The new mechanistic philosophy is divided into two largely disconnected projects. One deals with a metaphysical inquiry into how mechanisms relate to issues such as causation, capacities and levels of organization, while the other deals with epistemic issues related to the discovery of mechanisms and the intelligibility of mechanistic representations. Tudor Baetu explores and explains these projects, and shows how the gap between them can be bridged. His proposed account is compatible both with the assumptions and practices of experimental (...) design in biological research, and with scientifically accepted interpretations of experimental results. (shrink)

This paper investigates the Generalized Traveling Salesman Problem (GTSP), which is an extension of the well-known Traveling Salesman Problem (TSP), and it searches for an optimal tour in a clustered graph, such that every cluster is visited exactly once. In this paper, we describe a novel Memetic Algorithm (MA) for solving efficiently the GTSP. Our proposed MA has at its core a genetic algorithm (GA), completed by a Chromosome Enhancement Procedure (CEP), which is based on a TSP solver and the (...) Shortest Path (SP) algorithm and for improving the convergence characteristics of the GA, a Local Search (LS) operation is applied for the best chromosomes in each generation. We tested our algorithm on a set of well-known instances from the literature and the achieved results prove that our novel memetic algorithm is highly competitive against the existing solution approaches from the specialized literature. (shrink)

The frequency of cyberattacks has been rapidly increasing in recent times, which is a significant concern. These attacks exploit vulnerabilities present in the software components that constitute the targeted system. Consequently, the number of vulnerabilities within these software components serves as an indicator of the system’s level of security and trustworthiness. This paper compares the accuracy, trainability and stability to configuration parameters of several neural network architectures, namely Long Short-Term Memory, Multilayer Perceptron and Convolutional Neural Network. These architectures are utilized (...) for forecasting the number of software vulnerabilities within a specified timeframe for a specific software product. By evaluating these neural network models, our aim is to provide insights into their performance and effectiveness in vulnerability forecasting. (shrink)

The Fukushima nuclear accident from 2011 provided an occasion for the public display of radiation maps generated using decision-support systems for nuclear emergency management. Such systems rely on computer models for simulating the atmospheric dispersion of radioactive materials and estimating potential doses in the event of a radioactive release from a nuclear reactor. In Germany, as in Japan, such systems are part of the national emergency response apparatus and, in case of accidents, they can be used by emergency task forces (...) for planning radioprotection countermeasures. In this context, the paper addresses the epistemology of dose projections by critically analyzing some of the sources of epistemic opacity and non-knowledge affecting them, and the different methods and practices used by German radioprotection experts to improve their trustworthiness and reliability. It will be argued that dose projections are part of an entire radioprotection regime or assemblage built around the belief that the effects of nuclear accidents can be effectively mitigated thanks to the simulation technologies underlying different protocols and practices of nuclear preparedness. And, as the Fukushima experience showed, some of these expectations will not be met in real emergencies due to the inherent uncertainties entailed by the use of dose projections when planning protective countermeasures. (shrink)

University life is colourful, filled with a plethora of memorable moments both academic and non-academic. During the COVID-19 pandemic, however, first-year university students’ academic experiences may have differed from their expectations due to being conducted fully online. The COVID-19 pandemic denied first-year students the opportunity to join in-person classes and become involved in university activities in a physical setting. All activities were moved to virtual settings, and students could only contact their classsmates and lecturers via social media platforms. This derailment (...) of expectations may dampen students’ enthusiasm and impact their levels of motivation and happiness. To explore this phenomenon, a study was conducted with 143 first-year psychology students to examine their self-reported motivational and happiness levels before and after seven weeks of online classes. This study included 113 females and 30 males with a mean age of 20.68. Data collected revealed that students’ motivation and happiness levels declined significantly after their online classes. Based on the level of agreement with one item—‘Overall, I am happy with my university life’—48 students agreed, 76 were neutral, and 19 indicated dissatisfaction. This study may assist the university and relevant authorities in understanding students’ perceptions of dealing with academic and life challenges while learning online during the COVID-19 pandemic. Therefore, psychological strategies should be considered to enhance first-year students’ motivation and happiness levels when faced with online classes in their new first semester. (shrink)

In this paper we investigate a particular two-stage supply chain network design problem with fixed costs. In order to solve this complex optimization problem, we propose an efficient hybrid algorithm, which was obtained by incorporating a linear programming optimization problem within the framework of a genetic algorithm. In addition, we integrated within our proposed algorithm a powerful local search procedure able to perform a fine tuning of the global search. We evaluate our proposed solution approach on a set of large (...) size instances. The achieved computational results prove the efficiency of our hybrid genetic algorithm in providing high-quality solutions within reasonable running-times and its superiority against other existing methods from the literature. (shrink)

But to explain. Dissipation inspires the wrath of the moralist and the envy of most others; for the physicist, however, it is merely faintly depressing. We call something dissipative if it looses energy to waste-heat. (Technically: if volume in the phase space is not conserved.) The famous Second Law of Thermodynamics amounts to saying that, if something is isolated from the rest of the world, it will dissipate all the free energy it has. Equivalently, it maximizes its entropy. Thermal equilibrium (...) is the state of maximum entropy. (shrink)

The paper discusses methodological guidelines for evaluating mechanistic explanations. According to current accounts, a satisfactory mechanistic explanation should include all of the relevant features of the mechanism, its component entities and activities, and their properties and organization, as well as exhibit productive continuity. It is not specified, however, how this kind of mechanistic completeness can be demonstrated. I argue that parameter sufficiency inferences based on mathematical model simulations provide a way of determining whether a mechanism capable of producing the phenomenon (...) of interest can be constructed from mechanistic components organized, acting, and having the properties described in the mechanistic explanation. (shrink)

An important strategy in the discovery of biological mechanisms involves the piecing together of experimental results from interventions. However, if mechanisms are investigated by means of ideal interventions, as defined by James Woodward and others, then the kind of information revealed is insufficient to discriminate between modular and non-modular causal contributions. Ideal interventions suffice for constructing webs of causal dependencies that can be used to make some predictions about experimental outcomes, but tell us little about how causally relevant factors are (...) organized together and how they interact with each other in order to produce a phenomenon. I argue that lab research relies on more elaborated types of interventions targeting in a controlled fashion multiple variables at the same time in order to probe the temporal organization of causally-relevant factors along distinct causal pathways and to test for non-modular interaction effects, thus providing crucial spatial-temporal constraints guiding the formulation of more detailed mechanistic explanations. (shrink)

David Chalmers advocates the view that the phenomenon of consciousness is fundamentally different from all other phenomena studied in the life sciences, positing a uniquely hard problem that precludes the possibility of a mechanistic explanation. In this paper, I evaluate three demarcation criteria for dividing phenomena into hard and easy problems: functional definability, the puzzle of the accompanying phenomenon, and the first-person data of subjective experience. I argue that none of the proposed criteria can accurately discriminate between the phenomenon of (...) consciousness and mechanistically explainable phenomena. (shrink)

Hierarchical structures are rapidly and flexibly built up in the domains of human language and music. These domains require a tree-building capacity – “dendrophilia” – to dynamically infer hierarchical structures from sensory input, based on subunits stored in a lexicon. This dynamic process involves a crucial class of abstracta overlooked in the target article.

Savage et al. make a compelling case, Mehr et al. less so, for social bonding and credible signalling, respectively, as the main adaptive function of human musicality. We express general advocacy for the former thesis, highlighting: overlap between the two; direct versus derived biological functions, and aspects of music embedded in cultural evolution, for example, departures from tonality.

Istoria ideii de geniu.--Simbolul artistic.--Tezele unei filozofii a operei.

The article analyses in detail the Meselson–Stahl experiment, identifying two novel difficulties for the crucial experiment account, namely, the fragility of the experimental results and the fact that the hypotheses under scrutiny were not mutually exclusive. The crucial experiment account is rejected in favour of an experimental-mechanistic account of the historical significance of the experiment, emphasizing that the experiment generated data about the biochemistry of DNA replication that is independent of the testing of the semi-conservative, conservative, and dispersive hypotheses. _1_ (...) Introduction _2_ The Meselson–Stahl Experiment _3_ Some Difficulties for the Crucial Experiment Account _3.1_ Additional experiments were required _3.2_ Simplicity considerations are unconvincing _3.3_ The fragility of the experimental results _3.4_ The problematic interpretation of falsifyng results _3.5_ Not all possible hypotheses considered or tested _3.6_ The tested hypotheses were not mutually exclusive _4_ The Historical and Scientific Significance of the Meselson–Stahl Experiment _4.1_ The challenge for the crucial experiment account _4.2_ A mechanistic perspective on the experiment _4.3_ The experimental design and its independence from theoretical speculations _4.4_ The advantages of a ‘bottom-up’ mechanistic account _5_ Conclusion. (shrink)

Both clinical research and basic science rely on the epistemic practice of extrapolation from surrogate models, to the point that explanatory accounts presented in review papers and biology textbooks are in fact composite pictures reconstituted from data gathered in a variety of distinct experimental setups. This raises two new challenges to previously proposed mechanistic-similarity solutions to the problem of extrapolation: one pertaining to the absence of mechanistic knowledge in the early stages of research and the second to the large number (...) of extrapolations underpinning explanatory accounts. An analysis of the strategies deployed in experimental research supports the conclusion that while results from validated surrogate models are treated as a legitimate line of evidence supporting claims about target systems, the overall structure of research projects also demonstrates that extrapolative inferences are not considered definitive or sufficient evidence, but only partially justified hypotheses subjected to further testing. 1 Introduction2 Surrogate Models2.1 What exactly is a surrogate model?2.2 Why use surrogate models?3 Prior Validation of Surrogate Models3.1 The validation and ranking of surrogate models in the early stages of basic research3.2 The validation of surrogate models in later stages of basic research and in clinical research4 ‘Big Picture’ Accounts and the Extrapolations Underpinning Them4.1 The mosaic nature of mechanistic descriptions in basic science4.2 Challenges for mechanistic-similarity-based validation protocols5 Retrospective Testing of Extrapolated Knowledge5.1 Holistic confirmation5.2 Fallback strategies6 Conclusions. (shrink)

Current debates surrounding the virtues and shortcomings of randomization are symptomatic of a lack of appreciation of the fact that causation can be inferred by two distinct inference methods, each requiring its own, specific experimental design. There is a non-statistical type of inference associated with controlled experiments in basic biomedical research; and a statistical variety associated with randomized controlled trials in clinical research. I argue that the main difference between the two hinges on the satisfaction of the comparability requirement, which (...) is in turn dictated by the nature of the objects of study, namely homogeneous or heterogeneous populations of biological systems. Among other things, this entails that the objection according to which randomized experiments fail to provide better evidence for causation because randomization cannot guarantee comparability is mistaken. (shrink)

A survey of models in immunology is conducted and distinct kinds of models are characterized based on whether models are material or conceptual, the distinctiveness of their epistemic purpose, and the criteria for evaluating the goodness of a model relative to its intended purpose. I argue that the diversity of models in interdisciplinary fields such as immunology reflects the fact that information about the phenomena of interest is gathered from different sources using multiple methods of investigation. To each model is (...) attached a description specifying how information about a phenomenon of interest has been acquired, highlighting points of commonality and difference between the methodological and epistemic histories of the information encapsulated in different models. These points of commonality and difference allow investigators to integrate findings from different models into more comprehensive explanatory accounts, as well as to troubleshoot anomalies and faulty accounts by going back to the original building blocks. (shrink)

Examples from the sciences showing that mechanisms do not always succeed in producing the phenomena for which they are responsible have led some authors to conclude that the regularity requirement can be eliminated from characterizations of mechanisms. In this article, I challenge this conclusion and argue that a minimal form of regularity is inextricably embedded in examples of elucidated mechanisms that have been shown to be causally responsible for phenomena. Examples of mechanistic explanations from the sciences involve mechanisms that have (...) been shown to produce phenomena with a reproducible rate of success. By contrast, if phenomena are infrequent to the point that they amount to irreproducible observations and experimental results, they are indistinguishable from the background noise of accidental happenings. The inability to detect or measure the phenomenon of interest against the background noise of accidental correlations makes it impossible to elucidate a mechanism by experimental means, to demonstrate that a proposed mechanism actually produces the phenomenon, and ultimately to justify why a hypothetical scenario involving an irregular mechanism should be preferred over attributing irreproducible happenings to chance. (shrink)

The pore‐forming BCL‐2 family proteins are effectors of mitochondrial poration in apoptosis initiation. Two atypical effectors—BOK and truncated BID (tBID)—join the canonical effectors BAK and BAX. Gene knockout revealed developmental phenotypes in the absence the effectors, supporting their roles in vivo. During apoptosis effectors are activated and change shape from dormant monomers to dynamic oligomers that associate with and permeabilize mitochondria. BID is activated by proteolysis, BOK accumulates on inhibition of its degradation by the E3 ligase gp78, while BAK and (...) BAX undergo direct activation by BH3‐only initiators, autoactivation, and crossactivation. Except tBID, effector oligomers on the mitochondria appear as arcs and rings in super‐resolution microscopy images. The BH3‐in‐groove dimers of BAK and BAX, the tBID monomers, and uncharacterized BOK species are the putative building blocks of apoptotic pores. Effectors interact with lipids and bilayers but the mechanism of membrane poration remains elusive. I discuss effector‐mediated mitochondrial poration. (shrink)

Multidisciplinary models aggregating ‘lower-level’ biological and ‘higher-level’ psychological and social determinants of a phenomenon raise a puzzle. How is the interaction between the physical, the psychological and the social conceptualized and explained? Using biopsychosocial models of pain as an illustration, I argue that these models are in fact level-neutral compilations of empirical findings about correlated and causally relevant factors, and as such they neither assume, nor entail a conceptual or ontological stratification into levels of description, explanation or reality. If inter-level (...) causation is deemed problematic or if debates about the superiority of a particular level of description or explanation arise, these issues are fueled by considerations other than empirical findings. (shrink)

Multidisciplinary models aggregating ‘lower-level’ biological and ‘higher-level’ psychological and social determinants of a phenomenon raise a puzzle. How is the interaction between the physical, the psychological and the social conceptualized and explained? Using biopsychosocial models of pain as an illustration, I argue that these models are in fact level-neutral compilations of empirical findings about correlated and causally relevant factors, and as such they neither assume, nor entail a conceptual or ontological stratification into levels of description, explanation or reality. If inter-level (...) causation is deemed problematic or if debates about the superiority of a particular level of description or explanation arise, these issues are fueled by considerations other than empirical findings. (shrink)

Kenneth Waters and Marcel Weber argue that the joint use of distinct gene concepts and the transfer of knowledge between classical and molecular analyses in contemporary scientific practice is possible because classical and molecular concepts of the gene refer to overlapping chromosomal segments and the DNA sequences associated with these segments. However, while pointing in the direction of coreference, both authors also agree that there is a considerable divergence between the actual sequences that count as genes in classical genetics and (...) molecular biology. The thesis advanced in this paper is that the referents of classical and molecular gene concepts are coextensive to a higher degree than admitted by Waters and Weber, and therefore coreference can provide a satisfactory account of the high level of integration between classical genetics and molecular biology. In particular, I argue that the functional units/cistrons identified by classical techniques overlap with functional elements entering the composition of molecular transcription units, and that the precision of this overlap can be improved by conducting further experimentation. (shrink)

The positions Ross & Spurrett (R&S) take on issues of information, causality, functionalism, and emergence are actually implicit in the theory and practice of statistical physics, specifically in the way it relates macroscopic collective coordinates to microscopic physics. The reasons for taking macroscopic physical variables like temperature or magnetization to be real apply equally to mental properties like pain.

Looking from a critical race perspective at Wittig’s lesbian, in this article, I draw two conclusions. First, I suggest that it is actually trans exclusionary lesbians' own transphobia that makes them cis-gendered. And second, it becomes clear that the politicisation of choosing and refusing gender needs to acknowledge racism’s shaping role in the construction of gender. My approach not only intervenes in transphobic feminisms that are obsessed with simplistic understandings of sexual violence, but also questions rigid cis/trans binaries and rejects (...) accounts of trans/gender that ignore the role of racialisation for the emergence of gender. The main question that I address is: how to conceptualise the complex im/possibilities of refusing and choosing in relation to gender? It is my aim to connect seemingly disparate knowledge productions on genderqueer, trans and other ‘impossible’ genders and sexualities. I am particularly interested in a phenomenon that can be described as ‘lesbian haunting’: the ambivalences one will find in tracing lesbian theory in relation to transing gender. With this, it is my attempt to rethink lesbian, queer and trans feminist approaches on violence, and to investigate the role of sexual violence within broader concepts of violence. More specifically, in order to understand both ‘gender’ and ‘transing gender’ as always already racialised, my approach builds on theories that identify ‘ungendering’ as an effect of normative racial violence (e.g. Spillers, 1987; Lewis, 2017; Snorton, 2017). (shrink)

We have created the homunculus and have seen the monstrous being. Forty days the sperm lay buried in manure and each day at noon the Master turned his magnet across it, muttering foreign words. Then, on the fortieth day he showed me the resemblance of a man, but it was transparent, without a corpus. He told me we should feed the loathsome object for exactly forty weeks, and all this time allow it to lie in its bed of manure in (...) a continual and even temperature, so that its every member might develop. This we did, much against my will. And it grew into a human child, though much smaller than any born of Woman. Now, my friends ask me to make one for them That they may be as horrified as I. I would do so for their admiration, except that I am merely the apprentice of the Master, and I am afraid. (shrink)

Recommended: Edo Airoldi, David M. Blei, Stephen E. Fienberg, Anna Goldenberg, Eric P. Xing and Alice X. Zheng (eds.), Statistical Network Analysis: Models, Issues, and New Directions [Disclaimer: contains one of my papers .] Aaron Clauset and Cristopher Moore, "Accuracy and Scaling Phenomena in Internet Mapping", cond-mat/0410059 = Physical Review Letters 94 (2005).

"Chuang Tzu" means "Master Chuang". If we are to believe traditional accounts (like those in the Records of the Historian , by Ssu-ma Ch'ian), he lived in the fourth century BC, contemporary with Plato and Aristotle. He was from a place called Meng, probably in the state of Sung, where he was "an official in the lacquer garden"; nobody knows what that means. Chuang Chou is also recorded as being a member of the Chi-Hsia academy maintained by the larger and (...) more advanced state of Ch'i, along with many of his most famous philosophical contemporaries, like Mencius and Hui Shih. And that is about it, so far as Chuang Chou goes. (shrink)

Causal pluralism can be defended not only in respect to causal concepts and methodological guidelines, but also at the finer-grained level of causal inference from a particular source of evidence for causation. An argument for this last variety of pluralism is made based on an analysis of causal inference from randomized experiments (RCTs). Here, the causal interpretation of a statistically significant association can be established via multiple paths of reasoning, each relying on different assumptions and providing distinct elements of information (...) in favour of a causal interpretation. (shrink)

This article identifies and analyses links between conceptualisations of trans-gender and trans-national, and aims for a critical redefinition of political agency. Through an examination of theories on transing, passing and performativity in queer-, trans- and transnational feminist knowledge production—illustrated by discursive examples from transgender communities and Romanian migrant communities—I call for a conceptualisation of entangled power relations that does not rely on fixed, pre-established categories, but defines subjectivity through risk in political struggle. I suggest that ‘transing’ the nation and ‘transing’ (...) gender could be thought as critical moves for a radical deconstruction of gendered and national belonging. Rather than provide a static definition of the term ‘transnationalism’, the article explores potentials and limits of going beyond ‘the national’ and ‘gender’, and intervenes in forms of minority nationalism that reproduce racism, sexism, heteronormativity and gender binary as the norm of Western national belonging. In particular, building on Jasbir Puar's (2007) conceptualisation of homonationalism, the article shows how forms of nationalism in Western transgender and migrant communities rely on a combination of heteronormative binary gendering and the exertion of racism. While a conventionalised approach to transnationalism defines the term as a political strategy based on transnational politics, I play with suggesting different dimensions of transnationalism: it could mean ‘transgender nationalism’; the ‘assimilation of transgendered persons to the Western nation’; or ‘cross-border-nationalism’, a form of nationalism often established in migrant communities that constructs the diaspora as a nationalist extension of the homeland. My focus, therefore, is on analysing privilegings, contradictions and ambivalences in gendering, racialising and nationalising ascriptions of (non)belonging. Overall, and as an alternative to romanticised knowledge productions of crossing national and gendered borders, I suggest a power-sensitive epistemological and methodological shift in thinking entangled power relations, belonging and subjectivity in transnational feminist knowledge productions. (shrink)

Human stories lie at the heart of professional practice in the human, social services, though these are often discounted when it comes to researching such services and sharing practice through publication. This article identifies and addresses certain methodological and epistemological biases and consequent challenges in human science research, and discusses the importance of story (autoethnography) and discovery (heuristics) in research which can inform practice, meaningfully and ethically. It considers this by addressing both research and publication, illustrating both the challenges and (...) the solutions from the authors’ own experiences. The article argues for reclaiming the subjective and the subjectivist dimension in human, social science, and, therefore, the experiential, in both research and publication; and addresses four problems with regard to publishing in the human sciences, namely: privilege, quality, anonymity in peer-review, and capital. (shrink)

I argue that informational models of consciousness, including those proposed by the Integrated Information Theory, don’t presuppose or entail any particular view about the physical or metaphysical nature of consciousness. Such models only tell us how certain properties of consciousness can be mathematically described, thus providing a quantitative characterization of the phenomenon of consciousness that may contribute to the development of new methods of assessment and guide the explanatory project by supplying additional constraints on theoretical proposals. While informational models are (...) in principle compatible with multiple physical interpretations, a preliminary argument in favour of the continuity between informational approaches and the mechanistic project in neuroscience can be made based on historical precedents. (shrink)

In this article, I argue that genomic programs are not substitutes for multi-causal molecular mechanistic explanations of inheritance, but abstract representations of the same sort as mechanism schemas already described in the philosophical literature. On this account, the program analogy is not reductionistic and does not ignore or underestimate the active contribution of epigenetic elements to phenotypes and development. Rather, genomic program representations specifically highlight the genomic determinants of inheritance and their organizational features at work in the wider context of (...) the mechanisms of genome expression. (shrink)

Emergent antireductionism in biological sciences states that even though all living cells and organisms are composed of molecules, molecular wholes are characterized by emergent properties that can only be understood from the perspective of cellular and organismal levels of composition. Thus, an emergence claim (molecular wholes are characterized by emergent properties) is thought to support a form of antireductionism (properties of higher-level molecular wholes can only be understood by taking into account concepts, theories and explanations dealing with higher-level entities). I (...) argue that this argument is flawed: even if molecular wholes are characterized by emergent properties and even if many successful explanations in biology are not molecular, there is no entailment between the two claims. (shrink)