<abstract>
<title style='display:none'>Abstract</title>
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.
</abstract>

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

<abstract>
<title style='display:none'>Abstract</title>
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

No <italic>Homo</italic>: Why Theistic Evolution Fails

<abstract>
<title style='display:none'>Abstract</title>
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.
</abstract>

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

<abstract>
<title style='display:none'>Abstract</title>
It is often argued both by scientists and the lay public that it is extremely unlikely for life or minds to arise spontaneously, but this argument is hard to quantify. In this paper I make this argument more rigorous, starting with a review of the concepts of information and entropy, and then examining the specific case of Maxwell's demon and how it relates to living systems. I argue that information and entropy are objective physical quantities, defined for systems as a whole, which allow general arguments in terms of physical law. In particular, I argue that living systems obey the same rules as Maxwell's demons.
</abstract>

Spontaneous Appearance of Life and the Second Law of Thermodynamics

Review of Philip Goff, <italic>Why? The Purpose of the Universe</italic>, (Oxford University Press, 2023)

<abstract>
<title style='display:none'>Abstract</title>
Evolutionary creationism (EC) formerly known as theistic evolution is a widely held view of the harmony between science and faith among theists of many denominations. Arguments against EC based on the fact that there is only one extant species of the genus Homo, or that human beings were not favored by God to survive, are strawmen, and are both scientifically and theologically refuted.
</abstract>

Evolutionary Creation Does Not Fail: A Response to ‘No Homo: Why Theistic Evolution Fails’

<abstract>
<title style='display:none'>Abstract</title>
The emergence of glycomolecules in nature coincided with the dawning of the ribonucleic acid (RNA) and deoxyribonucleic acid (DNA) world, along with the development of a colossal assortment of related monosaccharide building blocks, which vastly exceed the building blocks for any other class of macromolecules. The elaboration of glycomolecules by unicellular organisms, inside cells and on their surfaces and secretions, led to an explosion of diversity, in which unique types of glycomolecules evolved to be highly expressed in all kingdoms of life – monera, protists, fungi, plant and animal. In addition to nucleic acids, glycomolecules include glycoproteins, glycolipids, oligo- and polysaccharides, glycosylated RNA (glycoRNA), and many others. The glyco-modification of amino acids in proteins overcame the limitation inherent in the genetic code, which restricts protein structures to 20 amino acids. Thus, the virtually unlimited nature of protein glycosylation greatly expands the structures and functions of proteins. A highlight in the evolution of glycomolecules is the diversity in glycan structures, as each cell type in nature, from unicellular organisms to cells in metazoans and humans, generates incredibly complex and varied glycan structures. Thus, a central paradigm of glycomolecular evolution is that the collective glycan structures are the defining features unique to each organism. This article touches on the marvelous diversity of glycans and glycomolecules in nature that led to their dominance in the landscape of biology, as well as thoughts on evolution that likely gave rise to their elaboration, diversity, and evolutionary success.
</abstract>

Evolution and Diversity of Glycomolecules from Unicellular Organisms to Humans

<abstract>
<title style='display:none'>Abstract</title>
The post-genomic era raises questions about neo-Darwinian genetic determinism. Instead, open aspects of macroevolution become intelligible by Evo-Devo research. At all developmental levels, self-organization acts robustly towards “wholeness”, as exemplified by organoid technologies. In retinal reaggregates histotypical features are reached along different formative routes. Thus, tissue formation is not merely gene-directed, but channeled by unpredictable external conditions. These insights restrict conceptions of onto- and phylogenesis. Neither is characterized by unlimited randomness nor by finite genocentrism. A re-examination of Driesch’s drive to wholeness, i.e., robustness and intentionality, appears timely, while his teleologic postulates remain undecidable by reductionist reasoning.
</abstract>

Post-genomics, Evo-Devo and the recurrence of teleologic thought<xref ref-type="aff" rid="j_biocosmos-2022-0002_fn_003">†</xref>

<abstract>
<title style='display:none'>Abstract</title>
Highly accurate self-replication of cellular phenotype is a requirement for biological evolution. I previously investigated the degree of self-replication fidelity needed in a viable, evolving population of living cells. Here I present a phase transition approach from non-living chemical complexity to evolving living creatures and illustrate the necessary non-continuity of whatever process led to the origin of evolution. A theoretical approach to the relationship between replication fidelity, survival probability and the capacity to grow and evolve is presented consistent with previous data from experimental simulations. The implications for the origin of life to include explanations for non-continuity are discussed.
</abstract>

Evidence for Phase Transitions in Replication Fidelity and Survival Probability at the Origin of Life

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BioCosmos: New perspectives on the origin and evolution of life

Interdisciplinary approaches from biosciences, chemistry, physics, and philosophy

 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...

 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...

BioCosmos: New perspectives on the origin and evolution of life

Interdisciplinary approaches from biosciences, chemistry, physics, and philosophy

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