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Antievolution.org Discussion Board > From the Panda's Thumb > After the Bar Closes... > The Gang of Four at the Gateway of Life

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charlie wagner Posts: 24 Joined: Aug. 2008 (Permalink) Posted: Sep. 12 2008,10:49    Quote That is just so much handwaving BS. The genome (a string of DNA) of any creature is not an automaton. You could argue that a ribosome is an automaton. DNA is a sequence of instructions, but the instructions set in not "Turing complete" because there is no looping construct. There is no way to tell the ribosome to go back thirty codons or forward five. The ribosomal automaton reading the DNA sequence cannot make any other biochemical machine. It can make linear strings of 20 amino acids. Many drugs are not proteins. Sugars and fats are not proteins. All biochemistry does not equal protein chemistry. Further, these amino acids are not infinite in variety. They are 20 out of many many more. We can create biochemical machines that use amino acids that no genome codes for, no tRNA transcribes. The analogy of computers to biology is often overstated. You have done so. How do you know that a genome is not an automaton? How do you know that a genome cannot make any other biochemical machine? How do you know that amino acids are not infinite in variety? How do you know that biological processes are not analogous to our concept of computers? The human brain is an analog computer and much research has been done with DNA computers: http://en.wikipedia.org/wiki/Computational_Genes Talk about "hand-waving"!

charlie wagner Posts: 24 Joined: Aug. 2008 (Permalink) Posted: Sep. 12 2008,11:10    This is worth printing out here. (from Wikipedia) What is a Computational Gene ? A computational gene is a molecular automaton consisting of a structural and functional part which is designed such that it might work in a cellular environment. The structural part is a naturally occurring gene, which is used as a skeleton to encode the input and the transitions of the automaton. The conserved features of a structural gene (e.g., DNA polymerase binding site, start and stop codons, and splicing sites) serve as constants of the computational gene, while the coding regions, the number of exons and introns, the position of start and stop codon, and the automata theoretical variables (symbols, states, and transitions) are the design parameters of the computational gene. The constants and the design parameters are linked by several logical and biochemical constraints (e.g., encoded automata theoretic variables must not be recognized as splicing junctions). The input of the automaton are molecular markers given by single stranded DNA (ssDNA) molecules. These markers are signalling aberrant (e.g., carcinogenic) molecular phenotype and turn on the self-assembly of the functional gene. If the input is accepted, the output encodes a double stranded DNA (dsDNA) molecule, a functional gene which should be successfully integrated into the cellular transcription and translation machinery producing a wild type protein or an anti-drug.  Otherwise, a rejected input will assemble into a partially dsDNA molecule which cannot be translated.

Reciprocating Bill Posts: 4265 Joined: Oct. 2006 (Permalink) Posted: Sep. 12 2008,12:11    Quote (charlie wagner @ Sep. 12 2008,11:24) Quote Now address my question regarding how this postulated combination of stored algorithms and mostly (but not entirely) stored inputs manages to generate organisms that are adapted to highly contingent, unforeseeable environments that arise millions and/or billions of years after the pre-storage of those algorithms. Sorry to disappoint you but I don't know. The only thing I know for sure is that I don't know everything.   Quote One thing only I know, and that is that I know nothing. Socrates But that's the most important question Darwin originally, and evolutionary theory since, have answered. Vague talk about automatons and algorithms that goes no distance to address this central question gets you nowhere if you can't offer a more compelling explanation than the one we have in hand. -------------- Myth: Something that never was true, and always will be. "The truth will set you free. But not until it is finished with you." - David Foster Wallace "Here’s a clue. Snarky banalities are not a substitute for saying something intelligent. Write that down." - Barry Arrington

dvunkannon Posts: 1377 Joined: June 2008 (Permalink) Posted: Sep. 12 2008,12:52    Quote (charlie wagner @ Sep. 12 2008,11:49)       Quote That is just so much handwaving BS. The genome (a string of DNA) of any creature is not an automaton. You could argue that a ribosome is an automaton. DNA is a sequence of instructions, but the instructions set in not "Turing complete" because there is no looping construct. There is no way to tell the ribosome to go back thirty codons or forward five. The ribosomal automaton reading the DNA sequence cannot make any other biochemical machine. It can make linear strings of 20 amino acids. Many drugs are not proteins. Sugars and fats are not proteins. All biochemistry does not equal protein chemistry. Further, these amino acids are not infinite in variety. They are 20 out of many many more. We can create biochemical machines that use amino acids that no genome codes for, no tRNA transcribes. The analogy of computers to biology is often overstated. You have done so. How do you know that a genome is not an automaton? Because I've read descriptions of the genetic machinery of the cell. The genome is stored information, not the machine that reads the information.       Quote How do you know that a genome cannot make any other biochemical machine? Because we know that the product of the ribosome is a linear string of amino acids, and we know that there are other biochemical objects that are not linear strings of amino acids.     Quote How do you know that amino acids are not infinite in variety? Because we've counted the amino acids used in protein synthesis, there are 20. We know others, but protein chemistry only uses 20. There are only 64 slots in the code table of the gemone, some amino acids are specified more than once.   Quote How do you know that biological processes are not analogous to our concept of computers? No analogy is perfect. The instructon set of the genome is not Turing complete.       Quote The human brain is an analog computer and much research has been done with DNA computers: http://en.wikipedia.org/wiki/Computational_Genes Talk about "hand-waving"! Yup, that article is full of it. Full of speculation. But note that no genome has a "computational gene", this is a human invention (yet to be proved) that leverages existing natural functions, but adds things that have never existed in a natural genome. -------------- 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

cewagner Posts: 41 Joined: April 2005 (Permalink) Posted: Sep. 29 2008,18:04    http://enigma.charliewagner.com Monday, September 29, 2008 Out Of Her League Sunday, September 21, 2008 These People are Friggin' CRAZY!!!

simmi Posts: 38 Joined: Aug. 2007 (Permalink) Posted: Sep. 29 2008,19:03    Quote (dvunkannon @ Sep. 12 2008,13:52)           Quote How do you know that a genome cannot make any other biochemical machine? Because we know that the product of the ribosome is a linear string of amino acids, and we know that there are other biochemical objects that are not linear strings of amino acids. Hate to be pedantic, but this is not strictly true.  The ribosome itself is a gene product, and it's not (only) a protein.  The catalytic part consists of RNA.  The genome doesn't only produce proteins - it also produces RNA, some of which is catalytic (ribozymes), others which play other roles (mRNA, tRNA). Everything else you said was correct, and even what I said above fits into what you said - RNA polymerase can be thought of as an automaton, just like the ribosome.

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