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Synonymous mutations in a protein coding gene lead to a remarkably similar average “collateral” mutation effect size across alternative reading frames (1). Here we quantify the rarity of this feature among possible block structure codes as 0.77%. Then we develop a simple model of evolutionary search with two types of mutation. Across different mutation step sizes and ratios of the two types, the fitness-maximizing region corresponds to using a single average mutation value. The analogous constant average collateral mutation effect observed for the standard genetic code may likewise facilitate evolutionary search in alternative frame sequences.
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Highly Similar Average Collateral Effect of Synonymous Mutations Across Alternative Reading Frames: A Potential Role In Evolvability

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How close are we really to a human-engineered self-replicating machine? A couple of thought experiments are proposed which help explain why such machines are still far beyond current human technology. And I conclude that we are unlikely to be successful in explaining how the self-replicating machines we see everywhere in the living world could have arisen through entirely natural causes, when we still do not know how such machines could be designed.
</abstract>

Human-Engineered Self-Replicating Machines

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In 2007, I published a hypothesis about mechanisms of evolution of large taxonomic groups of the Kingdom Animalia, which was based on advances in paleontology genome analysis, genetics and embryology that are difficult to understand within Darwinian intuition. According to this model that I called a Universal Genome hypothesis: (a) the Universal Genome that encodes major developmental programs essential for various phyla of Metazoa emerged in a unicellular or a primitive multicellular common ancestral organism shortly before the Cambrian period; (b) The Metazoan phyla, all having similar gene sets, are nonetheless very morphologically distinct because each utilize specific combinations of developmental programs. A highly counterintuitive prediction of this idea, which strictly dissociates it from the classical evolutionary model, is that latent developmental programs should exist in genomes of lower Metazoan taxa. These latent programs control the development of organs and other morphologies that would emerge in evolutionary higher taxa. Potentially such programs could be activated by mutations or application of signaling molecules, and thus be revealed in lower taxa. A paper on the embryology of fins published in the Cell journal provides an evidence for existence of such a latent developmental program. Here I comment of this discovery and its implication in our understanding of evolution.
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Existence Of A Latent Developmental Program: Revisiting The Universal Genome Model Of Evolution Of Metazoa

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BioCosmos: New perspectives on the origin and evolution of life

 BioCosmos is an on-line, peer-reviewed, open access journal that currently does not charge authors for publishing. The journal aims to present a wide variety of novel perspectives on the origins and nature of life that go beyond the standard neo-Darwinian paradigm of biological evolution. The focus is on theoretically innovative, data-driven analysis and experimental results from biology and biochemistry, although broader perspectives from philosophy and physics are also represented.   BioCosmos encourages high quality scientific research and debate, which results in novel theoretical or experimental approaches that deal with unsolved problems of the standard biological theories. To bring about this aim, the journal’s peer review process takes to heart Newton’s ‘Hypotheses non fingo’. In other words, it judges the theoretical claims proposed by authors in terms of the results rather than in terms of how standard theorists deal with the same results. Inevitably, the range of research potentially covered by this journal is very wide. The tableau below provides a sense of this range.   The journal publishes original research articles, reviews, commentaries, letters to the editor and conference reports. Further details, along with instructions for submission, can be found under JOURNAL INFORMATION.   Biosciences:    Systems Biology   Theoretical Biology   Historical Biology   Cell Biology and Molecular Machines   Biological Fine-tuning   Biochemical Complexity   Bioinformatics   Population Genetics   Evolutionary Biology and Evolutionary Theory   Extended Synthesis   Simulated Evolution   Phylogenetics and Phylogenomics   Functional Morphology   Computational Biology   Paleontology   Astrobiology   RNA World    Physics and Cosmology:    Cosmology and Fine tuning   Quantum Cosmology    Chemistry:    Prebiotic Scenarios   Origin of Life Studies   Autocatalysis   Prebiotic catalysis   Amphiphilic assembly   Astrochemistry    Philosophy:    Teleology and Final Causes   Design Arguments   Anti- and Alt-Materialisms   Systems and Complexity Theory   Category and Information Theory      Archiving   Sciendo archives the contents of this journal in Portico - digital long-term preservation service of scholarly books, journals and collections.   Plagiarism Policy   The editorial board is participating in a growing community of Similarity Check System's users in order to ensure that the content published is original and trustworthy. Similarity Check is a medium that allows for comprehensive manuscripts screening, aimed to eliminate plagiarism and provide a high standard and quality peer-review process. 

BioCosmos: New perspectives on the origin and evolution of life

Volume 3 (2023): Issue 1 (January 2023)

Biological Fine-tuning

Highly Similar Average Collateral Effect of Synonymous Mutations Across Alternative Reading Frames: A Potential Role In Evolvability

Origin of Life Studies

Human-Engineered Self-Replicating Machines

Phylogenetics and Phylogenomics

Existence Of A Latent Developmental Program: Revisiting The Universal Genome Model Of Evolution Of Metazoa

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