Commentaries on genome-level arguments, mutation, heredity, molecular machines, information, and comparative genetics.
55 commentaries in this topic.
Paper: Seeing through the eyes of the sabertooth Thylacosmilus atrox (Metatheria, Sparassodonta)
A recent paper in Communications Biology presents a fascinating puzzle from the fossil record: the skull of the extinct sabertooth marsupial, Thylacosmilus atrox . The authors, Charlène Gaillard et al., rightly identify…
Read commentary: A Predator with the Eyes of a Cow? Thylacosmilus Skull Points to Design, Not DarwinismPaper: Environmental Epigenetics and a Unified Theory of the Molecular Aspects of Evolution: A Neo-Lamarckian Concept that Facilitates Neo-Darwinian Evolution
The paper "Environmental Epigenetics and a Unified Theory of the Molecular Aspects of Evolution: A Neo-Lamarckian Concept that Facilitates Neo-Darwinian Evolution" by Skinner (2015) attempts to integrate environmental…
Read commentary: Epigenetics and Evolution: A Confused NarrativePaper: Historical perspective on the development and evolution of eyes and photoreceptors
The origin of the eye has haunted evolutionary theory since Darwin, who confessed that the idea of its formation by natural selection "seems, I freely confess, absurd in the highest degree." Modern evolutionists believe…
Read commentary: Shared Genes, Different Designs: Why the Pax-6 "Master Gene" Points to a Common Designer, Not Common AncestryPaper: New Perspectives on Eye Development and the Evolution of Eyes and Photoreceptors
In a celebrated 2005 paper, "New Perspectives on Eye Development and the Evolution of Eyes and Photoreceptors," the late Walter J. Gehring summarized his team's groundbreaking research on the genetics of eye formation.…
Read commentary: The Pax6 Gene: Master Control for a Master Plan, Not Master-less EvolutionPaper: Tracking interspecies transmission and long-term evolution of an ancient retrovirus using the genomes of modern mammals
A 2016 paper in the journal eLife by William E. Diehl and colleagues, "Tracking interspecies transmission and long-term evolution of an ancient retrovirus using the genomes of modern mammals," claims to use viral…
Read commentary: Viral 'Fossils' Reveal Designed Decay, Not Darwinian AscentPaper: Light modulated cnidocyte discharge predates the origins of eyes in Cnidaria
Evolutionary biologists seek to explain the origin of complex biological structures, like the animal eye, through a gradual, step-by-step process. A popular narrative suggests that the component parts of these systems…
Read commentary: Pre-existing Systems or Pre-programmed Designs? Cnidarian Stinging Fails to Illuminate Eye OriginsPaper: How Darwinian models inform therapeutic failure initiated by clonal heterogeneity in cancer medicine
The 2010 paper in the British Journal of Cancer by M. Gerlinger and C. Swanton, "How Darwinian models inform therapeutic failure initiated by clonal heterogeneity in cancer medicine," is presented as a clear…
Read commentary: Cancer's "Evolution" a Case Study in Degeneration, Not CreationPaper: Punctuated equilibrium theory represents shifting balance theory (of macro and quantum evolution) and invalid Darwin’s theory
The 2017 paper "Punctuated equilibrium theory represents shifting balance theory… and invalid Darwin's theory" by Md. Abdul Ahad in the Journal of Entomology and Zoology Studies argues that the evolutionary theories of…
Read commentary: Punctuated Equilibrium: A Confirmation of Genetic Decay, Not Unguided EvolutionPaper: A rugged yet easily navigable fitness landscape
A recent paper in the prestigious journal Science by Andrei Papkou and colleagues presents a fascinating, high-resolution map of an evolutionary "fitness landscape." By creating and testing over 260,000 variants of a…
Read commentary: Navigating a Dead End: Why a "Rugged" Fitness Landscape Shows the Limits, Not the Power, of EvolutionPaper: Candidate Genes, Quantitative Trait Loci, and Functional Trait Evolution in Plants
The 2003 paper "Candidate genes, quantitative trait loci, and functional trait evolution in plants" by David L. Remington and Michael D. Purugganan is a comprehensive review of how modern molecular techniques can…
Read commentary: Plant Genetics Reveals Designed Adaptability, Not Unguided EvolutionPaper: Expanded encyclopaedias of DNA elements in the human and mouse genomes
The ENCODE (Encyclopedia of DNA Elements) project is a monumental achievement of operational science, a meticulous effort to map the functional landscape of the human and mouse genomes. This landmark paper summarizes…
Read commentary: ENCODE's Encyclopedia of Decay: Why Pervasive Function Spells Doom for DarwinismPaper: The evolution of eyes: major steps. The Keeler lecture 2017: centenary of Keeler Ltd
The eye, in its stunning variety and functional precision, has long been a focal point in the debate over biological origins. In his 2017 Keeler lecture, "The evolution of eyes: major steps," Dr. IR Schwab offers a…
Read commentary: An Eye for Design: Why Schwab's 'Evolution of Eyes' Points to Engineering, Not Unguided ProcessesPaper: New Perspectives on Eye Development and the Evolution of Eyes and Photoreceptors
The discovery that a single gene, Pax6 , acts as a high-level controller for eye development in creatures as different as flies and mice is often presented as one of the most compelling proofs of the grand evolutionary…
Read commentary: Pax6 and the Eye: Evidence for a Master Gene or a Master Designer?Paper: Mutation-selection models of coding sequence evolution with site-heterogeneous amino acid fitness profiles
In the quest to make the theory of evolution mathematically rigorous, scientists develop ever-more-complex models to describe how life’s machinery might change over time. The 2010 PNAS paper, "Mutation-selection models…
Read commentary: The Engineer's Signature: Why Sophisticated Models of Gene Evolution Reveal Design, Not DarwinismPaper: A cyanosulfidic origin of the Krebs cycle
The Krebs cycle is a masterpiece of metabolic engineering, a central hub of cellular respiration that generates energy and provides molecular building blocks for a vast array of other biomolecules. For this reason,…
Read commentary: Krebs Cycle Chemistry: A Roadblock, Not a Pathway, to Unguided OriginsPaper: The evolution of the Krebs cycle: A promising subject for meaningful learning of biochemistry
The 2016 paper, "The Evolution of the Krebs Cycle: A Promising Subject for Meaningful Learning of Biochemistry," presents a laudable pedagogical goal: to make the Krebs cycle more engaging for students by framing it…
Read commentary: The Krebs Cycle: A Testament to Design, Not Unguided EvolutionPaper: Natural selection and evolution: evolving concepts
In their commentary "Natural selection and evolution: evolving concepts," Andre van Wijnen and Eric Lewallen engage in a philosophical discussion about whether to classify natural selection as a "law" and evolution as a…
Read commentary: Evolving Definitions Cannot Evade the Question of OriginsPaper: The genius of Roger Stanier
The esteemed microbiologist Roger Stanier is rightly celebrated as a pioneer whose work brought microbiology into the mainstream of the biological sciences. The tribute article, "The genius of Roger Stanier," provides a…
Read commentary: The Genius of Design: How Roger Stanier's Work Reveals the Limits of EvolutionPaper: There’s plenty of time for evolution
In a paper titled "There's plenty of time for evolution," mathematicians Herbert Wilf and Warren Ewens present a model that purports to solve the longstanding "waiting time" problem that plagues evolutionary theory. The…
Read commentary: The "Plenty of Time" Fallacy: Why a Mathematician's Model Fails to Solve Darwin's Information CrisisPaper: The population genetics of mutations: good, bad and indifferent
The 2010 paper "The population genetics of mutations: good, bad and indifferent" by Laurence Loewe and William G. Hill provides a comprehensive overview of a field fundamental to the modern evolutionary synthesis. The…
Read commentary: Population Genetics: A Study in Variation and Decay, Not Unguided CreationPaper: Evolution by gene duplication of<i>Medicago truncatula PISTILLATA</i>-like transcription factors
A central tenet of modern evolutionary theory is that gene duplication provides the raw material for innovation. The story goes that after a gene is copied, one copy is free to maintain the original function while the…
Read commentary: Duplication and Decay: Why Plant Genes Fail to Demonstrate Darwinian InnovationPaper: Comparative Evidence of an Exceptional Impact of Gene Duplication on the Developmental Evolution of Drosophila and the Higher Diptera
A 2018 paper in Frontiers in Ecology and Evolution by Riyue Bao and colleagues examines the impact of gene duplication on the evolution of fruit flies and their relatives. The study is presented as evidence for a key…
Read commentary: Gene Duplication in Fruit Flies: Photocopying a Blueprint Is Not EngineeringPaper: RNA polymerase I is essential for driving the formation of 3D genome in early embryonic development in mouse, but not in human
A recent paper in Genome Medicine by Hou et al. provides a fascinating, high-resolution look into the earliest moments of life, comparing the way 3D genome architecture is established in mouse and human embryos. The…
Read commentary: Designed Differences: Why Human and Mouse Embryos Defy a Common Evolutionary StoryPaper: Genome-wide mapping of spontaneous DNA replication error-hotspots using mismatch repair proteins in rapidly proliferating <i>Escherichia coli</i>
A recent paper in Nucleic Acids Research provides a fascinating high-resolution map of where spontaneous DNA replication "errors" occur in the E. coli genome. Using a clever experimental setup, the authors identified…
Read commentary: Study of Bacterial "Errors" Reveals Not Randomness, but the Signature of a Pre-Programmed SystemPaper: Long-Term Experimental Evolution in Escherichia coli. XII. DNA Topology as a Key Target of Selection
The Long-Term Evolution Experiment (LTEE) founded by Richard Lenski is frequently presented as the gold-standard demonstration of "evolution in action." By tracking generations of E. coli in a controlled lab…
Read commentary: Tweaking the Engine: Why E. coli's Adaptations Don't Build New MachinesPaper: Evolution of Natural Agents: Preservation, Advance, and Emergence of Functional Information
In a 2016 paper in the journal Biosemiotics , researcher Alexei A. Sharov attempts to rescue evolutionary theory from the simplistic, gene-centric model of the 20th-century Modern Synthesis. He proposes a sophisticated…
Read commentary: A Theory of Evolution That Looks Exactly Like EngineeringPaper: BRS1 Function in Facilitating Lateral Root Emergence in Arabidopsis
Studies detailing the function of a single gene are often celebrated as snapshots of evolution. By understanding how a part works, the story goes, we can better understand how it came to be through an unguided process.…
Read commentary: Coordinated Control: How Plant Root Growth Reveals Engineering, Not EvolutionPaper: Emergence of FRESH 3D printing as a platform for advanced tissue biofabrication
The rapid advancement of technologies that manipulate biological materials is often presented as evidence for the plausibility of unguided, molecules-to-man evolution. By demonstrating our own growing ability to…
Read commentary: FRESH Bioprinting: A Masterclass in Engineering, Not Unguided EvolutionPaper: Novel Genes from Formation to Function
The quest to find observable evidence for large-scale evolution—the fabled "molecules-to-man" journey—often leads proponents to the field of genetics, seeking a mechanism that can create genuinely new biological…
Read commentary: Recycled Parts, Not New Inventions: Why 'Novel' Genes Don't Support Unguided EvolutionPaper: Evolution of New Functions De Novo and from Preexisting Genes
The origin of new genes containing novel, functional information is a critical requirement for any molecules-to-man evolutionary narrative. A 2015 review paper by Dan Andersson and colleagues, "Evolution of New…
Read commentary: Guided Adaptation, Not Unguided Creation: A Sober Look at the Origin of New GenesPaper: Genomic analysis of a key innovation in an experimental Escherichia coli population
Richard Lenski's Long-Term Evolution Experiment (LTEE) is one of the most celebrated studies in modern biology, often presented as definitive proof of "evolution in action." In a key finding from this experiment, one of…
Read commentary: The E. coli Long-Term Experiment: A Case Study in the Limits of EvolutionPaper: Chromothripsis drives the evolution of gene amplification in cancer
The 2021 Nature paper "Chromothripsis drives the evolution of gene amplification in cancer" by Ofer Shoshani and colleagues is a landmark study in molecular oncology. Using a suite of advanced genomic and imaging…
Read commentary: Engineering Resistance: Why Cancer's 'Evolution' Is a Testament to Goal-Directed System ResponsesPaper: Divergent cis-regulatory evolution underlies the convergent loss of sodium channel expression in electric fish
The Master Framing Strategy: The Final Verdict The 2022 study by LaPotin et al. in Science Advances is a landmark achievement in molecular biology, meticulously reverse-engineering the control system that governs a key…
Read commentary: Engineered Deactivation: Electric Fish Showcase Goal-Directed Control of Biological SystemsThis 1998 study by Seehausen and van Alphen investigates mate selection in two very similar Lake Victoria cichlid species, which are anatomically almost identical except for the vibrant red or blue coloration of the…
Read commentary: Cichlid Mate Choice: Evidence for Pre-Programmed Logic, Not Unguided SpeciationDiane M. B. Dodd's 1989 paper presents a compelling observation: populations of the fruit fly Drosophila pseudoobscura , when physically separated and adapted to different diets, subsequently show a strong mating…
Read commentary: Programmed Preference, Not Unguided Process: A Re-Evaluation of the Dodd ExperimentA paper in Nature presents the butterfly Heliconius heurippa as a compelling case of "speciation by hybridization." The researchers observed that H. heurippa possesses a wing pattern and genetic makeup that appear to be…
Read commentary: Heliconius Hybrids: Evidence for Evolutionary Innovation or a Showcase of Programmed Genetic Modularity?The theory of synergistic selection, as articulated by Peter Corning and Eörs Szathmáry, attempts to provide a Darwinian framework for the evolution of biological complexity. The core claim is that the functional…
Read commentary: Synergistic Selection: A Powerful Filter, Not a Creative EngineA recent paper in PLOS Computational Biology claims to have found a "plausible pathway" for simple molecular networks to increase their complexity through Darwinian evolution. The authors, Kamiura et al., propose that…
Read commentary: From Tinkering to Teleology: Why Parasite-Host Dynamics Don't Build ThemselvesMichael Majerus's paper passionately defends the peppered moth ( Biston betularia ) as the "most easily understood example of Darwinian evolution in action." The central claim is that shifts in the moth population's…
Read commentary: The Peppered Moth's Palette Swap: A Case of Adaptation, Not CreationA recent paper by Rebecca Varney and colleagues presents the visual systems of chitons—marine mollusks with armored plates—as a powerful demonstration of the grand evolutionary narrative in action. The authors claim…
Read commentary: Pre-Wired Pathways: Why Chiton Vision Fails as a Showcase for Evolutionary InnovationA recent paper by Wenjun Sun and colleagues on the Auxin Response Factor (ARF) gene family in quinoa claims to provide insights into the "adaptive domestication" of crops. The study suggests that the expansion of this…
Read commentary: Copy, Don't Create: How Quinoa's Genetic Toolkit Reveals the Limits of Evolutionary TinkeringA recent paper in Science Advances , titled "Insights on the evolution and adaptation toward high-altitude and cold environments in the snow leopard lineage," claims to document the gradual emergence of the snow leopard…
Read commentary: Tinkering with the Panthera Chassis: Why Snow Leopard Fossils Don't Demonstrate Unguided InventionThis study in Science Advances puts forward the "Enhancer Capture-Divergence" (ECD) model to explain how new gene functions can arise following a gene duplication event. The authors propose that when a copy of a gene…
Read commentary: Relocating a File Is Not Writing New Code: Why 'Enhancer Capture' Fails to CreateA recent paper in Science Advances documents a fascinating shift in the morphology and flight performance of an extinct family of giant insects, the Palaeontinidae. The authors propose that these changes represent a…
Read commentary: Adaptation or Invention? Reinterpreting the Shifting Flight of Mesozoic Giant CicadasPaper: Chromosome-scale genome dynamics reveal signatures of independent haplotype evolution in the ancient asexual mite
<i>Platynothrus peltifer</i>
A recent study of the ancient asexual mite, Platynothrus peltifer , claims to have identified a key to its long-term evolutionary survival. The authors propose that the mite persists for millions of years without sex by…
Read commentary: A Tale of Two Copies: The Asexual Mite's Survival Highlights Conservation, Not CreationThe story of E. coli evolving the ability to eat citrate in the lab has been widely presented as a premier showcase for the grand evolutionary narrative. In the famous Long-Term Evolution Experiment, or LTEE, this trait…
Read commentary: Unlocking Latent Code: Why E. coli’s Rapid Citrate Adaptation Is a Feat of Engineering, Not Unguided EvolutionThe discovery of a new species of harvestman in Sri Lanka, as detailed in the paper by Prashant Sharma and Gonzalo Giribet, provides a fascinating glimpse into the biodiversity of these small, leaf-litter dwelling…
Read commentary: Pattern vs. Process: Why the Distribution of Harvestmen Eyes Fails to Illuminate Their OriginThe octopus is an icon of biological wonder, possessing a large brain, sophisticated problem-solving abilities, and a dynamic camouflage system that are profoundly different from its fellow molluscs. The 2015 sequencing…
Read commentary: The Octopus Genome: Reconfiguring a Blueprint, Not Writing a New OnePaper: Detecting riparian habitat preferences in “savanna” chimpanzees and associated Fauna with strontium isotope ratios: Implications for reconstructing habitat use by the chimpanzee‐human last common ancestor
The authors of this study present a technically sophisticated method for using strontium isotope ratios to trace the dietary habits and habitat use of animals in a mosaic environment. By analyzing vegetation and water…
Read commentary: Isotope Tracking: A Map of Behavior, Not a Blueprint for EvolutionPaper: Complete sequencing of ape genomes
A recent, technically impressive paper in Nature titled "Complete sequencing of ape genomes" presents the first comprehensive, telomere-to-telomere (T2T) comparison of the genomes of humans and our supposed closest…
Read commentary: Complete Ape Genomes Reveal Common Design, Not Common DescentThis analysis examines a technical paper on microbial genetics, "Towards understanding the first genome sequence of a crenarchaeon," to see if its findings support the idea that microbes can evolve into more complex…
Read commentary: Shuffling the Deck, Not Writing the BookA 2000 paper in PNAS by Adami, Ofria, and Collier, titled " Evolution of biological complexity ," uses a computer simulation called Avida to argue that genomic complexity is forced to increase over time. While the…
Read commentary: Digital Complexity: What Computer Simulations Can't ExplainWhat the Paper Claims This study reviews how blind Mexican cavefish ( Astyanax mexicanus ) adapted to low-oxygen cave environments. Researchers compare cave-dwelling populations to surface-dwelling counterparts, noting…
Read commentary: Cavefish Adaptations: Evidence of Design, Not Darwinian MacroevolutionWhat the Paper Claims The study identifies a nonsense mutation (W49X) in the SLC2A11B gene as responsible for pearl iris color in domestic pigeons. Researchers claim this mutation originated ~5,400 years ago through…
Read commentary: Pigeon Eye Color Study Reveals Limits of Mutation-Driven ChangeWhat the Paper Claims This comprehensive study of six bat species' genomes claims to reveal "the evolution of bat adaptations" and provide insights into how bats supposedly evolved their remarkable abilities like…
Read commentary: Bat Genomes Reveal Sophisticated Design, Not Evolutionary Innovation