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Francisco Ayala: “You’re a heretic and blasphemer, but don’t ask me what I am.”

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Darwin's Gift to Science and ReligionFrancisco Ayala has taken an aggressive theological stance against intelligent design, even using words like “blasphemy” and “atrocity” to characterize it (go here). But if Ayala feels entitled to make such strong accusations against ID, one might wonder what Ayala’s own theological views are. I therefore emailed him and copied Michael Ruse:

Dear Prof. Ayala,

I’m writing to inquire whether in any of your writings you lay out your present religious faith (and, if so, where?). I’m copying my friend Michael Ruse because I find his criticisms of ID parallel your own, and yet he makes clear that he himself is an atheist. You, on the other hand, regularly cite your background in the Roman Catholic Church as a priest. Yet you left the priesthood and it’s not clear what aspects of the Christian faith you retain. Do you, for instance, believe in a personal God who created the world? Do you believe that humans experience continued conscious existence after they die? Do you believe that Jesus was God incarnate? I would appreciate any clarifications you can provide. Thank you.

Blessings,
Bill Dembski

Ruse got back to me first and suggested that Ayala would not be forthcoming about his religious views, whereupon Ayala got back to me, agreeing with Ruse: “What Michael Ruse told you about my not asserting publicly my religious convictions is correct. I have stated that on numerous occasions, quoted in all sorts of publications from The New York Times and Scientific American to religious journals and periodicals.”

Interesting that Ayala is willing publicly to acknowledge his former theological views as a Roman Catholic priest (presumably he embraced RCC dogma). And yet his present theological views are off limits. Perhaps when Dover II rolls around, Ayala will be an expert witness and under deposition be required to state his theological views. In the mean time, Ayala’s reticence about his present religious faith (or lack thereof) is at best a convenient ploy.

Comments
Why the Quantum? It from Bit? A Participatory Universe? Excerpt: In conclusion, it may very well be said that information is the irreducible kernel from which everything else flows. Thence the question why nature appears quantized is simply a consequence of the fact that information itself is quantized by necessity. It might even be fair to observe that the concept that information is fundamental is very old knowledge of humanity, witness for example the beginning of gospel according to John: “In the beginning was the Word.” Anton Zeilinger – a leading expert in quantum teleportation: http://www.petworlds.net/category/fish/petworlds
November 22, 2018
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Cassandra @ 300 "We can measure the Shannon information in a particular nucleotide sequence and we can see that that sequence is generated by known chemical and physical laws. How, then, can you continue to assert that information cannot be explained by the laws of physics? What, exactly, is your definition of information and how, exactly, can it be measured in a nucleotide sequence?" Francis Crick, Of Molecules and Men, page 41. "The flow of information thus goes: DNA -> RNA -> protein." OMM, page 43. "…we have, in effect, to translate the information from a four-letter language into a twenty-letter language, and this is by no means easy." OMM, page 57. "…so that the language that is used in the nucleic acid polymers is universal." Richard Dawkins, River Out of Eden, page 11. "You can treat the genetic code as a dictionary in which sixty-four words in one language (the sixty-four possible triplets of a four-letter alphabet) are mapped onto twenty-one words in another language (twenty amino acids plus a punctuation mark)." ROE, page 19. "Life is just bytes and bytes and bytes of digital information." ROE, page 150. "Indeed, the whole DNA/protein-based information technology is so sophisticated – high tech, it has been called by the chemist Graham Cairns-Smith – that you can scarcely imagine it arising by luck, without some other self-replicating system as a forerunner." Dawkins, The Selfish Gene, viii. "This reason is that we animals are the most complicated and perfectly designed pieces of machinery in the known universe." Information Theory, Evolution, and The Origin of Life, Hubert P. Yockey, page 2. "The reason that there are principles of biology that cannot be derived from the laws of physics and chemistry lies simply in the fact that the genetic information content of the genome for constructing even the simplest organisms is much larger than the information content of these laws. ITEOOL, page 2. "The existence of a genome and the genetic code divides the living organisms from nonliving matter. There is nothing in the physico-chemical world that remotely resembles reactions being determined by a sequence and codes between sequences." ITEOOL, page 3. "Information theory and coding theory and their tools of measuring the information in the sequences of the genome and the proteome are essential to understanding the crucial questions of the nature and the origin of life." ITEOOL, page 5. "The belief of mechanist-reductionists that the chemical processes in living matter do not differ in principle from those in dead matter is incorrect. There is no trace of messages determining the results of chemical reactions in inanimate matter. If genetical processes were just complicated biochemistry, the laws of mass action and thermodynamics would govern the placement of amino acids in the protein sequences." ITEOOL, page 6. "Information, transcription, translation, code, redundancy, synonymous, messenger, editing, and proofreading are all appropriate terms in biology. They take their meaning from information theory (Shannon, 1948) and are not synonyms, metaphors, or analogies." ITEOOL, page 7. "The genetic information system is the software of life and, like the symbols in a computer, it is purely symbolic and independent of its environment. Of course, the genetic message, when expressed as a sequence of symbols, is nonmaterial but must be recorded in matter or energy." ITEOOL, page 8. "Life is guided by information and inorganic processes are not." ITEOOL, page 20. "The Central Dogma (ever hear of that???) states that information can be transferred from DNA to DNA, DNA to mRNA, and mRNA to protein." ITEOOL, page 94. "…They find the genetic code to be very near or possibly at a global optimum for error minimization." ITEOOL, page 118. "…no natural chemical procedure exists to form an optically active biochemistry." ITEOOL, page 187. "Let us remind ourselves that the laws of physics and chemistry are much like the rules of grammar. They must be obeyed, but there is not enough information in the rules of grammar to produce Lincoln's Gettysburg Address." Should I go on??? All three of these authors are, or were, darwinists. They "get it." Information and life are inextricably linked. Can't have one without the other. Go argue with Crick, Dawkins, and Yockey. Well the alive one of the three, go argue with him. And lastly, you say: "The fact that we can model certain processes using terms like “information” and “language” does not justify equivocating on those terms." Surely you jest. Equivocating? That's rich. Go into any biology department in the country or world for that matter and tell them there is no such thing as biological information or a genetic language. hee hee. May I also suggest a Google search of the term "bioinformatics." Pity. All these universities spending all this time, effort, and money to develop these programs. Be pretty embarrassing for them when they find out THERE'S NO SUCH THING AS BIOLOGICAL INFORMATION. You're killing me. No really, you are. Nice... By the way, did you mention what universe you are from? I'd like to tell the other earthlings before it's too late... Oh wait, there go Johns Hopkins and Boston University. Not to mention the Oxford journal of Bioinformatics. Darn. I'm sure there are others. Somebody help... We've got to stop them... They need to know... They'll make fools of themselves... I have a solution. They all just need to go back and rewrite everything ala Richard Dawkins. You know, with him it's all "apparent" design and the "illusion" of purpose. So now I suppose we'll be treated to the "apparent" information in the genome and the "illusion" of a genetic language. They can use "find and replace" on the illusion of their copy of MS Word or the apparent Mac word processor. Shouldn't take long. Let me know when they're finished. I'm sure they'll all be grateful to know this...tgpeeler
June 7, 2010
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gpuccio @ 308, I appreciate the effort you put in your responses to me but keep in mind that I am in the moderation queue and can't address long posts properly. Let's try to come to agreement one single step at a time. Here is my re-labeled example. [DNA_1]=100....0....111 [DNA_2]=100....1....111 Notice there is a single-bit change in the "code". The "codes" are 1 million bits long in my "lab-designed" life-form. Only one bit can change each generation. What are the odds of getting from DNA_1 to DNA_2 with a population of 1 million? I say it is likely that you will hit your target with the very next generation. Notice that there is no lower-level detail involving real-world chemistry required at all since the example works on the same level as the Dembski-Marks papers. This comment addresses only the one single ID point, that evolution cannot generate information without intelligent intervention. Here we see that the Evo position, that environmental feedback and random mutation are quite capable of modifying "information", is viable. Any argument refuting the sudden appearance of a one million bit string of data from a "random starting point" is not refuting evolution, since it is addressing the random mutation component only. Evolution is not random at all, only mutation can be considered in some way, random.Toronto
June 7, 2010
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Sorry, I messed with the tags again. In my previous post, Toronto's quote is up to: "Are 2 hydrogen atoms and an oxygen atom in a molecule, a code for water, or is that water?", while my post starts at: "I don’t understand why you ask such obvious things. Maybe you are not familiar with biology."gpuccio
June 7, 2010
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Toronto: Where is your decoder? If DNA is a code, something must convert that coded symbol to the real entity before use. If there is no decoder, then DNA is not a symbolic code for the component used in a chemical process, it already is that component. Are 2 hydrogen atoms and an oxygen atom in a molecule, a code for water, or is that water? I don't understand why you ask such obvious things. Maybe you are not familiar with biology. The answers are very simple. DNA is a code (I am obviously sepaking of the protein coding genes). It contains in its sequence the information for the proteins, coded according to what is correctly called by everybody the genetic code. The real entity is the protein, not the DNA. The decoder is the translation apparatus. It is formed by about 100 proteins and the ribosomal RNA. But the part which specifically keeps the key to the translation of the code is formed by the "Aminoacil RNS synthases", a set of 20 different proteins, each of them very long and complex and multidomain, which form two different classes of 10 each. Each protein of this set is specific for one aminoacid, and has, in a different part of the molecule, the correct anticodon to recognize the specific codons in mRNA. Without this very complex decoder system, the information in DNA is completely useless. And DNA, in itself, is a very inert molecule, its only real role is to be a mass memory for functional information. And finally, just to be clear, "2 hydrogen atoms and an oxygen atom in a molecule" are just a molecule of water. They don't code for anything.gpuccio
June 7, 2010
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Toronto: Why unrelated? I thought I had specified why: "Let’s assume that you have to arrive to a new sequence (B), with a new fold and fucntion, from an existing sequence (A). Let’s assume that A and B have no significant homology (the standard case for two different folds and superfamilies)." In other words, I was modeling the transition which only could give rise to a new fold in a new superfamily. Is that clear. Again I quote from my post: "In this simple reference context, which must have happened, if any new protein fold has been discovered by darwinian mechanisms, RV acts on the starting sequence A by single random events (each of which can change one or more AAs) in time." Proteins in different superfamilies are unrelated. You must remember that the primary sequence of many proteins is perfectly known. It is not a mystery. Everybody can use BLAST or any other similar tool to compare them. And protein domains and folds are unrelated. They have no significant homology. The ASTRAL SCOP Genetic Domain Sequence tool, version 1.75 (the latest) gives the following numbers: a) 1195 domains which represent each fold b) 1961 domains which represent each superfamily c) 6041 domains filtered with E values >=10 d) 6258 domains with less than 10% identity All these criteria are guarantee that the structures are unrelated. Even if we take the strictest, the difference in folds, we still have at least 1195 independent structures whose emergence we have to explain. And remember two key points: 1)About half of these domains seem to have been already present in LUCA 2) The average single domain length is about 100 -150 AAs, with range 36 - 692 I have to remind you that the two binary sequences you give in you post #306 are not only extremely short, but also heavily related (75% identity). I really don't know what they were supposed to show. So, maybe you should stop playing tricks with binary sequences, and start discussing seriously.gpuccio
June 7, 2010
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Toronto,
"If DNA is a code, something must convert that coded symbol to the real entity before use. If there is no decoder, then DNA is not a symbolic code for the component used in a chemical process, it already is that component. Are 2 hydrogen atoms and an oxygen atom in a molecule, a code for water, or is that water?"
Keep going Toronto...you'd be an IDer soon.Upright BiPed
June 7, 2010
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gpuccio @ 305,
The new sequence is modeled as emerging from a pre-existing, unrelated sequence.
Why unrelated? What is the probablity of getting from [stateN] to [stateN+1] in the following... [stateN]........1011 [stateN+1]......1111 ...if only one bit changes each generation? Your answer should 1 in 4, not 1 in 16. For a length of 32 bits it would be one in 32, while N bits would be 1 in N. Where is your decoder? If DNA is a code, something must convert that coded symbol to the real entity before use. If there is no decoder, then DNA is not a symbolic code for the component used in a chemical process, it already is that component. Are 2 hydrogen atoms and an oxygen atom in a molecule, a code for water, or is that water?Toronto
June 7, 2010
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Cassandra (#299): I’m afraid you haven’t. It’s quite clear that the one calculation you provided is for the odds of a particular nucleotide sequence (or the protein it transcribes to) appearing ex nihilo. Any calculation that reflects observed evolutionary mechanisms will have a time component. Wrong. The time component is not relevant. What is relevant is the number of trials in the random search, which is always taken in consideration in all ID discourses, usually under the term "probabilistic resources". In other words, the model is simple: Let's assume that you have to arrive to a new sequence (B), with a new fold and fucntion, from an existing sequence (A). Let's assume that A and B have no significant homology (the standard case for two different folds and superfamilies). Let's assume that the engine of variation is only random variation (random events of any type). That's the standard neo darwinist assumption. Let's assume, for simplicity, that A and B are of the same length (approximately). In this simple reference context, which must have happened, if any new protein fold has been discovered by darwinian mechanisms, RV acts on the starting sequence A by single random events (each of which can change one or more AAs) in time. Now, let's assume that the intermediaries between A and B are not functional, or not functional enough to undergo positive selection. That rules out NS form this specific scenario. Obviously, NS can start to act as soon as we get B. At any moment, in a real scenario, anybody can prove that some intermediary is selectable. In that case, the scenario will be "resized" to the transition from A to, let's say, A', and then from A' to B. But only on evidence, or at least reasonable assumnption, that A' is selectable. Finally, please take notice that B is not a single sequence, but a subset of sequences in the search space: all sequences which exhibit the new fold and the new function. Let's call it "the B target space". That is the model. Now, each v ariation event, whenever it happens, can be considered as a random trial in the search space (you get a different sequence form the search space, in a random way). The result of that trial can be evaluated in a binary way, as a success (you got B; you found the B target space). Or a fialure (you didn't). The probability of success in a single trial is simply the ratio between target space and search space (assuming a practically uniform distribution, which is the only reasonable assumption in this context). But you have time. Correct. And you can repeat your trials many times. Correct. Again, time is not the relev ant factor- The number of trials is the relevant factor. There is no difference if you toss a coin 1000 times in one hour or in one year, the probabilities of getting some specific result remain the same. You can get an estimate of the probabilities of getting B in n trials by a statistical calculation, taking into consideration the probability in each single trial and the number of trials. Again, time is not relevant, and nobody is modeling the new sequence as appearing ex nihilo (that would be true in an OOL scenario). The new sequence is modeled as emerging from a pre-existing, unrelated sequence. Time can be considered only when, after having calculated the probability of the supposed transition, we have to evaluate if the time available in our model is enough to allow sufficient trials to get to a vaguely reasonable probability of final success. Further, you have failed to answer my simple questions from my 238, echoing Petrushka’s 227: I’m a bit confused about how you quantify FAI. What units ins it measured in and can you give me an example of a measurement? Under what circumstances would a point mutation change the quantity of FAI? Does anyone else use this unit? What is the mathematically rigorous definition of FAI? Can you please provide an example or two of calculating FAI for a real world biological organism or even a subsystem? Strange, I would say I have done exactly that in my post 239, with further information in all ny following posts on this thread. Have we read different threads? I have also taken again the discussion in greater detail on the new thread on Andy MacIntosh's paper, in answer to Petrushka. You can check that btoo, for reference. Please note that just from the start of my post 239 I have clarified that FAI does not mean anything, and that we should speak of CSI and of its subsets FSCI and dFSCI (and BA, who had in some way used the expression "you have no mechanism to generate functional algorithmic information by material processes" seems to agre that he was not trying to define a new category). So, all my discussion is about dFSCI. Of that I have given a rigorous definition, a way to measure it, examples of application of the measure to proteins and even to Hamlet! What can I do more? :) So, instead to just state that I have failed to answer, you could more correctly say that you don't agree with my answers. That would be fair. And, if you want, you could also explain why.gpuccio
June 7, 2010
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Cassandra there was nothing particularly criptic in what you seem to imply. I simply wanted to establish that you haven't even a conceptual clue as to a physico-chemical explanation for the existence of funtional nucleic sequencing. Telling us something can change over time is hardly an explanation for its existence. The hood on my car will rust away given enough time. I will be able to describe it's demise by purely chemical laws, but there is nothing in the metal that will tell me how it came to be a hood on a car.Upright BiPed
June 6, 2010
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Cassandra: "We can measure the Shannon information in a particular nucleotide sequence and we can see that that sequence is generated by known chemical and physical laws." 1. That makes no sense. Shannon information is merely a measure of decrease in uncertainty -- basically measuring bit storage capacity. This does not tell us anything about the pattern in question either resulting or not resulting from physics or chemistry or from chance or anything else for that matter. The generation of the pattern is a completely separate issue. 2. A nucleotide sequence is not defined by the physical properties of the nucleotides, in the same way that the sequence of letters in this paragraph of mine is not defined by the properties of the pixels used to "write" the letters. 3. The fact that life operates according to laws of physics and chemistry does not mean that it can organize itself utilizing only physics and chemistry. A running, operational computer also operates according to the laws of physics and chemistry, yet its organization and sequencing is not defined by the physical properties of the material which is utilized in its construction. At the information processing level of life -- especially concerning nucleotides -- we also see the same type of "non-lawful" organization as is seen in the computer example. In fact, if a sequence of nucleotides were constrained by the laws of physics and chemistry there would be no degrees of freedom for it to carry information. We would merely have a rigid crystalline structure with no potential for variability and evolution. Is this making sense so far?CJYman
June 6, 2010
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Upright BiPed (301),
“We can measure the Shannon information in a particular nucleotide sequence and we can see that that sequence is generated by known chemical and physical laws.” Really? You can show the physical and chemical laws that lead to the origin of functional nucleotide sequences from their non-functional counterparts? Let me see it. Thanks.
Your restatement of my claim is inaccurate. I said nothing about the "origin of functional nucleotide sequences from their non-functional counterparts." If you have a question about what I actually said, I'll be happy to answer it.Cassandra
June 6, 2010
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"We can measure the Shannon information in a particular nucleotide sequence and we can see that that sequence is generated by known chemical and physical laws." Really? You can show the physical and chemical laws that lead to the origin of functional nucleotide sequences from their non-functional counterparts? Let me see it. Thanks.Upright BiPed
June 6, 2010
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tgpeeler (297),
Cassandra says: “You seem to be asserting that DNA is a code that cannot be explained by means of natural laws, but that’s exactly the question under consideration. When we look at the internals of a cell, we see normal (bio)chemistry in action. You can model the nucleotides as a code, but what’s really happening is chemical reactions and physics. That’s as natural as it gets.” What do you not understand? OF COURSE there are chemical reactions described and prescribed by physical laws. But the biological INFORMATION, which is expressed in the GENETIC CODE/LANGUAGE is not explained by the laws of physics.
We can measure the Shannon information in a particular nucleotide sequence and we can see that that sequence is generated by known chemical and physical laws. How, then, can you continue to assert that information cannot be explained by the laws of physics? What, exactly, is your definition of information and how, exactly, can it be measured in a nucleotide sequence? By the way, your implicit assertion that DNA contains a language comes dangerously close to assuming your conclusion (again). The fact that we can model certain processes using terms like "information" and "language" does not justify equivocating on those terms.Cassandra
June 6, 2010
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gpuccio (292),
First of all, I have answered Aleta’s “objection” in my previous post.
I'm afraid you haven't. It's quite clear that the one calculation you provided is for the odds of a particular nucleotide sequence (or the protein it transcribes to) appearing ex nihilo. Any calculation that reflects observed evolutionary mechanisms will have a time component. Further, you have failed to answer my simple questions from my 238, echoing Petrushka's 227:
I’m a bit confused about how you quantify FAI. What units ins it measured in and can you give me an example of a measurement? Under what circumstances would a point mutation change the quantity of FAI? Does anyone else use this unit?
What is the mathematically rigorous definition of FAI? Can you please provide an example or two of calculating FAI for a real world biological organism or even a subsystem?Cassandra
June 6, 2010
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Apollow (290),
Are you taking issue with any of my statements at #286? … 1) that you were question begging in your accusation of circular reasoning;
I ignored that as a silly and patently unsupportable attempt at a tu quoque.
2) that there are two putatively plausible, basically opposing, and competing explanations for the source of coded information;
You are here assuming facts not in evidence, to use lawyerly jargon. It is certainly possible to model nucleotide sequences as codes. That does not justify the equivocation of treating them as intelligently designed codes.
3) that there are two ways of verifying empirically that chance acting in accordance with natural law is the best explanation for coded information (I’m open to any other explanations that would show why intelligence is an unnecessary component of abstract functional specification);
I'm not asking about codes. I'm asking for a mathematically rigorous definition of CSI (or FSCI, or dFSCI, or whatever the acronym de jour might be) so that it is possible to determine if various known types of mutations can increase or decrease that quantity.
4) that we have empirical evidence, already present and abundant, that intelligence is the only verifiable source of coded information apart from the phenomenon of subject?
Let's start with some rigorous definitions and measurements before skipping ahead to conclusions, shall we?Cassandra
June 6, 2010
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Cassandra @ 283 "You seem to be assuming your conclusion by saying that codes are only the result of intelligent design. If you define “code” in that way then your conclusion is trivially true but irrelevant to what we observe in DNA." And Aleta @ 284 "Cassandra is exactly right. tgpeeler assumes the conclusion. And, he writes, “At the risk of oversimplifying, …” Yes, vastly oversimplifying." I've probably got better things to do but because I care, I'm going to point out the egregious flaw in both of your statements. Cassandra for making it and Aleta for agreeing without, apparently, either of you actually bothering to read what I said. The argument is not circular. IF I said that a code was only intelligently designed and the way I knew something was a code was that it was intelligently designed, then that would indeed be circular. Unfortunately for you, that is not what I said. I said a code uses symbols and rules (look it up) and that there is no way to explain a code, any code, in terms of the laws of physics. Hardly the same thing, now, is it? Let me reiterate and use M-W so you don't think I'm making this up. code: a system of signals or symbols for communication (note that I am not claiming a code is something that is intelligently designed, yet) Claim: there is no way natural processes, as described by the laws of physics, natural laws, however you want to say it, can explain a code (or a language) BECAUSE, BECAUSE the laws of physics describe, HELLO, physical things, the interactions of sub-atomic particles in energy fields. The laws of physics have NOTHING TO SAY about why a symbol, or set of symbols, means one thing and another combination of them means another. In other words, ABSTRACT things. Remember this little mantra, it may help. Physics explains physical things and minds explain abstract things. Let me spell it out for you in another way. Physics is all about the material world. Information is abstract. It is encoded into physical substrates by means of a code or language for transmission and decoding on the other end. It is a fundamental categorical mistake to expect to explain the abstract (information) in terms of the physical. It can't be done. It can't ever be done. It's IRRATIONAL to try, or claim that it can be done. Particularly when it has been explained ad nauseum. NOW comes the part where I say that only a mind can explain a code, or a language. I offered you the opportunity to prove me wrong by giving us an example of a code described by physical laws, but NOOOO, you twisted what I said, making what is called a straw man argument, and completely ignored what the real argument was. You are both either extremely careless or lack any kind of intellectual integrity. Please address the argument if you care to continue with this discussion. p.s. Cassandra says: "You seem to be asserting that DNA is a code that cannot be explained by means of natural laws, but that’s exactly the question under consideration. When we look at the internals of a cell, we see normal (bio)chemistry in action. You can model the nucleotides as a code, but what’s really happening is chemical reactions and physics. That’s as natural as it gets." What do you not understand? OF COURSE there are chemical reactions described and prescribed by physical laws. But the biological INFORMATION, which is expressed in the GENETIC CODE/LANGUAGE is not explained by the laws of physics. Get it? Information MUST BE encoded in a physical substrate of some kind but it's APART from the physical substrate. I'm honestly pretty amazed that neither of you apparently grasp this elementary point. I don't know how to make it any plainer.tgpeeler
June 5, 2010
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Cassandra: If you want, you can check the following old thread: https://uncommondescent.com/intelligent-design/ev-ware-dissection-of-a-digital-organism/ and the discussion on Mark Frank's blog, which I referred to previously: http://mark_frank.blogspot.com/2009/01/lets-calculate-some-csi.htmlgpuccio
June 5, 2010
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Aleta, Cassandra et al: I paste here another post of mine form another recent thread, which can be relevant to the present discussion. The main point I would like to emphasize here is the quantitative evaluation of the power which can be assigned to different causal models, on the basis of both theoretical and empirical considerations. The key concept is the number of coordinated mutations which are necessary for a new selectable trait to appear, in other words the number of random variation events which must be present at the same time (even if randomly generated in successive steps) for a new selectable function to be added to a previous context. Behe has shown very convincingly (in TEOE) that, on the basis of purely empirical data, the threshold of what RV can accomplish in the extremely favourable context of bacterial or protist environment (extremely big populations, extremely high reproduction rate) can be reasonably put at 2-3 coordinated mutations. That is a very important point, because it means that any supposed darwinist scenario for any specific moleculary macroevolutionary transition (if and when darwinist will care to offer one) will have to deconstruct the transition in single selectable steps which are not more than 2-3 coordinated mutations distant one from the other. Good luck! Anyway, here is my post (from the thread about neo-Lamarckism): To steer back to Lamarckism, a brief summary/proposal. Three procedures which can modify the genome: 1) Random Variation + Natural Selection (RV+NS). Traditional neo-darwinist theory. Minimal power (small changes, usually acts mainly through negative NS of non functional mutations, but can fix and expand minimal, non complex mutations which can, in particular contexts, confer some benefits, usually through some concomitant loss of function: example, antibody resistance due to point mutation of target structures). 2) Adaptation + NS. Adaptation takes place probably through pre-existing structures and algorithms of response which allow the incorporation and utilization of external information to create a selective genome modification. Power: discreet. Possible examples: antibody resistance or other functions obtained through HGT, including the algorithmic tweaking of existing information to accommodate new, slightly different targets (plasmid information, emergence of nylonase from penicillinase); antibody affinity maturation. The adaptational algorithms must be already present in the living being. They can be rigidly deterministic, or use partial random search in the context of a deterministic algorithm, and they usually incorporate external information: in antibody affinity maturation, for example, controlled random hypermutation acts on specific segments of the genome, and the information present in the external antigen is used to effect an intelligent selection of the results. 3) Intelligent design. Power: limited only by the knowledge available to the designer and by his power of implementation. Here the input of information comes from an external source (the designer), who is a conscious intelligent being of some kind. The designer must have previous information about the result to be obtained, and must have access to some modality of manipulation of the physical support of biological information. The information inputted by the designer can be of different kinds (one does not esclude the others): a) Previous knowledge of the final information to be implemented (for instance, previous knowledge of the exact sequence of nucleotides/aminoacids which allows the desired function. b) Previous knowledge of the desired function, which can be used to effect intelligent selection after a controlled random search, especially if point a) is not available. c) Previous knowledge about the search space structure for the desired functional ouptut, which can allow a controlled and more efficient random search by defining specific constraints and procedures. In other words, some knowledge of the desired function must always be present (teleologism) for design to be implemented. Knowledge of the detailed information which confers the fucntion can allow a process of direct implementation of that information (point a). On the contrary, knowledge of the function but not of the detailed information needed in the output, and/or knowledge of the structure of the search space, will allow indirect design, with the use of intelligent search algorithms, incorporating possibly controlled random variation, and usually intelligent selection. Finally, if the indirect search algorithm is not used directly by the designer, but only incorporated in the genome for future use, if and when new external information will be available, then we are again in point 2, adaptation. In this case the role of the designer is only to design the algorithm, which will automatically produce the necessary output as soon as it is activated by the input of the pertinent external information.gpuccio
June 4, 2010
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slightly off topic but not by much: Image of The invisible - Thrice (with LYRICS) http://www.youtube.com/watch?v=WWery1h7e1Qbornagain77
June 4, 2010
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Cassandra (#287): do you accept that the processes involved in gene expression are explained by chemistry and physics? First of all, I think that Apollos was talking about the origin of DNA code, and of DNA's coded information, that is the origin of the information in the genes. That's not the same thing as the "gene expression", which seems to relate more to gene regulation and transcription. So, if we are speaking of the origin of protein genes, for instance, I would definitely say that it is not expalined by chemistry and physics. That's usually a very well understood point. Chemistry and physics can explain well how nucleotides (or aminoacids) join to form long sequences, provided that the correct cell machinery for that is present. But they can in no way explain wht they form that specific sequence which is functional. For proteins, the only explanation is that the sequence is written in DNA. For DNA, the sequence was written in previous instances of DNA, and is copied down. Nobody knows how the functional sequences originated. That's exactly the problem we debate here. There are fundamentally two approaches: one mechanichal, based on RV and NS, which for many reasons does not work. And one based on the concept of design, which has all the potentialities to describe correctly what we observe. That's what all the debate is about.gpuccio
June 4, 2010
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Cassandra: First of all, I have answered Aleta's "objection" in my previous post. You say: Thanks for the detailed response. Could you please point out the specific posts on the other threads where you provided a detailed mathematical definition of FAI or FSCI and where you have calculated this quantity for a real biological system of some sort? I have pasted in my #239 many significant points from two recent posts of mine in recent threads. I refer you also to my posts #185 and #188 in this thread for othe rimportant points. In the past, I have debated these things in great detail with many of different opinion, but as I have been absent form UD for a few months, I would not know how to point you to those old threads. A very interesting quantitative debate took place, some time ago, on Mark Frank's personal blog, with some good darwinists, the best of which IMO (without offence for the others) was Zachriel. Those discussions were interesting, and I think they should be still available on Mark's blog. KF, BA, StephenB and many others have debated these points many time, in great detail, and I must say with great patience, with all the kinds of interlocutors: strict darwinists, theistic evolutionists, religious people of all kinds, atheists of all kinds, or just with silly trolls whose only purpose was to provoke and blindly criticize. I have cooperated with KF and StephenB to the realization of the section "Frequently Raised But Weak Arguments Against Intelligent Design", in the Quick Reference Resources of this blog, where you can again find our views about the quantitative problem of CSI. Axe, Abel, Trevors, Durston and others have published very good papers in peer reviewed literature about these points. I have referenced the most important in my posts in this thread. I would definitely add the non ID paper suggested by Zach Bailey at #236. We in ID have always been interested in a detailed discussion of the quantitative measurement of CSI in proteins. We have spent hours and hours debating that in as much detail as possible with everyone interested. Frankly, seeing people like Aleta jump here out of the blue, and happily stating: Good luck, Petrushka – no one here has ever answered that, or any similar, question about a biological entity. and similar false platitudes, in a thread where a lot of long posts had already been offered on the subject, in a blog where hundreds of long and detailed posts have been offered on the subject, is not a comforting sign. As you can see, Aleta has at least offered some reasoning, and I have offered my answer. That, for me, is constructive exchange, and I am ready to go on, even on the dangerous limit of 290 posts.gpuccio
June 4, 2010
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Aleta (#273): That’s the answer that you don’t want to accept. Wrong. I accept very easily what you say, only it is not an answer. I will try to clarify why. The problem is simple. The causal model of neo darwinisms assumes two different moments which happen sequentially: RV generates functional information, and NS fixes and expands it. It is obvious that the working of NS is based on necessity, and cannot be evaluated in terms of probability and statistics. Nobody denies that, least of all we at ID. But the fact is that NS can only select new function which is already present. Moreover, the function must be relevant enough to be selectable in terms of increased reproduction and survival. Any change which has not such properties cannot be even "seen" by NS for a positive selection. Obviously, NS acts also negatively, eliminating variation when it is "detectable" in terms of sufficient loss of function. But negative selection alone, while useful to mitigate genetic entropy, cannot help generate new information. Positive selection is necessary for that. Well, the point is that, while NS certainly acts according to necessity, RV is by definition random, and can certainly be evaluated according to a scientific, quantitative analysis, in terms of probability and statistics. In other words, a model which implies a random search as part of its explanation must be credible from a statistical point of view for the part of the model itself which implies a random search. It's that simple. Nobody is trying to analyze the NS part in terms of probability. We are only trying to analyze the RV part, something that darwinists apparently do not to want to do. In my analysis, I have repeatedly stated that I was referring to the functional unit in proteins, protein domains. The work by Axe has the same approach. Our point is that protein domains are already complex enough to be beyond the possibility of a random search. When we measure the functional complexity of protein domains, or of simple domain proteins, it is perfectly correct to ask: how was that functional information discovered? How was the search problem solved? Darwinists have no credible answer. They continue to hope that there exists some path where single steps are selectable, but that is simply not true. They speak of smooth transitions form one island to another, but the primary sequences of proteins which we know tell us that such selectable transitions do not exist. So, the simplest problem in the proteome, the emergence of thousands of different protein folds and domains, has no credible answer in terms of RV and NS, simply because RV cannot find the information which NS ought to recognize. It's as simple as that. Therefore, all our discourses about dFSCI are perfectly legit, because they apply only to the RV part of the model. As soon as, or as far as, darwinists can show clearly definable selective steps which are credibly selectable at the molecular level, we will happily restrict our quantitative analysis to the transition between such steps, in other words, again to the purely random part. Therefore, your objection: All calculations of CSI et al are simple probability calculations that all the component parts of whatever is being considered came together simultaneously and entirely by chance. They do not take into consideration any causal chain of events that could have brought the thing under consideration into existence through a set of steps. is simply not pertinent and not true. First of all, for a statistical analysis there is no need at all that the events happen simultaneously. You can have as many steps as you want, but if they are random they are random, and you can evaluate the probabilities of a specific result, given the search space and the probabilistic resources. A causal chain of events becomes non random only if specific laws, like NS, act on the events. In other words, the steps must be selectable (or obey to any other known law of necessity). Otherwise, the process remains perfectly random. You say: Since no one believes that anything happens by a whole bunch of parts just coming to together by chance, such calculations of CSI are irrelevant: they eliminate a hypothesis (pure chance) that no one thinks happened anyway. That's not true. Darwinists do believe that the information in proteins, or genomes, originated by pure chance, until something could be selected. Darwinists do believe that new protein domains, new proteins, new functions, must be found by random variation, in random steps, until a new selectable step is achieved. Remember, NS is not like the Weasel algorithm: it does not know the solution. Otherwise, it would be intelligent selection. NS is blind to anything which is not a detectable function powerful enough to affect reproduction and survival. In all the rest of the procedure, RV is absolutely alone.gpuccio
June 4, 2010
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Cassandra, typically the phrase, "to be perfectly clear," is followed by a clarifying statement, and not another question. ;-) Are you taking issue with any of my statements at #286? ... 1) that you were question begging in your accusation of circular reasoning; 2) that there are two putatively plausible, basically opposing, and competing explanations for the source of coded information; 3) that there are two ways of verifying empirically that chance acting in accordance with natural law is the best explanation for coded information (I'm open to any other explanations that would show why intelligence is an unnecessary component of abstract functional specification); 4) that we have empirical evidence, already present and abundant, that intelligence is the only verifiable source of coded information apart from the phenomenon of subject? Or something else? Thanks in advance for any clarification.Apollos
June 4, 2010
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Cassandra- " Is your contention that the processes themselves could not have arisen without intelligent intervention?" This is the whole point. :-/Phaedros
June 4, 2010
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Apollos (286), To be perfectly clear, do you accept that the processes involved in gene expression are explained by chemistry and physics? Is your contention that the processes themselves could not have arisen without intelligent intervention?Cassandra
June 4, 2010
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Cassandra accuses Peeler of circular reasoning in #282, and then turns right around and begs the question in regard to the source of DNA code. The item on the table is the source of DNA's coded information, and there are two explanatory paradigms in competition: 1) Coded information is the result of known or unknown natural laws. If known, these laws should be demonstrated. If unknown, they are scientifically invalid until discovered. 2) Coded information is the result of active input by an intelligent agent. There are two ways to confirm explanation #1: a) demonstrate/elucidate the laws which govern the spontaneous formation of coded information -- absent intelligent input; b) Prove empirically that intelligence is purely the result of natural law. Explanation #2 has empirical support already: coded information is the result of intelligent intervention, and no known laws exist which can explain its spontaneous generation. Anyone is welcome to exercise faith in regard to finding a natural law, independent of agency, which governs/explains coded information. However until such faith is confirmed by hard evidence, design remains the best explanation for the presence of coded information.Apollos
June 4, 2010
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ps. kairosfocus has repeatedly refuted the objections presented by cassandra. At some point it get's rather boring to say and hear the same old stuff over and over again.above
June 4, 2010
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But aleta seems to so eager to ignore the blatant circularity of logic exibited by cassandra as indicated above by myself and others.above
June 4, 2010
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Cassandra is exactly right. tgpeeler assumes the conclusion. And, he writes, "At the risk of oversimplifying, ..." Yes, vastly oversimplifying.Aleta
June 4, 2010
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