Engineering Life Flipped Course Introduction: How did life evolve? How can we understand the principles of biological systems to create new proteins, new chemicals, biological structures, cells and tissues? The course title led me to think they might include the required information on energy-dependent base pair flipping that links atoms to ecosystems. See, for example: … Designing, engineering, and protecting biodiversity
De novo design of a transmembrane Zn2+-transporting four-helix bundle Excerpt 1) The de novo design of proteins is an important endeavor that critically tests our understanding of the principles underlying protein folding and function, while also laying the foundation for the design of proteins and molecular assemblies with desired properties. Much progress has been recently … Creating nothing but a theory
Luis P. Villarreal has led the way towards discovery of the “origins of life.” He has helped to elucidate what is currently known about how the epigenetic landscape becomes the physical landscape of DNA in the organized genomes of species from microbes to humans. Kudos to Suzan Mazur for admitting that she missed learning about … Luis P. Villarreal tells it like it is
I’ve been busy following the current research and attempting to discuss it, which led me to not finish this blog post. I started writing it last week. Since then, as I had anticipated, others have tried to sneak up from behind and stake their claims to links from physics to cell type differentiation that I … Sneaking up from behind
Relationship between protein thermodynamic constraints and variation of evolutionary rates among sites Excerpt: “…a two-variable model that combines stability and stress signi ficantly improves predictions. Therefore, both the overall stability [symbol] and the stress [symbol] seem to capture distinct thermodynamic constraints on protein evolution.” My comment: Proteins do not evolve. Nutrients are required. Metabolism of nutrients to … Thermodynamic constraints and ecological adaptations sans evolution
Why skin cells are skin cells and not neurons Excerpt: “…we’re using this approach to identify how the epigenome changes when plants are exposed to challenging environmental conditions, such as drought or high temperature, and how these changes might prime the plants for greater tolerance of subsequent exposures.” My comment: The ‘approach’ is DNA methylation … RNA eclipses the importance of DNA to cell type differentiation
RCas9: A programmable RNA editing tool Excerpt: “The researchers envision a wide range of potential applications for RCas9. For example, an RCas9 tethered to a protein translation initiation factor and targeted to a specific mRNA could essentially act as a designer translation factor to “up-” or “down-” regulate protein synthesis from that mRNA.” My comment: … RNA-mediated genetic engineering (Part 3)
Reappraisal of known malaria resistance loci in a large multicenter study Abstract excerpt: “The finding that G6PD deficiency has opposing effects on different fatal complications of P. falciparum infection indicates that the evolutionary origins of this common human genetic disorder are more complex than previously supposed.” Reported as: Long term genetic study finds geographical differences … Different physical locations and different molecular mechanisms of health and disease
Physics, Chemistry, and Molecular biology (PCMb) link ecological variation to ecological adaptations via a model of gene-cell-tissue-organ-organ system complexity that I first presented in 1992. After adding gene activation by pheromones, I co-authored a book that linked the pheromone-controlled physiology of reproduction across species from microbes to man: The Scent of Eros: Mysteries of Odor … Physics, Chemistry, and Molecular biology (PCMb)
The events depicted are now portrayed in the context of Genome Dynamics Events, which are biophysically-constrained RNA-mediated events. RNA-mediated events lead to amino acid substitutions that differentiate the cell types of species. For example: “…the so-called alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ … Physics denied; pseudoscientific nonsense accepted
