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Author
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Topic: Wheels of Life
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RBH
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Member # 380
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posted 26. June 2003 18:58
John asked quote:
RBH: do you agree or disagree with my point as it stands: about the simulation?
This is how I see it:
1. The experiment was run intentionally.
2. That the experiment produced results was also intentional.
3. The particular results that were produced (evolved programs capable of performing EQU) were not intentional. This was the question asked in the research: Would such programs evolve under the conditions of the simulation?
RBH
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Micah Sparacio
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posted 26. June 2003 19:00
I'm not sure that the concept of "intentionality" is being applied correctly in this thread. Intentionality means only this "directedness." It is only partially related to the common usage of "having an intention."
The ability to direct thoughts, plans, etc. towards a goal is an example of "intentionality." Cats have intentionality when they see a squirrel outside the window, plan an attack, and then pounce (banging their head on the window - my cat did this just today for the third day in a row!) Some actually argue that a smart bomb has a form of intentionality when it locks on to its target, though this would probably be viewed as derived intentionality.
Anyway, those are my 2 cents. I noticed that John and Argon are using slightly different concepts.
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charlie d.
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posted 26. June 2003 19:15
If the question is whether there was intentionality in how the simulation developed (as opposed to how the simulation was conceived and initiated), then the answer is "no". Similarly, there was no intentionality in how cannonballs fell of the Tower of Pisa, though of course it took some in bringing them up there, dropping them off the edge, and making the relevant observations about their motion.
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Argon
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posted 26. June 2003 21:00
Molehill. Let's move on.
[ 26. June 2003, 21:00: Message edited by: Argon ]
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Rex Kerr
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posted 26. June 2003 22:05
Good experimenters tend to be addressing some manner of question with their experiment, and intentionally construct the experiment to have some bearing on the question. Experiments therefore necessarily involve intentionality.
However, in setting up an experiment, there are certain degrees of freedom allowed. It is critical to distinguish intentionality that picks one option from those allowed by the experiment, and the intentionality of the experimenter that set up the allowable range of outcomes.
For example, I have a 12-sided die here, and I run an experiment to see which numbers come up: 11,3,9,9,6,11,3,6,12,6,11,11,2. Note that I never rolled 120357, or "fish", or "flagellum", but that doesn't mean that the die intended to roll what it did. Further, you may note that the rolls don't look entirely random: in fact, 3, 6, 9, 11, and 12 are all adjacent on the die. I didn't intend this, but the shape of 12-sided dice combined with the size of my hand makes rolling not a very randomizing process unless I roll quite hard--but this doesn't mean that I intended to get this distribution. (I forgot that 12-sided dice of that size have that property in my hands, and was rolling gently so as to not annoy other people in the office.) The experiment was certainly compatible with a more random-looking outcome.
So when we think about generating EQU, the outcome was intended in approximately the same way that I intended to show a random sequence of numbers. The system was intentionally set up to allow the possibility of developing EQU in an method that would allow indirect selection. This was the test: if there is an indirect pathway to an irreducibly complex outcome, can an evolutionary algorithm find it? So of course, the competent experimenter has to try to arrange things so that there is the possibility of an indirect pathway, or the experiment wouldn't be informative.
So there are two answers to the intentionality question: was an experiment done intentionally? Yes. Was the outcome of the experiment intentionally caused from among the possible outcomes? No.
Note that while we can't do experiments without involving intentionality, we can apply the intentionality-free aspect of the results to our observations of the world. charlie's cannonball example is a particularly succinct demonstration of this.
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With respect to the biowheel, there are some good criticisms that can be overcome with modifications, some misunderstandings, and some criticisms that don't seem to have much merit.
However, I think I'm going to abandon the biowheel since it is a case of somewhat ambiguous usefulness; one could make the claim that no efficient designer would bother making multiple specialized structures specifically for large vertebrates who live on salt flats.
Other examples are much clearer: for instance, the RF antenna. These allow long-range high-bandwidth communication--and this is far superior to sound, since auditory channels are polluted with so much other information. Almost everything makes noise. Of course, you need an auditory system, as these noises can be very informative, but for inter-organismal communication, RF is vastly superior.
Unfortunately, RF signals can't be produced on the molecular level. You need conductors of a size roughly comparable to the signals being produced, and a way to drive the system at high frequency. Why not design a biological system that could deposit an appropriate metal and which was driven by appropriate electronics coupled to neurons? The materials seem to be easy enough to come by; there's plenty of iron in our blood to make some small, thin wires, or one could possibly use massive bundles of DNA or another conductive polymer.
In any case, I don't think that this entire line of argumentation is very compelling, even if true. So some useful things weren't designed. Curious, isn't it? Why not? Perhaps the designer had goals other than utility in mind; or perhaps there was no designer; or perhaps our view of utility is shorter-term (or longer-term) than the designer. We can rule out an extremely explicit designer who builds the exact form of every species independently (unless it's a very quirky explicit designer) based on arguments like these, but not much else.
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Mike Gene
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posted 26. June 2003 22:43
Well, this thread is well off topic from my original posting and beyond my self-imposed 50 posting/thread limit. So let me add some final thoughts:
Charlie,
You write: It seems to me that more than to the data, you are responding to a certain aesthetics, that goes with the scientific and technological development of the time.
I think I have a better feel for what I respond to that you.
In fact, so do all of us, even mainstream scientists. But the only way to judge a technology we cannot replicate ourselves is "a complex-looking thing that does something", which would apply to cells even if they looked like bags of soup.
You appear to be thinking in black and white terms and this can be misleading when dealing with ambiguous topics. In this case, it looks to me like you are arguing that we have a) a technology we can replicate or b) a technology we cannot replicate. If it’s the latter, then all we supposedly have to judge is the criterion of “complex looking that does something.” But just because we cannot replicate the technology does not mean there is no more to the overlap between technologies than “complex looking that does something.” The key is in the degree of overlap.
Nobody,
I enjoyed your comments/expansion on four of the points I brought to the table. Yes, I think as we advance in our nanotechnology, we will not only better understand how life works, but we’ll be in a better position to judge these analogies. My conservative side would have me wait it out, but my life-span won’t allow it. So I live on the edge and dare risk making bogus arguments. ![[Smile]](smile.gif)
You mention that the materials employed on the nanoscale will would also force different design parameters. Indeed. What’s more, I found a nice cite that highlights some of the implications of the molecular scale:
quote:
This is the region of scale where flow and diffusion are not clearly separated; where the concepts of temperature and molecular movement overlap; where it is not clear whether molecules move or are moved; where the ideas of active and passive lose their meaning'. – Denys N. Wheatley quoting RPC Johnson in The Journal of Experimental Biology 206, 1955-1961 (2003)
If life is designed, it makes sense that our own advanced designs represent the best models for life. But given that our own advanced models are still rather primitive and restricted to the macro-scale, we have to be careful when interpreting the meaning of stochastic processes, labile associations, inefficiency, etc.
In fact, speaking of inefficiency, sometimes this may represent a potential design solution to the noise that is far more problematic at the nanoscale. Here are some excerpts from Ertugrul M. Ozbudak1, Mukund Thattai1, Iren Kurtser2, Alan D. Grossman2 & Alexander van Oudenaarden. 2002. Regulation of noise in the expression of a single gene. Nature Genetics 31: 69 – 73.
quote:
Cell-to-cell variation in gene expression and flucuations over time in single cells have broad implications. Noise is often harmful, as it garbles cell signals, corrupts circadian clocks6 and disrupts the fine-tuned process of development. Cell signaling pathways13 and developmental switches14 have evolved so as to minimize the disruptive effect of such fluctuations, in ways that are only now beginning to be understood. Recently, Becskei and Serrano reported that variation in gene expression could be reduced by autoregulation15. We have shown that phenotypic variation can be controlled by genetic parameters: low translation rates will lead to reduced fluctuations in protein concentration. Because our control parameters are general, our results should be generally applicable. We suggest that several inefficiently translated regulatory genes (Table 3) have been naturally selected for their low-noise characteristics, even though efficient translation is energetically favorable16. For example, the cya gene of Escherichia coli, whose downstream product cyclic AMP (cAMP) is involved in several cellular regulatory processes, has a low translation rate. The unusual and inefficient RBS of cya is conserved across a variety of Gram-negative bacteria17, perhaps because it suppresses harmful fluctuations in cAMP levels that could have highly pleiotropic effects, including cell death18.
When viewed from certain contexts, inefficiency makes good design sense.
Also..
quote:
In some circumstances, noise can be highly desirable: an organism could use high translation rates and large concentration fluctuations as a means of creating nongenetic individuality in a population19, 20. This is seen with the cI gene of -phage4, 21: upon infection of a host cell, the cI mRNA is transcribed with an efficient RBS upstream of the initiation codon, thus creating a high-noise state; however, the lysogenic phenotype, once established, is maintained in a low-noise state (since transcription then begins at the initiation codon itself, producing inefficiently translated mRNA4).
And finally, an understanding of life’s design promises to illuminate problems faced in our developing designs:
quote:
Our experimental approach of creating low-noise genes through the use of inefficient RBSs mirrors the structure of these natural systems. The technique of translational noise control can be applied in the fast-growing field of artificial genetic networks22, 23. The current capabilities of artificially engineered circuits such as genetic toggle switches24 or ring oscillators5 are limited by intrinsic noise. New methods of noise reduction will allow these circuits to mimic the robust behavior of natural biological systems and will enable their practical application in areas such as biocomputation or the construction of genetic biosensors.
I originally pointed out the three differences between human design and life’s design because it demonstrates that the truth of life’s design does not entail that life’s design = our current designs. These are not criteria designed to function as escape hatches, but truths that follow from my hypothesis of originally designed cells. Any sincere methodology must work with them, rather than use them to score false positives (over-eager IDists) or false negatives (hyper-skeptical ID critics).
Finally, you ask if I think life is possible without DNA replication. Who really knows? The problem comes with the ambiguity inherent in the definition of life. I do think, however, that the type of biosphere we currently experience probably could not be generated without DNA-based organisms (or information molecules strongly analogous to DNA). DNA can be viewed as a molecule that serves more than the organism.
But that’s another topic.
I do agree that the original life forms were expressions of advanced biotechnology.
Anyway, the original focus of the thread was a response to Holliday’s argument about wheels and design.
I once again showed how to take a criticism of design and turn it into a positive research program, using the concept of design to again predict things about cell/molecular biology. It’s a fuzzy prediction, yet still rooted in ID (as explained in several postings above). I can close out this thread by simply repeating myself:
The odd thing about this debate is the lack of human-like structures on the macroscale is supposed to count against ID, but the presence of human-like structures on the microscale does not count for ID. I’m willing to agree that the lack of human-like structures on the macroscale works against ID at this level. Are my critics willing to agree that the presence of human-like structures on the microscale count for ID at this level. Of course not.
It’s a strange state of affairs. The problem on the cellular level is that the design is not exactly like something we design. But would a rabbit with something like an RF antenna sticking out of its head and lasers beams coming out of its eyes be exactly like something we design?
It may be very difficult to experimentally “address the question.” But one option is to note that a purely non-teleological approach is not needed to investigate reality and one can adopt a teleological approach instead. Eventually, it may be helpful to compare the pay-off of both approaches, once we adjust for pragmatic considerations that may be unequal. But I don’t think teleological design plus evolution looks a lot like non-design. Perspectives often depend on expectations. And yes, it’s quite clear that non-teleologists expect design to present itself as something so sensational that no one can reasonably doubt its existence. Anything less that this doesn’t count. We need rabbits with RF antennas to communicate where the wolves are. Once found, the bunnies circle the wolf on their all terrain tires and blast it with laser beams coming from their eyes. Since such creatures do not exist, design is to be dismissed. But to me, it looks like a lot of middle ground has just been leapt over.
See ya in the next thread...
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Nel
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posted 26. June 2003 23:05
Zygotecowboy,
Specification in Dembski's work can be said to be based on Kolmogorov's work. You can see this in the Caputo case, where Dembski was able to describe the event with a brief description. It's a simple pattern in one sense but a complex pattern in the probabilistic sense, as Dembski would say.
Dembski's complexity is not new, it asks how complex the thing really is. If chance and law could likely build the turboshaft then it isn't very complex at all, even if humans built it.
The filter isn't a crystal ball into the past. Dembski's filter asks how likely it is that a given chance hypothesis can account for the thing in question. That question can be asked regardless of whether we know it was designed or not. However, it is designed specifically to answer questions where we do not know the history. For example, a three letter word (like "the") can likely be accomplished by chance and law, and so if we don't know the causal history behind it we would attribute it to chance and law, if a guy comes up and says "but hey I wrote it" then we found a false negative, but thats ok. We can never say that that three letter word has 0 probability of occuring by chance even if we knew beforehand that it was designed. What we can say is a natural processes can likely form the word "the" and if we saw it without knowing who wrote it we wouldn't really raise an eyebrow.
You can see this in Dembski's writings when he makes the case that he is not arguing for logical impossibility. All of the machines under study by IDers can fail Dembski's tests for complexity and yet they could have been designed. Likewise, all of the machines under study by IDers can pass Dembski's tests for complexity and yet still have been formed by some wildly unlikely event.
So, to apply this to what you say above, it is more likely for chance and law to be able to form the turboshaft than the bacterial flagellum and that is true regardless of whether we know that the turboshaft was designed.
Note, IDers are allowed to base their complexity "hunches" on observation. Here specifically, I based my complexity "hunch" on the observation that the flagellum can build itself with a high degree of accuracy, that alone pointed to more complexity than the turboshaft. You can even see this in a calculation, I can do the calculation for the flagellum's ability to build itself, and how likely it is for chance and law to build a machine that can build itself. I can't do that for the turboshaft, it can't build itself. Already we see that we will have a lower number for the flagellum then we would have for the turboshaft.
Dembski's math is useful when you want to ask origin questions and when you want to pin down the complexity of the object in question precisely. It doesn't miraculously become the causal story, but it does point us in the direction we want to go when we don't know the causal story.
Put another way then, both the human design and the flagellum would probably fall below the probability bound, so I'm not saying that the turboshaft would likely be built by law and chance, just that it would have an even tougher time with the bacterial flagellum.
I don't know why I always get sucked into these off-topic discussions.
[ 26. June 2003, 23:29: Message edited by: Nelson-Alonso ]
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Pim van Meurs
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posted 26. June 2003 23:52
Nelson: If chance and law could likely build the turboshaft then it isn't very complex at all, even if humans built it.
That seems to be in contradiction to Dembski's design inference in which complexity, and more specifically specified complexity is what identifies intelligent design.
Nelson suggests that Dembski's approach works with respect to know cases but so far Dembski himself has applied his filter to a very limited set of cases making evaluation of the value of his filter somewhat limited. Combine this with the substantial criticism of his approach places some burden on the part of the ID proponent.
Nelson: Likewise, all of the machines under study by IDers can pass Dembski's tests for complexity and yet still have been formed by some wildly unlikely event.
But Dembski argues for no false positives. Or is he? Allowing the possibility of false positives severely undermines the design inference since there is no objective measure to determine the likelihood of failure thus for all we know all design inferences wrt biology may in fact be false positives.
It would be helpful if Dembski's ideas were actually put to a thorough test. Are you aware of any efforts to pursue such an approach?
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Nel
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posted 27. June 2003 00:03
Pim,
That quote does not contradict Dembski. It merely states that if something has high probability, it has low complexity.
With respect to false positives, here is how Dembski put it:
quote:
I argue that we are justified asserting specified complexity (and therefore design) once we have eliminated all known material mechanisms. It means that some unknown mechanism might eventually pop up and overturn a given design inference. But it also means that we have prima facie evidence of design and that we are justified in holding to this claim in the absence of such mechanisms being found.
[ 27. June 2003, 00:04: Message edited by: Nelson-Alonso ]
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RBH
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posted 27. June 2003 00:04
Nelson wrote quote:
Note, IDers are allowed to base their complexity "hunches" on observation. Here specifically, I based my complexity "hunch" on the observation that the flagellum can build itself with a high degree of accuracy, that alone pointed to more complexity than the turboshaft. You can even see this in a calculation, I can do the calculation for the flagellum's ability to build itself, and how likely it is for chance and law to build a machine that can build itself. I can't do that for the turboshaft, it can't build itself. Already we see that we will have a lower number for the flagellum then we would have for the turboshaft. (Emphases added)
Are you actually claiming that the flagellum is a von Neumann self-replicating machine? That's amazing! And given that von Neumann's goal was to formally describe a self-replicating automaton that could increase in complexity over cycles of reproduction, it's more than a little destructive of ID claims for the extant flagellum's history and origin.
RBH
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Nel
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posted 27. June 2003 00:08
RBH,
Bacterial flagella don't replicate themselves. They build themselves. Those are two different things.
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Mesk
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posted 27. June 2003 00:24
I'd tend to agree with Rex - the issue of whether or not specific non-existent biological structures could have been designed seems fairly irrelevant to the larger debate. The absence of biological macro-scale wheels is no more evidence against design than it is evidence against evolution. Wheels may not have evolved because of fundamental biological constraints, and likewise they may not have been designed because the designer simply didn't feel like it, or couldn't see the point, or didn't know how to. Either way, while this has been an extremely interesting thought experiment, it says little with respect to the possibility that life is designed.
The intentionality question is more difficult, and I think reflects a fundamental issue in the ID debate. To some extent, the accusation of intentionality is perfectly justified - we all know that Avida was carefully constructed and refined to model the process of evolution. No doubt its programmers spent considerable time tweaking its parameters until it generated outcomes which resemble things we see in the biological world. The program itself is clearly designed. Does this fact, in itself, invalidate its applications to the real world? Of course not. But the claims of intentionality are more specific: namely, that the researchers designed the program with the defined goal of generating virtual organisms which were capable of evolving EQU.
Knee-jerk denials aside, there may be a grain of truth to this. All of us who have ever been published in the scientific literature know that the publication is a poor reflection of the grunt work that went into the study - the false starts, misdirected experimental approaches, and endless optimisations that compose so much of the daily life of scientists are generally nowhere to be seen in their final publications. It is entirely possible that the researchers had to try a number of approaches to the program before they developed one which was capable of developing EQU, and their final results may in fact represent output from a program which had been subjected to considerable "fine-tuning" in order to get it to generate the published data.
In the absence of personal communication with Lenski et al. we are unlikely to ever know just how much tweaking was required. But how much difference does this make to the applicability of the results to the real world? This is the all-important question.
I submit that the process of fine-tuning the program probably does not significantly reduce the study's usefulness in addressing many important questions, so long as the tweaking was not directly aimed at influencing the precise manner in which Avida programs evolved EQU (and I find this unlikely, given that it would essentially invalidate the point of the study).
The Avida program, like all models of real-worl phenomena, is of limited applicability and needs to be interpreted with caution. However, I think that there is widespread agreement that the process used by Avida is at least broadly analogous to biological evolution, in that it represents the random generation of heritable variation which results in variation with respect to reproductive success in the organism's current environment. Over time, variants with the highest reproductive success increase steadily in frequency, and the process is repeated. Fundamentally there is no major difference in these aspects between Avida and real evolution.
In Avida, (as I understand it, anyway) the experimenter can specify particular organismal outcomes (i.e. logical functions) which boost the reproductive success of those organisms which possess them. This is analogous to particular organismal outcomes in the real world (such as, say, improved vision or reproductive strategies), although of course in the real world these outcomes do not need to be pre-specified by an experimenter.
This may be a point of contention, but I think pre-specification of desired outcomes is perfectly valid, and indeed necessary for any well-controlled experimental approach. It does not fundamentally change the applicability of the model's outcomes to real-world phenomena. It merely restricts the applicability of the output to situations in which the fitness landscape is similar. In the Lenski et al. simulation the fitness landscape was relatively smooth, but of course this is precisely what we expect for real-life biological systems - meaningful evolution does not occur in flat fitness landscapes, so of course to model evolution we need to use smooth landscapes. It is interesting to note that claims by some ID advocates that IC features represent "pinnacles" in a flat fitness landscape are seemingly resoundingly falsified by the Lenski et al. data (IMO, this is the most important conclusion that can be drawn from the study).
Intentionality aside, a more valid criticism of the experiment might be the possibility that the fitness landscape generated by Lenski et al. does not resemble anything seen in the biological world. I can see no particular reason why this would be the case, but I would be interested in hearing arguments to the contrary.
Mesk.
[Edited to tweak unclear grammar.]
[ 27. June 2003, 00:28: Message edited by: Mesk ]
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Pim van Meurs
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posted 27. June 2003 00:24
Nelson: Your claim that the flagellum 'builds itself' is already remarkable enough but how does this differ from 'replicate' itself?
I would be interested in a more detailed description and rebuttal.
Nelson:That quote does not contradict Dembski. It merely states that if something has high probability, it has low complexity.
Huh? What quote are you refering to and are you agreeing with me that an intelligently designed system has a high probability thus low complexity thus indicating that ID cannot be detected through such probabilistic approaches?
Your quote of Dembski does not help resolve the issue of false positives. If as Dembski claims the ID filter has no false positives then how does this fit in with your claims (you seem to accept false positives) and if there are false positives then how does one establish if something is not a false positive when its inference depends on elimination alone?
Clarification added: How does one establish a reliable design inference if there is an unknown probability of false positives? In case of an approach which is based on elimination, false positives form a major obstacle.
Nelson, are you saying that humans create things of low probability? And yet they created it thus suggesting a high probability for intelligent design? How can you accept the design inference when the probability of something intelligently designed is quite high and thus its complexity quite low?
Nelson suggests in the next posting that "The distinction is straightforward. Being able to build yourself from nothing is very different from being able to copy yourself. "
Could you address this in the context of the references to self replication? How is self replication different from building itself? And what is the evidence that the flagellum 'builds itself'?
So far your application of the terms specification, complexity etc leave a lot of uncertainty :-)
Nelson comments:
If something exhibits low probability it exhibits high complexity and vice versa (high probability = low complexity). Some human designed things exhibit low probability (turboshaft) and some human designed things exhibit high probability (a single two letter word for instance).
This seems to be at odds with Dembski's approach. How do we establish the low probability of a turbo shaft for instance? After all humans have created it so its probability seems to be quite high? Let's apply this to natural 'designed' objects and conclude that although the a-priori probability was low, the a posterio probability was high. Thus did nature "design" intelligently, a conclusion which seems inevitable using your arguments? Or should we reject any approach to probability since nothing really exhibits high specified complexity since either it arose naturally and thus its complexity would be low or it was created intelligently and thus its complexity was low. Or should we abandon appeal to probability as a measure of complexity which seems to lead in this case to some interesting conclusions.
Nelson found a website that suggests that the flagellum 'self assembles'? But does the flagellum self assemble or do these many proteins self assemble? Nelson's initial suggestion that the flagellum self assembles suggested a role for the flagellum. Now it seems that Nelson argues that the flagellum arose through self assembly of proteins.
As far as your a priori probabilities are concerned, how did you reach the conclusion that a turbo shaft is highly complex when in fact the probability of assembly by humans is quite high? Please explain since this is essential to the probabilistic argument of ID. My argument is that a conflation of probability and complexity results in any structure that was intelligently designed having a high probability and thus low complexity. Or perhaps Nelson could explain to us how we should calculcate the probability? We can then apply his approach to natural design and see if there is any difference between natural and intelligent design, or in fact as Wesley and others have argued intelligent design cannot eliminate a natural designer.
[ 27. June 2003, 01:14: Message edited by: Pim van Meurs ]
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Nel
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posted 27. June 2003 00:36
Pim,
The distinction is straightforward. Being able to build yourself from nothing is very different from being able to copy yourself. Thats all that needs to be said to clarify that distinction. Even so, self-replicating systems don't really damage an ID inference either. Considering the design specification that need to go into one:
http://www.zyvex.com/nanotech/selfRepJBIS.html
The quote in your reply to me is what I'm referring to, the first one. And no I'm not agreeing with you that designed systems exhibit high probability. I don't know where you got that from.
I can't make any sense out of your last paragraph. The claim of no false positives is if we don't know the causal history behind an object, but we find that it exhibits specified complexity, then we can be confident that it was designed that's what Dembski means by false positive. However, this does not mean that it is impossible for a wacky, freakish, improbable chance event to account for it, Dembski's claim of false positives is that these things do not regularly happen, that if it does, we should be surprised and be confident that it is not normally how such objects originate.
Saying that "humans create things thus they exhibit low probability" but they created it "thus they exhibit high probability" is a contradiction and I never said such a thing. If something exhibits low probability it exhibits high complexity and vice versa (high probability = low complexity). Some human designed things exhibit low probability (turboshaft) and some human designed things exhibit high probability (a single two letter word for instance).
I also never said that any probability can be determined a priori, probabilities can be determined by looking at the thing, it's parts, what the parts do, etc.
That the flagellum self-assembles is well known.
http://www.aip.org/mgr/png/2002/174.htm
[ 27. June 2003, 00:54: Message edited by: Nelson-Alonso ]
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