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Antievolution.org Discussion Board > From the Panda's Thumb > After the Bar Closes... > Complexity vs. Information

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JAM Posts: 517 Joined: July 2007 (Permalink) Posted: Aug. 31 2008,18:43    Quote (Daniel Smith @ Aug. 31 2008,15:02)   Quote (Zachriel @ Aug. 30 2008,14:34)             Quote (Daniel Smith @ Aug. 30 2008,12:47) I guess my problem is one of accuracy: what do these examples represent in regard to real world evolution? Not much, but Word Mutagenation is one of a class of evolutionary algorithms, and biological evolution can be modeled, in part, as an evolutionary algorithm. This is really the only debate I'm interested in.  I'd be intensely interested in an algorithm that mirrors real biological evolution. Hmmm...then why is it that you aren't at all interested in real biology? Quote I'm not really that interested at all in the debate about words - unless there's something that can be shown analogous to real world (non-theoretical) evolution. So we agree that the IDers' claims that the "genetic code" (which is not a code in biology; it's only a code when we offer letters to replace chemical structures) implies intelligence are bogus? Quote I guess what I'm saying is that every living organism and every organ is said to be the result of evolution. Your obsession with organs appears to be sexual. Quote What I'd like to see is a detailed account of how any one of these organs or organisms (or even the most basic biochemical systems within them) originated via evolution. It's in the sequences that you botched so badly. But as for seeing how complex organ systems can differ dramatically based on the dosage/activity/presence/absence of a very small number of genes, I suggest that you examine the dimorphism of human sexual organs. Quote I'd like to see a step-by-step analysis of evolution in action.  What was the precursor? The undifferentiated system. Quote What were the intermediate steps?  Why were they selected? Because they helped in reproduction.  Quote For instance, it's often said that lungs evolved from swim bladders.  So... What were the specific biochemical steps? Biochemical steps? You're just BSing now. You clearly don't even understand what the word "biochemical" even means. Quote Are lungs and swim bladders made of the same proteins? Almost entirely--but not the same proteins, orthologous proteins. There's a difference, but understanding that is probably beyond your curiosity, because you are afraid of learning enough to test your assumptions. Quote What are the differences?  How was each difference created step by viable step?  What was the selective advantage for each?  Can these steps be recreated or verified in the lab? No. Your request is stupid. What were the design steps, Dan? What was the intelligent rationale behind each step? Why are you such a dishonest hypocrite? Quote Are these steps able to be specified down to the biochemical level? More BS. You don't know what you're talking about. Quote What is the evidence in support from other fields such as paleontology?   The most important field is comparative genomics, one you ran away from studying, remember?

dogdidit Posts: 315 Joined: Mar. 2008 (Permalink) Posted: Aug. 31 2008,21:22    Quote (Daniel Smith @ Aug. 30 2008,12:47) As far as I'm concerned, all this talk about information, complexity, and specificity is irrelevant if it doesn't apply to real world biochemical systems. Erm - well, it does seem relevant in light of the attempts of the ID community to make various claims that the genetic code shows evidence of complex specified information having been injected into it (shh! don't say by who!) without a shred of science or measurement behind the words "complex" or "specified" and predicated on a listener's confusion or lack of understanding as to what "information" is and how it is measured in statistical terms. So the first order of business would be to clear the cobwebs of obfuscation out of the way. "Information" has a solid mathematical foundation beneath it; it even gets to be a "theory"! "Complexity"? "Specified"? Jury still out. As for:   Quote I'd be intensely interested in an algorithm that mirrors real biological evolution. Any simulation must be judged by the level of fidelity one is looking for, but would Blondie24 (Anaconda) fill the bill? Not an algorithm, really, but more of a process (which is what evolution is). Random variation and natural selection -- it's all there. No targets, no external fitness measure, no guidance, no CSI injected; just live (and spawn) or die. Close enough? -------------- "Humans carry plants and animals all over the globe, thus introducing them to places they could never have reached on their own. That certainly increases biodiversity." - D'OL

Richardthughes Posts: 11178 Joined: Jan. 2006 (Permalink) Posted: Aug. 31 2008,21:27    GAs have incredible utility as seen by their application in optimization. Funny how they're modelled on this thing that doesn't work, yet they do so well. Sure, we might completely understand the mechanism, but at least we have one. -------------- "Richardthughes, you magnificent bastard, I stand in awe of you..." : Arden Chatfield "You magnificent bastard! " : Louis "ATBC poster child", "I have to agree with Rich.." : DaveTard "I bow to your superior skills" : deadman_932 "...it was Richardthughes making me lie in bed.." : Kristine

Wesley R. Elsberry Posts: 4991 Joined: May 2002 (Permalink) Posted: Aug. 31 2008,22:09    Quote (Daniel Smith @ Aug. 31 2008,14:34) Quote (Wesley R. Elsberry @ Aug. 30 2008,13:38) You'd be whining ad nauseum if someone were offering an opinion on Schindewald without reading his work, so suck it up and learn something about what you presume to criticize. Did you mean "Schindewolf"?   I don't remember anyone here actually reading Schindewolf's book all the way through before they took to criticizing his work.  I know some who read a few chapters, others read Gould's foreword, yet I don't remeber one who began a counterargument with the statement "I'm thoroughly familiar with Schindewolf's work and I find it..."  Did you read his book? If not, then don't be a hypocrite: allow the uninformed debate to continue. It's not my standard that is a basis for a charge of hypocrisy; I've never stated that one cannot address particular issues on the basis of having read a relevant subset of someone's work. You, on the other hand, have been copiously documented saying that criticism of any issue cannot be done unless all of some book or all of someone's work has been read by the critic, at least for certain privileged sources. Others apparently don't merit even the minimal amount of respect that reading the material relevant to your completely uninformed claims would require. -------------- "You can't teach an old dogma new tricks." - Dorothy Parker

Quidam Posts: 229 Joined: Mar. 2008 (Permalink) Posted: Aug. 31 2008,22:26    Quote (Daniel Smith @ Aug. 31 2008,14:02) I'd be intensely interested in an algorithm that mirrors real biological evolution. How about a program that in each iteration generates an array of artificial life creatures  by mutations in its building rules ('genes') from a parent. The user selects one of the children in each generation to become the parent of the next generation. The user decides subjectively what sorts of traits  to select for. This simulates artificial, rather than natural, selection. I know where such an algorithm can be found. -------------- The organized fossils ... and their localities also, may be understood by all, even the most illiterate. William Smith, Strata. 1816

oldmanintheskydidntdoit Posts: 4999 Joined: July 2006 (Permalink) Posted: Sep. 01 2008,02:55    Quote (Daniel Smith @ Aug. 31 2008,15:02) I guess what I'm saying is that every living organism and every organ is said to be the result of evolution. I guess what I'm saying is that every living organism and every organ is said to be the result of Jesus.  What I'd like to see is a detailed account of how any one of these organs or organisms (or even the most basic biochemical systems within them) originated via Jesus.  I'd like to see a step-by-step analysis of Jesus in action.  What was the precursor?  What were the intermediate steps?  Why were they selected?   Well? -------------- I also mentioned that He'd have to give me a thorough explanation as to *why* I must "eat human babies". FTK if there are even critical flaws in Gauger’s work, the evo mat narrative cannot stand Gordon Mullings

Daniel Smith Posts: 970 Joined: Sep. 2007 (Permalink) Posted: Sep. 01 2008,15:21    I found a program called Stylus that attempts to bridge the gap between language and real biological function by using Chinese characters.  I've only just begun to read the article, but it appears to be an honest attempt at a realistic evolutionary algorithm. Abstract:   Quote The study of protein evolution is complicated by the vast size of protein sequence space, the huge number of possible protein folds, and the extraordinary complexity of the causal relationships between protein sequence, structure, and function. Much simpler model constructs may therefore provide an attractive complement to experimental studies in this area. Lattice models, which have long been useful in studies of protein folding, have found increasing use here. However, while these models incorporate actual sequences and structures (albeit non-biological ones), they incorporate no actual functions—relying instead on largely arbitrary structural criteria as a proxy for function. In view of the central importance of function to evolution, and the impossibility of incorporating real functional constraints without real function, it is important that protein-like models be developed around real structure–function relationships. Here we describe such a model and introduce open-source software that implements it. The model is based on the structure–function relationship in written language, where structures are two-dimensional ink paths and functions are the meanings that result when these paths form legible characters. To capture something like the hierarchical complexity of protein structure, we use the traditional characters of Chinese origin. Twenty coplanar vectors, encoded by base triplets, act like amino acids in building the character forms. This vector-world model captures many aspects of real proteins, including life-size sequences, a life-size structural repertoire, a realistic genetic code, secondary, tertiary, and quaternary structure, structural domains and motifs, operon-like genetic structures, and layered functional complexity up to a level resembling bacterial genomes and proteomes. Stylus is a full-featured implementation of the vector world for Unix systems. To demonstrate the utility of Stylus, we generated a sample set of homologous vector proteins by evolving successive lines from a single starting gene. These homologues show sequence and structure divergence resembling those of natural homologues in many respects, suggesting that the system may be sufficiently life-like for informative comparison to biology. Unfortunately, the software only runs on Unix/Linux operating systems so I have no way of testing it. -------------- "If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright "The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

Daniel Smith Posts: 970 Joined: Sep. 2007 (Permalink) Posted: Sep. 01 2008,16:22    Quote (Wesley R. Elsberry @ Aug. 31 2008,20:09) It's not my standard that is a basis for a charge of hypocrisy; I've never stated that one cannot address particular issues on the basis of having read a relevant subset of someone's work. You, on the other hand, have been copiously documented saying that criticism of any issue cannot be done unless all of some book or all of someone's work has been read by the critic, at least for certain privileged sources. Others apparently don't merit even the minimal amount of respect that reading the material relevant to your completely uninformed claims would require. Well, without going out and buying the book, I think I've managed at least a rudimentary understanding of Dawkins' purpose for the weasel algorithm.  He uses it solely as a demonstration for the power of cumulative selection vs. single step selection.  He also is quite clear that it does not mirror biological evolution:   Quote Although the monkey/Shakespeare model is useful for explaining the distinction between single-step selection and cumulative selection, it is misleading in important ways. One of these is that, in each generation of selective 'breeding', the mutant 'progeny' phrases were judged according to the criterion of resemblance to a distant ideal target, the phrase METHINKS IT IS LIKE A WEASEL. Life isn't like that. Evolution has no long-term goal. There is no long-distance target, no final perfection to serve as a criterion for selection, although human vanity cherishes the absurd notion that our species is the final goal of evolution. In real life, the criterion for selection is always short-term, either simple survival or, more generally, reproductive success. Dawkins admitted (according to the Wiki article I read anyway) that there has not been enough time since the universe began to produce the phrase METHINKS IT IS LIKE A WEASEL randomly via single/step selection.  So his phrase--of only 28 character length--required cumulative selection (of one letter resolution) in order to be produced from a random generator within a realistic time frame.  It would seem to me then that any biological system at least as complex as METHINKS IT IS LIKE A WEASEL, would require cumulative selection of each of its individual elements in order to be produced via random mutation in a sufficient amount of time.  Thus, each element must confer a selective advantage.  This would mean that each point mutation would have to confer an advantage in order to produce a specific 28bp sequence.  You could not just pull a good 28bp sequence out of space (single selection) as a starting point.  In fact, you could not pull an 8bp sequence out of space without significantly increasing the amount of time required to produce the functional sequence. Where have I gone wrong? -------------- "If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright "The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

Daniel Smith Posts: 970 Joined: Sep. 2007 (Permalink) Posted: Sep. 01 2008,16:26    Why is it that anytime I post a reply I'm redirected to the Bathroom Wall thread?  Is that a joke?  Some sort of warning perhaps?  Or is it happening to everyone and I'm just being paranoid? -------------- "If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright "The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

Lou FCD Posts: 5455 Joined: Jan. 2006 (Permalink) Posted: Sep. 01 2008,20:52    Quote (Daniel Smith @ Sep. 01 2008,17:22) Well, without going out and buying the book, ... Wait, weren't you just... nevermind. -------------- “Why do creationists have such a hard time with commas? Linky“. ~ Steve Story, Legend

JAM Posts: 517 Joined: July 2007 (Permalink) Posted: Sep. 01 2008,23:34    Quote (Daniel Smith @ Sep. 01 2008,16:26) Why is it that anytime I post a reply I'm redirected to the Bathroom Wall thread?  Is that a joke? Speaking of jokes, I'd like an answer to my question: did you read all of Schindewolf's book?

oldmanintheskydidntdoit Posts: 4999 Joined: July 2006 (Permalink) Posted: Sep. 02 2008,02:57    Quote (Daniel Smith @ Sep. 01 2008,16:22) Dawkins admitted (according to the Wiki article I read anyway) that there has not been enough time since the universe began to produce the phrase METHINKS IT IS LIKE A WEASEL randomly via single/step selection.   Would you like us to club together and purchase then send you a copy of the book? It'll only be a few $$$. There are many copy's. I'm in for $1. If you are in the UK I can post my copy today. -------------- I also mentioned that He'd have to give me a thorough explanation as to *why* I must "eat human babies". FTK if there are even critical flaws in Gauger’s work, the evo mat narrative cannot stand Gordon Mullings

Daniel Smith Posts: 970 Joined: Sep. 2007 (Permalink) Posted: Sep. 02 2008,19:07    Quote (JAM @ Sep. 01 2008,21:34) Speaking of jokes, I'd like an answer to my question: did you read all of Schindewolf's book? Yes JAM I did. -------------- "If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright "The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

Daniel Smith Posts: 970 Joined: Sep. 2007 (Permalink) Posted: Sep. 02 2008,19:46    Quote (JAM @ Aug. 31 2008,16:43)       Quote (Daniel Smith @ Aug. 31 2008,15:02)   I'd like to see a step-by-step analysis of evolution in action.  What was the precursor? The undifferentiated system.       Quote What were the intermediate steps?  Why were they selected? Because they helped in reproduction. Why is it JAM, that whenever I ask for specifics about evolution in forums like these, the answers get more vague?       Quote       Quote For instance, it's often said that lungs evolved from swim bladders.  So... What were the specific biochemical steps? Biochemical steps? You're just BSing now. You clearly don't even understand what the word "biochemical" even means. I don't think it's that hard a word to understand, it's just the chemicals that life is made of.  I know that all of life is essentially biochemical reactions.  A lot of it is dependent on a chemical's reaction to water molecules.  Protein folding seems to be largely dependent on keeping the correct amino acids on the outside for their ready interactions with water (among other things) and keeping the "oily" amino acids separated from water (among other things as well).  The strength/weakness of chemical bonds is probably the most important quality.     Quote     Quote Are lungs and swim bladders made of the same proteins? Almost entirely--but not the same proteins, orthologous proteins. There's a difference, but understanding that is probably beyond your curiosity, because you are afraid of learning enough to test your assumptions.       Quote What are the differences?  How was each difference created step by viable step?  What was the selective advantage for each?  Can these steps be recreated or verified in the lab? No. Your request is stupid. Why?  Why is it "stupid" to ask someone who firmly believes that all of life's systems are the product of evolution to explain how one of them came to be via evolution? Surely you have specific, lab-tested evolutionary pathways for scores of living systems.  After all, you are a scientist, correct?  Why not break one out for my amusement?   "Homologous sequences are orthologous if they were separated by a speciation event: when a species diverges into two separate species, the divergent copies of a single gene in the resulting species are said to be orthologous." (from Wiki) So what was the original sequence for the undifferentiated ancestor of modern lung/swim bladder species? You should be able to re-create the steps - correct?  What were they?     Quote What were the design steps, Dan? What was the intelligent rationale behind each step? Why are you such a dishonest hypocrite? Is this a dodge?  Are you attempting to change the subject?  You have not answered my questions with anything above the vaguest vaguery, yet you want me to get specific.       Quote     Quote Are these steps able to be specified down to the biochemical level? More BS. You don't know what you're talking about. Humor me.       Quote The most important field is comparative genomics, one you ran away from studying, remember? I don't remember "running away" from anything JAM.  A lot of it is over my head, but I am perfectly willing to discuss anything you have the patience to discuss with me. -------------- "If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright "The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

Henry J Posts: 5786 Joined: Mar. 2005 (Permalink) Posted: Sep. 02 2008,22:41    Quote Why?  Why is it "stupid" to ask someone who firmly believes that all of life's systems are the product of evolution to explain how one of them came to be via evolution? Asking a question isn't stupid. But, mplying that the validity of a theory depends on scientists having a detailed history of a particular series of event (esp. for events between .5 and 4.5 billion years ago) - that's unrealistic. It isn't so much that scientists "firmly believe" their conclusions, but (as I understand it) that they (1) note that the general concepts of the theory is consistent with all the relevant evidence (2) that is very unlikely to be the case if the theory is wrong, and (3) some of the implications of the theory were recognized before the confirming data was available (not all of the implications by any means; there will always be some implications that can't be directly tested). Henry

JAM Posts: 517 Joined: July 2007 (Permalink) Posted: Sep. 03 2008,00:46    Quote (Daniel Smith @ Sep. 02 2008,19:46)     Quote (JAM @ Aug. 31 2008,16:43)             Quote (Daniel Smith @ Aug. 31 2008,15:02)   I'd like to see a step-by-step analysis of evolution in action.  What was the precursor? The undifferentiated system.             Quote What were the intermediate steps?  Why were they selected? Because they helped in reproduction. Why is it JAM, that whenever I ask for specifics about evolution in forums like these, the answers get more vague? There was nothing vague about my answer. How can an intelligent person demand a step-by-step analysis of something in action that took hundreds of millions of years, Dan? And why can't you supply any specifics about design, given that you believe in it with your heart and soul? Your demand is a dishonest one and you know it.        Quote   Quote             Quote For instance, it's often said that lungs evolved from swim bladders.  So... What were the specific biochemical steps? Biochemical steps? You're just BSing now. You clearly don't even understand what the word "biochemical" even means. I don't think it's that hard a word to understand, it's just the chemicals that life is made of.  I know that all of life is essentially biochemical reactions. Right. So please explain why EVOLUTION would involve ANY "biochemical steps." You don't know what you're talking about.   Quote A lot of it is dependent on a chemical's reaction to water molecules.  Protein folding seems to be largely dependent on keeping the correct amino acids on the outside for their ready interactions with water (among other things) and keeping the "oily" amino acids separated from water (among other things as well). "Keeping"? There's no "keeping" going on at all. You're assuming design from the start, because you're afraid to test a design hypothesis. You have no real faith.   Quote The strength/weakness of chemical bonds is probably the most important quality. This is so vague as to be meaningless.   Quote           Quote           Quote Are lungs and swim bladders made of the same proteins? Almost entirely--but not the same proteins, orthologous proteins. There's a difference, but understanding that is probably beyond your curiosity, because you are afraid of learning enough to test your assumptions.             Quote What are the differences?  How was each difference created step by viable step?  What was the selective advantage for each?  Can these steps be recreated or verified in the lab? No. Your request is stupid. Why?  Why is it "stupid" to ask someone who firmly believes that all of life's systems are the product of evolution to explain how one of them came to be via evolution? Now you're being dishonest again. It's not a matter of firm belief like yours, it's a conclusion based on the evidence, none of which supports your firm belief. That's why you run away from evidence.   Quote Surely you have specific, lab-tested evolutionary pathways for scores of living systems. Why would I? We only have specific pathways for subsystems. The problem for you is, when we analyze a new subsystem, we don't find anything inconsistent with evolutionary pathways. You, of course, deal with this evidence by never analyzing any systems or subsystems. You are afraid to do so.   Quote After all, you are a scientist, correct? I am, and you reject the scientific method itself, correct?   Quote "Homologous sequences are orthologous if they were separated by a speciation event: when a species diverges into two separate species, the divergent copies of a single gene in the resulting species are said to be orthologous." (from Wiki) Cut/paste doesn't equal understanding.   Quote So what was the original sequence for the undifferentiated ancestor of modern lung/swim bladder species? This is gibberish. Sequence of what? Are you saying that lungs and swim bladders are species?   Quote You should be able to re-create the steps - correct? Why should I be able to do so?   Quote What were they? We extrapolate back to the nearest species to a common ancestor and it becomes obvious.   Quote   Quote What were the design steps, Dan? What was the intelligent rationale behind each step? Why are you such a dishonest hypocrite? Is this a dodge? It's a question. You firmly believe that lungs and swim bladders were designed and not descended from a common ancestor, don't you?   Quote Are you attempting to change the subject? No, I'm addressing your lack of faith in your position.   Quote You have not answered my questions with anything above the vaguest vaguery,... That's a lie. I've pointed out why they are sleazy and ignorant in very specific ways.   Quote   Quote           Quote Are these steps able to be specified down to the biochemical level? More BS. You don't know what you're talking about. Humor me. There aren't "biochemical steps" in evolution, you arrogant fool.             Quote   Quote The most important field is comparative genomics, one you ran away from studying, remember? I don't remember "running away" from anything JAM. You're delusional.   Quote A lot of it is over my head, but I am perfectly willing to discuss anything you have the patience to discuss with me. Then let's pick up your thread where it left off, and have you address the fact that not a single one of your predictions in comparative genomics were supported by the evidence. In fact, they all were completely inconsistent with the evidence. How have you changed your hypothesis to accommodate the evidence?

oldmanintheskydidntdoit Posts: 4999 Joined: July 2006 (Permalink) Posted: Sep. 03 2008,02:42    Why?  Why is it "stupid" to ask someone who firmly believes that all of life's systems are the product of design to explain how one of them came to be via design? Surely you have specific, lab-tested design pathways for scores of living systems.  After all, you are a Intelligent Design scientist, correct?  Why not break one out for my amusement?   well? Can you explain how a single "system" came to be via design Daniel? I expect it's turtles all the way down with your sort. -------------- I also mentioned that He'd have to give me a thorough explanation as to *why* I must "eat human babies". FTK if there are even critical flaws in Gauger’s work, the evo mat narrative cannot stand Gordon Mullings

Richard Simons Posts: 425 Joined: Oct. 2006 (Permalink) Posted: Sep. 03 2008,17:40    Quote Surely you have specific, lab-tested evolutionary pathways for scores of living systems. I have no idea what you mean by this. Do you mean someone must have carried out a selection program to, for example, convert a population of lunged organisms to a population with swim bladders? Have you the slightest idea of how much it would cost to maintain a suitable breeding population of lungfish to do what is essentially a pointless exercise? Even if this succeeds after millenia of selection (at a bare minimum), your spiritual descendents will complain that a detailed genomic analysis of each generation was not performed. Perhaps you could tell us exactly what it is you expect to have been done. -------------- All sweeping statements are wrong.

Daniel Smith Posts: 970 Joined: Sep. 2007 (Permalink) Posted: Sep. 03 2008,19:09    By "lab tested" I mean something that is tested period.  For instance, if two sets of genes are known, and are said to be from a common ancestor, it should be possible to extrapolate the common ancestral gene (and intermediate genes) via computer simulation.  Then you should be able to test the resultant genes for viability by altering and inserting the DNA into the living organisms. I'm sure there are many other ways to test for viable pathways.  If you don't test for a pathway though, you have nothing but comparable sequences, which may show common ancestry but do nothing to show how evolution occurred.  It could've been gradual step-by-step, or it could've been saltational.  Who knows?  You've established nothing in regard to mechanism. As for how things came to be via design; I'd imagine the methodology was very similar to the methods of design we observe and use every day.  We are able to take raw materials from the earth, refine them, and fit them together to make working machinery.  A cellular designer would do the same thing, but on a nano-scale.  Only the very first cellular lifeform on earth would have to be designed--IF--the designer was able to program the cell to differentiate via evolutionary mechanisms.  The tricky part would not be the putting together of the actual pieces of that first cell so much as it would be putting together the information that would cause the cell to replicate, grow and evolve.  That every cell on earth contains coded information is irrefutable evidence for design, unless you can show a way to get coded information from natural forces working on earthly elements.  (Oh and JAM, we know that DNA is a code because we are able to decode it.)  One thing we might expect to find if cellular information was designed would be that the genetic code could be described mathematically.  This is exactly what we do find - as outlined in this paper.  Abstract:     Quote From a mathematical point of view, the genetic code is a surjective mapping between the set of the 64 possible three-base codons and the set of 21 elements composed of the 20 amino acids plus the Stop signal. Redundancy and degeneracy therefore follow. In analogy with the genetic code, non-power integer-number representations are also surjective mappings between sets of different cardinality and, as such, also redundant. However, none of the nonpower arithmetics studied so far nor other alternative redundant representations are able to match the actual degeneracy of the genetic code. In this paper we develop a slightly more general framework that leads to the following surprising results: i) the degeneracy of the genetic code is mathematically described, ii) a new symmetry is uncovered within this degeneracy, iii) by assigning a binary string to each of the codons, their classification into definite parity classes according to the corresponding sequence of bases is made possible. This last result is particularly appealing in connection with the fact that parity coding is the basis of the simplest strategies devised for error correction in man-made digital data transmission systems. Follow-up paper -------------- "If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright "The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

G. cuvier Posts: 2 Joined: Sep. 2006 (Permalink) Posted: Sep. 03 2008,21:18    Quote (Daniel Smith @ Sep. 03 2008,19:09) As for how things came to be via design; I'd imagine the methodology was very similar to the methods of design we observe and use every day.  We are able to take raw materials from the earth, refine them, and fit them together to make working machinery.  A cellular designer would do the same thing,  (Oh and JAM, we know that DNA is a code because we are able to decode it.)  One thing we might expect to find if cellular information was designed would be that the genetic code could be described mathematically. Mmmmm.... that's some good tard. While berating actual scientists for vagueness, Daniel writes this incredibly specific prediction: Quote As for how things came to be via design; I'd imagine the methodology was very similar to the methods of design we observe and use every day.  We are able to take raw materials from the earth, refine them, and fit them together to make working machinery.  A cellular designer would do the same thing, Of course, he then tops that off with this, the veritable cherry on top of his sundae of comedy: Quote One thing we might expect to find if cellular information was designed would be that the genetic code could be described mathematically. It should be obvious to even the meanest Intelligence that the path of a falling stone can be "described mathematically". Since Daniel is probably not a believer in Intelligent Falling, I leave it to you all to work out the relative intelligence of the designer of this argument.

Henry J Posts: 5786 Joined: Mar. 2005 (Permalink) Posted: Sep. 03 2008,22:48    The methods that human engineers use every day would not produce single consistent nested hierarchy - it would produce lots of different hierarchies. It also would not tend to cluster close relatives near each other geographically. And it would likely produce lots of cases of exact copying of sequences. Also human engineers like to modularize things so that they can change one part with minimal risk of disruption of other parts. Henry

JAM Posts: 517 Joined: July 2007 (Permalink) Posted: Sep. 04 2008,00:22    Quote (Daniel Smith @ Sep. 03 2008,19:09) By "lab tested" I mean something that is tested period. So if I tested it outside the lab and in the field, you'd still call it "lab tested"? Quote For instance, if two sets of genes are known,... This is meaningless unless you define "sets" in this context. Quote ... and are said to be from a common ancestor, it should be possible to extrapolate the common ancestral gene (and intermediate genes) via computer simulation. We can extrapolate, but we can't be sure. But why extrapolate? Why not just take the gene from one species and see if it works in another? Quote Then you should be able to test the resultant genes for viability by altering and inserting the DNA into the living organisms. How would simply inserting a gene test it for viability? Do you even think about this stuff before you write it? Quote I'm sure there are many other ways to test for viable pathways. I'm just as sure that you haven't thought carefully about any of them. You're just throwing shit at this point. Quote If you don't test for a pathway though, you have nothing but comparable sequences, which may show common ancestry but do nothing to show how evolution occurred.  It could've been gradual step-by-step, or it could've been saltational.  Who knows?  You've established nothing in regard to mechanism. Gee, if we establish that homologous (not orthologous) biological phenomena have homologous mechanisms, what does that show? Quote As for how things came to be via design;... What Henry and Cuvier said. Pure tard. You can't even discriminate between design and manufacture. Psst...the term "code" is used metaphorically. There's nothing symbolic about it.

Mark Iosim Posts: 27 Joined: Oct. 2007 (Permalink) Posted: Sep. 04 2008,21:31    As long as scientists insist that there is no mystery in life phenomenon, ID proponents will have material to ridicule this science and promote their agenda. I am not ID supporter, but I also can’t separate life (and even spontaneous processes in general) from some sort of purpose. Just think about thermodynamic description of a chemical reaction: it occurs TO ACHIEVE a state of minimum of free energy of system. Does is sound like metaphysics? But I am more interested not in “ID vs. Natural Evolution” arguments, but in Complexity itself. If information is reduction in uncertainty, the complexity, I think, is a level of this uncertainty. In my opinion, the main problem with defining Complexity is in treating it as an objective category, while it should be regarded as relative to observer only. The Complexity, of a problem or task, cannot be separated from a specific intelligence that is solving this problem. In the same time we can’t define (and measure) intelligence without referring to a particular problem. Therefore the definitions of Complexity and Intelligence (and Information probably also) are inseparable and both categories aren’t absolute, but are relative to each other. The Intelligence is measured by interaction with a specific problem. For example if the problem to solve is a protein folding, then any single cell (or even molecule of protein) could be much more intelligent that we are. The same way a complexity of a specific problem could be measured only in reference to a specific intelligence that attempts to solve this problem. For example, what is more complex: to build a house, surgically remove an appendix, or solve a linear differential equation? The answer depends on whom you ask- Carpenter, Surgeon, or Mathematician.

qetzal Posts: 311 Joined: Feb. 2006 (Permalink) Posted: Sep. 04 2008,22:27    Quote (Daniel Smith @ Sep. 03 2008,19:09) By "lab tested" I mean something that is tested period.  For instance, if two sets of genes are known, and are said to be from a common ancestor, it should be possible to extrapolate the common ancestral gene (and intermediate genes) via computer simulation.  Then you should be able to test the resultant genes for viability by altering and inserting the DNA into the living organisms. Been done. Multiple times. Here's just one example: Quote J Mol Biol. 2007 Jun 15;369(4):1060-9. Epub 2007 Apr 5. Extremely thermophilic translation system in the common ancestor commonote: ancestral mutants of Glycyl-tRNA synthetase from the extreme thermophile Thermus thermophilus. Shimizu H, Yokobori S, Ohkuri T, Yokogawa T, Nishikawa K, Yamagishi A. Department of Molecular Biology, Tokyo University of Pharmacy and Life Science, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan. Based on phylogenetic analysis of 16 S and 18 S rRNAs, the common ancestor of all organisms (Commonote) was proposed to be hyperthermophilic. We have previously tested this hypothesis using enzymes with ancestral residues that are inferred by molecular phylogenetic analysis. The ancestral mutant enzymes involved in metabolic systems show higher thermal stability than wild-type enzymes, consistent with the hyperthermophile common ancestor hypothesis. Here, we have extended the experiments to include an enzyme of the translation system, glycyl-tRNA synthetase (GlyRS). The translation system often shows a phylogenetic tree that is similar to the rRNA tree. Thus, it is likely that the tree represents the evolutionary route of the organisms. The maximum-likelihood tree of alpha(2) type GlyRS was constructed. From this analysis the ancestral sequence of GlyRS was deduced and individual or pairs of ancestral residues were introduced into Thermus thermophilus GlyRS. The ancestral mutants were expressed in Escherichia coli, purified and activity measured. The thermostability of eight mutated proteins was evaluated by CD (circular dichroism) measurements. Six mutants showed higher thermostability than wild-type enzyme and seven mutants showed higher activity than wild-type enzyme at 70 degrees C, suggesting an extremely thermophilic translation system in the common ancestor Commonote. Note that it doesn't just show that the inferred ancestral sequence works. It shows that the inferred ancestral sequence has specific properties predicted based on evolution!

oldmanintheskydidntdoit Posts: 4999 Joined: July 2006 (Permalink) Posted: Sep. 05 2008,02:51    Quote (qetzal @ Sep. 04 2008,22:27) Quote (Daniel Smith @ Sep. 03 2008,19:09) By "lab tested" I mean something that is tested period.  For instance, if two sets of genes are known, and are said to be from a common ancestor, it should be possible to extrapolate the common ancestral gene (and intermediate genes) via computer simulation.  Then you should be able to test the resultant genes for viability by altering and inserting the DNA into the living organisms. Been done. Multiple times. Here's just one example:   Quote J Mol Biol. 2007 Jun 15;369(4):1060-9. Epub 2007 Apr 5. Extremely thermophilic translation system in the common ancestor commonote: ancestral mutants of Glycyl-tRNA synthetase from the extreme thermophile Thermus thermophilus. Shimizu H, Yokobori S, Ohkuri T, Yokogawa T, Nishikawa K, Yamagishi A. Department of Molecular Biology, Tokyo University of Pharmacy and Life Science, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan. Based on phylogenetic analysis of 16 S and 18 S rRNAs, the common ancestor of all organisms (Commonote) was proposed to be hyperthermophilic. We have previously tested this hypothesis using enzymes with ancestral residues that are inferred by molecular phylogenetic analysis. The ancestral mutant enzymes involved in metabolic systems show higher thermal stability than wild-type enzymes, consistent with the hyperthermophile common ancestor hypothesis. Here, we have extended the experiments to include an enzyme of the translation system, glycyl-tRNA synthetase (GlyRS). The translation system often shows a phylogenetic tree that is similar to the rRNA tree. Thus, it is likely that the tree represents the evolutionary route of the organisms. The maximum-likelihood tree of alpha(2) type GlyRS was constructed. From this analysis the ancestral sequence of GlyRS was deduced and individual or pairs of ancestral residues were introduced into Thermus thermophilus GlyRS. The ancestral mutants were expressed in Escherichia coli, purified and activity measured. The thermostability of eight mutated proteins was evaluated by CD (circular dichroism) measurements. Six mutants showed higher thermostability than wild-type enzyme and seven mutants showed higher activity than wild-type enzyme at 70 degrees C, suggesting an extremely thermophilic translation system in the common ancestor Commonote. Note that it doesn't just show that the inferred ancestral sequence works. It shows that the inferred ancestral sequence has specific properties predicted based on evolution! Do you accept evolution now Daniel? Now that you've been given the evidence that you asked for? -------------- I also mentioned that He'd have to give me a thorough explanation as to *why* I must "eat human babies". FTK if there are even critical flaws in Gauger’s work, the evo mat narrative cannot stand Gordon Mullings

Henry J Posts: 5786 Joined: Mar. 2005 (Permalink) Posted: Sep. 05 2008,13:26    Quote As long as scientists insist that there is no mystery in life phenomenon, Who the heck is claiming that there aren't any unanswered questions? If that ever happened, researchers would be out of jobs. Henry

dvunkannon Posts: 1377 Joined: June 2008 (Permalink) Posted: Sep. 05 2008,14:54    Quote (dogdidit @ Aug. 31 2008,22:22) As for:       Quote I'd be intensely interested in an algorithm that mirrors real biological evolution. Any simulation must be judged by the level of fidelity one is looking for, but would Blondie24 (Anaconda) fill the bill? Not an algorithm, really, but more of a process (which is what evolution is). Random variation and natural selection -- it's all there. No targets, no external fitness measure, no guidance, no CSI injected; just live (and spawn) or die. Close enough? Gil Dodgen of UD fame gives an amazingly positive Amazon review to Blondie24, back in 2001. Maybe he wasn't saved back then. -------------- I’m referring to evolution, not changes in allele frequencies. - Cornelius Hunter I’m not an evolutionist, I’m a change in allele frequentist! - Nakashima

dogdidit Posts: 315 Joined: Mar. 2008 (Permalink) Posted: Sep. 05 2008,16:14    Quote (dvunkannon @ Sep. 05 2008,14:54)     Quote (dogdidit @ Aug. 31 2008,22:22) As for:             Quote I'd be intensely interested in an algorithm that mirrors real biological evolution. Any simulation must be judged by the level of fidelity one is looking for, but would Blondie24 (Anaconda) fill the bill? Not an algorithm, really, but more of a process (which is what evolution is). Random variation and natural selection -- it's all there. No targets, no external fitness measure, no guidance, no CSI injected; just live (and spawn) or die. Close enough? Gil Dodgen of UD fame gives an amazingly positive Amazon review to Blondie24, back in 2001. Maybe he wasn't saved back then. No doubt by now Jebus has shown him where the CSI was injected. edited for spelling -------------- "Humans carry plants and animals all over the globe, thus introducing them to places they could never have reached on their own. That certainly increases biodiversity." - D'OL

dvunkannon Posts: 1377 Joined: June 2008 (Permalink) Posted: Sep. 05 2008,17:14    Quote (dogdidit @ Sep. 05 2008,17:14) Quote (dvunkannon @ Sep. 05 2008,14:54)       Quote (dogdidit @ Aug. 31 2008,22:22) As for:               Quote I'd be intensely interested in an algorithm that mirrors real biological evolution. Any simulation must be judged by the level of fidelity one is looking for, but would Blondie24 (Anaconda) fill the bill? Not an algorithm, really, but more of a process (which is what evolution is). Random variation and natural selection -- it's all there. No targets, no external fitness measure, no guidance, no CSI injected; just live (and spawn) or die. Close enough? Gil Dodgen of UD fame gives an amazingly positive Amazon review to Blondie24, back in 2001. Maybe he wasn't saved back then. No doubt by now Jebus has shown him where the CSI was injected. edited for spelling Artificial Chemistries - an old review, but might help Daniel if he wants to pursue the relevance of artificial models to the real world. -------------- I’m referring to evolution, not changes in allele frequencies. - Cornelius Hunter I’m not an evolutionist, I’m a change in allele frequentist! - Nakashima

Daniel Smith Posts: 970 Joined: Sep. 2007 (Permalink) Posted: Sep. 05 2008,18:28    Quote (qetzal @ Sep. 04 2008,20:27)     Quote (Daniel Smith @ Sep. 03 2008,19:09) By "lab tested" I mean something that is tested period.  For instance, if two sets of genes are known, and are said to be from a common ancestor, it should be possible to extrapolate the common ancestral gene (and intermediate genes) via computer simulation.  Then you should be able to test the resultant genes for viability by altering and inserting the DNA into the living organisms. Been done. Multiple times. Here's just one example:       Quote J Mol Biol. 2007 Jun 15;369(4):1060-9. Epub 2007 Apr 5. Extremely thermophilic translation system in the common ancestor commonote: ancestral mutants of Glycyl-tRNA synthetase from the extreme thermophile Thermus thermophilus. Shimizu H, Yokobori S, Ohkuri T, Yokogawa T, Nishikawa K, Yamagishi A. Department of Molecular Biology, Tokyo University of Pharmacy and Life Science, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan. Based on phylogenetic analysis of 16 S and 18 S rRNAs, the common ancestor of all organisms (Commonote) was proposed to be hyperthermophilic. We have previously tested this hypothesis using enzymes with ancestral residues that are inferred by molecular phylogenetic analysis. The ancestral mutant enzymes involved in metabolic systems show higher thermal stability than wild-type enzymes, consistent with the hyperthermophile common ancestor hypothesis. Here, we have extended the experiments to include an enzyme of the translation system, glycyl-tRNA synthetase (GlyRS). The translation system often shows a phylogenetic tree that is similar to the rRNA tree. Thus, it is likely that the tree represents the evolutionary route of the organisms. The maximum-likelihood tree of alpha(2) type GlyRS was constructed. From this analysis the ancestral sequence of GlyRS was deduced and individual or pairs of ancestral residues were introduced into Thermus thermophilus GlyRS. The ancestral mutants were expressed in Escherichia coli, purified and activity measured. The thermostability of eight mutated proteins was evaluated by CD (circular dichroism) measurements. Six mutants showed higher thermostability than wild-type enzyme and seven mutants showed higher activity than wild-type enzyme at 70 degrees C, suggesting an extremely thermophilic translation system in the common ancestor Commonote. Note that it doesn't just show that the inferred ancestral sequence works. It shows that the inferred ancestral sequence has specific properties predicted based on evolution! This is exactly what I've been looking for.  Thank you for posting that qetzal.  I only wish I could read the whole paper.  You say that experiments like these have been done multiple times: if you have any more links to papers such as this (preferably the full paper), I'm interested and would appreciate your posting them. Thanks again. -------------- "If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright "The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

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