Fredwin On Evolution

great post. I wonder if Fred is a Freeper.

I like this rebuttal was quite good. It hits all of the salient points.

I must have read something else. But I liked this part in response to the question "(1) Life was said to have begun by chemical inadvertence in the early seas. Did we, I wondered, really know of what those early seas consisted?"

Here's the response:

"For some billion year old oceans, we know about their acidity, their oxygen content, their organic content, and their radionuclide concentrations as well or better than we know of some major bodies of water on earth today."

First of all, according to the science I've read, prokaryotic life appeared at a minimum of 3.5 billion years ago and second of all I find the second claim the essence of just soism. It is so because he said it is so.

And so it goes.

Fred's right -- "the accretion of successful point mutations" is even according to what you say -- one of the ways evolution proceeds. Doesn't mean the only way.

To get started -- to develop the amino acids, the chains of acids, the fats, etc. would take that low level of development. And it continues. We see it all the time in metabolisms -- usually leads to sickness, cancer, death.

Genetic variability of higher, more complex sorts means you have genes and metabolisms inside cells that work with the genes. That's a lot of "a priori". And even those others sorts of complex modalities can be thought as point-wise, if the "point" is chosen to the more complex level.

My point about brownian motion -- I myself really don't see what point it was, yet that silly dance of dust motes is what fired off Einstein, and lead eventually iirc to quantum mechanics, the weight of the electron and other intellectual evolutions not so obvious.

Maybe that's just me.

I don't think so and I think you're a doggone honest guy.

Third, evolutionists are obsessed by Christianity and Creationism,

ROFL! Apparently this guy is ignorant of the fact that the majority of evolutionists in America are themselves *Christians*.

with which they imagine themselves to be in mortal combat.

Gee, might it have something to do with the way that evolution is under constant attack by folks calling themselves creationists? Or is that too obvious for the author to grasp?

This is peculiar to them.

Because the creationists' attacks are "peculiar to evolution" (not to mention "peculiar" in the other sense). I don't see anyone going to court to try to force astronomy textbooks to carry "disclaimers"... And I haven't heard of anyone starting an "anti-astronomy league".

Note that other sciences, such as astronomy and geology, even archaeology, are equally threatened by the notion that the world was created in 4004 BC. Astronomers pay not the slightest attention to creationist ideas.

Neither would evolutionists (and for a long time they *didn't*) if the creationists didn't keep popping out of the woodwork to attack evolution and evolutionists, including but not limited to in school boards and in the courts. Not surprisingly, the evolutionists are defending themselves from the attacks.

Nobody does—except evolutionists.

See above.

We are dealing with competing religions

Yawn -- *that* stupid claim again? Evolutionary biology is science. It only looks like "religion" to those people who are so steeped in their own religions that they can't conceive of any other way of acquiring knowledge. It's like the old saying, "when the only tool you have is a hammer, every problem looks like a nail."

—overarching explanations of origin and destiny. Thus the fury of their response to skepticism.

We've got absolutely no problem with "skepticism". Read any science journals and you'll see plenty of "skepeticism" of *everything*, including evolution. Science thrives on skepticism, it's part of the scientific method.

However, you will see some "fury of response" to the endless waves of IGNORANT, FLAWED, KNEE-JERK skepticism by people most of whom couldn't even pass a freshman biology course. It gets *really* old after the first several hundred times.

Speaking of things "peculiar to evolution", could someone tell me why it is that while most folks would never dream of presuming to know enough about, say, relativistic physics, to denounce that field of science as a "fraud" or "a religion" or "metaphysics", blah blah blah -- and yet endless waves of people seem to feel imminently qualified to make such pronoucements about evolutionary biology in complete confidence, without bothering to learn much if anything about it?

...and then you wonder why those of us who *do* know quite a bit about the field get a little cranky at the vast numbers of arrogant know-nothings who dismiss 150 years of research as "fraud" and worse?

The last straw for me was a post where a Freeper declared that even her nine-year old daughter was able to spot the "flaw" in evolution. My response to that post explains why evolutionists often get fed up to *here* with the frequent attacks an insults (note, a recent change at NCBI has broken a lot of these links, but you can still find those papers by Googling for their titles):

LOL.. well duh. My nine year old figured that out. LOL. She has seen my pics of micro- organisms plus the macroscopic world. With no federal funding and no advanced degrees- she figured out it would be statistically impossible no matter how many millions of years for each organism to develop from one common cellular structure. She thought that even after a gamillion years we would be lucky to have a small portion of living organisms today.
Yes, indeed, anti-evolutionist "analysis" is about on the level of sophistication and knowledge as a nine-year-old. Thanks for the example.
Meanwhile, could you ask your little girl for her critique of the following papers? It sure would be a boon to the world of science if your nine-year-old could shed some light on these ongoing productive lines of research. Thanks.

On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells William Martin and Michael J. Russell
Abstract: All life is organized as cells. Physical compartmentation from the environment and self-organization of self-contained redox reactions are the most conserved attributes of living things, hence inorganic matter with such attributes would be life’s most likely forebear. We propose that life evolved in structured iron monosulphide precipitates in a seepage site hydrothermal mound at a redox, pH and temperature gradient between sulphide-rich hydrothermal fluid and iron(II)-containing waters of the Hadean ocean floor. The naturally arising, three-dimensional compartmentation observed within fossilized seepage-site metal sulphide precipitates indicates that these inorganic compartments were the precursors of cell walls and membranes found in free-living prokaryotes. The known capability of FeS and NiS to catalyse the synthesis of the acetyl-methylsulphide from carbon monoxide and methylsulphide, constituents of hydrothermal fluid, indicates that pre-biotic syntheses occurred at the inner surfaces of these metal-sulphide-walled compartments, which furthermore restrained reacted products from diffusion into the ocean, providing sufficient concentrations of reactants to forge the transition from geochemistry to biochemistry. The chemistry of what is known as the RNA-world could have taken place within these naturally forming, catalyticwalled compartments to give rise to replicating systems. Sufficient concentrations of precursors to support replication would have been synthesized in situ geochemically and biogeochemically, with FeS (and NiS) centres playing the central catalytic role. The universal ancestor we infer was not a free-living cell, but rather was confined to the naturally chemiosmotic, FeS compartments within which the synthesis of its constituents occurred. The first free-living cells are suggested to have been eubacterial and archaebacterial chemoautotrophs that emerged more than 3.8 Gyr ago from their inorganic confines. We propose that the emergence of these prokaryotic lineages from inorganic confines occurred independently, facilitated by the independent origins of membrane-lipid biosynthesis: isoprenoid ether membranes in the archaebacterial and fatty acid ester membranes in the eubacterial lineage. The eukaryotes, all of which are ancestrally heterotrophs and possess eubacterial lipids, are suggested to have arisen ca. 2 Gyr ago through symbiosis involving an autotrophic archaebacterial host and a heterotrophic eubacterial symbiont, the common ancestor of mitochondria and hydrogenosomes. The attributes shared by all prokaryotes are viewed as inheritances from their confined universal ancestor. The attributes that distinguish eubacteria and archaebacteria, yet are uniform within the groups, are viewed as relics of their phase of differentiation after divergence from the non-free-living universal ancestor and before the origin of the free-living chemoautotrophic lifestyle. The attributes shared by eukaryotes with eubacteria and archaebacteria, respectively, are viewed as inheritances via symbiosis. The attributes unique to eukaryotes are viewed as inventions specific to their lineage. The origin of the eukaryotic endomembrane system and nuclear membrane are suggested to be the fortuitous result of the expression of genes for eubacterial membrane lipid synthesis by an archaebacterial genetic apparatus in a compartment that was not fully prepared to accommodate such compounds, resulting in vesicles of eubacterial lipids that accumulated in the cytosol around their site of synthesis. Under these premises, the most ancient divide in the living world is that between eubacteria and archaebacteria, yet the steepest evolutionary grade is that between prokaryotes and eukaryotes.
And:
The emergence of life from iron monosulphide bubbles at a submarine hydrothermal redox and pH front M. J. RUSSELL & A. J. HALL: Department of Geology and Applied Geology, University of Glasgow
Abstract: Here we argue that life emerged on Earth from a redox and pH front at c. 4.2 Ga. This front occurred where hot (c. 150)C), extremely reduced, alkaline, bisulphide-bearing, submarine seepage waters interfaced with the acid, warm (c. 90)C), iron-bearing Hadean ocean. The low pH of the ocean was imparted by the ten bars of CO2 considered to dominate the Hadean atmosphere/hydrosphere. Disequilibrium between the two solutions was maintained by the spontaneous precipitation of a colloidal FeS membrane. Iron monosulphide bubbles comprising this membrane were inflated by the hydrothermal solution upon sulphide mounds at the seepage sites. Our hypothesis is that the FeS membrane, laced with nickel, acted as a semipermeable catalytic boundary between the two fluids, encouraging synthesis of organic anions by hydrogenation and carboxylation of hydrothermal organic primers. The ocean provided carbonate, phosphate, iron, nickel and protons; the hydrothermal solution was the source of ammonia, acetate, HS", H2 and tungsten, as well as minor concentrations of organic sulphides and perhaps cyanide and acetaldehyde. The mean redox potential (ÄEh) across the membrane, with the energy to drive synthesis, would have approximated to 300 millivolts. The generation of organic anions would have led to an increase in osmotic pressure within the FeS bubbles. Thus osmotic pressure could take over from hydraulic pressure as the driving force for distension, budding and reproduction of the bubbles. Condensation of the organic molecules to polymers, particularly organic sulphides, was driven by pyrophosphate hydrolysis. Regeneration of pyrophosphate from the monophosphate in the membrane was facilitated by protons contributed from the Hadean ocean. This was the first use by a metabolizing system of protonmotive force (driven by natural ÄpH) which also would have amounted to c. 300 millivolts. Protonmotive force is the universal energy transduction mechanism of life. Taken together with the redox potential across the membrane, the total electrochemical and chemical energy available for protometabolism amounted to a continuous supply at more than half a volt. The role of the iron sulphide membrane in keeping the two solutions separated was appropriated by the newly synthesized organic sulphide polymers. This organic take-over of the membrane material led to the miniaturization of the metabolizing system. Information systems to govern replication could have developed penecontemporaneously in this same milieu. But iron, sulphur and phosphate, inorganic components of earliest life, continued to be involved in metabolism.
And:
The Path from the RNA World Anthony M. Poole, Daniel C. Jeffares, David Penny: Institute of Molecular Biosciences, Massey University
Abstract: We describe a sequential (step by step) Darwinian model for the evolution of life from the late stages of the RNA world through to the emergence of eukaryotes and prokaryotes. The starting point is our model, derived from current RNA activity, of the RNA world just prior to the advent of genetically-encoded protein synthesis. By focusing on the function of the protoribosome we develop a plausible model for the evolution of a protein-synthesizing ribosome from a high-fidelity RNA polymerase that incorporated triplets of oligonucleotides. With the standard assumption that during the evolution of enzymatic activity, catalysis is transferred from RNA M RNP M protein, the first proteins in the ``breakthrough organism'' (the first to have encoded protein synthesis) would be nonspecific chaperone-like proteins rather than catalytic. Moreover, because some RNA molecules that pre-date protein synthesis under this model now occur as introns in some of the very earliest proteins, the model predicts these particular introns are older than the exons surrounding them, the ``introns-first'' theory. Many features of the model for the genome organization in the final RNA world ribo-organism are more prevalent in the eukaryotic genome and we suggest that the prokaryotic genome organization (a single, circular genome with one center of replication) was derived from a ``eukaryotic-like'' genome organization (a fragmented linear genome with multiple centers of replication). The steps from the proposed ribo-organism RNA genome M eukaryotic-like DNA genome M prokaryotic-like DNA genome are all relatively straightforward, whereas the transition prokaryotic-like genome M eukaryotic-like genome appears impossible under a Darwinian mechanism of evolution, given the assumption of the transition RNA M RNP M protein. A likely molecular mechanism, ``plasmid transfer,'' is available for the origin of prokaryotic-type genomes from an eukaryotic-like architecture. Under this model prokaryotes are considered specialized and derived with reduced dependence on ssRNA biochemistry. A functional explanation is that prokaryote ancestors underwent selection for thermophily (high temperature) and/or for rapid reproduction (r selection) at least once in their history.
(Note: The above papers are a few years old -- anyone who tries to rebut them without familiarity with the amount of confirmation of those scenarios which has already come flooding in the past few years is only going to make an ass of themselves...)
Also:

The Evolution of Improved Fitness by random mutation plus selection
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
New insights into V(D)J recombination and its role in the evolution of the immune system
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
Layered evolution in the immune system. A model for the ontogeny and development of multiple lymphocyte lineages
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
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.
Reconstructing the evolution of vertebrate blood coagulation from a consideration of the amino acid sequences of clotting proteins
Evolutionary assembly of blood coagulation proteins
Exon and domain evolution in the proenzymes of blood coagulation and fibrinolysis
Evolution of proteolytic enzymes
Evolution of vertebrate fibrin formation and the process of its dissolution.
Common Parasite Overturns Traditional Beliefs About The Evolution And Role Of Hemoglobin
Scientists Discover How Bacteria Protect Themselves Against Immune System
The Evolution of Hemoglobin
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
Early evolution of microtubules and undulipodia
Flagellar beat patterns and their possible evolution
A temporary flagellate (mastigote) stage in the vahlkampfiid amoeba Willaertia magna and its possible evolutionary significance
The evolutionary origin and phylogeny of eukaryote flagella
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
Dynein family of motor proteins: present status and future questions
Origins of the nucleate organisms
The evolutionary origin and phylogeny of microtubules, mitotic spindles and eukaryote flagella
The evolution of cellular movement in eukaryotes: the role of microfilaments and microtubules
Kinesin Motor Phylogenetic Tree
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
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.
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 Event
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
Evolution of glycolysis
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
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
Molecular evolution of ruminant lysozymes
Adaptive evolution of lysozyme: changes in amino acid sequence, regulation
of expression and gene number
Evolution of stomach lysozyme: the pig lysozyme gene
The evolution of trichromatic color vision by opsin gene duplication in New World and Old World primates
The Evolution of Color Vision
Molecular basis for tetrachromatic color vision
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
Optimization, constraint, and history in the evolution of eyes
A pessimistic estimate of the time required for an eye to evolve
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
The evolution of eyes.
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
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.
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.
Reconstructing the evolution of vertebrate blood coagulation from a consideration of the amino acid sequences of clotting proteins
Determining divergence times of the major kingdoms of living organisms with a protein clock
The multiplicity of domains in proteins
Characterization, primary structure, and evolution of lamprey plasma albumin
The origins and evolution of eukaryotic proteins
Evolution of vertebrate fibrin formation and the process of its dissolution.
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
Evolution of an antifreeze glycoprotein
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.
A Classification of Possible Routes of Darwinian Evolution
Generation of evolutionary novelty by functional shift
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
Genetic Stowaways May Contribute To Evolutionary Change
Evolutionary Molecular Mechanism In Mammals Found
Complete Genomes
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
The origin and early development of biological catalysts
DNA secondary structures and the evolution of hypervariable tandem arrays
Episodic adaptive evolution of primate lysozymes
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
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
Speculations on the origin and evolution of metabolism
Probabilistic reconstruction of ancestral protein sequences
The contribution of slippage-like processes to genome evolution
Molecular evolution in bacteria
The structural basis of molecular adaptation.
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
Tiggers and DNA transposon fossils in the human genome
Gene competition and the possible evolutionary role of tumours
New Scientist Planet Science: Replaying life
Molecular evolution of an arsenate detoxification pathway by DNA shuffling
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
Evolution of Enzymes for the Metabolism of New Chemical Inputs into the Environment
Evolution of Amino Acid Metabolism Inferred through Cladistic Analysis
Integrating the Universal Metabolism into a Phylogenetic Analysis
Invertebrate Data Predict an Early Emergence of Vertebrate Fibrillar Collagen Clades and an Anti-incest Model
Tachykinin and Tachykinin Receptor of an Ascidian, Ciona intestinalis: EVOLUTIONARY ORIGIN OF THE VERTEBRATE TACHYKININ FAMILY
DNA Replication Fidelity
Serial segmental duplications during primate evolution result in complex human genome architecture
Phylogeny determined by protein domain content
Evolutionary Genomics of Nuclear Receptors: From Twenty-Five Ancestral Genes to Derived Endocrine Systems
Gene Loss, Protein Sequence Divergence, Gene Dispensability, Expression Level, and Interactivity Are Correlated in Eukaryotic Evolution
The Evolution of Controlled Multitasked Gene Networks: The Role of Introns and Other Noncoding RNAs in the Development of Complex Organisms
Phylogenetic Dating and Characterization of Gene Duplications in Vertebrates: The Cartilaginous Fish Reference
Dating the Tree of Life
An Insect Molecular Clock Dates the Origin of the Insects and Accords with Palaeontological and Biogeographic Landmarks
Diversity, taxonomy and evolution of medium-chain dehydrogenase/reductase superfamily
Molecular archaeology of the Escherichia coli genome
Comparative Genomics of the Eukaryotes
Millions of Years of Evolution Preserved: A Comprehensive Catalog of the Processed Pseudogenes in the Human Genome
Asymmetric Sequence Divergence of Duplicate Genes
The Genetic Core of the Universal Ancestor
Evolutionary History of Chromosome 20
The Complete Mitochondrial DNA Sequence of Scenedesmus obliquus Reflects an Intermediate Stage in the Evolution of the Green Algal Mitochondrial Genome
Reconstructing large regions of an ancestral mammalian genome in silico
Occurrence and Consequences of Coding Sequence Insertions and Deletions in Mammalian Genomes
The Origin of Human Chromosome 1 and Its Homologs in Placental Mammals
Sister grouping of chimpanzees and humans as revealed by genome-wide phylogenetic analysis of brain gene expression profiles
Genome Evolution at the Genus Level: Comparison of Three Complete Genomes of Hyperthermophilic Archaea
The Evolution of Trichromatic Color Vision by Opsin Gene Duplication in New World and Old World Primates
Obcells as Proto-Organisms: Membrane Heredity, Lithophosphorylation, and the Origins of the Genetic Code, the First Cells, and Photosynthesis (Journal of Molecular Evolution, Volume 53 - Number 4/5, 2001)
N-Carbamoyl Amino Acid Solid-Gas Nitrosation by NO/NO_x: A New Route to Oligopeptides via alpha-Amino Acid N-Carboxyanhydride. Prebiotic Implications (Journal of Molecular Evolution, Volume 48 - Number 6, 1999
Chemical interactions between amino acid and RNA: multiplicity of the levels of specificity explains origin of the genetic code (Naturwissenschaften, Volume 89 Number 12 December 2002)
The Nicotinamide Biosynthetic Pathway Is a By-Product of the RNA World (Journal of Molecular Evolution, Volume 52 - Number 1, 2001)
On the RNA World: Evidence in Favor of an Early Ribonucleopeptide World
Inhibition of Ribozymes by Deoxyribonucleotides and the Origin of DNA
Genetic Code Origin: Are the Pathways of Type Glu-tRNAGln to Gln-tRNAGln Molecular Fossils or Not?
Researchers Engineer A Way To Improve T-Cell Receptors
Digital Organisms Give Life To Questions Of Evolution
Lies, Damned lies, Statistics, and Probability of Abiogenesis Calculations
Purdue Study Breathes New Life Into Question Of How Life Began
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
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
Are the Odds Against the Origin of Life Too Great to Accept? : Addenda to Review of David Foster's The Philosophical Scientists
Really, the world of science is just dying for further helpful insights from your child on these active research topics. Please have her review these and get back to us with her dissertations on them. As your nine-year-old points out, evolution "obviously" couldn't have happened, so something *must* be wrong with all of these findings -- please have your nine-year-old identify the errors for us.
And that goes for the rest of the anti-evolution know-it-alls on this thread as well. Come on, folks, show us what ya got. Since you're such self-proclaimed experts on evolutionary biology, this should be a piece of cake for y'all. Now's your chance, go for it. If evolution is the nonsense you claim it is, feel free to point out what's wrong with each of these papers, and what theory you've got that better explains the results and observations (*ALL* of them, not just one or two isolated observations).
Once you've finished with those, I'll post a few thousand more for you, but hey, that should be no problem for you "experts", you've got it all figured out already, right?
[185JHP wrote:] The hoax is circling the drain. Nothing scientific rests on the hoax, which is a good thing b/c it's laughable nonsense, built on jibberjabber jargn: Blahblahblah "DNA" blahblahblah...
I'm truly impressed with the level of knowledge, rational argument, and unassailable evidence shown by the anti-evolutionists. How could I ever have doubted that you folks truly grasp a century-and-a-half of scientific knowledge well enough to be in a position to critique an entire field of science and declare it completely void of validity in its entirety? Clearly, you've been right all along, and those millions of biologists who have spent their entire careers studying this topic are foolishly mistaken in every respect. I'm really impressed with the way you folks have made your case.
Oh, wait, no I'm not.
...do you ever even *listen* to yourselves? Your towering arrogance on this subject is only equalled by your vast ignorance of it.
Attacking a field of knowledge that you barely know -- and much of what you "know" is wrong thanks to creationist misinformation -- is a waste of *everyone's* time, including your own. Stop mouthing off without knowing what in the hell you're talking about. A lot of us have better things to do than correct all the misinformation y'all spew here on a regular basis. And acting like frothing scientific illiterates (okay, maybe it's *not* an act) really does *not* help the conservative cause -- it turns off large numbers of potential Republican voters in the same way (and for the same reasons) as the wackjob/enviro/feminist/"new-age"/crystal-healing/holistic/etc. "don't-confuse-me-with-science" folks turn off potential Democrat voters.
So if you really do care about conservatism -- go find a new hobby...
Until momincombatboots's little girl knows the difference between an endogenous retrovirus and a retroposon -- and can cogently discuss the pros and cons of maximum parsimony bootstrap consensus tree analysis of each -- (among a ton of other skills and types of evidence) she is *really* unlikely to be able to add any novel insights to the current body of scientific knowledge on this subject. And yes, that goes for you other anti-evolutionists in the peanut gallery as well. You really, really don't understand this topic even a fraction as well as you believe you do.
But maybe you can help me with a question I've been unable to answer: Why is it that folks who wouldn't dream of thinking that they knew enough to attempt to identify any flaws in (for example) quantum physics, have no problem at all feeling "qualified" to "disprove" or outright dismiss just about *everything* in evolutionary biology?

I expanded on those points in replies to subsequent responses:

I think your style of debate is called "elephant hurling."
In a sense, maybe, but in this case I was responding to a specific allegation with an appropriate, to-the-point response.
In case it has somehow escaped your attention, the anti-evolutionists on these threads do an awful lot of claiming that there is "no evidence for evolution", that evolution is "not a science", that evolution is "empty" or a "house of cards" or "a theory in crisis" and is about to come crashing down any day now, that it's "only a theory" (in the sense of "guess"), that it "can't be tested", "can't be falsified", "doesn't make predictions", "can't be replicated", "can't be observed", "denies reality", blah blah blah blah blah.
In short, one of the anti-evolutionists' favorite mantra is to repeat the creationist *LIE* that there's really "nothing to" evolutionary biology, that it's just an empty suit masquerading as "real" science and there's actually "no" evidence for it. (How many hundred examples would you like me to repost here?)
The recent "even my nine-year-old can see that it's nonsense" post was just more of the same -- the implication is that evolutionary biology is such a ridiculous, empty shell that even little children can see through it.
In reply to that sort of allegation it is ENTIRELY APPROPRIATE to respond with "elephant hurling". The point is, "since you say this topic is so unsupported and insubstantial, perhaps you'll realize what an idiot you're being when I stampede this herd of elephants in your direction -- does *THAT* feel 'insubstantial'? And that was just a tiny, tiny fraction. There's plenty more where that came from, if you feel like persisting in your ignorant proclamations."
In short, as long as anti-evolutionists persist in pretending that there's "nothing to see" in evolutionary biology, it's entirely appropriate to show them that even a *sliver* of the field is actually overwhelmingly huge, and beyond their level of knowledge.
Look, I've made endless posts responding to "evolution is empty" accusations with "no it isn't, it's supported by overwhelming evidence and endless studies", but somehow that just bounces off the anti-evolutionists' foreheads with a sharp "ping". So fine -- if I have to hit them with a sledgehammer, if I have to stampede them with all the elephants in Africa just to get through to them for a change, so be it. Maybe *then* they'll stop saying these stupid things ad infinitum.
And if even just one anti-evolutionist says, even to himself, "ummm, it seems there's more to this subject than I was led to believe", and tones down the outright LIE of the "evolution is empty" mantra so that those of us who *do* know something about this topic don't have to keep responding to the same old dishonest horsecrap fifty times a day, then I've accomplished something worthwhile.
The questions remains, though (and my past experience does not lead me to be optimistic) -- is even a single one of you folks that smart?

And:

Your nine year old is far wiser than all the intellectually blind evolutionists put together.
You really think so? Then I'll add you to the list of people that post #158 is directed towards. I await your critique, since you've got it all figured out, at least better than "all the intellectually blind evolutionists put together"...
As an X-atheist, evolutionist myself, I can tell you the arrogance and hostility you will encounter here is to be expected.
And, of course, there's nothing "arrogant" or "hostile" about dismissing "all the intellectually blind evolutionists" as having, "put together", less smarts than a single nine-year-old girl, right? You're one hell of a big hypocrite, Jorge.
They are some of the most arrogant and bitter people I have ever encountered.
You don't sound all that humble and sanguine yourself, Jorge.
But hey, now's your chance to put "all us intellectually blind evolutionists" in our place, son -- point out the errors in the papers I list in post #158. As an "X-evolutionist" (is that anything like an "X-Box"?), you should already know this material, right? Go for it.

Any further questions about why evolutionists might get a tad cranky about idiotic and insulting attacks on evolutionary biology, and against the people who are familiar with and work in the field?

Ummm, I'm black, read the entire essay, and did not see one iota of racism.

Asserting that blacks are 30 IQ points dumber than whites doesn't seem like even "one iota of racism" to you? Ooookay.

Maybe that's just me.

I find it disgusting and the sort of thing that gives ammunition to FreeRepublic's enemies (who love posts that give them excuses to "prove" that we're racist rednecks, etc.), but "maybe that's just me".

Just so you know, I hit the abuse button on your post. Maybe you will be honored by this, as I only do it once a year or so. But I haven't addressed you at all. Your comment to me strikes me as the sort I would expect from a liberal. It really doesn't reflect well upon FR.

ML/NJ

"

We describe a sequential (step by step) Darwinian model for the evolution of life from the late stages of the RNA world through to the emergence of eukaryotes and prokaryotes.

Where'd the RNA world come from?

"It is apparent that ribose cannot be synthesized from formaldehyde by the Butlerow reaction in yields substantially higher than other pentoses and hexoses. Related syntheses may possibly give higher yields of ribose. However, sugars are known to be unstable in aqueous solution, but there are no kinetic data available. We therefore have measured the rate of decomposition of ribose at 60 to 120° and pH's between 4 and 8. The half-life of ribose at 100° and pH 7 is 73 minutes and 34 years at 0°. These results show that ribose is too unstable for prebiotic use unless it is used immediately after its synthesis. The other pentoses and hexoses decompose at a rate approximately proportional to their free aldehyde content. It therefore seems unlikely that sugars could have played a role in the first informational macromolecules." Professor Stanley Miller

That assertion was not in the article. It was an accusation in your post. You even quoted Rdb3 saying he'd not seen racism IN THE ARTICLE.

I suspect he's wondering what your accusation has to do with the article. Your comments came across as pure ad hominem.

"Black sub-Saharan Africans (say many evolutionists) have a mean IQ somewhere near 70"

Two thoughts.

The author says that evolutionists avow this number. Do they?

And secondly, is it true?

Fred's right -- "the accretion of successful point mutations" is even according to what you say -- one of the ways evolution proceeds. Doesn't mean the only way.

No, Fred's WRONG. When he writes:

Does a random point mutation cause the appearance of an extra vertebra? If so, which mutation? (It would have to be a pretty vigorous point mutation.)

...the parenthetical phrase was a lame attempt to get the reader nodding his head and saying, "hey, yeah, it *is* ridiculous to think that a 'random point mutation' could create a whole new vertebra... wow, what kind of miracles do those evolutionists expect us to swallow, anyway?"

This is a class "straw man" attack -- trying to make your opponent's position appear ridiculous by "beating up" a cheap imitation that you present *as* your opponent's actual position.

There's far more to evolutionary variation than just "point mutations". Fred's attempt to get the reader to doubt evolutionary processes by reducing them to *just* the mechanism of "random point mutations" and then implying that they seem inadequate to achieve things like the giraffe's neck is just cheap sophistry. Or maybe he's just an idiot arrogant enough to think he can actually shed some light on a subject that he knows very little about. But neither option inspires confidence.

And unfortunately, that's pretty much par for the course for "evolution doubters". People who actually have spent a few years *learning* the subject seldom have any real problems with it of this sort.

To get started -- to develop the amino acids, the chains of acids, the fats, etc. would take that low level of development.

What exactly is "that low level of development"?

And it continues. We see it all the time in metabolisms -- usually leads to sickness, cancer, death.

Huh? Try to be coherent.

Genetic variability of higher, more complex sorts means you have genes and metabolisms inside cells that work with the genes. That's a lot of "a priori". And even those others sorts of complex modalities can be thought as point-wise, if the "point" is chosen to the more complex level.

Uh huh...

My point about brownian motion -- I myself really don't see what point it was, yet that silly dance of dust motes is what fired off Einstein, and lead eventually iirc to quantum mechanics, the weight of the electron and other intellectual evolutions not so obvious.

So... you were making a point using brownian motion, despite "not seeing what point it was"? Fascinating.

Never mind, I found the answer to my question at the CharlesDarwinResearch.org

That assertion was not in the article.

Yes it was. I QUOTED THE ARTICLE saying that. Just how poor *is* your reading comprehension, anyway?

One MORE time, FROM THE ARTICLE:

"Black sub-Saharan Africans (say many evolutionists) have a mean IQ somewhere near 70, live in wretched poverty, and breed enthusiastically. White Europeans, reasonably bright at IQ 100 and quite prosperous, are losing population. Jews, very bright indeed at a mean IQ of 115 and very prosperous, are positively scarce, always have been, and seem to be losing ground."

Are we clear now?

It was an accusation in your post.

Yes it was. With good cause.

You even quoted Rdb3 saying he'd not seen racism IN THE ARTICLE.

Yup, I sure did. That's why I expressed surprise that he didn't find that assertion from the article racist.

I suspect he's wondering what your accusation has to do with the article.

I don't think he's wondering at all, since he responded to the post in which I QUOTED THE ARTICLE claiming that blacks have an IQ thirty points lower than that of whites.

Your comments came across as pure ad hominem.

I don't care how they come across to you. I care that RobRoy had the poor judgment to post to FreeRepublic an essay that makes a racist slur.

"Twaddle.

More twaddle."

Da**!! Ichneumon, "twaddle" is my word. I got in trouble for using it (the word I wanted to use was a bit .... stronger), but I bet you won't ;>).

There was nothing abusive in my post. There is nothing substantive in your posts.

Did you ever wonder how the baby giraffes survived until they could reach the tree tops? Or how a large increase in body mass accrues to survival during tough times? Or why a giraffe has to splay it's legs to drink from a stream?

I wonder about these things sometimes, but admittedly not too often.

You might grow up Pinhead.

Hit a nerve, did I?

Well thanks for the advice, but I grew up a long time ago. Judging from your prediliction for silly puerile labels like "Pinhead", however, not to mention your childish glee at receiving a bagful of ready-made schoolyard taunts like "It was like giving a bobcat a prostate exam" for your future use against people who disagree with you, I'm not sure the same can be said for you.

I am almost certainly older and better educated, officially and unofficially, than you.

Oh, yes, "certainly"... Excuse me while I snicker.

Regardless of your chronological age, though, the fact remains that you were immature enough to insult someone as being "Sad. Really sad" for daring to politely decline your desire that he spend *his* time coming to this thread at your call, reading an article that you yourself noted was quite "long", and then entertaining you with his reflections upon it, EVEN THOUGH he had already followed up and pinged you to a linked response by someone else that he thought you might find useful.

Now that I've had time to reconsider my original assessment of your insulting reply to him, and re-examine all the relevant posts, including your most recent one, all I can say is that I stand 100% by my original comment that you need to grow up.

Patrick Henry did not deserve the response you gave him.

The fact that you are so impatient that you cannot wait for me to reply to your own post

You seem to have poor reading comprehension (perhaps that wasn't covered in your allegedly extensive "education"). Nowhere did I express any impatience whatsoever about when you might reply to me -- if ever.

What I *WAS* pointing out, however, was that if you were really so disappointed in PatrickHenry's declining of your "invitation" -- if the reason for your insult to him was your grief over what you say here:

"I asked an honest question, but so far none of your sole-mates has offered an honest reply.

...then it's mighty, strange shall we say, that you responded by insulting PatrickHenry for not responding, instead of just taking up other people's offers to address your "honest question".

almost certainly confirms the truth of at least two of the three assertions in the previous paragraph,

And what does it instead "confirm" when it turns out that you were entirely mistaken about what you misunderstood as my "impatience"?

but I did reply to you (courteously, I think) before I saw the message to which I am now responding.

Yes, albeit *after* my observation that you had not, and thus my point at the time about how it appeared that you chose to insult PatrickHenry rather than seek answers.

Have at it, if you wish, but please avoid the ad hominems.

I'll do my best to respond in kind, as my next post.

I asked an honest question, but so far none of your sole-mates has offered an honest reply.

First, you hadn't actually *ASKED* any question ("honest" or otherwise) for the first three hours of the thread. If you mean your "invitation for comments" from PatrickHenry in particular, that seems less like a question than a call for papers.

Second, it was directed quite specifically to PatrickHenry personally, so it seems rather disingenuous for you to complain that "none of your sole-mates has offered an honest reply", especially since I had *already* offered *to* reply if you indicated that you wanted specific points addressed instead of just a "PatrickHenry review" in general.

Third, what's a "sole-mate" -- people who wear each other's shoes? People who fish for haddock together? (Sorry, I can't resist funny typos...)

Finally, you probably raised skepticism about just how "honest" your question(s) about the validity of the article might be, when your first post on this thread declared it a "Dynamite article", indicating you had already made up your mind and considered it stellar, and expressed your joy that it had "Lots of great pull-quotes" which ridiculed evolutionists.

So be really "honest" now -- just how "honest" are your questions about this "dynamite" article full of "great pull-quotes" to use as ammunition against evolution?

Excuse us for being just a bit dubious about your actual motivations.

You are being toooooooo nice.

You're right and I'm wrong.

I read it and somehow went right over that.

Read it again, he got the info from some Darwinists.