The emergence of the postgenomic gene

The identity and the existence of genes has been challenged by postgenomic discoveries. Specifically, the consideration of molecular and cellular phenomena in which genes are embedded has proved relevant for their understanding. In response to these challenges, I will argue that the complexity of genetic phenomena supports the weak emergence of genes from the DNA. In Section 2, I will expose what genes are taken to be in the postgenomic world. In Section 3, I will present the relevant account of emergence. I consider weak emergence as in Franklin and Knox (Studies for the History and Philosophy of Modern Physics, 64, 68–78, 2018), for which a phenomenon is emergent when it displays novelty and robustness. In Section 4, I will argue that genes are weakly emergent since they are novel, improving explanations, and robust in respect to some perturbations. Then, I will conclude in Section 5 that genes’ emergence is a way to allow genes’ flexibility and context dependency, without compromising their existence

Biochemical Kinds and the Unity of Science

The present thesis explores some metaphysical issues concerning biochemical kinds and the relations between chemical and biological properties and phenomena. The main result of this thesis is that there is something sui generis about biochemical kinds. This result is motivated by two theoretical steps. The first is characterising biochemical functions as weakly emergent from the chemical structure [Chapter 3, Chapter 6]. The second is via an account for which biochemical kinds are natural categories [Chapter 4, Chapter 7]. The thesis comprises four parts. Part I [Chapter 1, Chapter 2] aims to offer the methodological and conceptual tools that underpin this research. Chapter 1 presents the debate on the unity of science and the motivation of the research. Chapter 2 presents the account of natural kinds that will be used throughout the thesis. Part II [Chapter 3, Chapter 4] offers a detailed metaphysical analysis of the molecular gene. Chapter 3 argues that molecular genes are weakly emergent from nucleic acids. Chapter 4 argues that the category "molecular gene" can be deemed a natural kind, following the account presented in Chapter 2. Part III [Chapter 5, Chapter 6, Chapter 7] explores some of the themes related to biochemical kinds and generalises some of the results from Part II. Chapter 5 considers biochemical functions and how functional attribution should be interpreted for biochemical molecules. Chapter 6 considers the relation between biochemical functions and structure, spelt in terms of weak emergence and explores unity in biochemistry. Chapter 7 considers the topic of biochemical kinds per se and argues that biochemical kinds are natural categories. Part IV [Chapter 8] elucidates the main outcome and the implications that this research can have for future discussion in the philosophy and metaphysics of biochemistry and the unity of science

The Gene as a Natural Kind

What is a gene? Does it represent a natural kind, or is it just a tool for genomics? A clear answer to these questions has been challenged by postgenomic discoveries. In response, I will argue that the gene can be deemed a natural kind as it satisfies some requirements for genuine kindhood. Specifically, natural kinds are projectible categories in our best scientific theories, and they represent nodes in the causal network of the world (as in Khalidi. Natural Categories and Human Kinds: Classification in the Natural and Social Sciences. Cambridge University Press, Cambridge, 2013; Khalidi. Synthese 195: 1379–1396, 2018; Khalidi. Are Sexes Natural Kinds, In: Dasgupta S, Weslake B (eds) Current Controversies in Philoso-phy of Science. Routledge, New York, 2020; Khalidi. Philos Sci 88:1–21, 2021). In Sect. 2, I will present a brief history of the gene and the controversy over its status. In Sect. 3, I will introduce the account of natural kinds considered in this paper. In Sect. 4, I will first present the relevant definition of genes and how they can be classified. Then, I will argue that the gene can be considered a natural kind as it satisfies the criteria for natural kindhood. Section 5 concludes

Emergence in Complex Physiological Processes: The Case of Vitamin B12 Functions in Erythropoiesis

In this paper, we will explore the relation between molecular structure and functions displayed by biochemical molecules in complex physiological processes by using tools from the philosophy of science and the philosophy of scientific practice. We will argue that biochemical functions are weakly emergent from molecular structure by using an account of weak. In order to explore this thesis, we will consider the role of vitamin B12 in contributing to the process of erythropoiesis. The structure of the paper is the following: First, we will consider biochemical functions and why they cannot be easily reduced to their chemical realisers. We will suggest weak emergence as an alternative while also accounting for the relevance of the context, in our case, systemic and organisational. The paper will conclude by considering (1) how the usage of tools from the philosophy of science, such as weak emergence, can aid our understanding of the relations between the components of complex phenomena, such as erythropoiesis, and (2) how the philosophy of scientific practice sheds light on the explanatory role of processes that are dynamically stabilised and the different levels of organisation implied

COVID-19 calls for virtue ethics

The global spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) or coronavirus disease 19 (COVID-19) has led to the imposition of severely restrictive measures by governments in the Western hemisphere. We feel a contrast between these measures and our freedom. This contrast, we argue, is a false perception. It only appears to us because we look at the issue through our contemporary moral philosophy of utilitarianism and an understanding of freedom as absence of constraints. Both these views can be substituted with more sophisticated alternatives, namely an ethics of virtue and a notion of freedom of the will. These offer a fuller picture of morality and enable us to cooperate with the current restrictions by consciously choosing to adhere to them instead of perceiving them as draconian and immoral. We ask whether we should collaborate with the restrictions and argue that considerations of virtue will lead to an affirmative answer. More broadly, virtue ethics permits to deal with the practical concerns about how an individual should behave during this pandemic, given the current lockdown measures or lack thereof. In section 1, we present how utilitarianism and a notion of freedom as negative liberty support the opposition to restrictive measures. In section 2, we outline an alternative based on an ethics of virtue and a more elaborated notion of free will. In the concluding section 3, we argue that considerations of virtue should guide the individual and public response to the emergency

A hierarchical Naïve Bayes Model for handling sample heterogeneity in classification problems: an application to tissue microarrays

BACKGROUND: Uncertainty often affects molecular biology experiments and data for different reasons. Heterogeneity of gene or protein expression within the same tumor tissue is an example of biological uncertainty which should be taken into account when molecular markers are used in decision making. Tissue Microarray (TMA) experiments allow for large scale profiling of tissue biopsies, investigating protein patterns characterizing specific disease states. TMA studies deal with multiple sampling of the same patient, and therefore with multiple measurements of same protein target, to account for possible biological heterogeneity. The aim of this paper is to provide and validate a classification model taking into consideration the uncertainty associated with measuring replicate samples. RESULTS: We propose an extension of the well-known Naïve Bayes classifier, which accounts for biological heterogeneity in a probabilistic framework, relying on Bayesian hierarchical models. The model, which can be efficiently learned from the training dataset, exploits a closed-form of classification equation, thus providing no additional computational cost with respect to the standard Naïve Bayes classifier. We validated the approach on several simulated datasets comparing its performances with the Naïve Bayes classifier. Moreover, we demonstrated that explicitly dealing with heterogeneity can improve classification accuracy on a TMA prostate cancer dataset. CONCLUSION: The proposed Hierarchical Naïve Bayes classifier can be conveniently applied in problems where within sample heterogeneity must be taken into account, such as TMA experiments and biological contexts where several measurements (replicates) are available for the same biological sample. The performance of the new approach is better than the standard Naïve Bayes model, in particular when the within sample heterogeneity is different in the different classes

Assessment of the Impact of a New Industrial Discharge on an Urban Wastewater Treatment Plant: Proposal for an Experimental Protocol

Assessing the compatibility of industrial discharges with the biological process of a municipal wastewater treatment plant (WWTP) may represent a critical task. Indeed, either focusing only on chemical characterization or ecotoxicity tests designed to assess the impact on surface waters may lead to questionable or misleading conclusions. The feasibility of an industrial connection to the sewer should better take into account the features of the downstream WWTP, in particular by studying the potential effects on the biomass of that specific plant. With this aim, a multi-step experimental protocol applicable by water utilities has been proposed: (step 1) calculation of the flow rate/load ratio between industrial discharge (ID) and urban wastewater (WW); (step 2) analysis of the modified operating conditions of the biological stage; (step 3) experimental assessment of the impact of the ID on the WWTP biomass by means of respirometric tests. An application of this protocol is presented in this work as a case study, namely a new ID (average flowrate 200 m3 d−1) coming from an aqueous waste treatment plant (AWTP) to be connected to the public sewer. The integrated evaluation of results showed that no negative impacts could be expected on the downstream urban activated sludge WWTP (treating a flow rate of around 45,000 m3 d−1)