Modern Synthesis Review

"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 Formation: How oft...

Epigenetics calls for a different view of common ancestry by challenging the Modern Synthesis of evolution, primarily through the mechanism of transgenerational epigenetic inheritance. While the traditional view in the modern synthesis centers evolutionary change on random genetic mutations (alterations to the DNA sequence) and natural selection, epigenetics introduces a layer of heritable information that is independent of the DNA sequence, allowing for a more dynamic and potentially rapid response to the environment. The Epigenetic Challenge to Inheritance Common ancestry suggests all life shares a single ancestor, with diversification driven over eons by genetic changes. Epigenetics, the study of changes in gene expression that do not involve changes in the underlying DNA sequence, challenges the strict interpretation of the Epigenetics breaches the 120 year old Weismann barrier, the idea that changes acquired by an organism during its lifetime in its somatic (body) cell...

The field of genetic phylogenetics, which aims to reconstruct evolutionary relationships between organisms, has historically focused almost exclusively on changes in DNA sequences. However, a growing body of evidence indicates that epigenetic modifications, which alter gene expression without changing the underlying DNA sequence, can also play a significant role in evolution. This realization has led to a recent surge in interest in incorporating epigenetics into phylogenetic analyses. Here's a breakdown of how and why this shift is occurring: Traditional Phylogenetics and its Limitations: DNA-centric view: Traditional phylogenetics relies heavily on comparing DNA sequences to infer evolutionary relationships. The assumption is that changes in these sequences, through mutations, are the primary drivers of evolutionary divergence. This approach has been successful in reconstructing evolutionary trees for many groups of organisms. Neglecting Epigenetics: For a long time, ...

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...