Organisms. Journal of Biological Sciences

Single-cell Molecular Analysis: When an Experimental Technique Generates Conceptual Controversies

Andras Paldi, Laëtitia Racine — Tue, 14 Nov 2023 00:00:00 +0000

The last decade has witnessed a rapid evolution of highly sensitive single-cell molecular analysis techniques. These techniques allow the simultaneous detection and quantification of mRNA and protein molecules in a large number of individual cells. Some of these methods are already commercialized, making them readily available to any interested lab. While the pitfalls concerning the experimental extraction of biocomponents (mRNA and protein) and analytical bioinformatic methods are widely discussed in the literature, little is known regarding the conceptual difficulties raised by single-cell methodologies. Considered and treated as pure technical difficulties, these issues are rarely discussed explicitly. This is a problem as conceptual difficulties precede technical ones and contribute, to a large extent, to the failure of techniques. Consequently, a new theoretical framework is urgently needed to make sense of the ever-increasing amount of data.

Do Single-cell Experiments Challenge the Concept of Cell Type?

Fridolin Gross — Tue, 14 Nov 2023 00:00:00 +0000

Recent debates among biologists have highlighted problems with the traditional concept of cell type, which is considered vague and subjective. Single-cell technologies reveal the limitations of the current concept by exposing a high degree of heterogeneity in cell populations. At the same time, some biologists believe that these technologies provide the basis for a more objective and precise concept of cell type that is not dependent on prior theoretical assumptions. In this paper, I explore the impact that single-cell experiments and analyses will have on the concept of cell type. Drawing on the practices of biologists using these methods, but also on more principled arguments, I argue that the idea of a purely theory-free classification is unlikely to be realized. However, single-cell technology may affect the concept of cell type in more subtle ways.

The Contrasting Role of Single-cell Studies in the Theoretical Debate on Determinism in Molecular Biology

Thomas Heams — Tue, 14 Nov 2023 00:00:00 +0000

In experimental biology, the last three decades have seen a flood of techniques dedicated to study biological phenomena at the single-cell level, and this article aims to reflect on how these technical advances can contribute to the renewal of theoretical perspectives in biology. The case studied here is that of the critique of the genetic determinism of molecular biology. The demonstration of unpredictability in gene expression at the single-cell level, a phenomenon known as stochastic gene expression, even in clonal populations, initially appeared to be a decisive indication that cells do not actually behave as predicted by deterministic frameworks. However, single-cell techniques have also revealed other sources of genetic variation that nuance this picture. The role of single-cell studies thus appears contrasted, and can be used to support or challenge the paradigm of genetic determinism (GDP). This opens up a more general debate on the practical ability of molecular biologists to criticize their own paradigms.

The Common Origin of Multicellularity and Cancer: Lessons from the Fossil Record

Daniela Montagna, Raúl Ruggiero — Tue, 14 Nov 2023 00:00:00 +0000

Despite the methodological limitations in the study of fossil record and some confusion in the literature about the diagnostic distinction between real neoplasia and other types of proliferation or even malformations in species very distant from mammals, paleopathological studies have revealed many cases of bona fide benign as well as malignant neoplasms in animals and land plants since Paleozoic Era onwards. Further, almost all types of modern neoplastic diseases have been documented in ancient Homo sapiens bone remains. It is worth to note that, despite the major changes in the structure of animal populations, the prevalence of malignant as well benign neoplasms has remained relatively constant (and in some cases it has even increased), among the different taxa of animals for hundred million years suggesting that malignancies as well as benign neoplasms are rooted quite deeply in the evolutionary life of organisms. This seemingly unremarkably fact represents a remarkable riddle for evolutionary biologists. If natural selection, working on living organisms has been powerful enough to produce complex adaptations, from the eye to the immune system, why has it been unable to eliminate or even reduce the incidence of cancer, even though many apparently less harmful traits have been eliminated during species evolution. Based on the fact that, both today and in the fossil record, cancer seems to occur in organs that have experienced a decline or loss of their regenerative ability we suggested that it may be an ultimate, even futile, reparative attempt. Therefore, the permanence of cancer by hundred million years might be understood if its existence is coupled to the normal regenerative mechanisms of the organisms without which no pluricellular organism could survive. This interpretation, encoded in the so-called hypothesis of the biological sense of cancer, was built within the broad framework of tissue organization field theory (TOFT) by assuming that cancer is primarily a disease of higher levels of organization, that is, an organismic, organ or tissue-based disease rather than a cellular one.

New Genetically Modified Organisms (GMOs): Towards a “scientific precautionary principle”

Giuseppe Longo — Tue, 14 Nov 2023 00:00:00 +0000

To the ordinary precautionary principle, we should add a more precise “scientific precautionary principle”. In short, we cannot act on nature based on ‘dogmas’ that are either manifestly false or are implicitly adopting an uncritical way of thinking. Science is the invention of a new way of thinking, of new theoretical frameworks, starting from a critical review of the principles mobilized, which are themselves well explained. Without this, technoscience, in all its power, becomes a nightmare, as it is totally unsuited to make us live in an ecosystem with all its complexity. The case of New Genetic Technologies, whose application to agriculture is under discussion in Europe, is paradigmatic and urgent.

*A preliminary version of this paper was published in French in Philosophy World Democracy, 1/9/23, www.philosophy-world-democracy.org/articles-1/les-nouveaux-organismes-genetiquement-modifies-ogm-pour-un-principe-de-precaution-scientifique.

Celebrating Evelyn Fox Keller: “The Toronto Statement"

Tue, 14 Nov 2023 00:00:00 +0000

With much anticipation, in time and spirit, a group of historians and philosophers of biology, and theoretical and experimental biologists, met at the Institute for the History and Philosophy of Science and Technology at the University of Toronto, Canada, on 22 and 23 September 2023, to pay homage to Evelyn Fox Keller for her contributions to theoretical biology. The conference was supported and sponsored by the Department of Philosophy, Institute for the History and Philosophy of Science and Technology, Faculty of Arts and Science (all at University of Toronto), as well as the Social Sciences and Humanities Research Council of Canada. The workshop was an in-person celebration complementing the publication of a volume celebrating her work (Vicedo & Walsh 2020a, 2020b), which includes the following contributions: (Herrington & Jablonka 2020; Longo & Mossio 2020; Radick 2020; Riskin 2020; Soto & Sonnenschein 2020; Walsh 2020). After introductory remarks by Denis Walsh and a short video in which Evelyn Fox Keller thanked us for this homage and wished us well, we learned of her death.

Process-philosophical Perspectives on Biology: Intuiting Life (Edited by Spyridon A. Koutroufinis and Arthur Araujo)—Philosophical Intuitions for a New Understanding of Life

Mariano Bizzarri — Tue, 14 Nov 2023 00:00:00 +0000

Book review

Special Issue, “Single-cell Analysis: Epistemological Inquiries”

Caroline Angleraux, Matteo Mossio — Tue, 14 Nov 2023 00:00:00 +0000

Editorial