Epigenetic Lamarck

The article "Nucleosome conformation dictates the histone code" by Matthew Marunde argues that the conformation of the nucleosome, the basic repeating unit of chromatin, plays a critical role in determining how histone post-translational modifications (PTMs) are read by chromatin-associated proteins (CAPs). PTMs are modifications made to the amino acid residues of histones, which can alter their structure and function. PTMs can occur anywhere on the histone proteins, but they are most commonly found on the histone tails, which protrude from the nucleosome core. CAPs are proteins that bind to chromatin and play a variety of roles in gene regulation, including transcription, DNA replication, and DNA repair. CAPs contain specialized domains called reader domains, which recognize and bind to specific PTMs on histones. Traditionally, the histone code has been studied by isolating reader domains and histone peptides and testing their binding affinity for each other. Ho...

The paper "The molecular and mathematical basis of Waddington's epigenetic landscape: A framework for post-Darwinian biology?" by Sui Huang  discusses the relationship between Waddington's epigenetic landscape and gene regulatory networks (GRNs). Waddington's epigenetic landscape is a metaphor for the developmental process, with different phenotypes represented by valleys and ridges. GRNs are complex networks of interactions between genes that control gene expression. Huang argues that GRNs can be used to model the epigenetic landscape, and that this can provide a framework for understanding post-Darwinian biology. One of the key ideas of the paper is that GRNs are non-linear and stochastic. This means that the output of a GRN can be unpredictable, even if the inputs are known. This is because the interactions between genes can be complex and non-additive. Huang argues that this non-linearity and stochasticity is essential for understanding...

"It is doubtful, however, whether even the most statistically minded geneticists are entirely satisfied that nothing more is involved than the sorting out of random mutations by the natural selective filter." - Conrad Waddington, father of Epigenetics, Letter to Nature journal the year the MS (theory of evolution) was released in '42 S cientists rejected Waddington's epigenetics for 70 years. There are a few reasons for this: Waddington's ideas were ahead of their time. In the 1960-70's, scientists were focused on the central dogma of molecular biology, which stated that DNA was the only blueprint for life and that genes could only be expressed in one way.  Waddington's ideas about epigenetics, which suggested that genes could be regulated by external factors, went against this prevailing dogma. There was little experimental evidence to support Waddington's claims. The technology to study epigenetics did not exist until the l...

Extracellular vesicle analysis Hendrix et al., Nature Reviews Methods Primers (2023) Extracellular vesicles (EVs) are nanoscale membrane-bound structures that are secreted by all cells. They contain a variety of biomolecules, including proteins, nucleic acids, and lipids, and play a role in cell-cell communication, signaling, and transport. EVs have been implicated in a wide range of physiological and pathological processes, including cancer, inflammation, and immunity. EVs can be isolated from a variety of biological fluids, including blood, plasma, serum, urine, saliva, and cerebrospinal fluid. There are a number of different methods for EV isolation, each with its own advantages and disadvantages. The most common methods include ultracentrifugation, density gradient centrifugation, and size-exclusion chromatography. Once EVs have been isolated, they can be characterized using a variety of methods, including microscopy, flow cytometry, and proteomics. Microscopy can be us...

M any evolutionists believe that epigenetics challenges neo-Darwinism. Neo-Darwinism is the prevailing theory of evolution, and it states that evolution is driven by natural selection, which acts on random mutations in the DNA sequence. Epigenetics, on the other hand, is the study of changes in gene expression that are not caused by changes in the DNA sequence itself. Epigenetic changes can be passed down from parents to offspring, and they can be influenced by the environment. This raises a number of challenges for neo-Darwinism. First, it challenges the view that natural selection is the only driving force in evolution. Epigenetic changes can occur without mutations in the DNA sequence, so they can provide a way for organisms to adapt to their environment more quickly than natural selection alone can explain. Second, it challenges the view that evolution is a gradual process. Epigenetic changes can be large and sudden , and they can have a significant impact on an ...