Stephen Meyer on ID’s Scientific Bona Fides

_{William Dembski
July 13, 2010

Intelligent Design}_{Categories
Intelligent Design}

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---Acipenser: “StephenB: We have been discussing a sand formation. Can any combination of naturalistic forces [wind, water, erosion, time etc.] (meaning without the help of an intelligent agent) produce the specific model in question?” ---"Oh, a sand sculpture. I’ve already asnwered this question, Stephen." No, you have not. You have reframed the question in order to avoid answering it. ---"There is one and only one answer to this question. The sand sculpture of any make automobile (engine or not) is an artistic expression of humans." I didn't ask you who sculpted the sand image of the 1959 Ford, so I don't know why you continue answering a question I didn't ask. ---"Human(s) built the sand sculpture I appreciate that fact that you think you know who did the sculpting, but that is not the question on the table. Again, here is the question: Is it possible [within the bounds of reasonable probability] that naturalistic forces such as wind, air, water, erosion and time could form the sand image of a 1959 Ford.StephenB_{July 19, 2010
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I am not sure what is emerging here. Could you specify?
The problem is to deduce water and all its properties before you know water exists. Working backward doesn't count. The designer of first life must know that life is possible before it exists. Humans will never be in that situation. We have enought trouble with reverse engineering. Perhaps your son can invent a new molecule with really surprising properties.Petrushka_{July 19, 2010
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That’s why I believe in common descent.
Fine. I'll accept that we have no detailed history of the origin of protein domains. I won't try to dissuade you from believing they are the work of some invisible agent, working at unknown times, etc. For most of them them to have been present two billion years ago, about one new one would have to arise every million years or so.Petrushka_{July 19, 2010
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Gaz: <So, StephenB – was the weasel-shaped cloud designed? Answer that one, and I’ll give you the rest of my answer on the car. If I may intrude, I would state again that if we want detailed quantitative analysis, we should stick to dFSCI (digital functionally specified functional information). The principles of design detection are alawys the same, but analogic information and other-than-functional specifications create greater problems. So, why not stick to the simpler case? (also because that case is more than enough to treat biological information, which both in the genome and the proteome is of the dFSCI type).gpuccio_{July 19, 2010
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Petrushka: In fact, as more species are sequenced, it is becoming increasingly difficult to find examples of coding or regulatory sequences that are isolated by more than a couple of mutations from sequences found in other species. What an example of false reasoning! Protein superfamilies are isolated, and there are thousands of them. Obviously, the same protein with the same functions is passed form one species to another, and the differences in sequence will be caused mainly by neutral mutations, or maybe by some tweaking in different species. That's why I believe in common descent. So you have hundreds of myoglobims, slightly different one form the other, sometimes different enough, but they are always myoglobins. The folding is the same, the function is the same. If you have seen the paper about the "big bang theory" for proteins, which I linked some time ago, you can see how new protein domains appear, and then in time they "travel" thorugh their own functional spcae, bearing a variety of different proteins which have the same structure and function. But protein domains and superfamilies are isolated one from the other. Were you nor present in the long tghread about Axe's paper?gpuccio_{July 19, 2010
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Petrushka:
I will not that I have not fired a barrage. I have brought up approximately three questions for which I think ID should have a response. 1. How do you eliminate false positives from design detection? I’ve presented a number of scenarios, but haven’t seen the math. It appears to be intuitive. 2. How does the designer meet the challenge of large numbers — the same large numbers that presumably rule out chance? 3. How does the designer deduce emergent properties? Or the effects of small changes in a complex ecosystem?
To sum up: 1. By choosing an appropriate threshold of complexity for functionally specified strings. That rules out false positives, while false negatives remain. 2. Using intelligent methods, as I have argued, and therefore optimized search. 3. The designer can deduce, or more often infer, according to his previous knowledge. And he can also use a trial and error method.gpuccio_{July 19, 2010
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Petruahka: It’s going to run into the problem of big numbers rather rapidly, unless you cheat and do it with evolution. Not true. Protein top7 was calculated. Folding can be calculated. Take a simple case: deduce the properties of water from the properties of hydrogen and oxygen. Or find someone who knows how to do it. I think that many properties of water can be calculated from the laws of physics. I am not a physicist, but my son, who is, agrees with that. It can be true that some aspects can defy present computational power, or present knowledge, but most are not. The properties of water depend on the properties of the molecule. the structure of the molecule is known, and depends on the properties of its constituents, on how the electron orbitals are formed, and so on. I am not sure what is emerging here. Could you specify?gpuccio_{July 19, 2010
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Of course they can be solved through evolution. I asked you how you would solve a problem and your answer was directed evolution. Yes, that's correct. And so? Directed evolution is design.gpuccio_{July 19, 2010
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Reproductive advantage must be defined in some environment. In my lab model, the lab system is the environment. So, the model is consistent. If you want to do the experiment in the open air, and in geological times, be my guest.
Already in progress.Petrushka_{July 19, 2010
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Folding can be computed. Biochemical binding can be understood and computed. It’s not easy, but it can be done.
It's going to run into the problem of big numbers rather rapidly, unless you cheat and do it with evolution.
Emergent properties like those ones (if they are emergent properties, I really can’t undersatnd the meaning of that concept in any clear-cut sense) can be deduced.
Take a simple case: deduce the properties of water from the properties of hydrogen and oxygen. Or find someone who knows how to do it. A related problem is that of mathematical complexity, the rapid divergence of system behavior starting from small changes.Petrushka_{July 19, 2010
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Petrushka: Reproductive advantage must be defined in some environment. In my lab model, the lab system is the environment. So, the model is consistent. If you want to do the experiment in the open air, and in geological times, be my guest.gpuccio_{July 19, 2010
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Petrushka: If this is true, then one ought to be able to distinguish samples of artificially bred animals from those that exist without human intervention. Isn’t that what design detection is about, separating things that would not exist without intelligent intervention, from those that exist without intervention? Ahh! Again with bred animals. Let's go back to dFSCI. I have told you many times that the laws of design detection are always the same, but that if you want a rigorous, easy and quantitative analysis it is better to stick to digictal functional information. Dog breeding "could" be analyzed, but it is difficult to do that. But I think that protein information is a better model, and nearer to the true problem, don't you agree? So, very simple: a string of 500 - 1000 bits, of pseudo-random nature (not significantly compressible), which has a recognizable and measurable function encoded in the whole string, for which no credible necessity model is known, and for which the ratio "target functional space / search space" is lower than some conventional, appropriate threshold (defined according to the empirical context: for biological strings, I would suggest something like 10^-50, just to stay on the safe side) is a designed object. There are no false positives. There are no counter-examples to that.gpuccio_{July 19, 2010
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There are some specifical problems, especially mathemathical, which cannot be solved algorithmically in a finite time, but biological problems are not like that. Protein engineers are out there, working: they are not planning suicide because their work is doomed to failure. Please, don’t repeat any more this silly concept.
Of course they can be solved through evolution. I asked you how you would solve a problem and your answer was directed evolution.Petrushka_{July 19, 2010
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Petrushka: How does a designer calculate the effects of changing a sequence that codes for a protein? First: through a top down process: protein top7 is an example. Protein folding can be computed: it's long, it's complex, but it can be done. Second: through a bottom up process: the Szostac way. That's probably easier, at least for now. Is it even possible to design from first principles? I’m not aware that anyone in the field of physics or chemistry thinks that emergent properties can be deduced. Folding can be computed. Biochemical binding can be understood and computed. It's not easy, but it can be done. Emergent properties like those ones (if they are emergent properties, I really can't undersatnd the meaning of that concept in any clear-cut sense) can be deduced. The challenge for design advocates is to demonstrate that it is possible to deduce emergent properties. We know that cut and try works. Inefficiently, but it works. You are just saying that top down methods cannot solve all problems. I don't agree for biological problems, but even if that were the case, you are forgetting that bottom up methods are design methods too. You make a fundamentsl mistake: you identify design with top down, deductive methods. That's simply not true. Top down methods are only a type of design, and moreover they are not wholly deductive: inferential reasoning is always important in all human empirical knowledge. And anyway, bottom up designs are designs just the same. You are really epistemologically confused. Is that what darwinism makes to human methodology?gpuccio_{July 19, 2010
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As far as petrushka falsely claiming (once again though he has been corrected before) that the flagellum is proof of evolution: The flagellum has steadfastly resisted all attempts to elucidate its plausible origination by Darwinian processes, much less has anyone ever actually evolved a flagellum from scratch in the laboratory; Genetic Entropy Refutation of Nick Matzke's TTSS (type III secretion system) to Flagellum Evolutionary Narrative: Excerpt: Comparative genomic analysis show that flagellar genes have been differentially lost in endosymbiotic bacteria of insects. Only proteins involved in protein export within the flagella assembly pathway (type III secretion system and the basal-body) have been kept... http://mbe.oxfordjournals.org/cgi/content/abstract/msn153v1 "One fact in favour of the flagellum-first view is that bacteria would have needed propulsion before they needed T3SSs, which are used to attack cells that evolved later than bacteria. Also, flagella are found in a more diverse range of bacterial species than T3SSs. ‘The most parsimonious explanation is that the T3SS arose later," Howard Ochman - Biochemist - New Scientist (Feb 16, 2008) Michael Behe on Falsifying Intelligent Design - video http://www.youtube.com/watch?v=N8jXXJN4o_A Genetic analysis of coordinate flagellar and type III - Scott Minnich and Stephen Meyer Molecular machines display a key signature or hallmark of design, namely, irreducible complexity. In all irreducibly complex systems in which the cause of the system is known by experience or observation, intelligent design or engineering played a role the origin of the system. https://www.discovery.org/f/389 STILL SPINNING JUST FINE: A RESPONSE TO KEN MILLER - William Dembski Excerpt: "Darwin's theory, without which nothing in biology is supposed to make sense, in fact offers no insight into how the flagellum arose." http://www.designinference.com/documents/2003.02.Miller_Response.htm Bacterial Flagella: A Paradigm for Design – Scott Minnich – Video http://www.vimeo.com/9032112 Flagellum - Sean D. Pitman, M.D. http://www.detectingdesign.com/flagellum.htmlbornagain77_{July 19, 2010
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It seems that petrushka is very selective of exactly which evidence he will consider. For example he considers sequence similarity to be a slam dunk for Darwinism yet neglects to mention that no one has ever actually observed any protein mutating amino acid by amino acid into another protein of a different function: “Mutations are rare phenomena, and a simultaneous change of even two amino acid residues in one protein is totally unlikely. One could think, for instance, that by constantly changing amino acids one by one, it will eventually be possible to change the entire sequence substantially… These minor changes, however, are bound to eventually result in a situation in which the enzyme has ceased to perform its previous function but has not yet begun its ‘new duties’. It is at this point it will be destroyed - along with the organism carrying it.” Maxim D. Frank-Kamenetski, Unraveling DNA, 1997, p. 72. (Professor at Brown U. Center for Advanced Biotechnology and Biomedical Engineering) "A problem with the evolution of proteins having new shapes is that proteins are highly constrained, and producing a functional protein from a functional protein having a significantly different shape would typically require many mutations of the gene producing the protein. All the proteins produced during this transition would not be functional, that is, they would not be beneficial to the organism, or possibly they would still have their original function but not confer any advantage to the organism. It turns out that this scenario has severe mathematical problems that call the theory of evolution into question. Unless these problems can be overcome, the theory of evolution is in trouble." Problems in Protein Evolution: http://www.cs.unc.edu/~plaisted/ce/blocked.html Nor has petrushka mentioned the severe constraints placed on proteins gradually evolving: Extreme functional sensitivity to conservative amino acid changes on enzyme exteriors - Doug Axe Excerpt: Contrary to the prevalent view, then, enzyme function places severe constraints on residue identities at positions showing evolutionary variability, and at exterior non-active-site positions, in particular. http://nsmserver2.fullerton.edu/departments/chemistry/evolution_creation/web/AxeProteinEvolution.pdf This following paper, and audio interview, shows that there is a severe "fitness cost" for cells to carry "transitional" proteins that have not achieved full functionality yet: Reductive Evolution Can Prevent Populations from Taking Simple Adaptive Paths to High Fitness - May 2010 Excerpt: Despite the theoretical existence of this short adaptive path to high fitness, multiple independent lines grown in tryptophan-limiting liquid culture failed to take it. Instead, cells consistently acquired mutations that reduced expression of the double-mutant trpA gene. Our results show that competition between reductive and constructive paths may significantly decrease the likelihood that a particular constructive path will be taken. http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2010.2 In fact, the Ribosome, which makes the myriad of different, yet specific, types of proteins found in life, is found to be severely intolerant to any "random mutations" occurring to proteins. The Ribosome: Perfectionist Protein-maker Trashes Errors Excerpt: The enzyme machine that translates a cell's DNA code into the proteins of life is nothing if not an editorial perfectionist...the ribosome exerts far tighter quality control than anyone ever suspected over its precious protein products... To their further surprise, the ribosome lets go of error-laden proteins 10,000 times faster than it would normally release error-free proteins, a rate of destruction that Green says is "shocking" and reveals just how much of a stickler the ribosome is about high-fidelity protein synthesis. http://www.sciencedaily.com/releases/2009/01/090107134529.htm nor did petrushka mention that, much like words in the English language, similar sequences of amino acids (similar to words that are spelled, or sound, the same way) can have completely different functions (meanings): A shining case in point being this: Kangaroo genes close to humans Excerpt: Australia's kangaroos are genetically similar to humans,,, "There are a few differences, we have a few more of this, a few less of that, but they are the same genes and a lot of them are in the same order," ,,,"We thought they'd be completely scrambled, but they're not. There is great chunks of the human genome which is sitting right there in the kangaroo genome," http://www.reuters.com/article/science%20News/idUSTRE4AH1P020081118 So petrushka should kangaroos be placed before or after primates in the cartoon drawings of man's supposed evolution??? to drive the point home down to level of proteins though (that similar sequences DO NOT establish functional, nor morphological relationship) Human Genes: Alternative Splicing (For Proteins) Far More Common Than Thought: Excerpt: two different forms of the same protein, known as isoforms, can have different, even completely opposite functions. For example, one protein may activate cell death pathways while its close relative promotes cell survival. http://www.sciencedaily.com/releases/2008/11/081102134623.htm As well it seems that petrushka failed to mention the over 1000 ORFan genes found that are completely unique to humans: This following site has a brief discussion on the biased methodology of the ORFan study: https://uncommondescent.com/intelligent-design/proteins-fold-as-darwin-crumbles/#comment-358505 As well petrushka seems to labor under the illusion that sequence similarity, when applied in a consistent manner, (As unbiased science would dictate it be done), supports his meta-narrative: "Why Darwin was wrong about the tree of life," New Scientist (January 21, 2009) Excerpt: Even among higher organisms, “the problem was that different genes told contradictory evolutionary stories,”,,,“despite the amount of data and breadth of taxa analyzed, relationships among most [animal] phyla remained unresolved.” ,,,,Carl Woese, a pioneer of evolutionary molecular systematics, observed that these problems extend well beyond the base of the tree of life: “Phylogenetic incongruities [conflicts] can be seen everywhere in the universal tree, from its root to the major branchings within and among the various taxa to the makeup of the primary groupings themselves.”,,, “We’ve just annihilated the (Darwin's) tree of life.” http://www.evolutionnews.org/2009/05/a_primer_on_the_tree_of_life_p_1.html#morebornagain77_{July 19, 2010
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Petrushka: ID rests on a foundation of big numbers and huge configuration space. But big numbers are a problem for designers. No one has explained how designers get around the problem. That's false. Thats' false. Thats' false. Designers do not work through random search, but through intelligent optimized search. They can both profit of their understanding of nature, of laws, os search spaces, and use random search in optimized ways. They can do a lot of things which RV + NS cannot do. How can you deny that? Are you blind? There are some specifical problems, especially mathemathical, which cannot be solved algorithmically in a finite time, but biological problems are not like that. Protein engineers are out there, working: they are not planning suicide because their work is doomed to failure. Please, don't repeat any more this silly concept.gpuccio_{July 19, 2010
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I could start a process of hypermutation on that protein, possibly after having duplicated it (targeted hypermutation), and periodically measure the function I need..</blockquote. In other words, you would use evolution. Just improve it a bit. But the question is about reproductive advantage, not reproductive speed. Reproductive advantage includes survival of the population in a dynamic environment and in an ecosystem that includes preditors that are also jockeying for reproductive advantage.
Petrushka_{July 19, 2010
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"StephenB: We have been discussing a sand formation. Can any combination of naturalistic forces [wind, water, erosion, time etc.] (meaning without the help of an intelligent agent) produce the specific model in question?" Oh, a sand sculpture. I've already asnwered this question, Stephen. There is one and only one answer to this question. The sand sculpture of any make automobile (engine or not) is an artistic expression of humans. Human(s) built the sand sculpture.Acipenser_{July 19, 2010
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That is, we see here an irreducibly complex set of core components that must all be present in a properly organised fashion for a successful self-replicating machine to exist.
Just a quick question. Does Spiegelman's Monster qualify?Petrushka_{July 19, 2010
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Petrushka: Wow, what an activity during the night! (my night, at least). I'll try to catch up... Suppose you are a designer and your boss says to increase the reproductive advantage of model 4573-A-23. What do you do? There are many possibilities. First of all I would consider what I know of the existing model. Than I would perform an analysis of the pros and cons of what already is there. Than I would device some possible ameliorations, based on my knowledgde of basic science and on the observed results os what already exists. Then I would try to implement some definite positive variation. Let's imagine that for that variation I need some radical modification of an existing protein to nobtain a new function. I could start a process of hypermutation on that protein, possibly after having duplicated it (targeted hypermutation), and periodically measure the function I need, promoting the mutations which exhibit a higher level of function. Something similar to what Szostac did, and other protein engineers do. But it is imnportant that I have a plan in mind for the new protein and the new function. That plan should include integration of the new function with what already exists. And if I work well, my boss will be satisfied.gpuccio_{July 19, 2010
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PS: Goal-post shifting! Really now. every scientific endeavour is subject to adjustment or correction in light of further evidence.
. I appreciate your comments on the barrage of objections and the requirement of science to modify hypotheses based on evidence. Good points for any debate.Petrushka_{July 19, 2010
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PS: Goal-post shifting! Really now. every scientific endeavour is subject to adjustment or correction in light of further evidence. Solutions we do have in hand are not obviated by problems we have not yet solved -- demanding full daylight instead of using candlelight to do what we can in the meanwhile will not do. And so on, we are seeing recirculated objections that have already been adequately answered [e.g. on alleged false positives -- while the real case is being ignored again and again . . . ], yet another case of refusing to read and take seriously what is right in front of the relevant darwinist advocates. Selective hypersketpicism in short.kairosfocus_{July 19, 2010
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Onlookers: Back for a moment. First it is plain that Petrushka refuses to simply read the discussion surrounding Fig I.1 (and the following two figures), which provide a discussion on the reason for FSCI [and linked organisation] as a reliable empirical sign of design. WITHOUT THAT SORT OF GIVE AND TAKE, A REASONED DISCUSSION IS NOT POSSIBLE. This is an impasse, and it is occasioned by refusal of evolutionary materialist advocates to be reasonable. As for the barrage of objections to the work of Behe, there is a whole universe of exchanges on the topic, and the balance is that the concept of irreducible complexity is plainly valid and indeed a commonplace of technology: we usually have parts in machines because they do a necessary job, and jointly achieve the overall core function. Objections on co-optation typically fail to address the issue of co-ordination and mutual adaptation of parts to work together successfully. They don't begin to touch on the issue of automatic self-assembly in living organisms, and they don't ever deal with the root IC question of all: self-replication rests on a cluster of hard and soft ware components that are the premise for being able to metabolise AND replicate the metabolising entity. For, a von Neumann replicator (as has already been pointed out but pointedly and studiously ignored) requires:
(i) an underlying storable code to record the required information to create not only (a) the primary functional machine [[here, a Turing-type “universal computer”] but also (b) the self-replicating facility; and, that (c) can express step by step finite procedures for using the facility; (ii) a coded blueprint/tape record of such specifications and (explicit or implicit) instructions, together with (iii) a tape reader [[called “the constructor” by von Neumann] that reads and interprets the coded specifications and associated instructions; thus controlling: (iv) position-arm implementing machines with “tool tips” controlled by the tape reader and used to carry out the action-steps for the specified replication (including replication of the constructor itself); backed up by (v) either: (1) a pre-existing reservoir of required parts and energy sources, or (2) associated “metabolic” machines carrying out activities that as a part of their function, can provide required specific materials/parts and forms of energy for the replication facility, by using the generic resources in the surrounding environment.
Note, parts (ii), (iii) and (iv) are each necessary for and together are jointly sufficient to implement a self-replicating machine with an integral metabolic capacity required as well. That is, we see here an irreducibly complex set of core components that must all be present in a properly organised fashion for a successful self-replicating machine to exist. [[Take just one core part out, and self-replicating functionality ceases: the self-replicating machine is irreducibly complex (IC).]. This irreducible complexity is compounded by the requirement (i) for codes, requiring organised symbols and rules to specify both steps to take and formats for storing information, and (v) for appropriate material resources and energy sources. Immediately, we are looking at islands of organised function for both the machinery and the information in the wider sea of possible (but mostly non-functional) configurations. In short, outside such functionally specific -- thus, isolated -- information-rich target zones, want of correct components and/or of proper organisation and/or co-ordination will block function from emerging or being sustained across time from generation to generation. So, once the set of possible configurations is large enough and the islands of function are credibly sufficiently specific/isolated, it is unreasonable to expect such function to arise from chance, or from chance circumstances driving blind natural forces under the known laws of nature. Further, let us consider a tape of 1,000 bits (= 125 bytes), which is plainly grossly insufficient to specify the parts and instructions for a von Neumann replicator. However, the number of possible configurations of 1,000 bits is 1.07 * 10^301, more than ten times the square of the 10^150 states the 10^80 atoms of our observed universe would take up across a reasonable estimate of its lifespan. So, viewing our observed universe as a search device, it would scan less than 1 in 10^150th part of even so “small” a configuration space. That is, it would not carry out a credible “search” for islands of function, making such islands sufficiently isolated to be beyond the reasonable reach of a blind search. The Darwinian tree of life has no credible root. And since major body plan innovasions require upwards of 10 MB of new DNA bases, and coordinated functional integration that is embryologically feasible, there is no credible mechanism for the major branches as well. This is joined by the persistent general absence of links for such body plan innovations in the fossil record, when we should stumble across them every time we go out the front door. In short there is something rather rotten in the state of Darwinland. GEM of TKIkairosfocus_{July 19, 2010
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I will not that I have not fired a barrage. I have brought up approximately three questions for which I think ID should have a response. 1. How do you eliminate false positives from design detection? I've presented a number of scenarios, but haven't seen the math. It appears to be intuitive. 2. How does the designer meet the challenge of large numbers -- the same large numbers that presumably rule out chance? 3. How does the designer deduce emergent properties? Or the effects of small changes in a complex ecosystem?Petrushka_{July 19, 2010
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The real false positive on the specific case of the blood clotting cascade was the claimed dismissal. (As I recall, the point that has the irreducible core was AFTER the point that was highlighted in the attempted rebuttal, look it up.)
That's called moving the goalposts. Where are you going to move the goalposts when further subsets of clotting proteins are found?Petrushka_{July 19, 2010
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PS: One must beware the fallacy of the barrage of objections.
Good point.Petrushka_{July 19, 2010
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With the flagellum, the TTSS, the claimed antecedent that was to have been co-opted and augmented, tu4rns out to be derivative.
Perhaps, but derivitave of what? There are dozens of cilia and partial flagella employing many different subsets of the E.coli proteins. Many of the proteins are used in other organisms for purposes other than locomotion.Petrushka_{July 19, 2010
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PS: One must beware the fallacy of the barrage of objections. Issues in science are not like ships that can be blown up and sunk by a lucky shot. And when so many fallacies of distractive irrelevance are being committed it points to a great weakness on the central matter on the part of the evolutionary materialism advocates. It is obvious that hey cannot bring themselves to acknowledge that the question of empirically reliable signs of intelligence in action is a valid scientific question, and one that has significant import for those of us who wish to restore science to its proper course as an unfettered pursuit of the truth about our world based on empirical evidence and uncensored reasoned analysis.kairosfocus_{July 19, 2010
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As to the claim that we are ignoring relevant cases, evidently Petrushka has yet to examine Fig. I.1 in the repeatedly linked before making adverse comments.
I seem to be unable to find the generalized method for distinguishing art from natural objects. Is there some math involved, or is it, "I know it when I see it"? I assume you have taken into account the fact that most human produced art is not photographically representational.Petrushka_{July 19, 2010
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AM
PDT}

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