Darwinian Research Articles

A network analysis of early arthropod evolution and the potential of the primitive

It is often thought that the primitive is simpler, and that the complex is generated from the simple by some process of self-assembly or self-organization, which ultimately consists of the spontaneous and fortuitous collision of elementary units. This idea is included in the Darwinian theory of evolution, to which is added the competitive mechanism of natural selection. To test this view, we studied the early evolution of arthropods. Twelve groups of arthropods belonging to the Burgess Shale, Orsten Lagerstätte, and extant primitive groups were selected, their external morphology abstracted and codified in the language of network theory. The analysis of these networks through different network measures (network parameters, topological descriptors, complexity measures) was used to carry out a Principal Component Analysis (PCA) and a Hierarchical Cluster Analysis (HCA), which allowed us to obtain an evolutionary tree with distinctive/novel features. The analysis of centrality measures revealed that these measures decreased throughout the evolutionary process, and led to the creation of the concept of evolutionary developmental potential. This potential, which measures the capacity of a morphological unit to generate changes in its surroundings, is concomitantly reduced throughout the evolutionary process, and demonstrates that the primitive is not simple but has a potential that unfolds during this process. This means for us the first empirical evolutionary evidence of our theory of evolution as a process of unfolding.

An Assessment of the Influence of Special Needs Education Resources on Management of Inclusive Education in Public Primary Schools in Nakuru East Sub-County, Kenya

Inclusive education has become a worldwide practice because it boosts child rights, especially the right to basic education. Management of inclusive education in primary schools is critical if the education sector is to realize set objectives. The purpose of the study was to examine the influence of special needs education (SNE) resources on the management of inclusive education in public primary schools in Nakuru East Sub-County, Kenya. The specific objectives included establishing the influence of available teaching and learning resources for SNE and SNE teachers' competence in the management of inclusive education in public primary schools in Nakuru East Sub-County. The study was supported by two theories, namely Classical Liberal Theory of Equal Opportunity and Social Darwinism and Systems Theory. The research used a mixed-methods approach. This study used a descriptive, explanatory research design. The target population was 520 respondents, including 437 pupils with disabilities, one quality assurance officer, 4 guidance and counselling teachers, and 4 head teachers. A sample of 170 respondents was selected. Questionnaires for Headteachers, Guidance and counselling Teachers, and Pupils with disabilities and interview schedules for Quality assurance officers were adopted to collect primary data. After cleaning this data by looking for errors in the entries, different descriptive statistics like the variation of coefficient, frequencies, standard deviation, mean score and percentages were assessed for all the quantitative information and variables presented using tables. Inferential statistics such as regression analysis were computed using Statistical Package for Social Sciences version 27. On the other hand, qualitative information was analyzed through the use of content analysis. Regarding the availability of teaching and learning resources for SNE, the study found that the schools had adequately adapted textbooks and hearing aids for SNE. Further, regarding the SNE teachers' competence, the study established that it was uncertain whether many of the teachers at their schools had received special education training. The study concluded that SNE teachers' competence (β=0.737, p-value=0.006<0.05) had the greatest influence on the management of inclusive education in public primary schools in Nakuru East Sub-County, while available teaching and learning resources for SNE (β=0.541, p-value=0.003<0.05) had the least influence on the management of inclusive education in public primary schools in Nakuru East Sub-County. The study recommended that head teachers and teachers should be taken for some SNE management training by the government through seminars organized by the Ministry of Education in order to be able to cater to the learners with special needs in regular schools. The findings might be used by the Ministry of Education and education stakeholders to enhance the quality of inclusive education in public primary schools in Nakuru East Sub-County, Kenya.

Hypothesis of Genetic Diversity Selection in the Occurrence and Development of Lung Cancer: Molecular Evolution and Clinical Significance

So far, the monoclonal hypothesis of tumor occurrence and development cannot be justified. The genetic diversity selection hypothesis for the occurrence and development of lung cancer links Mendelian genetics with Darwin's theory of evolution, suggesting that the genetic diversity of tumor cell populations with polyclonal origins-monoclonal selection-subclonal expansion is the result of selection pressure. Normal cells acquire mutations in oncogenic driver genes and have a selective advantage over other cells, becoming tumor initiating cells; In the interaction with the tumor microenvironment (TME), the vast majority of initiating cells are recognized and killed by the human immune system. If immune escape occurs, the incidence of malignant tumors will greatly increase, and subclonal expansion, intratumour heterogeneity, etc. will occur. This article proposed the hypothesis of genetic diversity selection and analyzed its clinical significance. .

Early Muslim Encounters with Darwinian Theory of Evolution in South Asia: A Study of Shibli Nomani’s Response

Early Muslim Encounters with Darwinian Theory of Evolution in South Asia: A Study of Shibli Nomani’s Response

More than Body Composition: A Darwinian Theory of Somatotype, Applied to a DII Track and Field Outdoor Season

More than Body Composition: A Darwinian Theory of Somatotype, Applied to a DII Track and Field Outdoor Season

Interelasi Teori Evolusi Manusia dan Tafsir Al-Mishbah: Pemahaman Mendalam tentang Penciptaan Manusia

Interrelation of Human Evolution Theory and Al-Mishbah Interpretation: In-depth Insights into the Creation of HumanityThis study explores the concept of human creation in the Qur'an and the widely discussed human evolution theory. It addresses the interpretation of human creation according to Quraish Shihab and the interrelation between Quraish Shihab's interpretation and evolutionary theory, leading to the emergence of connections between evolutionary theory and Al-Mishbah interpretation, which can be explored by interpreters. Building upon these issues, the study reveals that evolutionary theory not only explains human evolution but is also related to all living beings in nature. Unlike Darwin's theory, which suggests that humans originated from apes, this study emphasizes the correlation between human evolution theory and Al-Mishbah's interpretation of human creation, both for the first human and subsequent generations. This is evident in the Qur'an's depiction of human creation after Prophet Adam, detailing the inevitable changes from infancy to old age. Human evolution is closely linked to the Qur'an, contrasting with Darwinian evolution, as the Qur'an specifies the origin of humans, as interpreted by Quraish Shihab. The research employs a literature review methodology, drawing data from relevant sources

Darwinian evolution has become dogma; AI can rescue what is salvageable

Artificial Intelligence (AI), as an academic discipline, is traceable to the mid-1950s but it is currently exploding in applications with successes and concerns. AI can be defined as intelligence demonstrated by computers, with intelligence difficult to define but it must include concepts of ability to learn, reason, and generalize from a vast amount of information and, we propose, to infer meaning. The type of AI known as general AI, has strong, but unrealized potential both for assessing and also for solving major problems with the scientific theory of Darwinian evolution, including its modern variants and for origin of life studies. Specifically, AI should be applied first to evaluate the strengths and weaknesses of the assumptions and empirical information underpinning theories of the origin of life and probability of its evolution. AI should then be applied to assess the scientific validity of the theory of how abundant life came to be on earth.

Narration of Evolutionary Theory and Educational Thought

Darwin's theory of evolution not only challenged the omnipotence of the Western Christian God but also eroded anthropocentrism, causing identity anxiety and crises of belonging among Christian believers in Britain. This influence extended to literature, where Victorian children's literature authors like Kingsley, Carroll, and Kipling engaged in a dialogue with evolutionary theory. They explored the fantasy nature of children's literature and the proximity of children to animals to address the anxieties and confusion arising from evolution. Embracing Darwin's ideas, these authors argued that anatomy, morphology, and even language could not distinguish humans from animals; only morality, emotions, imagination, and creativity facilitated human evolution. They warned against moral decline leading to evolutionary reversal and emphasized the need for education to focus on these qualities rather than rote memorization.

Orchestration and theranostic applications of synthetic genome with Hachimoji bases/building blocks.

Synthetic genomics is a novel field of chemical biology where the chemically modified genetic alphabets have been considered in central dogma of life. Tweaking of chemical compositions of natural nucleotide bases could be developed as novel building blocks of DNA/RNA. The modified bases (dP, dZ, dS, and dB etc.) have been demonstrated to be adaptable for replication, transcription and follow Darwinism law of evolution. With advancement of chemical biology especially nucleotide chemistry, synthetic genetic codes have been discovered and Hachimoji nucleotides are the most important and significant one among them. These additional nucleotide bases can form orthogonal base-pairing, and also follow Darwinian evolution and other structural features. In the Hachimoji base pairing, synthetic building blocks are formed using eight modified nucleotide (DNA/RNA) letters (hence the name "Hachimoji"). Their structural conformations, like polyelectrolyte backbones and stereo-regular building blocks favor thermodynamic stability and confirm Schrodinger aperiodic crystal. From the structural genomics aspect, these synthetic bases could be incorporated into the central dogma of life. Researchers have shown Hachimoji building blocks were transcribed to its RNA counterpart as a functional fluorescent Hachimoji aptamer. Apart from several unnatural nucleotide base pairs maneuvered into its invitro and invivo applications, this review describes future perspective towards the development and therapeutic utilization of the genetic codes, a primary objective of synthetic and chemical biology.

"The effect of gravity on the evolution of life on earth based on general relativity and the low of free fall "

The radius of the universe can be determined by combining the Einstein formulas, which determine the degree of gravitational redshift and describe the angle of refraction of a beam of light running along celestial bodies. The relationship between the two equations is made by the ratio of the total angle to the angle of deflection of the beam of light passing by the Earth according to the rules of Euclidean geometry (2∙π/α). The so-called Darwinian evolutionary distances measured from the color changes of the respiratory pigments of biological creatures (in connection with the phase of their circulation) can be paralleled with this. It is possible to measure these to the radius of the universe determined in this way. During the nearly 4-billion-year uninterrupted process of Darwinian evolution, living organisms presumably adapted to surface gravity during mutations as well as to any other environmental factor. In this way, they can accelerate continuously along the imaginary straight line from the origin of life to the appearance of the human race, i.e., within the short evolutionary distance, due to the attractive effect of gravity. During the free fall from the past to the present, the curvature of space-time may gradually appear in their physiological processes and anatomical structure. Specifically in their circulatory system, the rate of evolution would correspond to the most qualitatively advanced level, i.e., the velocity of human blood circulation. In this way, the evolution accelerating to almost the speed of light is reduced to 5.23 cm/s due to an enormous time dilation (as a proportion of angles; α/2/π). With this average human blood flow velocity, together with data from cardiac and circulatory procedures, a toroidal, or even more refined, ‘interlocking figure 8 model’ can be constructed. It reflects the dimensions, flow and pressure conditions of the pulmonary and systemic circulation, as well as the work of the heart.

The Evolutionary Theory along the Phylogenetic Tree of Unicellular Organisms

In parallel to the advancement of molecular biology suggesting the evolutionary route from the RNA world to the DNA-RNA-protein world through the RNA-protein world, the analysis on the nucleotide base changes in ribosomal RNA genes revels that the divergence of prokaryote and eukaryote first occurred in the DNA-RNA-protein world but the divergence of present-day lineages in eukaryotes occurred after the ancestral eukaryote has acquired the mitochondria as the endosymbionts of O2-respiratory eubacteria. These results strongly suggest that the divergence of unicellular organisms is closely related with the drastic changes in cell contents such as the formation of ribosome, the generation of RNA genes, the conversion from the RNA genes to DNA genes, gene duplication or the endosymbiosis. In the present paper, such drastic changes in evolution of unicellular organisms are theoretically formulated on the basis of the concept of biological activity which consists of the acquired energy, stored energy and systematization. Upon the drastic change in cell contents, the biological activity of an organism is first lowered by the increase in stored energy, but it is gradually recovered as the systematization advances to increase the acquired energy overcoming the increased stored energy and negative entropy due to the systematization itself. Throughout this process, the divergence of new style organisms occurred utilizing new material and energy sources. Such evolutionary process will be explained in detail at the main divergence points in the phylogenetic tree. The relation of such drastic changes in evolution with Darwinian evolution is also clarified.

A History of Biology

A History of Biology

Genes and environment: An old pair in a new era.

What is the relationship between our genes and the environment we live in with regard to health? Like the debate about nature or nurture in the determination of our personality and behavior, the issue of genes and environment has been discussed intensely in the last two centuries. Is it Darwin or Lamarck who is right about the basic determinants of our health, especially as we age in a rapidly changing environment? Evolutionary biology as proposed by Darwin with natural selection at its core may not be able to explain almost instant adjustments of phenotypic traits to the pressures of the environment. Epigenesis, a concept that dates from Aristotle, provides a mechanism for the environment to affect variation in genetic traits that may become heritable. Indeed, Lamarck first described the inheritance of acquired characteristics. Thus, it appears that in contemporary genetics, both Darwin and Lamarck are right: environmental pressures may affect our genes through epigenetics, in ways that allow for inheritance of the changes, a Lamarckian concept; however, evolution through natural selection is the basis for incorporation (or rejection) of new traits and their sustained inheritance, a Darwinian concept. In this review, we present the synthesis of Darwin's and Lamarck's theories, the only way to understand how our health, and that of our progeny, responds to challenging and fast-changing environmental cues. In addition, we present other examples of environment-driven changes in disease frequency or expression.

Cyclophospholipids Enable a Protocellular Life Cycle.

There is currently no plausible path for the emergence of a self-replicating protocell, because prevalent formulations of model protocells are built with fatty acid vesicles that cannot withstand the concentrations of Mg2+ needed for the function and replication of nucleic acids. Although prebiotic chelates increase the survivability of fatty acid vesicles, the resulting model protocells are incapable of growth and division. Here, we show that protocells made of mixtures of cyclophospholipids and fatty acids can grow and divide in the presence of Mg2+-citrate. Importantly, these protocells retain encapsulated nucleic acids during growth and division, can acquire nucleotides from their surroundings, and are compatible with the nonenzymatic extension of an RNA oligonucleotide, chemistry needed for the replication of a primitive genome. Our work shows that prebiotically plausible mixtures of lipids form protocells that are active under the conditions necessary for the emergence of Darwinian evolution.

A High-Risk Subgroup Multiple Myeloma Classification Based on the Detection of PR Minor Subclones

In the last two decades several classifications of Multiple Myeloma (MM) have been proposed based on gene expression signatures. These include the supervised translocation and cyclin D (TC) molecular subgroup approach or unsupervised methods to elucidate the molecular heterogeneity of MM and identify high risk subgroups. In particular, two RNA based gene expression studies have identified 8 to 10 unique subtypes, including the MS, MAF, CD1, CD2, and PR subtypes. The PR subgroup represents a highly proliferative gene signature that is associated with very poor survival outcomes. However, assigning this PR subgroup based on bulk transcriptome signatures can be challenging giving the mixture of genetic backgrounds that can be observed within this subtype. Furthermore, the presence of a minor PR subclone can often be missed with bulk genomic studies leading to the misclassification of a patient as standard risk. We here postulated that minor PR subclones expand under selective therapeutic pressures to become the predominant clones at subsequent relapses and the presence of PR subclones can impact any of the molecular subgroups pertaining poor survival outcomes. Bulk RNA or single cell RNA (scRNAseq) analysis were performed in bone marrow sorted primary MM cells obtained from 718 patients from the CoMMpass trialand 32 relapse/refractory MM patients, respectively. For scRNAseq, serial samples with paired baseline and relapse samples were available in 18 cases. Bone marrow plasma cells samples were separated from bone marrow aspirates using positive sorting selection of CD138 + cells. For bulk RNA-seq we used the mRNA HyperPrep kit (Kapa Biosystems) with RNA from 50,000 cells.For scRNA studiesunbiased mRNA profiling was conducted using the GemCode system (10x Genomics). Cell Ranger and Seurat were used for sample de-multiplexing, barcode processing, single-cell 3' gene and data analysis. Sequencing was performed on Illumina. By performing GSEA at the single cell level using the Zhan gene data set we have classified patients in the appropriate TC groups. FISH data was used to insure accurate calls. For the survival analysis OS was analyzed by the Kaplan-Meier method. In the CoMMpass dataset, with bulk RNA sequencing, the PR subtype contained 7.1% of patients with an admixture of classic genetic subtypes and very poor clinical outcome, with a median OS of 21.3 months. High proliferation index scores were concentrated in this subtype. There was also a strong tendency for patients to transition to the PR subtype at progression, with 25.5% of patients in a non-PR subtype at diagnosis transitioning to PR. Regardless of original subtype, patients that transitioned to the PR subtype rapidly succumbed to their disease with a median OS after the detected progression of 88 days. Using subtype prediction weight we could identify non-PR patients with PR subtype weights above 5% and these patients have a significantly shorter OS of 50 months compared to patients with <5% PR. At the single cell level, investigating the relapsed patients cohort, we have analyzed 92,139 cells and identified 59 clusters. A PR signature (defined as present in ≥15% of cells) was identified in 38% of cases despite baseline favorable prognostic group by FISH cytogenetics (7% HP, 28% t(11;14), and 57% normal FISH). A good concordance with FISH data was observed. In serially relapsed paired samples, all the PR patients maintain their signature overtime and 44% of patients transitioned to PR at subsequent relapse (Fig1A). Survival analyses were performed to evaluate how the presence of minor PR clones at the single cell level relate to clinical outcomes. Notably, the overall survival of patients classified as PR was dramatically reduced with a median OS of 6 months compared to 34 months for non-PR patients (Fig1B). In conclusion, we here show that minor PR clones defined by transcriptional signature through bulk or scRNA may be detectable in patients with variable MM molecular subgroups, including those classified as standard risk by the currently adopted classifications. We also show that the presence of these PR minor clones pertains adverse outcomes with very poor survivals. At relapse, most acquired PR cases originated from standard-risk presentations consistent with a Darwinian clonal evolution. Future classifications should account for the presence of these PR subclones for a better disease prognostication and developments of novel therapeutics.

Endless forms of endless formation — The morphogenesis of organisms and scientific objects

The present article proceeds from the premises that living forms and abstract formalization come into being by similar mechanisms (e.g., random variation, selection, conventions) and have similar properties (e.g., semiosis, stasis and complexity). These convergences justify the comparative analysis of form's development, evolution and action in both fields. Here we shall focus on the notion of “endless forms” advanced by Darwin's seminal work in evolutionary biology “On The Origin of Species” to discuss the various ways in which it relates to biological formation. I shall explore the idea of “infinitude of evolved forms” through the lens of the five connotations of the word “endless” provided by the Merriam-Webster Thesaurus dictionary, which are: perpetual; incomputable; manifold; unfinished; steady. From each synonym chosen, a new iteration of dictionary search was made to produce a list of terms that are used in the reviewed literature to describe biological morphogenetic features, which are respectively: reproducible, unpredictable, additive, undetermined, the end of their own formation. In conclusion, I propose a tentative mapping between each of these five connotations and the biological processes at work in their making, which are, respectively: 1) copying organic information; coding organic signs; manufacturing organic meaning 2) natural variation, natural selection, natural conventions; 3) multilevel organization, differentiation/development, complexity; 4) ambiguity, degeneracy, semiotic thresholds; 5) homeostasis, autopoiesis, codepoiesis. The processes discussed here gained salience as developments, additions, or nuances to Darwin's original theory. It must be noted that, even though the discussion is mainly framed by Code Biology as a source of conceptualization, inputs from a wide range of theoretical perspectives will be given emphasis when suitable.

What Obstacles Stands in the Way of the Achievement of Socialism

The aim of this paper is to show that a system of democratically managed firms is the model of socialism best tailored to human nature. From the author’s perspective, considering that the retention of markets in such a system allows selfish drives of individuals to act themselves out to the full, its establishment would come up against fewer obstacles than those standing in the way of the creation of a centrally planned one. An additional thesis advanced in the paper is that that the process leading to the advent of such a system can be looked upon as a socialist revolution consistent with the principles of Darwinian evolutionism.

Redefining the Evolutionary History of the Rock Dove, Columba livia, Using Whole Genome Sequences.

The domestic pigeon's exceptional phenotypic diversity was key in developing Darwin's Theory of Evolution and establishing the concept of artificial selection. However, unlike its domestic counterpart, its wild progenitor, the rock dove Columba livia has received considerably less attention. Therefore, questions regarding its domestication, evolution, taxonomy, and conservation status remain unresolved. We generated whole-genome sequencing data from 65 historical rock doves that represent all currently recognized subspecies and span the species' original geographic distribution. Our dataset includes 3 specimens from Darwin's collection, and the type specimens of 5 different taxa. We characterized their population structure, genomic diversity, and gene-flow patterns. Our results show the West African subspecies C. l. gymnocyclus is basal to rock doves and domestic pigeons, and suggests gene-flow between the rock dove's sister species C. rupestris, and the ancestor of rock doves after its split from West African populations. These genomes allowed us to propose a model for the evolution of the rock dove in light of the refugia theory. We propose that rock dove genetic diversity and introgression patterns derive from a history of allopatric cycles and dispersion waves during the Quaternary glacial and interglacial periods. To explore the rock dove domestication history, we combined our new dataset with available genomes from domestic pigeons. Our results point to at least 1 domestication event in the Levant that gave rise to all domestic breeds analysed in this study. Finally, we propose a species-level taxonomic arrangement to reflect the evolutionary history of the West African rock dove populations.

Analisis Teori Darwin Ditinjau dari Konsep Waktu

The development of a science cannot be separated from the development of technology, as well as the development of the theory of evolution as a branch of pure biology which studies the existence of changes in the structure of living creatures which until now continues to experience development. This article uses a literature review approach by examining Darwin's theory of evolution based on the philosophy of science in the study of past, present and future time. Darwin's theory is striking in the excellence of its findings, such as the development of empirical data on an organism, even though it has had many controversies in the development of its science. The results of the study and analysis show that Darwin's theory of evolution can still be used today and is compatible with other existing theories.

A Nexus between Genetic and Non-Genetic Mechanisms Guides KRAS Inhibitor Resistance in Lung Cancer.

Several studies in the last few years have determined that, in contrast to the prevailing dogma that drug resistance is simply due to Darwinian evolution-the selection of mutant clones in response to drug treatment-non-genetic changes can also lead to drug resistance whereby tolerant, reversible phenotypes are eventually relinquished by resistant, irreversible phenotypes. Here, using KRAS as a paradigm, we illustrate how this nexus between genetic and non-genetic mechanisms enables cancer cells to evade the harmful effects of drug treatment. We discuss how the conformational dynamics of the KRAS molecule, that includes intrinsically disordered regions, is influenced by the binding of the targeted therapies contributing to conformational noise and how this noise impacts the interaction of KRAS with partner proteins to rewire the protein interaction network. Thus, in response to drug treatment, reversible drug-tolerant phenotypes emerge via non-genetic mechanisms that eventually enable the emergence of irreversible resistant clones via genetic mutations. Furthermore, we also discuss the recent data demonstrating how combination therapy can help alleviate KRAS drug resistance in lung cancer, and how new treatment strategies based on evolutionary principles may help minimize or even preclude the emergence of drug resistance.