My lengthy response is ripening, at least.

` Despite my stuffy nose and being confined to the bathroom lately, I have nearly managed to complete my response to Anonymous Dawn. After all, she apparently has not even heard of scientific demonstrations of mechanisms whereby complex cellular structures can evolve.
` I wonder why that could be.... This reminds me of something Michael Behe once wrote (pg179, Darwin’s Black Box):

There has never been a meeting, or a book, or a paper on details of the evolution of complex biochemical systems.

` Also;

There is no publication in the scientific literature – in prestigious journals, specialty journals, or books – that describes how molecular evolution of any real, complex, biochemical system either did occur or even might have occurred.

` Surely, Anonymous Dawn is well aware of his statements to this point, which are really interesting, because, for example, the Journal of Biological Chemistry has quite a few articles about evolution, many of which I am sure are the type Behe says are nonexistent.
` I don't have any time to check them out, however, as this draft has become unwieldy (extremely slow) from formatting and I only have a mere hour-long allotment for internet time each day. It is barely enough to do anything, though feel free to glance at the sheer number of this small sampling of articles I have come across in the JBC online:

Melissa L. Geddie and Ichiro Matsumura
Rapid Evolution of -Glucuronidase Specificity by Saturation Mutagenesis of an Active Site Loop
J. Biol. Chem., Jun 2004; 279: 26462 - 26468 ; doi:10.1074/jbc.M401447200

Catherine TomHon, Wei Zhu, David Millinoff, Kenji Hayasaka, Jerry L. Slightom, Morris Goodman, and Deborah L. Gumucio
Evolution of a Fetal Expression Pattern via cis Changes near the Globin Gene
J. Biol. Chem., May 1997; 272: 14062 - 14066 ; doi:10.1074/jbc.272.22.14062

Simon R. Andrews, Edward J. Taylor, Gavin Pell, Florence Vincent, Valérie M.-A. Ducros, Gideon J. Davies, Jeremy H. Lakey, and Harry J. Gilbert
The Use of Forced Protein Evolution to Investigate and Improve Stability of Family 10 Xylanases: THE PRODUCTION OF Ca2+-INDEPENDENT STABLE XYLANASES
J. Biol. Chem., Dec 2004; 279: 54369 - 54379 ; doi:10.1074/jbc.M409044200

Lawrence P. Wackett
Evolution of Enzymes for the Metabolism of New Chemical Inputs into the Environment
J. Biol. Chem., Oct 2004; 279: 41259 - 41262 ; doi:10.1074/jbc.R400014200

Christian Mitri, Marie-Laure Parmentier, Jean-Philippe Pin, Joël Bockaert, and Yves Grau
Divergent Evolution in Metabotropic Glutamate Receptors: A NEW RECEPTOR ACTIVATED BY AN ENDOGENOUS LIGAND DIFFERENT FROM GLUTAMATE IN INSECTS
J. Biol. Chem., Mar 2004; 279: 9313 - 9320 ; doi:10.1074/jbc.M310878200

Enrico Negrisolo, Alberto Pallavicini, Roberto Barbato, Sylvia Dewilde, Anna Ghiretti-Magaldi, Luc Moens, and Gerolamo Lanfranchi
The Evolution of Extracellular Hemoglobins of Annelids, Vestimentiferans, and Pogonophorans
J. Biol. Chem., Jul 2001; 276: 26391 - 26397 ; doi:10.1074/jbc.M100557200

Angela Schulz and Torsten Schöneberg
The Structural Evolution of a P2Y-like G-protein-coupled Receptor
J. Biol. Chem., Sep 2003; 278: 35531 - 35541 ; doi:10.1074/jbc.M303346200

Ronald E. van Kesteren, Cornelis P. Tensen, August B. Smit, Jan van Minnen, Lee. F. Kolakowski, Jr., Wolfgang Meyerhof, Dietmar Richter, Harm van Heerikhuizen, Erno Vreugdenhil, and Wijnand P. M. Geraerts
Co-evolution of Ligand-Receptor Pairs in the Vasopressin/Oxytocin Superfamily of Bioactive Peptides
J. Biol. Chem., Feb 1996; 271: 3619 - 3626 ; doi:10.1074/jbc.271.7.3619

Andrew P. Spicer and John A. McDonald Characterization and Molecular Evolution of a Vertebrate Hyaluronan Synthase Gene Family J. Biol. Chem. 1998 273: 1923-1932.

Catherine TomHon, Wei Zhu, David Millinoff, Kenji Hayasaka, Jerry L. Slightom, Morris Goodman, and Deborah L. Gumucio Evolution of a Fetal Expression Pattern via cis Changes near the Globin Gene J. Biol. Chem. 1997 272: 14062-14066.

Chien-Chia Wang, Andrey Pavlov, and Jim D. Karam Evolution of RNA-binding Specificity in T4 DNA Polymerase J. Biol. Chem. 1997 272: 17703-17710.

David R. Gang, Hiroyuki Kasahara, Zhi-Qiang Xia, Kristine Vander Mijnsbrugge, Guy Bauw, Wout Boerjan, Marc Van Montagu, Laurence B.Davin, and Norman G. Lewis Evolution of Plant Defense Mechanisms. RELATIONSHIPS OF PHENYLCOUMARAN BENZYLIC ETHER REDUCTASES TO PINORESINOL-LARICIRESINOL AND ISOFLAVONE REDUCTASES J. Biol. Chem. 1999 274: 7516-7527.

Elizabeth A. Bucher, Gurtej K. Dhoot, Mark M. Emerson, Margaret Ober, and Charles P. Emerson, Jr. Structure and Evolution of the Alternatively Spliced Fast Troponin T Isoform Gene J. Biol. Chem. 1999 274: 17661-17670.

Florence Magrangeas, Gilles Pitiot, Sigrid Dubois, Elisabeth Bragado-Nilsson, Michel ChŽrel, SŽverin Jobert, Benoit Lebeau, Olivier Boisteau, Bernard LethŽ, Jacques Mallet, Yannick Jacques, and StŽphane Minvielle Cotranscription and Intergenic Splicing of Human Galactose-1-phosphate Uridylyltransferase and Interleukin-11 Receptor -Chain Genes Generate a Fusion mRNA in Normal Cells. IMPLICATION FOR THE PRODUCTION OF MULTIDOMAIN PROTEINS DURING EVOLUTION J. Biol. Chem. 1998 273: 16005-16010.

James E. Hagstrom, Michael P. Fautsch, Monique Perdok, Anne Vrabel, and Eric D. Wieben Exons Lost and Found. UNUSUAL EVOLUTION OF A SEMINAL VESICLE TRANSGLUTAMINASE SUBSTRATE J. Biol. Chem. 1996271: 21114-21119.

Juan Ausi— Histone H1 and Evolution of Sperm Nuclear Basic Proteins J. Biol. Chem. 1999 274: 31115-31118.

M. Neale Weitzmann, Kerry J. Woodford, and Karen Usdin DNA Secondary Structures and the Evolution of Hypervariable Tandem Arrays J. Biol. Chem. 1997 272: 9517-9523.

Marieta Costache, Pol-AndrŽ Apoil, Anne Cailleau, Anders Elmgren, Gšran Larson, Stephen Henry, Antoine Blancher, Dana Iordachescu, Rafael Oriol, and Rosella Mollicone Evolution of Fucosyltransferase Genes in Vertebrates J. Biol. Chem. 1997 272: 29721-29728.

Medeiros, Edward G. Rowan, Alan L. Harvey, and AndrŽ MŽnez On the Convergent Evolution of Animal Toxins. CONSERVATION OF A DIAD OF FUNCTIONAL RESIDUES IN POTASSIUM CHANNEL-BLOCKING TOXINS WITH UNRELATED STRUCTURES J. Biol. Chem. 1997 272: 4302-4309.

Ronald E. van Kesteren, Cornelis P. Tensen, August B. Smit, Jan van Minnen, Lee. F. Kolakowski, Jr., Wolfgang Meyerhof, Dietmar Richter, Harm van Heerikhuizen, Erno Vreugdenhil, and Wijnand P. M. Geraerts Co-evolution of Ligand-Receptor Pairs in the Vasopressin/Oxytocin Superfamily of Bioactive Peptides J. Biol. Chem. 1996 271: 3619-3626.

Sandra K. Parker and H. William Detrich III Evolution, Organization, and Expression of -Tubulin Genes in the Antarctic Fish Notothenia coriiceps. ADAPTIVE EXPANSION OF A GENE FAMILY BY RECENT GENE DUPLICATION, INVERSION, AND DIVERGENCE J. Biol. Chem. 1998 273: 34358-34369.

Stefanie Brumme, Volker Kruft, Udo K. Schmitz, and Hans-Peter Braun New Insights into the Co-evolution of Cytochrome c Reductase and the Mitochondrial Processing Peptidase J. Biol. Chem. 1998 273: 13143-13149.

Stephan M. MŸhlebach, Thomas Wirz, Urs BrŠndle, and Jean-Claude Perriard Evolution of the Creatine Kinases J. Biol. Chem. 1996 271: 11920-11929.

Zhe Lu, Elisa Cabiscol, Nuria Obradors, Jordi Tamarit, Joaquim Ros, Juan Aguilar, and E. C. C. Lin Evolution of an Escherichia coli Protein with Increased Resistance to Oxidative Stress J. Biol. Chem. 1998 273: 8308-8316.


` Hmm. Looks promising. Indeed, here is a list someone has long since compiled of Behe's nonexistent meetings, books and papers:


Books
· Cells, Embryos, And Evolution: Towards a Cellular and Developmental Understanding of Phenotypic Variation and Evolutionary Adaptability - a recent textbook by John Gerhart and Marc Kirschner (1997 Blackwell Science) - "In writing Cells, Embryos, and Evolution, our aim has been to continue what Darwin started: to understand not only the influence of selection on the path of evolution, but also the capacity of the organism to generate heritable variation upon which selection can act."Preface / amazon.com bookstore
· Four Billion Years An Essay on the Evolution of Genes and Organisms by Willam F. Loomis
· Vital Dust : Life As a Cosmic Imperativeby Christian De Duve
· Many of these books suggested by David Ussery, Ph.D (thanks!):
· +Molecular Strategies in Biological Evolution - Proceedings of a New York Academy ofSciences conference, June 27-29, 1998. Lynn Helena Caporale, Editor.
· + Molecular Approaches to Ecology and Evolution by by Rob Desalle (Editor), B. Schierwater (Editor) (98)
· + Molecular Evolution by Wen-Hsiung Li (97)
· + Patterns in Evolution: The New Molecular View by Roger Lewin (96)
· + Chemical Evolution: Physics of the Origin and Evolution of Life (96)
· + Tracing Biological Evolution in Protein and Gene Structures (96)
· + Molecular Evolution (Biomathematics V. 24) by Vadim Aleksandrovich Ratner (Editor) (96)
· +GENE FAMILIES STRUCTURE FUNCTION GENETICS AND EVOLUTION Proceedings of the VIII International Congress on Isozymes (95)
· + Genetics and Evolution The Molecules of Inheritance (New Encyclopedia of Science) (95)
· + The Causes of Molecular Evolution (94)
· + The Origins of Order Self-Organization and Selection in Evolution by Stuart A. Kauffman (92)
· + Molecular Evolution of the Major Histocompatibility Complex (92)
· + Molecular Evolution on Rugged Landscapes; Proteins RNA and the Immune System by Stuart A. Kauffman (91)
· + Evolution at the Molecular Level by Robert K. Selander, Andrew G. Clark, Thomas S. Whittam (Editor) (91)
· + Evolution of Life: Fossils Molecules and Culture by S. Osawa, T. Honjo (Editor) (91)
· + Molecular Theory of Evolution (85)
· + Multidomain Proteins Structure and Evolution
· +Evolutionary Design by Computers edited by Peter J. Bentley. Book & CD-ROM edition (May 1999) Amazon.com or Amazon.co.uk- Yes, evolution does produce irreducible complexity!
o Author's Book Page with related links, Author's home page, More Ordering Information
· + Search for Life on Mars by Malcolm Walter, 1999 - contains origins of life scenarios

Conferences
· + Do Genomes Enhance Their Own Evolution? - "At a conference on molecular strategies in biological evolution, researchers discussed how evolutionary strategies can evolve, making the process of evolution more efficient."
· + New Passion for Evo-Devo - Fifth Annual Meeting of the Society for Molecular Biology and Evolution

Immune System
· +The Evolution of Improved Fitness by random mutation plus selection by Edward E. Max, M.D., Ph.D. [Talk.Origins archive] Michael Behe likes to talk about the human immune system, but what lessons should we really learn from such a system?
· Immunity and the Invertebrates - "the fabulously complex immune systems of humans and other mammals evolved over hundreds of millions of years - in sometimes surprising ways. Scientific American Nov 1996
· Sharks and the Origins of Vertebrate Immunity. Scientific American Nov 1996
· + Ancient Jumping DNA May Have Evolved Into Key Component Of Human Immune System
· + Transposition mediated by RAG1 and RAG2 and its implications for the evolution of the immune system
· Evolution of immune reactions - "The history and evolutionary pathways of defense reactions among various forms of life are reconstructed"
· New insights into V(D)J recombination and its role in the evolution of the immune system - no abstract avail
· Evolution and developmental regulation of the major histocompatibility complex
· Evolution of the IL-6/class IB cytokine receptor family in the immune and nervous systems - "we speculate on a plausible molecular pathway"
· Layered evolution in the immune system. A model for the ontogeny and development of multiple lymphocyte lineages - no abstract avail
· Development of an immune system
· The ancestor of the adaptive immune system was the CAM system for organogenesis
· The evolutionary origins of immunoglobulins and T-cell receptors: possibilities and probabilities - no abstract avail
· Evolutionary perspectives on amyloid and inflammatory features of Alzheimer disease
· Organization of the human RH50A gene (RHAG) and evolution of base composition of the RH gene family.
· Molecular evolution of the vertebrate immune system.
· Morphostasis: an evolving perspective.
· Rapid evolution of immunoglobulin superfamily C2 domains expressed in immune system cells.

Blood Coagulation
· Reconstructing the evolution of vertebrate blood coagulation from a consideration of the amino acid sequences of clotting proteins - no, this is not the "ying and yang" presentation from Behe's book
· Evolutionary assembly of blood coagulation proteins - no abstract avail
· Exon and domain evolution in the proenzymes of blood coagulation and fibrinolysis - no abstract avail
· Evolution of proteolytic enzymes
· Evolution of vertebrate fibrin formation and the process of its dissolution.

Globin
· + Common Parasite Overturns Traditional Beliefs About The Evolution And Role Of Hemoglobin - "reveals that hemoglobin evolved first and foremost to handle the molecule nitric oxide (NO) rather than oxygen"
· + Scientists Discover How Bacteria Protect Themselves Against Immune System - "So we are now providing an understanding of the evolutionary basis of hemoglobin and the original function of the hemoglobin family - to detoxify nitric oxide."
· + The Evolution of Hemoglobin by Ross Hardison, (Abstract) American Scientist, March-April 1999
· Globins in nonvertebrate species: dispersal by horizontal gene transfer and evolution of the structure-function relationships
· Reduction of two functional gamma-globin genes to one: an evolutionary trend in New World monkeys
· Evolutionary history of introns in a multidomain globin gene
· Hemoglobin A2: origin, evolution, and aftermath - no abstract avail

Flagella and Cilium
· Early evolution of microtubules and undulipodia
· Flagellar beat patterns and their possible evolution - "The most sophisticated flagellar mechanisms are best explained as having been evolved for the collection of particulate food"
· A temporary flagellate (mastigote) stage in the vahlkampfiid amoeba Willaertia magna and its possible evolutionary significance
· The evolutionary origin and phylogeny of eukaryote flagella - no abstract avail
· + Molecular analysis of archael flagellins: similarity to the type IV pilin-transport superfamily widespread in bacteria
· Molecular evolution of the C-terminal cytoplasmic domain of a superfamily of bacterial receptors involved in taxis - "The gene coding for the C-terminal cytoplasmic domain of these proteins apparently evolved through gene duplication from a common ancestor"
· Dynein family of motor proteins: present status and future questions - evolution of Dynein via gene duplication
· Origins of the nucleate organisms - "The phylogeny supports the hypotheses that the flagellum developed from the spindle system"
· The evolutionary origin and phylogeny of microtubules, mitotic spindles and eukaryote flagella - no abstract avail
· The evolution of cellular movement in eukaryotes: the role of microfilaments and microtubules - no abstract avail

Other Motor Proteins
· +Kinesin Motor Phylogenetic Tree - Behe likes to play down the importance of sequence comparisons. It's no wonder - just click around this diagram for a while. It becomes obvious that an important motor protein like kinesin has gradually evolved across many species. From the Kinesin HomePage.

Actin
· Evolution of a dynamic cytoskeleton
· Isolation, characterization and evolution of nine pufferfish (Fugu rubripes) actin genes
· Evolution of chordate actin genes: evidence from genomic organization and amino acid sequences
· Structural comparisons of muscle and nonmuscle actins give insights into the evolution of their functional differences

Cell Membrane - Receptors, Pumps, etc.
· + Molecular evolution of glutamate receptors: a primitive signaling mechanism that existed before plants and animals diverged.
· Co-evolution of ligand-receptor pairs in the vasopressin/oxytocin superfamily of bioactive peptides
· The evolution of the synapses in the vertebrate central nervous system
· Evolutionary origins of multidrug and drug-specific efflux pumps in bacteria.
· A comprehensive evolutionary analysis based on nucleotide and amino acid sequences of the alpha- and beta-subunits of glycoprotein hormone gene family.

Citric Acid Cycle (Krebs Cycle)
· The puzzle of the Krebs citric acid cycle: assembling the pieces of chemically feasible reactions, and opportunism in the design of metabolic pathways during evolution
· The evolution of metabolic cycles
· Evolution of the first metabolic cycles
· Chemical evolution of the citric acid cycle: sunlight photolysis of the amino acids glutamate and aspartate
· Speculations on the origin and evolution of metabolism
· The Molecular Anatomy of an Ancient Adaptive Eventby Anthony M. Dean (American Scientist Jan-Feb 1998) - "Using a combination of the modern techniques of structural biochemistry and protein engineering, combined with molecular phylogeny, the author recreates the story of this very ancient event."

Amino Acid Biosynthesis
· New prospects for deducing the evolutionary history of metabolic pathways in prokaryotes: aromatic biosynthesis as a case-in-point
· Biochemical pathways in prokaryotes can be traced backward through evolutionary time
· Enzyme specialization during the evolution of amino acid biosynthetic pathways
· Enzyme recruitment in evolution of new function

Gylcolysis
· Evolution of glycolysis - no abstract available
· Bioenergetics: the evolution of molecular mechanisms and the development of bioenergetic concepts
· Theoretical approaches to the evolutionary optimization of glycolysis--chemical analysis
· The evolution of kinetoplastid glycosomes

Photosynthesis
· Stepwise molecular evolution of bacterial photosynthetic energy conversion
· Evolution of photosynthetic reaction centers and light harvesting chlorophyll proteins
· Evolution of photosynthetic reaction centers
· Early evolution of photosynthesis: clues from nitrogenase and chlorophyll iron proteins
· Evolution of the control of pigment and plastid development in photosynthetic organisms
· Chemical evolution of photosynthesis

Lysozome
· Molecular evolution of ruminant lysozymes
· Adaptive evolution of lysozyme: changes in amino acid sequence, regulationof expression and gene number
· Evolution of stomach lysozyme: the pig lysozyme gene

Vision
· + The evolution of trichromatic color vision by opsin gene duplication in New World and Old World primates
· The Evolution of Color Vision - byMickey Rowe from the Talk.Origins archive.
· Molecular basis for tetrachromatic color vision - rhodopsins diverged from cone-type pigment
· Molecular evolution of the Rh3 gene in Drosophila
· Interphotoreceptor retinoid-binding protein. Gene characterization, protein repeat structure, and its evolution
· Spectral tuning and molecular evolution of rod visual pigments in the species flock of cottoid fish in Lake Baikal
· The evolution of rhodopsins and neurotransmitter receptors - another example of the importance of sequence comparisons in studying evolution. Behe dismisses comparisons as a limited tool in determining lines of descent.
· Optimization, constraint, and history in the evolution of eyes
· A pessimistic estimate of the time required for an eye to evolve - remember the last claim to irredicible complexity?
· Sequence analysis of teleost retina-specific lactate dehydrogenase C: evolutionary implications for the vertebrate lactate dehydrogenase gene family
· The eye of the blind mole rat (Spalax ehrenbergi): regressive evolution at the molecular level - no abstract avail
· The evolution of eyes. - "...The presence of homologous constituent molecules in nonhomologous structures reminds us that molecules are not eyes."

Development
· + Programming the Drosophila embryo
· + Evolution of chordate hox gene clusters
· + Hox genes in brachiopods and priapulids and protostome evolution.
· +Radical evolutionary change possible in a few generations
· + Evolution Re-Sculpted Animal Limbs By Genetic Switches Once Thought Too Drastic For Survival - "Today's finding marks the first time that changes in the control of homeotic genes have been shown to underlie an evolutionary trend leading to novel body structures." (also here: Animal Limb Evolution)
· + Flatworms Are Oldest Living Ancestors To Those Of Us With Right And Left Sides Researchers Report In Science
· The origin and evolution of animal appendages
· Hox genes in evolution: protein surfaces and paralog groups
· Evolution of the insect body plan as revealed by the Sex combs reduced expression pattern
· Sea urchin Hox genes: insights into the ancestral Hox cluster
· Theoretical approaches to the analysis of homeobox gene evolution
· Teleost HoxD and HoxA genes: comparison with tetrapods and functional evolution of the HOXD complex
· Evolutionary origin of insect wings from ancestral gills
· Tracing backbone evolution through a tunicate's lost tail
· Classification and phylogeny of the MADS-box multigene family suggest defined roles of MADS-box gene subfamilies in the morphological evolution of eukaryotes
· Modification of expression and cis-regulation of Hoxc8 in the evolution of diverged axial morphology.
· The ParaHox gene cluster is an evolutionary sister of the Hox gene cluster.

Transcription / Translation / Duplication
· Gene duplications in evolution of archaeal family B DNA polymerases
· Adaptive amino acid replacements accompanied by domain fusion in reverse transcriptase
· Molecular evolution of genes encoding ribonucleases in ruminant species
· Studies on the sites expressing evolutionary changes in the structure of eukaryotic 5S ribosomal RNA
· Evolution of a Transfer RNA Gene Through a Point Mutation in the Anticodon
· Archaeal translation initiation revisited: the initiation factor 2 and eukaryotic initiation factor 2B alpha-beta-delta subunit families
· Universally conserved translation initiation factors
· Genetic code in evolution: switching species-specific aminoacylation with a peptide transplant.
· Evolution of transcriptional regulatory elements within the promoter of a mammalian gene.
· Codon reassignment and amino acid composition in hemichordate mitochondria.

From Russell F. Doolittle
· Reconstructing the evolution of vertebrate blood coagulation from a consideration of the amino acid sequences of clotting proteins - no, this is not the "ying and yang" presentation from Behe's book
· Determining divergence times of the major kingdoms of living organisms with a protein clock - At least Behe thinks that common descent is "reasonable".
· The multiplicity of domains in proteins - evolution via domain shuffling
· Characterization, primary structure, and evolution of lamprey plasma albumin - protein evolution via gene duplication
· The origins and evolution of eukaryotic proteins
· Evolution of vertebrate fibrin formation and the process of its dissolution.
Drug resistance is biochemical evolution
· +HIV Mutating Too Fast For Drug Cocktail - "Because of HIV's high mutation rate, it provides a unique opportunity to study the processes of evolution,"
· The Challenge of Antibiotic Resistance. SciAm, March 98

Other
· + Vastly Different Virus Families May Be Related
· + Selective sweep of a newly evolved sperm-specific gene in Drosophila
· + Activated acetic acid by carbon fixation on (Fe,Ni)S under primordial conditions
· Molecular evolution of the histidine biosynthetic pathway
· Accelerated evolution in inhibitor domains of porcine elafin family members
· Tandem arrangement of the human serum albumin multigene family in the sub-centromeric region of 4q: evolution and chromosomal direction of transcription
· The B12-dependent ribonucleotide reductase from the archaebacterium Thermoplasma acidophila: an evolutionary solution to the ribonucleotide reductase conundrum
· Ancient divergence of long and short isoforms of adenylate kinase: molecular evolution of the nucleoside monophosphate kinase family
· Convergent evolution of antifreeze glycoproteins in Antarctic notothenioid fish and Arctic cod
· + Evolution of antifreeze glycoprotein gene from a trypsinogen gene in Antarctic notothenioid fish - "We have found that the antifreeze glycoproteins (AFGPs) of the predominant Antarctic fish taxon, the notothenioids, evolved from a pancreatic trypsinogen. We have determined the likely evolutionary process..."
· + Evolution of an antifreeze glycoprotein (no abstract)
· A model for the evolution of the plastid sec apparatus inferred from secY gene phylogeny
· The evolutionary history of the amylase multigene family in Drosophila pseudoobscura
· Accelerated evolution of Trimeresurus okinavensis venom gland phospholipase A2 isozyme-encoding genes
· The evolution of an allosteric site in phosphorylase
· Molecular evolution of fish neurohypophysial hormones: neutral and selective evolutionary mechanisms
· Pseudogenes in ribonuclease evolution: a source of new biomacromolecular function?
· Evolution of hemopoietic ligands and their receptors. Influence of positive selection on correlated replacements throughout ligand and receptor proteins
· Evolutionary relationships of the carbamoylphosphate synthetase genes
· The molecular evolution of the small heat-shock proteins in plants
· Phylogenetic analysis of carbamoylphosphate synthetase genes: complex evolutionary history includes an internal duplication within a gene which can root the tree of life
· Duplication and functional divergence in the chalcone synthase gene family of Asteraceae: evolution with substrate change and catalytic simplification
· Evolutionary history of the 11p15 human mucin gene family.
· Molecular evolution of the aldo-keto reductase gene superfamily.
· Molecular evolution allows bypass of the requirement for activation loop phosphorylation of the Cdc28 cyclin-dependent kinase.

General
· +A Classification of Possible Routes of Darwinian Evolution by Richard T. Thornhill and David W. Ussery, Journal of Theoretical Biology, 203:111-116, 2000 - "...This classification provides a conceptual framework within which to investigate the accessibility by Darwinian evolution of complex biological structures." (For the record, I don't agree with their conclusion that Orr's proposed route can not produce irreducible complexity - John C)
· + Generation of evolutionary novelty by functional shift+Evolutionary Insights Stem From Sloppy Copy Discovery
· + Mobile DNA Sequences Could Be The Cause Of Chromosomal Mutations During The Evolution Of Species
· + A domain model for eukaryotic DNA organization: a molecular basis for cell differentiation and chromosome evolution.
· + The domain model for eukaryotic DNA organization. 2: A molecular basis for constraints on development and evolution.
· +Minor Shuffle Makes Protein Fold - "the finding makes the evolution of new protein shapes easier to understand, because it implies that proteins can adapt through small changes and preserve some structural elements while discarding others."
· + Genetic Stowaways May Contribute To Evolutionary Change
· +Evolutionary Molecular Mechanism In Mammals Found
· +Complete Genomes - "This page contains the results of in-depth analysis of complete genome sequences of cellular life forms"
· Genetic redundancy caused by gene duplications and its evolution in networks of transcriptional regulators
· Strong evolutionary conservation of broadly expressed protein isoforms in the troponin I gene family and other vertebrate gene families
· Cases of ancient mobile element DNA insertions that now affect gene regulation
· Punctuated evolution caused by selection of rare beneficial mutations
· The origin of programmed cell death - no abstract avail
· The origin and early development of biological catalysts
· DNA secondary structures and the evolution of hypervariable tandem arrays
· Episodic adaptive evolution of primate lysozymes - testing for adaptation
· Genome plasticity as a paradigm of eubacteria evolution
· Evolutionary motif and its biological and structural significance
· Neutral and nonneutral mutations: the creative mix--evolution of complexity in gene interaction systems
· Exon shuffling and other ways of module exchange and Domain organizations of modular extracellular matrix proteins and their evolution
· Introns and gene evolution
· New Drosophila introns originate by duplication.
· Evolution and the structural domains of proteins
· The role of constrained self-organization in genome structural evolution
· A possible origin of newly-born bacterial genes: significance of GC-rich nonstop frame on antisense strand
· The coevolution of gene family trees
· The evolution of metabolic cycles
· The emergence of major cellular processes in evolution
· A hardware interpretation of the evolution of the genetic code - "A quantitative rationale for the evolution of the genetic code is developed considering the principle of minimal hardware" - note that "minimizing hardware" is one plausible path to evolving "irreducibly complex" systems.
· Speculations on the origin and evolution of metabolism
· Probabilistic reconstruction of ancestral protein sequences and Search for ancient patterns in protein sequences
· The contribution of slippage-like processes to genome evolution
· Molecular evolution in bacteria
· The structural basis of molecular adaptation.

Someone say Intelligent?
· Mitochondrial DNA: molecular fossils in the nucleus
· Cases of ancient mobile element DNA insertions that now affect gene regulation
· Tiggers and DNA transposon fossils in the human genome
· The eye of the blind mole rat (Spalax ehrenbergi): regressive evolution at the molecular level - no abstract avail
· Tiggers and DNA transposon fossils in the human genome

Cancer as Molecular Evolution
· Gene competition and the possible evolutionary role of tumours

Test Tube and Artificial Evolution
· + New Scientist Planet Science: Replaying life -At last, we can watch evolution happen over and over again in the microworlds of the lab. And in playing God, we are laying bare the very forces that shape all living things, says Kate Douglas
· Molecular evolution of an arsenate detoxification pathway by DNA shuffling - "These results show that DNA shuffling can improve the function of pathways by complex and unexpected mutational mechanisms that may be activated by point mutation. These mechanisms may be difficult to explain and are likely to be overlooked by rational design"
· UB Researcher Developing Method That Employs Evolution To Develop New Drug Leads
· Directed evolution of a type I antifreeze protein expressed in Escherichia coli with sodium chloride as selective pressure and its effect on antifreeze tolerance
· Directed evolution of biosynthetic pathways. Recruitment of cysteine thioethers for constructing the cell wall of Escherichia coli
· Exploring the functional robustness of an enzyme by in vitro evolution
· Evolutionary algorithms in computer-aided molecular design
· Mutations to the Rescue - unintelligent design
· + Researchers Engineer A Way To Improve T-Cell Receptors - using Darwinian selection
· + Digital Organisms Give Life To Questions Of Evolution (The Avida Artificial Life Group Home Page)

Origin of Life and Cells
· +Good intro: Lies, Damned lies, Statistics, and Probability of Abiogenesis Calculations
· +Purdue Study Breathes New Life Into Question Of How Life Began - self-replicating peptides
· + Ammonia From The Earth's Deep Oceans A Key Step In The Search For Life's Origins
· + Whitehead Study Supports Existence Of Ancient RNA World Helps Provide Insight Into Early Evolution Of Life
· + Yale Scientists Recreate Molecular Fossils Now Extinct That May Have Existed At The Beginning Of Life
· +A whole old world - new evidence for "The RNA World"
· The path from the RNA world.
· Relics from the RNA world.
· A supersymmetric model for the evolution of the genetic code.
· The hydrogen hypothesis for the first eukaryote.
· + Kick-start for life on earth
· The Beginnings of Life on Earth by Christian de Duve
· +Are the Odds Against the Origin of Life Too Great to Accept? : Addenda to Review of David Foster's The Philosophical Scientists by Richard C. Carrier. From Bad Science Worse Philosophy the Quackery and Logic-Chopping of David Foster's The Philosophical Scientists


` Nothing indeed!

In effect, the theory of Darwinian molecular evolution has not published, and so it should perish.

` Oh, I suppose you’re right, Dr. Behe. Excuse me, I’ll forget I ever saw those.

` I hope you see my point, Dawn; It seems as though Behe does not want this research to exist so that he can tell people it doesn’t! Whether he is largely oblivious to it, or if his pants are brilliantly aflame is immaterial – almost all of what he says about lack of research is not true.
` Similarly, a lot of what he says about existing research is also not true, a bit of which I describe in my response.
` Which is coming, flagella and all. Soon enough.