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Author
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Topic: Bacterial Colonies and Intelligent Design
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Nelson Alonso
Member
Member # 52
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posted 07. March 2002 18:45
Hello all. I've been away for a month or so from both ARN and ISCID, and I came back today to find that there are now two great discussion boards to post on! Great idea, ISCID.
I noticed that one of the news items mentions Eschel Ben-Jacob's Cybernetic's group. It is interesting that both Ben-Jacob and Dr. James Shapiro are often credited with finding that bacteria are actually social rather than individuals.
In this link, Mike Gene states about one of Shapiro's papers:
quote:
Shapiro envisions evolution as the deployment of this "natural genetic engineering" toolkit that functions to redesign the system architecture of the genome and thus facilitate rather significant and rapid evolutionary transitions.
http://www.idthink.net/arn/shap/index.htm
Ben-Jacob seems to echo these thoughts:
quote:
"the cell carries a complete set of tools for genetic self-reconstruction: plasmids, phages, transposons, and too many others to mention, the same tools, in fact, used in the lab today for genetic engineering."
Both Shapiro and Ben-Jacob's work seems to state that each bacteria carries a package of genes that works like a computer, but are able to do more than what even modern computers can do, in that it can solve new problems by changing itself.
Ben-Jacob summarizes these points:
quote:
"evolutionary progress is not a result of
successful accumulated mistakes"
Rather, when the genome is faced with a new problem it forms a "super-mind",
quote:
". It is known that in a stressed colony, some of the bacteria become competent by rendering their membrane more permeable to genetic material, while other bacteria go through lysis: break open and deposit their genetic material in the media [14,13]. In addition, direct genetic connections between the bacteria are formed by means of conjugation or transduction [14,13]. We propose that these features indicate that the stressed colony turns into a genetic network, which is the highest level of colony cooperation. To emphasize that the network is composed of agents (each genome is by itself a cybernetic agent) I refer to it as a ``genomic web''. I further assume, that in order to establish the genomic web, the bacteria produce (or activate) special cybernators enhancing the efficient and sophisticated genomic communication. Once formed, the genomic web is a "super-mind" relative to the individual genome. Thus, a paradox for the genome is a solvable problem for the web. The web, being more complex than the individual genome, can design and construct a new and more advanced genome relative to the original ones, i.e., perform a vertical genomic leap. Such a leap is best described as a cooperative self-improvement or cooperative evolution.
."
This brings about an interesting problem with respect to Gödel's Theorem. Basically it comes from the idea that if you use a turing machine to generate mathematical statements and another turing machine to prove these statements true or false given a certain group of axioms, then Godel's theorem will tell you that some of these statements will be true but unable to be proved true by the second turing machine. In other words, no computer can make one superior to itself. However, Ben-Jacob seems to have an answer to this:
quote:
But, if we truly regard the colony as a multicellular organism, it will be in contradiction with the extension of Gödel's theorem; if we regard the colony as our system, it would imply that a system is capable of designing a system more advanced than itself. I believe that the colony of the new bacteria can only be improved relative to the original colonies, and not more complex. In order to keep the picture consistent, we have to assume that genetic communication between many colonies of the same bacteria, or a number of colonies of different bacteria, are required for the design of a vertical leap on the colonial level.
Ben Jacob shows how the bacterial genome is "interpreting and assigning meaning" to its computations using "an advanced language with self-reference to sentences and grammar," and by possessing "information about the past and present abilities of the system, which it can apply when searching for a solution to a current" dilemma.
There are many interesting observations here, such as how colonies of bacteria send out a signal for the colony to form "troops" in order to go out and find food when the supply is depleted. They form exploratory parties called "random walkers" and other specialized groups which analyze the environment. They use chemotactic information exchange and quorum sensing to bring the thousands of bacteria into a "creative web".
In conclusion, Ben-Jacob writes:
quote:
The emergence of the new picture involves a shift from the pure reductionistic point of view to a rational holistic one, in which creativity is well within the realm of Natural sciences.
You can see this echoed in Mike's essay above:
quote:
Shapiro's views don't just amount to a important functional role for "junk DNA" and the growing irrelevance of the Modern Synthesis, but they also hold great potential for a very positive fruition of a robust teleological interpretation of life's history. As science moves in this direction, its difference from ID dwindles. This can be appreciated if one begins to ponder the huge implications entailed in the way Shapiro introduced his topic as discussed at a conference:
'the debate moved toward thinking of "evolution as biological function" rather than of evolution as accidental changes captured by selection.'
[ 07 March 2002, 18:58: Message edited by: Nelson Alonso ]
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Frances
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Member # 169
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posted 07. March 2002 23:07
Great post and thanks for the reference. I have found the relevant papers. Could you please explain to me the relevance of this work to ID? Shapiro's work shows us how bacteria are organized, provide for signaling etc. How does this relate to ID though?
I believe that these findings may raise some interesting issues about single-multicellular evolution.
Actually the whole issue in which this paper appeared is a great read.
"Annals of the New York Academy of Sciences
MOLECULAR STRATEGIES IN BIOLOGICAL EVOLUTION
Volume 870 published May 1999 Editors: Lynn Helena Caporale "
Look at the following papers
MIROSLAV RADMAN, IVAN MATIC, and FRANÇOIS TADDEI
Evolution of Evolvability Ann NY Acad Sci 1999 870: 146-155
Predictability of Mutant Sequences: Relationships between Mutational Mechanisms and Mutant Specificity Ann NY Acad Sci 1999 870: 159-172
Mechanisms of Genome-Wide Hypermutation in Stationary Phase Ann NY Acad Sci 1999 870: 275-289
Detecting Alien Genes in Bacterial Genomes
Ann NY Acad Sci 1999 870: 314-329.
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Nelson Alonso
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Member # 52
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posted 08. March 2002 09:54
Francis:
Could you please explain to me the relevance of this work to ID?
Nelson:
As I mentioned in my post, we are seeing that mutations are not all random. That evolution proceeds not through an accumalation of mistakes but through purposeful "natural genetic engineering". If such primitive creatures are capable of such complex tasks then what we are seeing could be the makings of a paradigm shift, from a reductionist perspective, to a teleological perspective. As my quote states:
quote:
Shapiro's views don't just amount to a important functional role for "junk DNA" and the growing irrelevance of the Modern Synthesis, but they also hold great potential for a very positive fruition of a robust teleological interpretation of life's history. As science moves in this direction, its difference from ID dwindles.
What we could be seeing is a glimpse of the designer's engineering skills, much like those of AI programmers.
Francis:
Shapiro's work shows us how bacteria are organized, provide for signaling etc. How does this relate to ID though?
Nelson:
Shapiro's work doesn't show that bacteria are organized. What he showed was that with respect to solving complex problems, we are:
quote:
"thinking of genomes as complex interactive information systems, in many ways comparable to those involving computers."
J. A. Shapiro. Natural genetic engineering in evolution. Genetica, 86:99-111,
1992.
Thanks for your references, however, I'm not quite sure I see the relevance. The relevance for ID is quite obvious. We are dealing with packages of genes that serve as a computer, that are able to compute better then the best parallel computers we have. It seems as though the primitive=simple concept is becoming more and more outdated.
The genetic code seems to follow set algorithms that are well known in AI and neural networks where programmers have basically taken their design methodologies from nature itself. Anyone who has worked with sophisticated AI systems knows the difficulties involved to make the system learn "efficiently" from its environment as well as from its mistakes, i.e., where it selected the wrong options along a chosen path and then acknowledges the quality of its choice (or the lack of it) by making the necessary programming adjustments.
This is, I think, what Mary Jane West-Eberhard is trying to get across in the quote below from her Commentary in Proc. Natl. Sci. USA.
quote:
"The idea of evolution of evolvability-that the ability to evolve can itself evolve-might be questioned by some evolutionary biologists because
it requires selection above the individual level."
Proc. Natl. Acad. Sci. USA
Vol. 95, pp. 8417-8419, July 1998
Commentary Evolution in the light of developmental and cell biology, and vice versa:
by
Mary Jane West-Eberhard
[ 08 March 2002, 10:37: Message edited by: Nelson Alonso ]
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Frances
Member
Member # 169
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posted 08. March 2002 12:17
quote:
Originally posted by Nelson Alonso:
Francis:
Could you please explain to me the relevance of this work to ID?
Nelson:
As I mentioned in my post, we are seeing that mutations are not all random. That evolution proceeds not through an accumalation of mistakes but through purposeful "natural genetic engineering".
One has to be careful when using the term 'random' and 'non-random'. As far as I can tell the non-randomness refers to position in the genome not function. Initially there seems to have been some excitement about adaptive mutations but the recent findings seem to suggest that adaptive mutations are due to hypermutations.
Secondly even assuming that mutations are non random in function, how would this provide support for ID? Are you saying that the intelligence is present in the organism?
quote:
If such primitive creatures are capable of such complex tasks then what we are seeing could be the makings of a paradigm shift, from a reductionist perspective, to a teleological perspective. As my quote states:
I would not call bacteria 'primitive'. They might be single cellular but they have undergone the longest period of evolution.
quote:
quote:
Shapiro's views don't just amount to a important functional role for "junk DNA" and the growing irrelevance of the Modern Synthesis, but they also hold great potential for a very positive fruition of a robust teleological interpretation of life's history. As science moves in this direction, its difference from ID dwindles.
What we could be seeing is a glimpse of the designer's engineering skills, much like those of AI programmers.
In this case the designer(s) seems to be the bacteria. How does the bacteria being a 'designer' help us determine if something designed the bacteria?
quote:
Francis:
Shapiro's work shows us how bacteria are organized, provide for signaling etc. How does this relate to ID though?
Nelson:
Shapiro's work doesn't show that bacteria are organized. What he showed was that with respect to solving complex problems, we are:
quote:
"thinking of genomes as complex interactive information systems, in many ways comparable to those involving computers."
J. A. Shapiro. Natural genetic engineering in evolution. Genetica, 86:99-111, 1992.
To me the question is: Is this analogy structural or superficial?
Thanks for your references, however, I'm not quite sure I see the relevance. The relevance for ID is quite obvious. We are dealing with packages of genes that serve as a computer, that are able to compute better then the best parallel computers we have. It seems as though the primitive=simple concept is becoming more and more outdated.
The genetic code seems to follow set algorithms that are well known in AI and neural networks where programmers have basically taken their design methodologies from nature itself. Anyone who has worked with sophisticated AI systems knows the difficulties involved to make the system learn "efficiently" from its environment as well as from its mistakes, i.e., where it selected the wrong options along a chosen path and then acknowledges the quality of its choice (or the lack of it) by making the necessary programming adjustments.
This is, I think, what Mary Jane West-Eberhard is trying to get across in the quote below from her Commentary in Proc. Natl. Sci. USA.
quote:
"The idea of evolution of evolvability-that the ability to evolve can itself evolve-might be questioned by some evolutionary biologists because
it requires selection above the individual level."
Proc. Natl. Acad. Sci. USA
Vol. 95, pp. 8417-8419, July 1998
Commentary Evolution in the light of developmental and cell biology, and vice versa:
by
Mary Jane West-Eberhard
[/QB][/QUOTE]
I agree that GA systems when applied to a large variety of problems are not always that succesful but in case of evolution we are talking about a relatively simple algorithm that has been shown to work quite efficiently.
Mary West-Eberhard continues
quote:
Adaptive evolution, however, concerns the genetically mediated spread of traits within populations, species, or clades (39). Several evolutionary biologists (e.g., 24, 43) have argued cogently in favor of clade selection for evolvability with reference to genetic aspects. The mechanisms of flexibility discussed by Kirschner and Gerhart seem to be especially good candidates for clade-level selection because the mechanisms can become established within species due to the immediate, individual advantages of flexibility and then be favored secondarily at higher levels (see ref. 44) because of their contributions to speciation, diversification, and major (macroevolutionary) change (27, 36). Darwin (2) was the first to argue in favor of selection for variability per se as part of his "principle of divergence," which included the idea that processes that contribute to intraspecific diversification also would enhance the differential survival and multiplication of descendent clades.
Eberhard references Marc Kirschner and John Gerhart's work:
quote:
Today, we see the survivors of lineages that underwent multiple radiations. These lineages have diversified by maintaining a core of highly conserved processes and modifying others. The core processes have unusual capacities to deconstrain change in other processes and components. This has proven to be a powerful strategy for the variation side of Darwin's variation and selection principle of evolution.
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Nelson Alonso
Member
Member # 52
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posted 08. March 2002 12:49
Francis:
One has to be careful when using the term 'random' and 'non-random'. As far as I can tell the non-randomness refers to position in the genome not function.
Nelson:
Non-randomness as it is discussed here is "not an accumalation of mistakes". This refers to function, mutations that are not mistakes. These are changes that are made to overcome a particular problem. There is growing evidence of this:
Kiely, Tom. 1990. "Rethinking Darwin." Technology Review.
Lipkin, Richard. 1995. "Stressed Bacteria Spawn Elegant Colonies," Science News.
Francis:
Initially there seems to have been some excitement about adaptive mutations but the recent findings seem to suggest that adaptive mutations are due to hypermutations.
Nelson:
Hypermutations are incompatible with most models of Darwinian evolution. Usually they either kill off the organism or are too limited to an area of the genome. In this context hypermutations are obviously "neutral" although restricted to only a small part of the genome.
Francis:
Secondly even assuming that mutations are non random in function, how would this provide support for ID? Are you saying that the intelligence is present in the organism?
Nelson:
I'm saying that the robustness of the organism, the ability for these colonies to compute better than any parrallel processor that even exists today, is due to intelligent design.
Nelson:
If such primitive creatures are capable of such complex tasks then what we are seeing could be the makings of a paradigm shift, from a reductionist perspective, to a teleological perspective.
Francis:
I would not call bacteria 'primitive'. They might be single cellular but they have undergone the longest period of evolution.
Nelson:
Perhaps you misunderstood. By primitive I meant "old". Darwinian evolution goes from simplest to complex, so the older the organism, it is usually, said , the more simple it probably is.
quote:
Shapiro's views don't just amount to a important functional role for "junk DNA" and the growing irrelevance of the Modern Synthesis, but they also hold great potential for a very positive fruition of a robust teleological interpretation of life's history. As science moves in this direction, its difference from ID dwindles.
Nelson:
What we could be seeing is a glimpse of the designer's engineering skills, much like those of AI programmers.
Francis:
In this case the designer(s) seems to be the bacteria. How does the bacteria being a 'designer' help us determine if something designed the bacteria?
Nelson:
The bacteria is the parrallel processor. In that it is a designed computer, we can see a concept of how the designer designed these computers to proliferate life billions of years ago.
Francis:
Shapiro's work shows us how bacteria are organized, provide for signaling etc. How does this relate to ID though?
Nelson:
Shapiro's work doesn't show that bacteria are organized. What he showed was that with respect to solving complex problems, we are:
"thinking of genomes as complex interactive information systems, in many ways comparable to those involving computers."
J. A. Shapiro. Natural genetic engineering in evolution. Genetica, 86:99-111, 1992.
Francis:
To me the question is: Is this analogy structural or superficial?
Nelson:
This is a false dichotomy. If we view these packages of genes as information processors, then it is absolutely correct to call them computers.
Francis:
I agree that GA systems when applied to a large variety of problems are not always that succesful but in case of evolution we are talking about a relatively simple algorithm that has been shown to work quite efficiently.
Nelson:
Perhaps you misunderstood. My point was not that genomes are not always successful, but that they are able to change themselves, form a "super-mind" in order to solve new problems. It is not a "simple algorithm" that works efficiently. The quotes below don't seem to have any relevance to my discussion here either.
[ 08 March 2002, 12:51: Message edited by: Nelson Alonso ]
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Janitor@MIT
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Member # 125
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posted 08. March 2002 13:29
Hi, Nelson Alonso, I am interested in the “representation problem” in evolutionary biology and evolutionary computation and how it relates to the “intelligent” solution of problems.
The Blind Watchmaker suffers from more than one disability. He’s not only blind, he’s a bit “dim,” if you what I mean. He doesn’t only lack the faculty of sight, he also lacks foresight, planning, prediction, etc.; everything we would characterize as “intelligence.” Yet, strangely enough, his productions never fail to impress us for their artistry, ingenuity, and technical sophistication! The received theory, informed by this “ethos” of dysteleological “dumbing down,” must be constantly revised as we discover the computational power and sophistication of genomic representations. The prevailing paradigm isn’t merely an anachronism, it’s an impediment.
But even if we assume that these “representations” are sophisticated we face a problem: representations are inherently limited. If the representation is limited its evolution is limited. I’m interested in how the representation is expanded, how it evolves. I suggested in another topic that the representation problem is insoluble in traditional terms and that an AI or machine learning approach is warranted, especially as it only offers the potential for the “open-ended” evolution we believe in.
Evolution is invariably the problem of “evolving” intelligent solutions to problems. Whereas the limitations of the former approach are well explored. The limitations are exactly because every problem is specified to the nth degree, every problem must be “hand-tooled,” “tailored,” and requires constant appeals to an “Oracle” or designer. The whole field of evolutionary computation, bound by the Darwinian program ends up as an ironic appeal to “special creationism”! The Designer is omnipresent and omnipotent, even if he isn’t omniscient!
The continued existence and evolution of living organisms and populations is not so obviously dependent on the designer. They are autonomous. Now if I was an “intelligent designer” I can’t imagine why I would do it any other way! Maybe that bears repeating: If life is intelligently designed, I can’t imagine that it would be any differently designed than it is. I can’t say this about Darwinian evolution. I have no idea why such “intelligent” solutions are arrived at by such an “unintelligent” process. Of course, I wouldn’t have come to that conclusion if the Blind Watchmaker hadn’t proven to be such an inept and incompetent designer in vitro and in silico. (The Blind Watchmaker kinda reminds me of Uri Geller. Try to get him to do his magic under controlled conditions and the magic disappears and the flop sweat flows in torrents.)
Back to the “representation problem: my primary interest now is how the design of the code and the “system architecture” of the genome is an idealized platform (universally pre-adapted) for implementing adaptive/learning strategies: e.g., how the (Turing complete) code scheme bounds and conditions system response, buffers against random perturbations, stabilizes and distributes the system, drives searches forward, and facilitates recoding, etc. You’ll notice that all of these are principal concerns in AI and machine learning, but are barely touched upon in the Darwin-driven program of evolutionary computation. But that’s changing.
Evolution is applied science, not 18th century natural atheology.
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Bryan Cross
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Member # 51
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posted 08. March 2002 15:34
Nelson,
Imagine a computer that was programmed to edit its software depending upon its conditions. Such a software feature would not per se indicate ID. Nor would it per se indicate irreducible teleological features of the software. Likewise, imagine a computer that was programmed to link up with other computers and share data during certain conditions. Such a software feature per se would not indicate ID or irreducible teleology. Why? Because the possibility that these software features could have 'evolved' by random mutations + natural selection has not been ruled out. The same reasoning applies to the bacteria. As long as the bacterial toolkits and social activity have not been shown to be irreducible to ateleological activities, they are no more evidence for ID or teleology than they are for naturalism and ateleology. Per se, they give us absolutely no reason to expand the present scientific paradigm.
- Bryan
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Nelson Alonso
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Member # 52
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posted 08. March 2002 15:42
Great post Janitor.
Hello Bryan,
Possibilty in science is the worst argument you could possibly give in defense of a theory. I do not need to prove Darwinian evolution impossible in order to propose intelligent agency as the mechanism for such complexity. We have not observed, and it seems extremely unlikely that chance and contingency would produce such complexity.
It is ironic that critics of ID pooh pooh Behe, Dembski, et. al. for criticizing Darwinism, and yet in the same breath they demand that we prove evolution impossible before we propose ID.
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Nelson Alonso
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Member # 52
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posted 08. March 2002 15:57
Janitor your post reminds me of a syllabus for a course in machine learning that I once came across:
Machine learning is concerned with the design of algorithms that, rather than encoding explicit instructions or programs for the solution of specific problems, encode inductive mechanisms whereby solutions to broad classes of problems may be derived from examples. Whether the approach is inspired by biology (e.g., artificial neural networks) or by cognitive psycholog (e.g., traditional AI), machine learning aims at building computer systems capable of adapting to new tasks and learning from their experience.
Machine learning has found increasing applicability in fields as varied as banking, medicine, marketing, condition monitoring, vision, programming and robotics. Skilled professionals and researchers, who can apply machine learning technology to current business problems and push the limits of what computers can effectively do further, are in demand.
Objectives:
===========
At the end of this course, students will be able to:
- Determine and justify, given a problem, the suitability of machine
learning techniques to the solution of that problem
- Select, given a specific application, the most appropriate machine
learning technique to use
- Design and implement machine learning solutions to suitable problems
- Discuss the limitations of current approaches to machine learning
- Demonstrate creativity by suggesting ways to improve existing
techniques or developing new techniques and algorithms
- Communicate ideas and concepts clearly both orally and in writing
[ 08 March 2002, 16:04: Message edited by: Nelson Alonso ]
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Bryan Cross
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Member # 51
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posted 08. March 2002 16:27
quote:
Possibilty in science is the worst argument you could possibly give in defense of a theory. I do not need to prove Darwinian evolution impossible in order to propose intelligent agency as the mechanism for such complexity.
I'm not saying you can't propose it. You can propose anything you like. I'm saying that your argument carries no weight to a naturalist, because you are proposing an increase in ontology without showing that such an ontological increase is necessary. The principle of parsimony requires that the explanatory power of your proposal outweighs the ontological cost entailed by your proposal. IDers don't just want to produce arguments and evidence that are viewed as evidence for ID only by IDers. Suppose someone says, "I don't need to show that those crop circles weren't made by humans in order to propose that they were made by extra-terrestrials". Of course, but he's not going to convince anyone who doesn't already believe him unless he practically shows it to be impossible for humans to have done it. Likewise, if you want to convince anyone (who doesn't already believe you) that X cellular feature is intelligently designed, you have to do more than assert it.
quote:
We have not observed, and it seems extremely unlikely that chance and contingency would produce such complexity.
That is just an assertion that begs the question against the naturalist. If you are saying that this complexity is IC or CSI, that's different. But then your evidence is a simply a case of IC or CSI; not a sui generis argument for ID or irreducible teleology.
quote:
It is ironic that critics of ID pooh pooh Behe, Dembski, et. al. for criticizing Darwinism, and yet in the same breath they demand that we prove evolution impossible before we propose ID.
It is not ironic; it is quite rational given the principle of parsimony. The inference to intelligent design has to meet a higher standard than the inference to law or chance. This is why in Dembki's explanatory filter, the data *first* runs through the law and chance filters. You first rule out law and chance before you conclude that X was intelligently designed.
- Bryan
[ 08 March 2002, 16:32: Message edited by: Bryan Cross ]
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Nelson Alonso
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posted 08. March 2002 16:39
Bryan:
I'm not saying you can't propose it. You can propose anything you like. I'm saying that your argument carries no weight to a naturalist, because you are proposing an increase in ontology without showing that such an ontological increase is necessary.
Nelson:
A naturalist is free to have faith in his/her mechanism. But as far as I am concerned, I am proposing an inference to the best explanation, not a philosphy.
Bryan:
The principle of parsimony requires that the explanatory power of your proposal outweighs the ontological cost entailed by your proposal. IDers don't just want to produce arguments and evidence that are viewed as evididence for ID only by IDers. Suppose someone says, "I don't need to show that those crop circles weren't made by humans in order to propose that they were made by extra-terrestrials". Of course, but he's not going to convince anyone who doesn't already believe him unless he practically shows it to be impossible for humans to have done it. Likewise, if you want to convince anyone (who doesn't already believe you) that X cellular feature is intelligently designed, you have to do more than assert it.
Nelson:
The problem is that I didn't assert it. I showed how we have evidence of what is basically a super computer. And that super computers is best explained by intelligent design. We observe designers producing such systems, the system is obviously complex, and although more research is necessary, it is safe to propose intelligent agency as the mechanism. You are trying to shift the burden and have Darwinian evolution as the default explanation, I don't buy it.
Nelson:
We have not observed, and it seems extremely unlikely that chance and contingency would produce such complexity.
Bryan:
That is just an assertion that begs the question against the naturalist.
Nelson:
This is not an assertion, there is no evidence that the Darwinian mechanism can produce such complexity. We have observed no such thing.
Bryan:
If you are saying that this complexity is IC or CSI, that's different. But then your evidence is a simply a case of IC or CSI; not a sui generis argument for ID or irreducible teleology.
Nelson:
I think it would be interested to find the CSI, or the various IC systems needed to bring this about. And thats why I am here. Whether I do or do not does not take away from the observations, the machine properties, of the ability of these colonies.
Nelson:
It is ironic that critics of ID pooh pooh Behe, Dembski, et. al. for criticizing Darwinism, and yet in the same breath they demand that we prove evolution impossible before we propose ID.
Bryan:
It is not ironic; it is quite rational given the principle of parsimony. The inference to intelligent design has to meet a higher standard than the inference to law or chance. This is why in Dembki's explanatory filer, the data *first* runs through the law and chance filters. You first rule out law and chance before you conclude that X was intelligently designed.
Nelson:
It is parsimonous to contradict yourself in your own breath? We are not allowed to criticize Darwinism because it is negative evidence. And yet we are to prove evolution impossible. That is not a higher standard that is called "cheating". If someone proposes a mechanism for how this might have arisen through law and chance, then I would be more than willing to discuss it with respect to the mechanism I am proposing. I would then make predictions based on the the mechanism we do observe that does build things like machines, and machine learning principles. Based on ID we make predictions that guide investigations and we see who has the better track record that guides further research. You can hold ID to a higher standard than that if you want, but I don't have to. I'm not here to convince anyone, I'm here to discuss complex systems.
As far as parsimony goes, I have learned to question such concepts. If what at first seems to be a simple explanation turns out to be fantasy, we need to look at other explanations. Science should be about finding the correct path, not the wrong one just because it seems to be the simplest.
[ 08 March 2002, 17:01: Message edited by: Nelson Alonso ]
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Bryan Cross
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posted 08. March 2002 17:31
quote:
A naturalist is free to have faith in his/her mechanism. But as far as I am concerned, I am proposing an inference to the best explanation, not a philosphy.
Hopefully by 'best' here you mean best simpliciter, and not merely 'best from your point of view'. Part of what makes an explanation better simpliciter is that it entails less ontological stuff.
quote:
The problem is that I didn't assert it. I showed how we have evidence of what is basically a super computer. And that super computers is best explained by intelligent design.
Well, supercomputers of the electronic sort are definitely best explained by intelligent designers. That per se does not mean that communities of bacteria operating like a supercomputer are best explained by intelligent design. Just because ID is the best explanation of X does not mean that ID is the best explanation of anything that is in some sense similar to X. Arguments from analogy are weak, *especially* when an increase in ontology is being proposed.
quote:
We observe designers producing such systems, the system is obviously complex, and although more research is necessary, it is safe to propose intelligent agency as the mechanism. You are trying to shift the burden and have Darwinian evolution as the default explanation, I don't buy it.
Whether you buy it or not, the principle of parsimony requires that non-intelligent causes first be shown to be insufficient (to a significant extent). If this is not done, then appeals to ID are mere assertions.
quote:
This is not an assertion, there is no evidence that the Darwinian mechanism can produce such complexity. We have observed no such thing.
This looks very much like an argument from ignorance.
quote:
It is parsimonous to contradict yourself in your own breath?
I am not contradicting myself. Perhaps you misunderstood me, or I wasn't clear. I'm not defending dogmatism. I am pointing out that it is rational and right for critics of ID to expect from IDers objective arguments and evidence that show why the move to ID is worth the accompanying ontological cost. Anybody can "criticize Darwinism"; that's easy. It is much harder to provide objective evidence showing what Darwinism cannot do. That's the kind of thing Behe has done.
quote:
If someone proposes a mechanism for how this might have arisen through law and chance, then I would be more than willing to discuss it with respect to the mechanism I am proposing.
Ok. Let's say it developed through mutation and natural selection.
quote:
I'm not here to convince anyone, I'm here to discuss complex systems.
Does this mean that you don't want to convince those who do not hold your view to adopt your view?
- Bryan
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Nelson Alonso
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posted 08. March 2002 18:32
Bryan:
Hopefully by 'best' here you mean best simpliciter, and not merely 'best from your point of view'. Part of what makes an explanation better simpliciter is that it entails less ontological stuff.
Nelson:
No I mean best with respect to the observations.
Bryan:
Well, supercomputers of the electronic sort are definitely best explained by intelligent designers. That per se does not mean that communities of bacteria operating like a supercomputer are best explained by intelligent design. Just because ID is the best explanation of X does not mean that ID is the best explanation of anything that is in some sense similar to X. Arguments from analogy are weak, *especially* when an increase in ontology is being proposed.
Nelson:
The problem is that I'm not using an analogy. I'm not saying X is like Y, but Y is X. These algorithms and computation, as the Ben-Jacob himself, are better than even our own parrallel processors. "Of the electronic sort" is irrelevant here, I'm referring to function.
Nelson:
We observe designers producing such systems, the system is obviously complex, and although more research is necessary, it is safe to propose intelligent agency as the mechanism. You are trying to shift the burden and have Darwinian evolution as the default explanation, I don't buy it.
Bryan:
Whether you buy it or not, the principle of parsimony requires that non-intelligent causes first be shown to be insufficient (to a significant extent). If this is not done, then appeals to ID are mere assertions.
Nelson:
No, an assertion is a statement that is unsupported. Parsimony is the simplest explanation, it has nothing to do with showing non-intelligent causes are insufficient. However, I am interested, and I think the very genomes and processes used by these organisms, show that non-intelligent causes are insufficient. Now I am interested in delving into these processes and as an aside showing how sterile the RM&NS explanation is, but I am just as interested in positively proposing ID. And as I say in my previous post, I'm not interested in the simplest explanation, I'm interested in the correct one.
Nelson:
This is not an assertion, there is no evidence that the Darwinian mechanism can produce such complexity. We have observed no such thing.
Bryan:
This looks very much like an argument from ignorance.
Nelson:
Ignorance is usually defined as something that you are unaware of. There is a difference between being unaware of the evidence, and the evidence being non-existent.
Nelson:
It is parsimonous to contradict yourself in your own breath?
Bryan:
I am not contradicting myself. Perhaps you misunderstood me, or I wasn't clear. I'm not defending dogmatism. I am pointing out that it is rational and right for critics of ID to expect from IDers objective arguments and evidence that show why the move to ID is worth the accompanying ontological cost. Anybody can "criticize Darwinism"; that's easy. It is much harder to provide objective evidence showing what Darwinism cannot do. That's the kind of thing Behe has done.
Nelson:
As I have shown above, I am more interested in proposing a positive mechanism for an observation. But even this observation shows several things, such as the fact that what we are seeing is that not all mutations are truly random. We are seeing computations that are much more sophistiticated then even our modern computers. Both Ben-Jacob and Shapiro state this:
quote:
'the debate moved toward thinking of "evolution as biological function" rather than of evolution as accidental changes captured by selection.'
and
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The emergence of the new picture involves a shift from the pure reductionistic point of view to a rational holistic one, in which creativity is well within the realm of Natural sciences.
Now I'm not interested in proving negatives, in that I am not saying going to show you how evolution is impossible (until I do a study of the systems involved or of CSI, that is). I don't need to. To show evolution is sufficiently unlikely to produce such a system is enough.
Nelson:
If someone proposes a mechanism for how this might have arisen through law and chance, then I would be more than willing to discuss it with respect to the mechanism I am proposing.
Bryan:
Ok. Let's say it developed through mutation and natural selection.
Nelson:
Yes..go on.., I'm beginning to think you have no argument at all. For three posts now you have added nothing to this discussion.
Nelson:
I'm not here to convince anyone, I'm here to discuss complex systems.
Bryan:
Does this mean that you don't want to convince those who do not hold your view to adopt your view?
Nelson:
Not if the person in question simply makes assertions and then says "I am right, prove me wrong". I'm not interested in convincing people like that, they are already convinced.
[ 08 March 2002, 18:39: Message edited by: Nelson Alonso ]
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Jack Foster
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Member # 79
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posted 08. March 2002 20:16
quote:
Frances: . . . but in case of evolution we are talking about a relatively simple algorithm that has been shown to work quite efficiently.
Your "simple argorithm" is demonstrably not sufficient to produce evolvability. Janitor has it right:
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Janitor: I have no idea why such "intelligent" solutions are arrived at by such an "unintelligent" process. Of course, I wouldn’t have come to that conclusion if the Blind Watchmaker hadn’t proven to be such an inept and incompetent designer in vitro and in silico.
With AL, a sufficient genotype – phenotype map (g-p map) is a necessary condition for an AL organism to have evolvability. A sufficent g-p map constrains search space in a evolutionarily friendly way. Potential evolutionary trajectories are internally derived by the mapping, and only culled by selection. Without internally derived trajectories, Frances, your "relatively simple algorithm" is completely incapable of producing evolutionary progress. RM & NS, though clearly part of the answer, cannot be the complete answer.
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Frances
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Member # 169
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posted 09. March 2002 00:49
quote:
Originally posted by Jack Foster:
quote:
Frances: . . . but in case of evolution we are talking about a relatively simple algorithm that has been shown to work quite efficiently.
Your "simple argorithm" is demonstrably not sufficient to produce evolvability. Janitor has it right:
Did the simple algorithm produce CSI or not? Is it sufficient to produce evolvability? I'd say it is. Look at the results.
quote:
Janitor: I have no idea why such "intelligent" solutions are arrived at by such an "unintelligent" process. Of course, I wouldn’t have come to that conclusion if the Blind Watchmaker hadn’t proven to be such an inept and incompetent designer in vitro and in silico.
With AL, a sufficient genotype – phenotype map (g-p map) is a necessary condition for an AL organism to have evolvability. A sufficent g-p map constrains search space in a evolutionarily friendly way. Potential evolutionary trajectories are internally derived by the mapping, and only culled by selection. Without internally derived trajectories, Frances, your "relatively simple algorithm" is completely incapable of producing evolutionary progress.
An interesting assertion and I am looking forward to you providing some supporting evidence. But let's go back to the original issues: Did the algorithm produce CSI or not?
RM & NS, though clearly part of the answer, cannot be the complete answer.
Why not?
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