Modern Synthesis Review

The discovery of transgenerational epigenetic inheritance of acquired cold tolerance in rice offers compelling molecular evidence for a concept long dismissed by mainstream evolutionary biology: the inheritance of acquired characteristics, a cornerstone of Lamarckism. The original study, which selected cold-sensitive rice over three generations under cold stress, yielded stable lines with enhanced cold tolerance that persisted for at least five generations even after the stress was removed. This rapid, environmentally induced, and heritable adaptation points toward a mechanism beyond traditional Mendelian genetics, giving credence to neo-Lamarckian concepts. How Epigenetics Affects Cold Adaptation in Rice The core of this transgenerational adaptation lies in epigenetics, specifically DNA methylation, which are chemical tags on the DNA that regulate gene expression without altering the underlying DNA sequence. The Epigenetic Mechanism The study identified a gene, ACT1 (Acqu...

The honeybee hive is a marvel of biological engineering and social complexity, nowhere more evident than in the dramatic life-history difference between the fertile, long-lived queen and her genetically identical, sterile, short-lived worker sisters. These two distinct female castes, or morphs, emerge from the same genome purely through a difference in early larval diet. This phenomenal example of phenotypic plasticity—where a single genotype can produce multiple distinct phenotypes in response to environmental cues—is governed by the molecular machinery of epigenetics. The key environmental signal is Royal Jelly (RJ), a nutrient-rich secretion from the head glands of worker bees, which holds the 'secret' to queen development. How Epigenetics Affects Honeybee Caste Differentiation Epigenetics refers to heritable changes in gene expression that occur without altering the underlying DNA sequence. These mechanisms act as a critical interface between the environment (in...

Zane Koch's proposition of somatic mutations as a primary driver of epigenetic aging presents a compelling alternative perspective to traditional, neo-Darwinian explanations of senescence. While neo-Darwinism primarily focuses on the accumulation of deleterious genetic mutations over generations, impacting reproductive fitness and thus influencing the evolutionary trajectory of aging, Koch's hypothesis shifts the focus to the individual, highlighting the role of accumulated somatic mutations in disrupting epigenetic regulation throughout a lifespan. Neo-Darwinism, in its classical form, suggests that aging is not actively selected for, but rather a byproduct of declining selective pressure on traits expressed later in life.  Genes that benefit an organism early in life, promoting reproduction, are favored, even if they have detrimental effects later on.  This theory, known as the "mutation accumulation" theory, posits that late-acting deleteri...

A recent, strongly-worded critique of mainstream evolutionary theory has emerged from the pages of Progress in Biophysics and Molecular Biology. In his 2024 paper , "Cooperative genes in smart systems: Toward an inclusive new synthesis in evolution," systems scientist Peter A. Corning argues for the complete abandonment of the long-standing "Modern Synthesis" and its popular counterpart, the "Selfish Gene" concept. Corning contends that these frameworks are no longer tenable in the face of mounting evidence and proposes a new, more inclusive paradigm that re-centers the agency of living organisms and the power of cooperation in shaping the grand narrative of life. For over half a century, the Modern Synthesis has provided the dominant framework for understanding evolution, wedding Darwinian natural selection with Mendelian genetics. This model, in essence, views evolution as a process driven primarily by the random mutation of genes, with natur...

"We conclude that epigenetic mutational bias challenges the pevailing paradigm that mutation is a DIRECTIONLESS force in evolution. Our discovery yields a new account of the forces driving patterns of natural variation, CHALLENGING a LONG-STANDING PARADIGM regarding the randomness of mutation." Nature 1/22 The intricate dance between genetics and environment shapes the phenotypic expression of an organism. While genetics provides the blueprint, epigenetics acts as a dynamic modulator, influencing how genes are expressed without altering the underlying DNA sequence.  One crucial role of epigenetics is its contribution to maintaining genomic stability by mitigating the impact of random mutations. This essay delves into the mechanisms by which epigenetics modulates the reduction of random mutations, ensuring the fidelity of genetic information across generations. Understanding Random Mutations Random mutations are alterations in the DNA sequence that occur stochastic...

"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...