1
|
Konsman JP. Expanding the notion of mechanism to further understanding of biopsychosocial disorders? Depression and medically-unexplained pain as cases in point. STUDIES IN HISTORY AND PHILOSOPHY OF SCIENCE 2024; 103:123-136. [PMID: 38157672 DOI: 10.1016/j.shpsa.2023.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 11/24/2023] [Accepted: 12/16/2023] [Indexed: 01/03/2024]
Abstract
Evidence-Based Medicine has little consideration for mechanisms and philosophers of science and medicine have recently made pleas to increase the place of mechanisms in the medical evidence hierarchy. However, in this debate the notions of mechanisms seem to be limited to 'mechanistic processes' and 'complex-systems mechanisms,' understood as 'componential causal systems'. I believe that this will not do full justice to how mechanisms are used in biological, psychological and social sciences and, consequently, in a more biopsychosocial approach to medicine. Here, I propose, following (Kuorikoski, 2009), to pay more attention to 'abstract forms of interaction' mechanisms. The present work scrutinized review articles on depression and medically unexplained pain, which are considered to be of multifactorial pathogenesis, for their use of mechanisms. In review articles on these disorders there seemed to be a range of uses between more 'abstract forms of interaction' and 'componential causal system' mechanisms. I therefore propose to expand the notions of mechanisms considered in medicine to include that of more 'abstract forms of interaction' to better explain and manage biopsychosocial disorders.
Collapse
Affiliation(s)
- Jan Pieter Konsman
- ImmunoConcEpT, CNRS UMR 5164, University of Bordeaux, 33076, Bordeaux, France.
| |
Collapse
|
2
|
Jiao F, Guo R, Beckmann JS, Yan Z, Yang Y, Hu J, Wang X, Xie S. Great future or greedy venture: Precision medicine needs philosophy. Health Sci Rep 2021; 4:e376. [PMID: 34541334 PMCID: PMC8439431 DOI: 10.1002/hsr2.376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 08/06/2021] [Accepted: 08/16/2021] [Indexed: 11/07/2022] Open
Abstract
INTRODUCTION Over the past decade, we have witnessed the initiation and implementation of precision medicine (PM), a discipline that promises to individualize and personalize medical management and treatment, rendering them ultimately more precise and effective. Despite of the continuing advances and numerous clinical applications, the potential of PM remains highly controversial, sparking heated debates about its future. METHOD The present article reviews the philosophical issues and practical challenges that are critical to the feasibility and implementation of PM. OUTCOME The explanation and argument about the relations between PM and computability, uncertainty as well as complexity, show that key foundational assumptions of PM might not be fully validated. CONCLUSION The present analysis suggests that our current understanding of PM is probably oversimplified and too superficial. More efforts are needed to realize the hope that PM has elicited, rather than make the term just as a hype.
Collapse
Affiliation(s)
- Fei Jiao
- Department of Biochemistry and Molecular BiologyBinzhou Medical UniversityYantaiChina
| | - Ruoyu Guo
- Department of Biochemistry and Molecular BiologyBinzhou Medical UniversityYantaiChina
| | | | - Zhonghai Yan
- Department of Medicine, College of Physicians and SurgeonsColumbia UniversityNew YorkNew YorkUSA
| | - Yun Yang
- Department of Biochemistry and Molecular BiologyBinzhou Medical UniversityYantaiChina
| | - Jinxia Hu
- Department of Biochemistry and Molecular BiologyBinzhou Medical UniversityYantaiChina
| | - Xin Wang
- Department of Clinical Laboratory & Center of Health Service Training970 Hospital of the PLA Joint Logistic Support ForceYantaiChina
| | - Shuyang Xie
- Department of Biochemistry and Molecular BiologyBinzhou Medical UniversityYantaiChina
| |
Collapse
|
3
|
Global quantitative biology can illuminate ontological connections between diseases. QUANTITATIVE BIOLOGY 2017. [DOI: 10.1007/s40484-017-0104-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
4
|
From Systems to Organisations. SYSTEMS 2017. [DOI: 10.3390/systems5010023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
5
|
|
6
|
Brigandt I. Systems biology and the integration of mechanistic explanation and mathematical explanation. STUDIES IN HISTORY AND PHILOSOPHY OF BIOLOGICAL AND BIOMEDICAL SCIENCES 2013; 44:477-492. [PMID: 23863399 DOI: 10.1016/j.shpsc.2013.06.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Revised: 06/12/2013] [Accepted: 06/14/2013] [Indexed: 06/02/2023]
Abstract
The paper discusses how systems biology is working toward complex accounts that integrate explanation in terms of mechanisms and explanation by mathematical models-which some philosophers have viewed as rival models of explanation. Systems biology is an integrative approach, and it strongly relies on mathematical modeling. Philosophical accounts of mechanisms capture integrative in the sense of multilevel and multifield explanations, yet accounts of mechanistic explanation (as the analysis of a whole in terms of its structural parts and their qualitative interactions) have failed to address how a mathematical model could contribute to such explanations. I discuss how mathematical equations can be explanatorily relevant. Several cases from systems biology are discussed to illustrate the interplay between mechanistic research and mathematical modeling, and I point to questions about qualitative phenomena (rather than the explanation of quantitative details), where quantitative models are still indispensable to the explanation. Systems biology shows that a broader philosophical conception of mechanisms is needed, which takes into account functional-dynamical aspects, interaction in complex networks with feedback loops, system-wide functional properties such as distributed functionality and robustness, and a mechanism's ability to respond to perturbations (beyond its actual operation). I offer general conclusions for philosophical accounts of explanation.
Collapse
Affiliation(s)
- Ingo Brigandt
- Department of Philosophy, University of Alberta, 2-40 Assiniboia Hall, Edmonton, AB T6G2E7, Canada.
| |
Collapse
|
7
|
van Heeswijk WC, Westerhoff HV, Boogerd FC. Nitrogen assimilation in Escherichia coli: putting molecular data into a systems perspective. Microbiol Mol Biol Rev 2013; 77:628-95. [PMID: 24296575 PMCID: PMC3973380 DOI: 10.1128/mmbr.00025-13] [Citation(s) in RCA: 159] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
We present a comprehensive overview of the hierarchical network of intracellular processes revolving around central nitrogen metabolism in Escherichia coli. The hierarchy intertwines transport, metabolism, signaling leading to posttranslational modification, and transcription. The protein components of the network include an ammonium transporter (AmtB), a glutamine transporter (GlnHPQ), two ammonium assimilation pathways (glutamine synthetase [GS]-glutamate synthase [glutamine 2-oxoglutarate amidotransferase {GOGAT}] and glutamate dehydrogenase [GDH]), the two bifunctional enzymes adenylyl transferase/adenylyl-removing enzyme (ATase) and uridylyl transferase/uridylyl-removing enzyme (UTase), the two trimeric signal transduction proteins (GlnB and GlnK), the two-component regulatory system composed of the histidine protein kinase nitrogen regulator II (NRII) and the response nitrogen regulator I (NRI), three global transcriptional regulators called nitrogen assimilation control (Nac) protein, leucine-responsive regulatory protein (Lrp), and cyclic AMP (cAMP) receptor protein (Crp), the glutaminases, and the nitrogen-phosphotransferase system. First, the structural and molecular knowledge on these proteins is reviewed. Thereafter, the activities of the components as they engage together in transport, metabolism, signal transduction, and transcription and their regulation are discussed. Next, old and new molecular data and physiological data are put into a common perspective on integral cellular functioning, especially with the aim of resolving counterintuitive or paradoxical processes featured in nitrogen assimilation. Finally, we articulate what still remains to be discovered and what general lessons can be learned from the vast amounts of data that are available now.
Collapse
|
8
|
Melham T. Modelling, abstraction, and computation in systems biology: A view from computer science. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2013; 111:129-36. [DOI: 10.1016/j.pbiomolbio.2012.08.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2012] [Accepted: 08/21/2012] [Indexed: 01/14/2023]
|
9
|
Mazzocchi F. Complexity and the reductionism-holism debate in systems biology. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2012; 4:413-27. [PMID: 22761024 DOI: 10.1002/wsbm.1181] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Reductionism has largely influenced the development of science, culminating in its application to molecular biology. An increasing number of novel research findings have, however, shattered this view, showing how the molecular-reductionist approach cannot entirely handle the complexity of biological systems. Within this framework, the advent of systems biology as a new and more integrative field of research is described, along with the form which has taken on the debate of reductionism versus holism. Such an issue occupies a central position in systems biology, and nonetheless it is not always clearly delineated. This partly occurs because different dimensions (ontological, epistemological, methodological) are involved, and yet the concerned ones often remain unspecified. Besides, within systems biology different streams can be distinguished depending on the degree of commitment to embrace genuine systemic principles. Some useful insights into the future development of this discipline might be gained from the tradition of complexity and self-organization. This is especially true with regards the idea of self-reference, which incorporated into the organizational scheme is able to generate autonomy as an emergent property of the biological whole.
Collapse
|
10
|
Pernu TK. Minding matter: how not to argue for the causal efficacy of the mental. Rev Neurosci 2012; 22:483-507. [PMID: 21967516 DOI: 10.1515/rns.2011.043] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The most fundamental issue of the neurosciences is the question of how or whether the mind and the body can interact with each other. It has recently been suggested in several studies that current neuroimaging evidence supports a view where the mind can have a well-documented causal influence on various brain processes. These arguments are critically analyzed here. First, the metaphysical commitments of the current neurosciences are reviewed. According to both the philosophical and neuroscientific received views, mental states are necessarily neurally based. It is argued that this leaves no room for a genuine interaction of the mental and the neural. Second, it is shown how conclusions drawn from recent imaging studies are in fact compatible with the fully physicalistic notion of mental causation and how they can thus be easily accommodated to the received view. The fallacious conclusions are argued to be a result of an overly vague grasping of the conceptual issues involved. The question of whether the fundamental physical principles exclude outright the ability of mental states to have causal influence on the physical world is also addressed and the reaction of appealing to the apparent loophole provided by quantum physics is assessed. It is argued that linking psychology to quantum physics contradicts many basic tenets of the current neurosciences and is thus not a promising line of study. It is concluded that the interactionist hypothesis benefits from neither conceptual nor empirical support.
Collapse
Affiliation(s)
- Tuomas K Pernu
- Department of Biosciences, Physiology and Neuroscience, University of Helsinki, P.O. Box 65, FI-00014 University of Helsinki, Finland.
| |
Collapse
|
11
|
Groeneveld P, Stouthamer AH, Westerhoff HV. Super life--how and why 'cell selection' leads to the fastest-growing eukaryote. FEBS J 2009; 276:254-70. [PMID: 19087200 DOI: 10.1111/j.1742-4658.2008.06778.x] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
What is the highest possible replication rate for living organisms? The cellular growth rate is controlled by a variety of processes. Therefore, it is unclear which metabolic process or group of processes should be activated to increase growth rate. An organism that is already growing fast may already have optimized through evolution all processes that could be optimized readily, but may be confronted with a more generic limitation. Here we introduce a method called 'cell selection' to select for highest growth rate, and show how such a cellular site of 'growth control' was identified. By applying pH-auxostat cultivation to the already fast-growing yeast Kluyveromyces marxianus for a sufficiently long time, we selected a strain with a 30% increased growth rate; its cell-cycle time decreased to 52 min, much below that reported to date for any eukaryote. The increase in growth rate was accompanied by a 40% increase in cell surface at a fairly constant cell volume. We show how the increase in growth rate can be explained by a dominant (80%) limitation of growth by the group of membrane processes (a 0.7% increase of specific growth rate to a 1% increase in membrane surface area). Simultaneous activation of membrane processes may be what is required to accelerate growth of the fastest-growing form of eukaryotic life to growth rates that are even faster, and may be of potential interest for single-cell protein production in industrial 'White' biotechnology processes.
Collapse
Affiliation(s)
- Philip Groeneveld
- Department of Molecular Cell Physiology & Mathematical Biochemistry, Netherlands Institute for Systems Biology, Vrije Universiteit, Amsterdam, The Netherlands
| | | | | |
Collapse
|
12
|
Abstract
The developments in the molecular biosciences have made possible a shift to combined molecular and system-level approaches to biological research under the name of Systems Biology. It integrates many types of molecular knowledge, which can best be achieved by the synergistic use of models and experimental data. Many different types of modeling approaches are useful depending on the amount and quality of the molecular data available and the purpose of the model. Analysis of such models and the structure of molecular networks have led to the discovery of principles of cell functioning overarching single species. Two main approaches of systems biology can be distinguished. Top-down systems biology is a method to characterize cells using system-wide data originating from the Omics in combination with modeling. Those models are often phenomenological but serve to discover new insights into the molecular network under study. Bottom-up systems biology does not start with data but with a detailed model of a molecular network on the basis of its molecular properties. In this approach, molecular networks can be quantitatively studied leading to predictive models that can be applied in drug design and optimization of product formation in bioengineering. In this chapter we introduce analysis of molecular network by use of models, the two approaches to systems biology, and we shall discuss a number of examples of recent successes in systems biology.
Collapse
Affiliation(s)
- Frank J Bruggeman
- Molecular Cell Physiology, Institute for Molecular Cell Biology, BioCentrum Amsterdam, Faculty of Earth and Life Sciences, Vrije Universiteit, De Boelelaan 1085, NL-1081 HIV Amsterdam, The Netherlands.
| | | | | | | |
Collapse
|
13
|
Cadenasso M, Pickett S, Grove J. Dimensions of ecosystem complexity: Heterogeneity, connectivity, and history. ECOLOGICAL COMPLEXITY 2006. [DOI: 10.1016/j.ecocom.2005.07.002] [Citation(s) in RCA: 163] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
14
|
Callebaut W. Again, what the philosophy of biology is not. Acta Biotheor 2005; 53:93-122. [PMID: 16049731 DOI: 10.1007/s10441-005-5352-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2004] [Accepted: 03/21/2005] [Indexed: 10/25/2022]
Abstract
There are many things that philosophy of biology might be. But, given the existence of a professional philosophy of biology that is arguably a progressive research program and, as such, unrivaled, it makes sense to define philosophy of biology more narrowly than the totality of intersecting concerns biologists and philosophers (let alone other scholars) might have. The reasons for the success of the "new" philosophy of biology remain poorly understood. I reflect on what Dutch and Flemish, and, more generally, European philosophers of biology could do to improve the situation of their discipline locally, regionally, and internationally, paying particular attention to the lessons to be learned from the "Science Wars."
Collapse
Affiliation(s)
- Werner Callebaut
- Faculty of Sciences, Limburgs Universitair Centrum, Diepenbeek, Belgium.
| |
Collapse
|
15
|
|
16
|
Boogerd F, Bruggeman F, Jonker C, de Jong HL, Tamminga A, Treur J, Westerhoff H, Wijngaards W. Inter-level relations in computer science, biology, and psychology. PHILOSOPHICAL PSYCHOLOGY 2002. [DOI: 10.1080/0951508021000042012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|