Darwinian Research Articles

Household-Related Factors Leading to Students’ Dropout from Mixed-Day Secondary Schools in Bomet East Sub-County, Kenya

Education is a basic need to every citizen. However, dropout has been at the top barring all countries the world over in ensuring a hundred percent literacy rates. The Kenyan government has since independence come up with various policies in a bid to increase access and retention rate: Free primary Education (2003), Free Day Secondary Education (2008) and a 100% transition rate policy (2018) from primary school to secondary. This study sought to investigate Household – related factors leading to Students’ Dropout from Mixed-Day Secondary Schools in Bomet East Sub-County, Kenya for the period between the year 2020 and 2023. This study tried to determine the reasons as to why students drop out of school and suggested recommendations on what can be done about it. The study was based on The Classical Theory of Equal Opportunities and Social Darwinism that is predicated on a philosophy that everyone has fair and equal access to a good quality education regardless of social background, race, gender, or religion, and where people achieve success in education according to their efforts and ability, free from any form of discrimination. Descriptive Research Design was used. Questionnaires and interview schedules were used to collect data from the sampled respondents in sampled Mixed Day Secondary schools. Piloting was carried out. Percentages and Frequencies were used to analyze the data with the aid of Statistical Package for Social Sciences (SPSS). It was found out that the following household-related factors lead to student’s dropout; female genital mutilation, early marriages, child labour and cultural beliefs. The study suggests five recommendations to curb school dropouts. The findings are hoped to add new knowledge and benefit the teachers, school principals and other school stakeholders to put necessary measures in place to curb the dropout problem.

Nash equilibrium mapping vs. Hamiltonian dynamics vs. Darwinian evolution for some social dilemma games in the thermodynamic limit

Nash equilibrium mapping vs. Hamiltonian dynamics vs. Darwinian evolution for some social dilemma games in the thermodynamic limit

Claude Bernard's non reception of Darwinism.

The aim of this paper is to explain why, while Charles Darwin was well recognized as a scientific leader of his time, Claude Bernard never really regarded Darwinism as a scientific theory. The lukewarm reception of Darwin at the Académie des Sciences of Paris and his nomination to a chair only after 8years contrasts with his prominence, and Bernard's attitude towards Darwin's theory of species evolution belongs to this French context. Yet we argue that Bernard rejects the scientific value of Darwinian principles mainly for epistemological reasons. Like Darwin, Bernard was interested in hereditary processes, and planned to conduct experiments on these processes that could lead to species transformation. But the potential creation of new forms of life would not vindicate Darwinism since biologists can only explain the origin of morphotypes and morphological laws by the means of untestable analogies. Because it can be the object neither of experiments nor of any empirical observation, phylogeny remains out of science's scope. Around 1878 Bernard foresaw a new general physiology based on the study of protoplasm, which he saw as the agent of all basic living phenomena. We will analyze why Bernard regarded Darwinism as part of metaphysics, yet still referred to Darwinians in his latter works in 1878. Basically, the absence of a scientific reception of Darwinism in Bernard's work should not obscure its philosophical reception, which highlights the main principles of Bernard's epistemology.

Differential Genome Replication of a Unique Single-Amino-Acid Mutation in the Adenovirus-4 Component of the Live Oral Adenovirus Type 4 and Type 7 Vaccine.

The FDA-approved Adenovirus Type 4 and Type 7 Vaccine, Live, Oral is highly effective and essential in preventing acute respiratory diseases (ARDs) in U.S. military recruits. Our study revealed the presence of a previously undetected mutation, not found in the wild-type human adenovirus type 4 (HAdV-4) component of the licensed vaccine, which contains an amino acid substitution (P388T) in the pre-terminal protein (pTP). This study demonstrated that replication of the T388 HAdV-4 vaccine mutant virus is favored over the wild type in WI-38 cells, the cell type utilized in vaccine manufacturing. However, results from serial human stool specimens of vaccine recipients support differential genome replication in the gastrointestinal tract (GI), demonstrated by the steady decline of the percentage of mutant T388 vaccine virus. Since vaccine efficacy depends upon GI replication and the subsequent immune response, the mutation can potentially impact vaccine efficacy.

D’Arcy Thompson’s Morphological Transformations: Issues of Causality and Dimensionality

AbstractD’Arcy Thompson’s drawings showing coordinated differences between the shape of an individual of one species and the shape of an individual of another have been reproduced and discussed countless times. However, while they have been widely regarded as inspirational, their interpretation in causal terms has proved difficult, and there is as yet no consensus on this matter. Here, I approach these Thompsonian transformations from a particular angle, namely their dimensional insufficiency. I argue that this problem must be solved before the issue of causality can be considered. This approach leads to the conclusion that Thompsonian transformations—or “morphological transformations”—have not taken place in evolution, and logically can never do so, because they involve the direct conversion of theadultform of one species into that of another. In contrast, “developmental transformations” do occur in the short term, within the lifetime of a single individual. And “evolutionary transformations” occur in the long term, in a context that can be described, following Scott Gilbert, as five-dimensional. I argue that these two kinds of transformation—developmental and evolutionary—have different causal agencies. I consider the possible nature of these agencies and, related to that, the way in which Thompson’s work connects with Darwinian evolutionary theory.

Evolvability-enhancing mutations in the fitness landscapes of an RNA and a protein

Can evolvability—the ability to produce adaptive heritable variation—itself evolve through adaptive Darwinian evolution? If so, then Darwinian evolution may help create the conditions that enable Darwinian evolution. Here I propose a framework that is suitable to address this question with available experimental data on adaptive landscapes. I introduce the notion of an evolvability-enhancing mutation, which increases the likelihood that subsequent mutations in an evolving organism, protein, or RNA molecule are adaptive. I search for such mutations in the experimentally characterized and combinatorially complete fitness landscapes of a protein and an RNA molecule. I find that such evolvability-enhancing mutations indeed exist. They constitute a small fraction of all mutations, which shift the distribution of fitness effects of subsequent mutations towards less deleterious mutations, and increase the incidence of beneficial mutations. Evolving populations which experience such mutations can evolve significantly higher fitness. The study of evolvability-enhancing mutations opens many avenues of investigation into the evolution of evolvability.

Aquatic Ferrous Solutions of Prebiotic Mineral Salts as Strong UV Protectants and Possible Loci of Life Origin.

Liposomes are lipid-bilayer vesicles that spontaneously self-assemble from fatty acids (or other amphiphiles) in water by encapsulating surrounding aqueous media. After British scientist Alec Bangham described this phenomenon in the early 1960s, they became a prominent participant in the hypotheses on life origin, particularly in the Lipid World model. A novel scenario of self-sustained Darwinian liposome evolution is based on ever-present natural phenomena of cyclic day/night solar UV radiation and gravitational submersion of liposomes in the Archean aqueous media. One of the assumptions of the hypothesis is the UV-shielding ability of the Archean waters that could protect the submerged liposomes from the damaging solar UV radiation. To corroborate the idea, we measured UV absorption in aquatic solutions of several ferrous mineral salts assumed to be present in Archean pools. Single-agent solutions of simple salts such as FeCl2-iron dichloride, FeCl3-iron trichoride, Fe(NO3)3-ferric nitride, NH4Fe(SO4)2-ferric ammonium sulfate, and (NH4)5[Fe(C6H4O7)2]-ferric ammonium citrate were tested. These direct measurements of UV light absorption supplement and reinforce the proposed hypothesis.

Digitizing protocols into single reactors for the one-pot synthesis of nanomaterials

Digitizing protocols into single reactors for the one-pot synthesis of nanomaterials

Modeling emergence of Wolbachia toxin-antidote protein functions with an evolutionary algorithm.

Evolutionary algorithms (EAs) simulate Darwinian evolution and adeptly mimic natural evolution. Most EA applications in biology encode high levels of abstraction in top-down population ecology models. In contrast, our research merges protein alignment algorithms from bioinformatics into codon based EAs that simulate molecular protein string evolution from the bottom up. We apply our EA to reconcile a problem in the field of Wolbachia induced cytoplasmic incompatibility (CI). Wolbachia is a microbial endosymbiont that lives inside insect cells. CI is conditional insect sterility that operates as a toxin antidote (TA) system. Although, CI exhibits complex phenotypes not fully explained under a single discrete model. We instantiate in-silico genes that control CI, CI factors (cifs), as strings within the EA chromosome. We monitor the evolution of their enzymatic activity, binding, and cellular localization by applying selective pressure on their primary amino acid strings. Our model helps rationalize why two distinct mechanisms of CI induction might coexist in nature. We find that nuclear localization signals (NLS) and Type IV secretion system signals (T4SS) are of low complexity and evolve fast, whereas binding interactions have intermediate complexity, and enzymatic activity is the most complex. Our model predicts that as ancestral TA systems evolve into eukaryotic CI systems, the placement of NLS or T4SS signals can stochastically vary, imparting effects that might impact CI induction mechanics. Our model highlights how preconditions and sequence length can bias evolution of cifs toward one mechanism or another.

Which came first: the chicken, the egg, or guanine?

The main goal of the origin of life (OoL) hypothesis is to reconstruct the missing link between the primordial soup and the extant biology. However, the OoL itself is just the initial part of the link representing the bootstrapping operation of Darwinian evolution. The rest of the link is the emergence of the evolution to the present day primary biological system-the ribosome-based translation apparatus. A valid hypothesis must (i) not invoke Darwinian evolution in the bootstrapping and (ii) transform the ab initio life form into the translation apparatus without violating the principle of continuity (i.e., only incremental steps without foresight). Currently, no such hypothesis exists. Here, I discuss the Quadruplex World hypothesis, which fully complies with these requirements and suggests a spontaneous emergence of the ab initio life form. The spontaneity of OoL arises from the physicochemical properties of guanine monomers in a manner of causal determinism: each step of the process (i.e., scaffolding, polymerization, and folding) is caused by the most recent past step such that in the end only the specific 3D architecture forms. The architecture (i) has a length-independent folding pattern; (ii) can play the role of the predecessor of tRNA and single-handedly conduct a primitive form of translation; and (iii) can evolve into the extant translation apparatus without any paradoxes.

Evolution and Political Revolution in Blackwood's Periodical Poetry

Abstract: In May 1861, the middlebrow British monthly Blackwood's Edinburgh Magazine published a comic poem titled "The Origin of Species." While foregrounding Charles Darwin, the poem portrays evolution as teleological, progressive, and driven by the agency and desires of individual organisms—a misrepresentation of Darwin's theory. I argue that the poem undertakes this misrepresentation deliberately: the version of evolution it attributes to Darwin was associated with radical politics and threats to the social order. The Blackwood's poems call up these political associations to reduce the novelty of Darwin's theory and to hint at its dangerous social tendencies.

Racial misconceptions of the theory of evolution predict opposition to the theory and science in general among a sample of Zimbabwean university students

The theory of evolution has often been misconceived and often associated with racist undertones and insinuations towards Black Africans, who are assumed to be less evolved and thus closer to “apes” genetically than other, presumably more advanced racial groups. In this research was thus tested the hypothesis that misconceptions surrounding Charles Darwin's Theory of Evolution, particularly racial ones, would predict a lack of acceptance of the theory in particular, and the entirety of the science enterprise in general among a sample of Black Zimbabweans. We also tested the impact of spirituality on both acceptance of evolution and science. The hypotheses received support from the findings and they are discussed in line with pedagogy surrounding evolution and science. The findings of the most central importance were that racial misconceptions, general misconceptions and spirituality predicted both acceptance of evolution and science. In turn, the effects of all these exogenous variables on acceptance of science were mediated by lack of acceptance of evolution.

Synthetic Biology Pathway to Nucleoside Triphosphates for Expanded Genetic Alphabets.

One horizon in synthetic biology seeks alternative forms of DNA that store, transcribe, and support the evolution of biological information. Here, hydrogen bond donor and acceptor groups are rearranged within a Watson-Crick geometry to get 12 nucleotides that form 6 independently replicating pairs. Such artificially expanded genetic information systems (AEGIS) support Darwinian evolution in vitro. To move AEGIS into living cells, metabolic pathways are next required to make AEGIS triphosphates economically from their nucleosides, eliminating the need to feed these expensive compounds in growth media. We report that "polyphosphate kinases" can be recruited for such pathways, working with natural diphosphate kinases and engineered nucleoside kinases. This pathway in vitro makes AEGIS triphosphates, including third-generation triphosphates having improved ability to survive in living bacterial cells. In α-32P-labeled forms, produced here for the first time, they were used to study DNA polymerases, finding cases where third-generation AEGIS triphosphates perform better with natural enzymes than second-generation AEGIS triphosphates.

Genetics of behavioural evolution in giant mice from Gough Island.

The evolution of behaviour on islands is a pervasive phenomenon that contributed to Darwin's theory of natural selection. Island populations frequently show increased boldness and exploration compared with their mainland counterparts. Despite the generality of this pattern, the genetic basis of island-associated behaviours remains a mystery. To address this gap in knowledge, we genetically dissected behaviour in 613 F2s generated by crossing inbred mouse strains from Gough Island (where they live without predators or human commensals) and a mainland conspecific. We used open field and light/dark box tests to measure seven behaviours related to boldness and exploration in juveniles and adults. Across all assays, we identified a total of 41 quantitative trait loci (QTL) influencing boldness and exploration. QTL have moderate effects and are often unique to specific behaviours or ages. Function-valued trait mapping revealed changes in estimated effects of QTL during assays, providing a rare dynamic window into the genetics of behaviour often missed by standard approaches. The genomic locations of QTL are distinct from those found in laboratory strains of mice, indicating different genetic paths to the evolution of similar behaviours. We combine our mapping results with extensive phenotypic and genetic information available for laboratory mice to nominate candidate genes for the evolution of behaviour on islands.

Ontology as ideology: A critique of Butler's theory of precariousness

Ontology as ideology: A critique of Butler's theory of precariousness

Student Characteristics Leading to Students’ Dropout from Mixed-Day Secondary Schools in Bomet East Sub-County, Kenya

Kenya’s education sector has faced many bottlenecks one being school dropouts. In 2018, the Kenyan government came up with 100% transition rate from primary school to secondary school to increase access to secondary school education which was hoped to result in increased completion rates. This study aimed at investigating Student’s Characteristics Leading to Students’ Dropout from Mixed-Day Secondary Schools in Bomet East Sub-County, Kenya for the period between the year 2019 and 2022. This study investigated individual student’s reasons as to why students drop out of school and suggested recommendations on what can be done about it. This study was guided by the objective: to investigate the student’s-related factors leading to school dropout. The researcher based the study on The Classical Theory of Equal Opportunities and Social Darwinism which reiterates that each person is born with some ability that cannot be altered but can be nurtured and is unique to that particular individual. To collect data from Principals, teachers and students of the sampled Mixed Day Secondary schools, the researcher employed Descriptive Survey. Before embarking on actual research, Piloting was carried out. Questionnaires and interview schedules were used to collect data while Percentages and Frequencies were used to analyze the data. Analysis was done by Statistical Package for Social Sciences (SPSS). The study revealed that the following student’s characteristics lead to students’ dropout; financial problems, peer influence, pregnancy, drug abuse, operating motorcycle business, over age, community/ family, family child labour, negative attitude to schooling, migration and health issues. The study suggests six recommendations to curb school dropouts. The researcher hopes that the findings will benefit the teachers, school principals and other school managers and the Ministry of Education to put necessary measures in place to deal with the dropout problem. The findings will add .......

Zika virus-induces metabolic alterations in fetal neuronal progenitors that could influence in neurodevelopment during early pregnancy.

Cortical development consists of an orchestrated process in which progenitor cells exhibit distinct fate restrictions regulated by time-dependent activation of energetic pathways. Thus, the hijacking of cellular metabolism by Zika virus (ZIKV) to support its replication may contribute to damage in the developing fetal brain. Here, we showed that ZIKV replicates differently in two glycolytically distinct pools of cortical progenitors derived from human induced pluripotent stem cells (hiPSCs), which resemble the metabolic patterns of quiescence (early hi-NPCs) and immature brain cells (late hi-NPCs) in the forebrain. This differential replication alters the transcription of metabolic genes in both pools of cortical progenitors but solely upregulates the glycolytic capacity of early hi-NPCs. Analysis using Imagestream® revealed that, during early stages of ZIKV replication, in early hi-NPCs there is an increase in lipid droplet abundance and size. This stage of ZIKV replication significantly reduced the mitochondrial distribution in both early and late hi-NPCs. During later stages of ZIKV replication, late hi-NPCs show reduced mitochondrial size and abundance. The finding that there are alterations of cellular metabolism during ZIKV infection which are specific to pools of cortical progenitors at different stages of maturation may help to explain the differences in brain damage over each trimester.

ORIGIN OF LIFE UNRAVELLED

A clear meaning of "Life" is even more important for these two than the "Origin of Life," which is crucial to "Evolution" itself as an emergent property of matter where biology transcends computation. The idea of panspermia as a metaphysical proposition is in fact a scientific reality when one considers ‘Jyotish’ (Vedic Astrology). In the present study, it is established that the rationale behind the subject of Jyotish (A Vedānga) is astronomy, and its life side is astrobiology, the study of how electromagnetism interacts with matter to describe “life” as an emergent property of matter. The current study of panspermia focuses on the two most important aspects of advanced complex life on earth: the Cambrian explosion and the emergence of an even more complex and intricate human brain which refutes Darwin's Theory of Evolution and Natural Selection. Solar disturbances and their particle emissions are the most likely link between biological and extra-terrestrial events in both the Origin and Evolution of Life.

Alfred Russel Wallace's Unrealized Last Book: Insights from the Plan for Darwin and Wallace

In honour of the two hundredth birthday of naturalist Alfred Russel Wallace (1823–1913) we present a transcription and analysis of the plan for Wallace's unrealized final book. Recently come to light, Darwin and Wallace was to have been a volume of eight chapters published by the well-known London publishing house of John Murray in the spring of 1915, a project derailed by Wallace's death at the age of 90 in November 1913. Drawing on letters, manuscripts and contemporary published works, we show how the chapter outlines illuminate Wallace's late-life thinking about his and Darwin's working methods, the factors contributing to their independent discovery of natural selection and contemporary challenges to Darwin–Wallace evolutionary gradualism and natural selection by the neo-Lamarckian, mutationist and early Mendelian schools during the period dubbed the ‘eclipse of Darwinism’. Wallace's planned book provides insight into how the co-founder of modern evolutionary biology saw his legacy in relation to Darwin's, and his role as fierce and eloquent defender of his and Darwin's theory during a fascinating period in the history of evolutionary biology. In the emergence of neo-Darwinism in the ‘Modern Synthesis’ period, Wallace's contributions were largely omitted, an oversight that Darwin and Wallace may have prevented had it been realized.

Abstract 4284: Enhancing subclonal reconstruction algorithm for resolving complex tumor phylogenies from multi-sample tumor DNA sequencing

Abstract Cancer is characterized by the ongoing accumulation of somatic mutations, providing selective advantages that may lead to dysregulated cellular proliferation. While the cancer genome at diagnosis has been extensively studied, many cancer types still lack strong prognostic biomarkers. The continuous acquisition and selection for driver mutations in a population of cancer cells acts as a Darwinian process, resulting in clonal expansions of progressively more aberrant and fit phenotypes. Reconstructing tumor evolution allows us to understand key events that drive cancer progression and patterns of mutation co-occurrence within clones. These evolutionary features guide our understanding of fundamental mechanisms that lead to disease lethality. Inferring tumor evolution from DNA sequencing data is becoming part of routine analysis in cancer research. As sequencing costs drop, sequencing multiple tumor samples from a patient becomes routine. These multiple samples can represent different spatial regions of a tumor, longitudinal samples from a single region or a combination of both. This provides an opportunity to study tumor evolution in much greater detail and accuracy than was previously feasible through single-sample datasets. The most widely used methods to reconstruct the subclonal evolution of a tumor utilize stochastic-search algorithms. These approaches iterate through a parameter space to select phylogenetic solutions that maximize the likelihood of observed sequencing data. They are optimized for low complexity cases, where the size and number or subclones are relatively limited. As tumor subclonal structure increases in complexity, the parameter space grows exponentially, and stochastic-search algorithms become computationally intractable. For instance, recent benchmarking studies have revealed that many methods fail to reconstruct clone trees for data with as few as ten subclones. To circumvent current computational limitations, we developed a deterministic algorithm for subclonal reconstruction that leverages fundamental principles of cancer biology to encode heuristics that reduce the solution space to biologically plausible phylogenies. When applied to samples (4-36 tumors; median 16) from 12 patients with metastatic breast cancer, our method reduced the average runtime ten-fold. We were able to delineate the evolutionary history of up to 57 distinct subclones per patient, which is infeasible with most current methods. Benchmarking using methods developed for the SMCHet DREAM challenge on real and simulated datasets further quantifies the accuracy, resolution, and scalability. We have thus presented a novel method for rapid and optimized reconstruction of tumor evolutionary histories. Citation Format: Helena Winata, Daniel Knight, Juber A. Patel, Nicholas K. Wang, Pier Selenica, Stefan E. Eng, Caroline Kostrzewa, Jaron Arbet, Yingjie Zhu, Ronglai Shen, Jorge Reis-Filho, Pedram Razafi, Paul C. Boutros. Enhancing subclonal reconstruction algorithm for resolving complex tumor phylogenies from multi-sample tumor DNA sequencing. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4284.