Modern Synthesis Review

With all the new developments in genetics and especially epigenetics, I sometimes feel I practiced medicine with leeches for 30 years.  Advances in medicine have disproved the "practice" of leeches; maybe older evolutionary "practices" will also be disproved.  In June 2022, Nature journal published an article called "Synonymous mutations in representative yeast genes are mostly strongly non-neutral."  The authors claimed that 60 years of neo-darwinism, aka the modern synthesis, is challenged by declaring that most “silent” (synonymous) mutations were not neutral but harmful. The discovery of the genetic code in 1961 noted DNA had four nucleotides coding for only 20 amino acids that make up proteins.   Three-letter DNA units called "codons" code each of the 20 amino acids. DNA has 64 (3^4) codon combinations for 20 amino acids.  Figure codon table Why was this the case? Why a "redundant" 64 to 20 "code?"...

The human body, a marvel of biological engineering, comprises over 200 distinct cell types, each performing specialized functions crucial for life. This incredible cellular diversity arises not solely from the information encoded within our genes, but also from the dynamic interplay of epigenetics, a field that goes beyond the traditional neo-Darwinian framework. While neo-Darwinism focuses on genetic mutations and natural selection as the primary drivers of evolution, epigenetics reveals how gene expression can be modulated without altering the underlying DNA sequence, offering a deeper understanding of cellular differentiation and development. The human genome, the complete set of genetic instructions, provides the blueprint for building a human. However, this blueprint is not a rigid, pre-determined program. Instead, it is a flexible set of instructions that can be interpreted and executed differently depending on the context. This context is provided by the epigenome, a...

A new perspective is challenging the long-held tenets of neo-Darwinism, offering a more integrated and multi-layered understanding of the evolutionary process. This emerging framework, known as Hierarchical Evolutionary-Developmental Theory (H-Evo-Devo), repositions the organism and its developmental processes at the heart of evolutionary change. By incorporating principles of hierarchy and the crucial role of epigenetics, this theory presents a significant challenge to the gene-centric view that has dominated evolutionary thought for nearly a century, proposing a more holistic and dynamic picture of how life diversifies and innovates. At its core, H-Evo-Devo theory posits that evolution operates on multiple, nested levels of biological organization, from the familiar microevolutionary changes within populations to the grander macroevolutionary and even "mega-evolutionary" patterns that shape the entire tree of life. This contrasts sharply with the traditional neo...

The discovery that epimutations spontaneous,heritable changes in DNA methylation act as a fast-ticking molecular clock in plants represents a profound shift in our understanding of evolutionary timescales and inheritance. This "epimutation-clock" provides an unprecedented tool for studying evolutionary divergence over remarkably short periods, a scale largely inaccessible to traditional genetic methods. The core finding is that stochastic changes in DNA methylation at certain cytosine sites, particularly in CG dinucleotides, accumulate at a rate orders of magnitude faster than genetic mutations, yet remain sufficiently stable and neutral to serve as a reliable temporal marker. How Epigenetics Affects the Molecular Clock Epigenetics refers to heritable changes in gene function that occur without a change in the DNA sequence itself. The key epigenetic mechanism in the plant clock is DNA methylation, the addition of a methyl group to a cytosine base. Specifically, th...