Organisms. Journal of Biological Sciences

Single Cell Sequencing Techniques and Biological Explanation

2024-06-13T13:21:42+00:00

The aim of this paper is to examine the type of biological explanation implied by single-cell sequencing, using established frameworks in the philosophy of biology, particularly those of new mechanical and systems biology. While investigating the extent to which new mechanistic philosophy or systems biology represent theoretical frameworks that align with single-cell sequencing, a part of -omics sequencing techniques, I claim that the objective of single-cell sequencing corresponds with the zeitgeist in theoretical philosophies of biology. The zeitgeist is a stance that advocates for a broader perspective on living organisms and that rejects reductionism. However, there remains a disparity between the scientific narrative and the practical capabilities of single-cell sequencing. Consequently, the conclusion drawn in this paper is that while single-cell sequencing aligns with the zeitgeist in certain theoretical philosophies of biology, it also acknowledges their theoretical limitations.

Polyploidization, Gene Duplication, and the Origin of Variability: Where is the Evidence?

2024-06-12T16:09:00+00:00

The origin of molecular complexity and its bearings on organismal novelty by duplication of primordial, ancestral states replaced the ab initio modelling to solve the dilemma of protein structure and precedes by far the advent of genome research. The insights of Margaret O. Dayhoff (1966) let her to conclude that ferrodoxins and other proteins were derived by doubling of short peptides and that proteins´ first folded domains arose by duplication, fusion, and diversification of shorter, ancestral peptides. Here, recent genetic, cytogenetic, and genomic data on protein evolution, genome size, and Hox genes patterns are critically analyzed, and the evolutionary importance of polyploidy and its mega cytogenetic effects are stressed. The empirical results from synthetic allopolyploids serve as fundamental knowledge to contend that interlineage crossings are the causal phenomena underlying the origin of macroevolutionary variation. Patterns of gene/genome duplications, the origin of complex proteins and the duplicated Hox gene clusters are signatures of ancient polyploidization, not derived massive events of unequal crossing over or polymerase slippage. Allopolyploidy and ancient gene transfers among the three domains of life generate such a variation that mutation rates based on common descend loose preponderance and the notion of tree of life gets suffocated in an entangled genomic bush. In short, we contend that duplications constitute the resulting outcome; not the source phenomenon that explains protein´s evolutionary complexity and macro phenotypic innovations. Metonymy should be avoided every time that allopolyploidization, not its consequential pattern of genome duplication, is causal of phenotypic variation leading to macroevolutionary innovations.

Cancer, Cytologism and the Kinase Inhibitors Saga

2024-06-13T16:37:25+00:00

The role of kinases in the cell cycle of unicellular eukaryotes and cells of multicellular organisms has been the object of numerous studies involving normal and cancer cells. These studies described in detail how two daughter cells are generated from a single normal or cancer mother cell. Among the thousands of participants in the cell cycle, kinases play a crucial role in the dynamic aspects of the cell cycle thanks to the phosphorylation of substrates with which they react. Inhibitors of these kinases have figured prominently among the strategies to treat cancers. However, evidence shows that the benefits that cancer patients accrued from this therapeutic approach have been of a limited degree. In this article, we review the rationale for adopting such a strategy and the factors that contribute to its shortcomings.

The Role of Biological Plasticity in Model-based Translational Research

2024-06-13T14:49:19+00:00

Reports of low replicability and translatability of biomedical research have called the value of animal models into question. The problems are real, but abandoning animal research is not the solution. Rather, improving the translatability of model-based research requires attention to relevant differences between humans and models, and to attributes of the models themselves that are essential to both robust science and effective translation. One is biological plasticity, the responsiveness of individual organisms to complex and variable environments. Though under-represented in model systems (for both historical and practical reasons), plasticity is central to human biology. While there are good reasons to minimize environmentally-induced variation in model-based research, doing so may undermine its translatability by eliding the kinds of external influences that are critical to human development, health, and disease. Accounting for plasticity can strengthen both the replicability and the translatability of model-based studies; this paper identifies strategies for doing so at each stage of the research process.

Science Across the Abyss: Knitting Bridges with Butterflies

2024-06-13T16:16:21+00:00

Science is built on the pursuit of answers to fundamental questions and the constant expansion of our understanding of the world around us. However, this effort has not been without challenges and inequalities. This article critically examines the issue of diversity in science and the notable disparities that persist in global scientific knowledge. Throughout history, the contributions of scientists from diverse regions and cultures have been pivotal to scientific advancement. Nevertheless, significant gaps in terms of access, funding, and recognition in the global scientific community still endure. We use the concept of the "abyss," as a metaphor for the disparities in scientific practices across diverse regions of the world within the context of globalization. We seek to shed light on how the abyss influences the very essence of scientific inquiry, ranging from disparities in access to knowledge to the limitations imposed by technology and resources. This article addresses how socioeconomic, gender, and geographical disparities impact who has the opportunity to engage in and lead scientific research. The decolonization of science and the incorporation of indigenous and local perspectives in research are highlighted as crucial ways to address these disparities. Additionally, the concept of participative science is explored as an inclusive approach that allows diverse communities to take part in scientific research. Ultimately, this exploration of diversity in science and disparities in scientific knowledge seeks to inspire deeper reflection on how we can work together to ensure that science becomes a truly global and representative endeavor, enriched by a multitude of perspectives and the collaboration of people from all corners of the world.

Organicist Perspectives in Newly Published Biology Textbooks

2024-06-13T15:36:47+00:00

Review of Bernd Rosslenbroich (2023). Propertiesof Life: Toward a Theory of Organismic Biology. Vienna Series in Theoretical Biology. Boston: The MIT Press.