Joe G
Posts: 12011
Joined: July 2007
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| Quote (OgreMkV @ Nov. 17 2010,18:39) | Hey Joe:
One: I want a mathematical description of CSI, CSU, IC, whatever. Keep in mind that I sit next to 8 mathematicians (3 with masters and 1 with a PhD (and another who's about to graduate with a PhD). I can also get 3 people with PhDs in statistical analysis. So don't worry your little head about the math. I can take it. If I can't I can get help.
Two: Where's your answer to this:
Ask me a question about real science (not what you THINK (if that's even possible) and I'll provide you with so many citations, your pathetic little 486-66 will asplode.
hmmm... let me go ahead and start.
Evolution has been observed taking place in real world living organisms and documented doing so in peer reviewed scientific papers. From the literature on nylonase alone, we have this collection of scientific papers:
A New Nylon Oligomer Degradation Gene (nylC) On Plasmid pOAD2 From A Flavobacterium sp. by Seiji Negoro, Shinji Kakudo, Itaru Urabe, and Hirosuke Okadam, Journal of Bacteriology, 174(12): 7948-7953 (December 1992)
A Plasmid Encoding Enzymes For Nylon Oligomer Degradation: Nucleotide Sequence And Analysis Of pOAD2 by Ko Kato, Kinya Ohtsuki, Yuji Koda, Tohru Maekawa, Tetsuya Yomo, Seiji Negoro and Itaru Urabe, Microbiology, 141: 2585-2590 (1995)
Biodegradation Of Nylon Oligomers by Seiji Negoro, Applied Microbiology and Biotechnology, 54: 461-466 (26th May 2000)
Birth Of A Unique Enzyme From An Alternative Reading Frame Of The Pre-eEisted, Internally Repetitious Coding Sequence by Susumu Ohno, Proceedings of the National Academy of Sciences of the USA, 81: 2421-2425 (April 1984)
DNA-DNA Hybridization Analysis Of Nylon Oligomer-Degradative Plasmid pOAD2: Identification Of The DNA Region Analogous To The Nylon Oligomer Degradation Gene by Seiji Negoro, Shunichi Nakamura and Hirosuke Okada, Journal of Bacteriology, 158(2): 419-424 (May 1984)
Emergence Of Nylon Oligomer Degradation Enzymes In Pseudomonas aeruginosa PAO Through Experimental Evolution by Irfan J. Prijambada, Seiji Negoro, Tetsuya Yomo and Itaru Urabe, Applied and Environmental Microbiology 61(5): 2020-2022 (May 1995)
Insertion Sequence IS6100 On Plasmid pOAD2, Which Degrades Nylon Oligomers by Ko Kato, Kinya Ohtsuki, Hiroyuki Mitsuda, Tetsuya Yomo, Seiji Negoro and Itaru Urabe, Journal of Bacteriology, 176(4): 1197-1200 (February 1994)
No Stop Codons In The Antisense Strands Of The Genes For Nylon Oligomer Degradation by Tetsuya Yomo, Itaru Urabe and Hirosuke Okada, Proceedings of the National Academy of Sciences of the USA, 89: 3780-3784 (May 1992)
Nylon Oligomer Degradation Gene, nylC, On Plasmid pOAD2 From A Flavobacterium Strain Encodes Endo-Type 6-Aminohexanoate Oligomer Hydrolase: Purification And Characterisation Of The nylC Product by Shinji Kakudo, Seiji Negoro, Itaru Urabe and Hirosuke Okada, Applied and Environmental Microbiology, 59(11): 3978-3980 (November 1993)
Plasmid-Determined Enzymatic Degradation Of Nylon Oligomers by Seiji Negoro, Tomoyasu Taniguchi, Masaharu Kanaoka, Hiroyuki Kimura and Hirosuke Okada, Journal of Bacteriology, 155(1): 22-31 (July 1983)
The nylonase enzyme did not appear in these bacteria until the 1980s. Indeed, Nylon itself, and the oligomers associated with it that these bacteria metabolise, did not exist in the environment until 1935, which means that there was no reason for bacteria to possess a capability to metabolise these substances before that date. Moreover, the mechanism by which the nylonase gene came into being is well known and documented - it was the result of a frameshift mutation that generated a complete new gene that did not previously exist. This is merely one of many instances of evolution being observed taking place - the landmark paper in the field to date is this one:
Historical Contingency And Evolution Of A Key Innovation In An Experimental Population Of Escherichia coli by Zachary D. Blount, Christina Z. Borland and Richard E. Lenski, Proceedings of the National Academy of Sciences of the USA, 105(23): 7899-7906 (10th June 2008) [Full paper downloadable from here]
Quote
Blount, Borland & Lenski, 2008 wrote:
The role of historical contingency in evolution has been much debated, but rarely tested. Twelve initially identical populations of Escherichia coli were founded in 1988 to investigate this issue. They have since evolved in a glucose-limited medium that also contains citrate, which E. coli cannot use as a carbon source under oxic conditions. No population evolved the capacity to exploit citrate for >30,000 generations, although each population tested billions of mutations. A citrate-using (Cit+) variant finally evolved in one population by 31,500 generations, causing an increase in population size and diversity. The long-delayed and unique evolution of this function might indicate the involvement of some extremely rare mutation. Alternately, it may involve an ordinary mutation, but one whose physical occurrence or phenotypic expression is contingent on prior mutations in that population. We tested these hypotheses in experiments that ‘‘replayed’’ evolution from different points in that population’s history. We observed no Cit+ mutants among 8.4 × 1012 ancestral cells, nor among 9 × 1012 cells from 60 clones sampled in the first 15,000 generations. However, we observed a significantly greater tendency for later clones to evolve Cit+, indicating that some potentiating mutation arose by 20,000 generations. This potentiating change increased the mutation rate to Cit+ but did not cause generalized hypermutability.
Thus, the evolution of this phenotype was contingent on the particular history of that population. More generally, we suggest that historical contingency is especially important when it facilitates the evolution of key innovations that are not easily evolved by gradual, cumulative selection.
Direct Experimental Tests Of Evolutionary Concepts
A Model For Divergent Allopatric Speciation Of Polyploid Pteridophytes Resulting From Silencing Of Duplicate-Gene Expression by Charles R.E. Werth and Michael D. Windham, American Naturalist, 137(4): 515-526 (April 1991) - DEVELOPMENT OF A MODEL TO MATCH OBSERVED SPECIATION IN NATURE
A Molecular Reexamination Of Diploid Hybrid Speciation Of Solanum raphanifolium by David M. Spooner, Kenneth. J. Sytsma and James F. Smith, Evolution, 45(3): 757-764 - DOCUMENTATION OF AN OBSERVED SPECIATION EVENT
Cavefish As A Model System In Evolutionary Developmental Biology by William R. Jeffrey, Developmental Biology, 231:, 1-12 (1 Mar 2001) - contains experimental tests of hypotheses about eye evolution
Chromosome Evolution, Phylogeny, And Speciation Of Rock Wallabies, by G. B. Sharman, R. L. Close and G. M. Maynes, Australian Journal of Zoology, 37(2-4): 351-363 (1991) - DOCUMENTATION OF OBSERVED SPECIATION IN NATURE
Crystal Structure Of An Ancient Protein: Evolution By Conformational Epistasis by Eric A. Ortlund, Jamie T. Bridgham, Matthew R. Redinbo and Joseph W. Thornton, Science, 317: 1544-1548 (14 September 2007) - refers to the reconstruction of ancient proteins from extinct animals by back-tracking along the molecular phylogenetic trees and demonstrating that the proteins in question WORK
Evidence For Rapid Speciation Following A Founder Event In The Laboratory by James R. Weinberg Victoria R. Starczak and Danielle Jörg, Evolution 46: 1214-1220 (15th January 1992) - EXPERIMENTAL GENERATION OF A SPECIATION EVENT IN THE LABORATORY
Evolutionary Theory And Process Of Active Speciation And Adaptive Radiation In Subterranean Mole Rats, Spalax ehrenbergi Superspecies, In Israel by E. Nevo, Evolutionary Biology, 25: 1-125 - DOCUMENTATION OF OBSERVED SPECIATION IN NATURE
Experimentally Created Incipient Species Of Drosophila by Theodosius Dobzhansky & Olga Pavlovsky, Nature 230: 289 - 292 (2nd April 1971) - EXPERIMENTAL GENERATION OF A SPECIATION EVENT IN THE LABORATORY
Founder-Flush Speciation On Drosophila pseudoobscura: A Large Scale Experiment by Agustà Galiana, Andrés Moya and Francisco J. Alaya, Evolution 47: 432-444 (1993) EXPERIMENTAL GENERATION OF A SPECIATION EVENT IN THE LABORATORY
Genetics Of Natural Populations XII. Experimental Reproduction Of Some Of the Changes Caused by Natural Selection by Sewall Wright & Theodosius Dobzkansky, Genetics, 31(2): 125-156 (1946) - direct experimental tests of natural selection mechanisms
Hedgehog Signalling Controls Eye Degeneration In Blind Cavefish by Yoshiyuki Yamamoto, David W. Stock and William R. Jeffery, Nature, 431: 844-847 (14 Oct 2004) - direct experimental test of theories about eye evolution and the elucidation of the controlling genes involved
Initial Sequencing Of The Chimpanzee Genome And Comparison With The Human Genome, The Chimpanzee Genome Sequencing Consortium (see paper for full list of 68 authors), Nature, 437: 69-87 (1 September 2005) - direct sequencing of the chimpanzee genome and direct comparison of this genome with the previously sequenced human genome, whereby the scientists discovered that fully twenty-nine percent of the orthologous proteins of humans and chimpanzees are IDENTICAL
Origin Of The Superflock Of Cichlid Fishes From Lake Victoria, East Africa by Erik Verheyen, Walter Salzburger, Jos Snoeks and Axel Meyer, Science, 300: 325-329 (11 April 2003) - direct experimental determination of the molecular phylogeny of the Lake Victoria Superflock, including IDENTIFYING THE COMMON ANCESTOR OF THE 350+ SPECIES IN QUESTION and NAMING THAT ANCESTOR as Haplochromis gracilior
Phagotrophy By A Flagellate Selects For Colonial Prey: A Possible Origin Of Multicellularity by Martin.E. Boraas, Dianne.B. Seale and Joseph .E. Boxhorn, Evolutionary Ecology 12(2): 153-164 (February 1998 ) - direct experimental test of hypotheses about the origins of multicellularity
Pollen-Mediated Introgression And Hybrid Speciation In Louisiana Irises by Michael L. Arnold, Cindy M. Buckner and Jonathan J. Robinson, Proceedings of the National Academy of Sciences of the USA, 88(4): 1398-1402 (February 1991) - OBSERVATION OF A SPECIATION EVENT IN NATURE
Protein Engineering Of Hydrogenase 3 To Enhance Hydrogen Production by Toshinari. Maeda, Viviana. Sanchez-Torres and Thomas. K. Wood, Applied Microbiology and Biotechnology, 79(1): 77-86 (May 2008) - DIRECT EXPERIMENTAL APPLICATION OF EVOLUTION IN THE LABORATORY TO PRODUCE A NEW BIOTECHNOLOGY PRODUCT
Resurrecting Ancient Genes: Experimental Analysis Of Extinct Molecules by Joseph W. Thornton, Nature Reviews: Genetics, 5: 366-375 (5 May 2004) - direct experimental reconstruction in the laboratory of ancient proteins from extinct animals
Sexual Isolation Caused By Selection For Positive And Negative Phototaxis And Geotaxis In Drosophila pseudoobscura by E. del Solar, Proceedings of the National Academy of Sciences of the USA, 56: 484-487 (1966) - direct experimental test of selection mechanisms and their implications for speciation
Speciation By Hybridisation In Heliconius Butterflies by Jesús Mavárez, Camilo A. Salazar, Eldredge Bermingham, Christian Salcedo, Chris D. Jiggins and Mauricio Linares, Nature, 441: 868-871 (15th June 2006) - DETERMINATION OF A SPECIATION EVENT IN NATURE, FOLLOWED BY LABOARTORY REPRODUCTION OF THAT SPECIATION EVENT, AND CONFIRMATION THAT THE LABORATORY INDIVIDUALS ARE INTERFERTILE WITH THE WILD TYPE INDIVIDUALS
Speciation By Hybridization In Phasmids And Other Insects By Luciano Bullini and Guiseppe Nascetti, Canadian Journal of Zoology 68(8): 1747-1760 (1990) - OBSERVATION OF A SPECIATION EVENT IN NATURE
The Gibbons Speciation Mechanism by S. Ramadevon and M. A. B. Deaken, Journal of Theoretical Biology, 145(4): 447-456 (1991) - DEVELOPMENT OF A MODEL ACCOUNTING FOR OBSERVED INSTANCES OF SPECIATION
The Master Control Gene For Morphogenesis And Evolution Of The Eye by Walter J. Gehrig, Genes to Cells, 1: 11-15, 1996 - direct experimental test of hypotheses concerning eye evolution including the elucidation of the connection between the Pax6 gene and eye morphogenesis, and the experimental manipulation of that gene to control eye development
The Past As The Key To The Present: Resurrection Of Ancient Proteins From Eosinophils by Steven A. Benner, Proceedings of the National Academy of Sciences of the USA., 99(8): 4760-4761 (16 April 2002) - direct experimental reconstruction of ancient proteins from extinct animals
This list is by no means complete, because over eighteen thousand critically robust peer reviewed papers were published in evolutionary biology in 2007 alone. The number of papers published in the subject since Darwin first published The Origin of Species probably exceeds a million or so, if someone were ever to perform the requisite accounting.
As I recall, you have an issue with abiogensis. First, conflating evolutionary theory with abiogenesis is not only wrong, not only scientifically invalid, but why, as a common creationist fabrication, it too is regarded here with scorn and derision.
As for self replicating systems, if you think scientists have no clue about the formation of these, the following scientific papers will disabuse you of that farcical notion:
A Self-Replicating Ligase Ribozyme by Natasha Paul & Gerald F. Joyce, Proc. Natl. Acad. Sci. USA., 99(20): 12733-12740 (1st October 2002)
A Self-Replicating System by T. Tjivuka, P. Ballester and J. Rebek Jr, Journal of the American Chemical Society, 112: 1249-1250 (1990)
Catalysis In Prebiotic Chemistry: Application To The Synthesis Of RNA Oligomers by James P. Ferris, Prakash C. Joshi, K-J Wang, S. Miyakawa and W. Huang, Advances in Space Research, 33: 100-105 (2004)
Cations As Mediators Of The Adsorption Of Nucleic Acids On Clay Surfaces In Prebiotic Environments by Marco Franchi, James P. Ferris and Enzo Gallori, Origins of Life and Evolution of the Biosphere, 33: 1-16 (2003)
Darwinian Evolution On A Chip by Brian M. Paegel and Gerald F. Joyce, Public Library of Science Biology, 6(4): e85 (April 2008)
Emergence Of A Replicating Species From An In Vitro RNA Evolution Reaction by Ronald R. Breaker and Gerald F. Joyce, Proceedings of the National Academy of Sciences of the USA, 91: 6093-6097 (June 1994)
Information Transfer From Peptide Nucleic Acids To RNA By Template-Directed Syntheses by Jürgen G. Schmidt, Peter E. Nielsen and Leslie E. Orgel, Nucleic Acids Research, 25(23): 4794-4802 (1997)
Ligation Of The Hairpin Ribozyme In cis Induced By Freezing And Dehydration by Sergei A. Kazakov, Svetlana V. Balatskaya and Brian H. Johnston, The RNA Journal, 12: 446-456 (2006)
Mineral Catalysis And Prebiotic Synthesis: Montmorillonite-Catalysed Formation Of RNA by James P. Ferris, Elements, 1: 145-149 (June 2005)
Montmorillonite Catalysis Of 30-50 Mer Oligonucleotides: Laboratory Demonstration Of Potential Steps In The Origin Of The RNA World by James P. Ferris, Origins of Life and Evolution of the biosphere, 32: 311-332 (2002)
Montmorillonite Catalysis Of RNA Oligomer Formation In Aqueous Solution: A Model For The Prebiotic Formation Of RNA by James P. Ferris and Gözen Ertem, Journal of the American Chemical Society, 115: 12270-12275 (1993)
Nucelotide Synthetase Ribozymes May Have Emerged First In The RNA World by Wentao Ma, Chunwu Yu, Wentao Zhang and Jiming Hu, The RNA Journal, 13: 2012-2019, 18th September 2007
Prebiotic Amino Acids As Asymmetric Catalysts by Sandra Pizzarello and Arthur L. Weber, Science, 303: 1151 (20 February 2004)
Prebiotic Chemistry And The Origin Of The RNA World by Leslie E. Orgel, Critical Reviews in Biochemistry and Molecular Biology, 39: 99-123 (2004)
Prebiotic Synthesis On Minerals: Bridging The Prebiotic And RNA Worlds by James P. Ferris, Biological Bulletin, 196: 311-314 (June 1999)
Ribozymes: Building The RNA World by Gerald F. Joyce, Current Biology, 6(8): 965-967, 1996
RNA-Catalysed Nucleotide Synthesis by Peter J. Unrau and David P. Bartel, Nature, 395: 260-263 (17th September 1998)
RNA-Catalyzed RNA Polymerization: Accurate and General RNA-Templated Primer Extension by Wendy K. Johnston, Peter J. Unrau, Michael S. Lawrence, Margaret E. Glasner and David P. Bartel, Science, 292: 1319-1325, 18th May 2001
RNA-Directed Amino Acid Homochirality by J. Martyn Bailey, FASEB Journal (Federation of American Societies for Experimental Biology), 12: 503-507 (1998)
RNA Evolution And The Origin Of Life by Gerald F. Joyce, Nature, 338: 217-224 (16th March 1989)
Self Replicating Systems by Volker Patzke and Günter von Kiedrowski, ARKIVOC 5: 293-310, 2007
Self-Organising Biochemical Cycles by Leslie E. Orgel, Proceedings of the National Academy of Sciences of the USA, 97(23): 12503-12507 (7th November 2000)
Self-Sustained Replication Of An RNA Enzyme by Tracey A. Lincoln and Gerald F. Joyce, ScienceExpress, DOI: 10.1126/science.1167856 (8th January 2009)
Sequence- And Regio-Selectivity In The Montmorillonite-Catalysed Synthesis Of RNA by Gözen Ertem and James P. Ferris, Origins of Life and Evolution of the Biosphere, 30: 411-422 (2000)
Synthesis Of 35-40 Mers Of RNA Oligomers From Unblocked Monomers. A Simple Approach To The RNA World by Wenhua Huang and James P. Ferris, Chemical Communications of the Royal Society of Chemistry, 1458-1459 (2003)
Synthesis Of Long Prebiotic Oligomers On Mineral Surfaces by James P. Ferris, Aubrey R. Hill Jr, Rihe Liu and Leslie E. Orgel, Nature, 381: 59-61 (2nd May 1996)
The Antiquity Of RNA-Based Evolution by Gerald F. Joyce, Nature, 418: 214-221, 11th July 2002
The Case For An Ancestral Genetic System Involving Simple Analogues Of The Nucleotides by Gerald F. Joyce, Alan W. Schwartz, Stanley L. Miller and Leslie E. Orgel, Proceedings of the National Academy of Sciences of the USA, 84: 4398-4402 (July 1987)
The Descent of Polymerisation by Matthew Levy and Andrew D. Ellington, Nature Structural Biology, 8(7): 580-582, July 2001
The Origin And Early Evolution Of Life: Prebiotic Chemistry, The Pre-RNA World, And Time by Antonio Laczano and Stanley R. Miller, Cell, 85: 793-798 (14th June 1996)
The Origin Of Replicators And Reproducers by Eörs Szathmáry, Philosophical Transactions of the Royal Society Part B, 361: 1689-1702 (11th September 2006)
The Roads To And From The RNA World[/i] by Jason P. Dworkin, Antonio Lazcano and Stanley L. Miller, Journal of Theoretical Biology, 222: 127-134 (2003)
Transcription And Translation In An RNA World by William R. Taylor, Philosophical Transactions of the Royal Society Part B, 361: 1689-1702 (11th September 2006)
That's thirty-three scientific papers covering the emergence of self-replicating systems and their behaviour in a prebiotic environment. If you think this is a problem for scientists, then you obviously never paid attention in proper science classes.
Finally, I'll ask you, what is the shortest RNA chain that can catalyze metabolic and/or cellular functions. Until you answer that... go away.
Until you have read everyone of the papers I present and explained with references to other peer-reviewed work why the paper is wrong, you have no argument. You are just a sad little man with delusions of adequacy.
BTW: Remember, the challenge is SCIENTIFIC questions... not questions that you THINK are scientific.
Speaking, of which, why do you keep challenging us, when you can't man up and answer one simple question about ID?
Fuck off, Chicken Little. |
Hey ogre- you are an equivocating fuck, buddy.
"Evolution" isn't being debated, YEC and ID are OK with speciation and ID is OK with universal common descent.
Neither evidence for speciation nor evidence for UCD is evidence for any mechanism.
So perhaps you can find just ONE peer-reviewed paper that demonstrates an accumulation of genetic accidents, ie blind, undirected chemical processes, can construct a functional multi-part system.
As for your abiogenesis pap- it looks like it takes quite a bit of engineering to get those results- the first paper is all about engineering the ribozyme- Joyce and Lincoln engineered their replicating RNAs.
Not one paper deals with blind, undirected chemical processes producing anything.
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"Facts are Stupid"- Timothy Horton aka Occam's Afterbirth
"Genetic mutations aren't mistakes"-ID and Timothy Horton
Whales do not have tails. Water turns to ice via a molecular code- Â Acartia bogart, TARD
YEC is more coherent than materialism and it's bastard child, evolutionism
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