NeoDarwinian Review

Transcriptional regulation is a cornerstone of cellular function, orchestrating the precise expression of genes in response to diverse internal and external cues. This intricate process involves a series of meticulously coordinated events, each contributing to the final output of a functional protein or non-coding RNA . Understanding the schematic mechanisms of transcriptional regulation requires delving into the interplay of chromatin accessibility, transcription initiation, transcript elongation, and splicing, with the added complexity of the cohesin complex and the spatial organization of the genome through topologically associated domains (TADs). Chromatin accessibility is the first layer of control. DNA, tightly packaged around histone proteins to form chromatin, must be made accessible to transcription factors and RNA polymerase for gene expression to occur. This accessibility is regulated by various mechanisms, including histone modifications (e.g., acetylation, m...

  The 2019 Cell paper , "Small RNAs in the Transgenerational Inheritance of Epigenetic Information," presents a compelling challenge to the neo-Darwinian framework, which has long dominated evolutionary thought. Neo-Darwinism, the modern synthesis of Darwin's theory of evolution and Mendelian genetics, emphasizes random genetic mutations as the primary source of variation, with natural selection acting upon this variation to drive evolutionary change. While acknowledging the role of environmental factors in influencing an individual's phenotype, neo-Darwinism largely relegates such influences to a non-heritable, transient role. The Cell paper, however, suggests a mechanism by which environmental impacts can become heritable , potentially altering the evolutionary trajectory of populations. The central players in this challenge are small RNAs , a class of non-coding RNA molecules with diverse regulatory functions within cells. The researchers demonst...

Endogenous retroviruses (ERVs) have long been considered strong evidence for the common descent of humans and chimpanzees. These remnants of ancient viral infections, embedded in the genomes of both species, were once thought to be non-functional "junk DNA." The premise was that the shared presence of these seemingly random insertions in corresponding genomic locations could best be explained by a shared evolutionary history. However, recent research, such as the "Switching Sides" article published in May 2021, has challenged this assumption by demonstrating that ERVs play a functional role in the development of the human embryo and immune system. This discovery raises questions about the validity of using ERVs as primary evidence for common descent. The Traditional Argument for Common Descent The traditional argument for common descent based on ERVs rests on the following points: Random Insertion: Retroviral insertions are thought to occur randomly in...

Richard Dawkins' "The Selfish Gene" popularized a gene-centric view of evolution, arguing that natural selection operates at the level of the gene, not the individual or the species. Organisms, in this perspective, are merely vehicles for genes, their primary purpose being to replicate and transmit these genetic units to the next generation. The study of heritable changes in gene expression without alterations to the DNA sequence itself, presents a significant challenge to this gene-centric worldview . The selfish gene concept emphasizes the stability and fidelity of DNA transmission. Genes, as the fundamental units of heredity, are seen as relatively immutable entities, faithfully copied and passed on from parent to offspring. Mutations, random changes in DNA, are the primary source of genetic variation, providing the raw material upon which natural selection acts. This focus on the gene as the replicator and the organism as the vehicle implicitly minimize...