NeoDarwinian Review

The journal article "Epigenetic patterns in a complete human genome" presents a groundbreaking exploration of the human epigenome, utilizing the recently completed telomere-to-telomere (T2T) reference genome, T2T-CHM13 . This study provides an unprecedented high-resolution view of epigenetic modifications across previously unresolved genomic regions, shedding light on the intricate regulatory mechanisms that govern gene expression and cellular function. Unveiling the Hidden Epigenome: The T2T-CHM13 reference genome, a significant advancement over previous incomplete versions, enables researchers to investigate epigenetic patterns in regions that were previously inaccessible or poorly understood. These regions include repetitive sequences, segmental duplications, and the entirety of acrocentric chromosome short arms. By comprehensively mapping CpG methylation, DNA accessibility, and chromatin immunoprecipitation sequencing (ChIP-seq) peaks, the study reveals a w

"How could all of these pieces fall into place through the random processes of mutation, recombination, and neutral drift—or at least enough of these pieces to produce a protogene that was sufficiently useful for selection to take hold? One can imagine a process by which short, simple genes periodically arise de novo, then gradually become more complex over time.” -Darwinian Alchemy Evolutionary Trajectories of New Duplicated and Putative De Novo Genes: A Summary The study "Evolutionary trajectories of new duplicated and putative de novo genes" published in Molecular Biology and Evolution (May 2023) delves into the fascinating world of new gene formation and their subsequent evolutionary paths. This research sheds light on the dynamics of gene evolution, challenging some prevailing assumptions and offering fresh insights into the mechanisms shaping genetic novelty. Key Questions and Findings The study centers on two primary questions: Rate of New Gene For

Crick's "frozen accident" hypothesis, a cornerstone of molecular evolution, posited that the genetic code was established arbitrarily early in life's evolution and became fixed due to the detrimental effects of altering it. This theory, coupled with Motoo Kimura's neutral theory of molecular evolution, emphasized the neutrality of synonymous mutations (those that don't change the amino acid sequence) and their role in genetic drift. However, recent research revealing the non-neutral effects of these mutations has challenged this paradigm, opening new avenues for understanding evolutionary mechanisms. The frozen accident hypothesis implied that the genetic code, once established, remained largely unchanged due to the catastrophic consequences of altering it. This view was supported by the near-universality of the genetic code and the seemingly random relationship between codons and amino acids. Kimura's neutral theory further solidified this not

Horizontal gene transfer (HGT) is the transfer of genetic material between organisms that are not parent and offspring. HGT can play a significant role in convergent evolution in animals in several ways: Acquisition of Novel Traits:   Through HGT, animals can acquire new genes and genetic information from distantly related organisms. Horizontal gene transfer (HGT) has led to the acquisition of surprising traits in various animals: Tardigrades: These microscopic creatures, known for their extreme resilience, have acquired numerous genes from bacteria, fungi, and even plants, contributing to their ability to survive harsh conditions like dehydration and radiation. Sea slugs: Some species have incorporated genes from algae, allowing them to photosynthesize and gain energy directly from sunlight. This remarkable ability provides them with a significant advantage in nutrient-poor environments. Aphids: These insects have acquired genes from fungi that enable them to produce carot

In their 2021 journal article "Social Darwinism," Jeffrey O'Connell and Michael Ruse offer a comprehensive philosophical history of the term and its complex evolution. The article is featured in the collection "Elements in the Philosophy of Biology," edited by Grant Ramsey and Michael Ruse. This work delves into the origins, applications, and controversies surrounding Social Darwinism, providing valuable insights into this often misunderstood concept. Defining Social Darwinism O'Connell and Ruse begin by addressing the challenge of defining Social Darwinism, highlighting its contentious nature and diverse interpretations. They emphasize the importance of distinguishing between the descriptive and normative aspects of the term. Descriptively, Social Darwinism refers to applying evolutionary ideas, particularly natural selection and survival of the fittest, to human societies. Normatively, it implies a moral justification for laissez-faire capitali