Abstract: Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal-to-zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by post-transcriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs, this pathway does not fully explain mRNA clearance. We investigated how codon identity and translation affect mRNA stability during development and homeostasis. We show that the codon triplet contains translation-dependent regulatory information that influences transcript decay. Codon composition shapes maternal mRNA clearance during the maternal-to-zygotic transition in zebrafish, Xenopus, mouse, and Drosophila, and gene expression during homeostasis across human tissues. Some synonymous codons show consistent stabilizing or destabilizing effects, suggesting that amino acid composition influences mRNA stability. Codon composition affects both polyadenylation status and translation efficiency. Thus, the ribosome interprets two codes within the mRNA: the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.
Occam’s Razor – the problem solving principle in philosophy that suggests that the theory with fewest assumptions should be preferred at first – could be helpful here in judging each potential causal direction. For example in the gene duplication and genetic dispensability problem presented above, the evolutionary causal effect requires the extra assumption that dispensable genes are more likely to undergo gene duplication during evolution; this is non-trivial.
My comment: Pseudoscientists have trivialized the link from the speed of light on contact with water to the de novo creation of nucleic acids and all biodiversity, which links the creation of the innate immune system to supercoiled DNA. Science journalists report the trivialization in articles like this.
My comment: Nothing “drives” evolution across two billion years. Pennisi is in rare form.
She reports this:
Two billion years ago, an early cell swallowed an energy-producing microbe, giving birth to the mitochondria that are the hallmarks of all eukaryotes, from protists to people. Evolutionary biologists now think that was just the start of the influence that the cell’s “powerhouses” have on the tree of life.
In the same context, she reports:
…evidence that natural selection boosts mutation rates in the nucleus, apparently to keep up with mitochondrial evolution.
See for comparison: Virus-driven energy theft has been linked to all pathology in Epigenetics and Genetics of Viral Latency.
…viral latency is responsible for life-long pathogenesis and mortality risk…
My comment: All serious scientists know that ecological variation must be linked to nutrient energy-dependent RNA-mediated ecological adaptation via biophysically constrained protein folding chemistry in all living genera. Only pseudoscientists and science journalists continue to report results in the context of two billion years of mutations, natural selection, and evolution.
See also: Inching toward the 3D genome; All in the (bigger) family — both articles were written by Pennisi, and the links are to my comments on the articles
See also: Combating Evolution to Fight Disease
My comment: Science journalists like Pennisi are supporting neo-Darwinian nonsense each time they report research in the context of two billion years of evolution.
…we interpret the striking similarities in organismal morphology, community structure, habitat, and evident physiology between the ancient and modern sulfur-cycling biotas as evidencing stasis resulting from adaptation to a physically quiescent subseafloor environment that has remained essentially unchanged over billions of years.
A central process in evolution is the recruitment of genes to regulatory networks. We engineered immotile strains of the bacterium Pseudomonas fluorescens that lack flagella due to deletion of the regulatory gene fleQ. Under strong selection for motility, these bacteria consistently regained flagella within 96 hours via a two-step evolutionary pathway.
My comment: Compare the bacteria that recruited genes to re-evolve their flagellum via a two-step evolutionary process to the lack of any evolutionary process in the bacteria living in ocean sediments. What was the two-step evolutionary process that was required for the weekend evolution of the bacterial flagellum? Why did nothing change in the other bacteria for ~ 2 billion years? If you ask answers to the right questions, you will find that theories about mutations, natural selection, and evolution have no explanatory power.
…genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world. In this view of evolution there is no need of considering teleological elements (p. 199).
My comment: In that view of evolution, there is no need to consider anything except the ridiculous conclusion, which can be placed into the context of what serious scientists can see. Occam’s razor suggests that all serious scientists should view ecological variation in the context of observed ecological adaptation. If they cannot see that their observations should be placed into the context of what is known about biologically-based cause and effect, they may need to start looking under the light.
See for example: Gen9 “Our Founders“
The founders of Gen9 include people who are likely to know that femotosecond blasts of UV light are linked to RNA-mediated DNA repair of all virus-driven pathology via energy-dependent changes in base pairs and RNA-mediated amino acid substitutions. Unfortunately, most people cannot see how that fact is connected to this fact:
In the forward to the reprint of “What is Life?” Roger Penrose asks:
“How often do we still hear that quantum effects can have little relevance in the study of biology, or even that we eat food in order to gain energy?”
Others still report that learning more about mutations and natural selection is the key to understanding how evolution occurs across millions of years — even after the report on weekend evolution of the bacterial flagellum in Pseudomonas flourescens which fluoresces when exposed to UV light. It seems that neo-Darwinian theorists and other theorists are not interested in linking Darwin’s “conditions of life” from Schrodinger’s claims about sunlight to Dobzhansky’s claims about the light of evolution. Do the theorists intend to keep ignoring everything known to serious scientists about the energy-dependent links from angstroms to ecosystems?
See: Structural diversity of supercoiled DNA
Our cryo-ET, biochemical, and computational studies show the astounding versatility and dynamism of DNA depending on the degree of supercoiling. DNA simultaneously exists in a largely inactive B-form with bases tucked in and protected and an active, highly varied structure with exposed bases. Our data provide relative comparisons of supercoiling-dependent twisted, writhed, curved, and kinked conformations and associated base exposure. Each of these structural features may be differentially recognized by the proteins, nucleic acids, and small molecules that modulate DNA metabolic processes.
My comment: The differential structure features of DNA are RNA-mediated. Energy-dependent amino acid substitutions link angstroms to ecosystems in all living genera, and virus-driven energy theft links mutations to all pathology.
See for examples: Nutrient-dependent/pheromone-controlled adaptive evolution: a model
My comment: For details on the conserved molecular mechanisms that link RNA-mediated amino acid substitutions to cell type differentiation in all cell types of all individuals of all species, see my invited review of nutritional epigenetics: Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems
This atoms to ecosystems model of ecological adaptations links nutrient-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA / messenger RNA balance and chromosomal rearrangements. The nutrient-dependent pheromone-controlled changes are required for the thermodynamic regulation of intracellular signaling, which enables biophysically constrained nutrient-dependent protein folding; experience-dependent receptor-mediated behaviors, and organism-level thermoregulation in ever-changing ecological niches and social niches. Nutrient-dependent pheromone-controlled ecological, social, neurogenic and socio-cognitive niche construction are manifested in increasing organismal complexity in species from microbes to man.
See for comparison: This protein designer aims to revolutionize medicines and materials
Baker’s team has all but solved one of the biggest challenges in modern science: figuring out how long strings of amino acids fold up into the 3D proteins that form the working machinery of life.
Conclusion: Protein designers have shed nature’s constraints and are now only limited by their imagination. “We can now build a whole new world of functional proteins,” Baker says.”
My comment: RNA-mediated protein folding chemistry is biophysically constrained by nutrient energy-dependent microRNA flanking sequences, which link the details in our section on molecular epigenetics from our 1996 Hormones and Behavior review to all morphological and behavior diversity in all living genera via RNA-mediated amino acid substitutions.
Baker fails to mention that quantized energy is the link to energy-dependent changes and all links from angstroms to ecosystems via RNA-mediated protein folding chemistry in all living genera. That fact requires the ‘design’ of an innate immune system that protects all organized genomes from virus-driven energy theft and genomic entropy so that organisms can reproduce when enough food is available. If not enough food or energy is available to support the physiology of reproduction, metabolic networks cannot be linked to genetic networks via RNA-mediated amino acid substitutions and protein folding. But virus-driven energy theft can clearly be linked from the Zika virus to differences in craniofacial morphology and brain development by smaller skull size in victims of the transgenerational epigenetic inheritance of the virus.
The facts about the Zika virus-damaged DNA link virus-driven pathology to every aspect of development during life history transitions that are altered by the energy theft. Plasticity associated with olfactory input in this example, and many others, can be examined in the context of what is currently known to serious scientists, or it can be placed back into the context of the pseudoscientific nonsense touted by neo-Darwinian theorists.