. Computational chemistry grew in a new era of “desktop modeling,” which coincided with a growing demand for modeling software, especially from the pharmaceutical industry. Parameterization of models in computational chemistry is an arduous enterprise, and we argue that this activity leads, in this specific context, to tensions among scientists regarding the epistemic opacity transparency of parameterized methods and the software implementing them. We relate one flame war from the Computational Chemistry mailing List in (...) order to assess in detail the relationships between modeling methods, parameterization, software and the various forms of their enclosure or disclosure. Our claim is that parameterization issues are an important and often neglected source of epistemic opacity and that this opacity is entangled in methods and software alike. Models and software must be addressed together to understand the epistemological tensions at stake. (shrink)

Molecular models are typical topics of chemical research depending on the technical standards of observation, computation, and representation. Mathematically, molecular structures have been represented by means of graph theory, topology, differential equations, and numerical procedures. With the increasing capabilities of computer networks, computational models and computer-assisted visualization become an essential part of chemical research. Object-oriented programming languages create a virtual reality of chemical structures opening new avenues of exploration and collaboration in chemistry. From an epistemic point of view, (...) virtual reality is a new computer-assisted tool of human imagination and recognition. (shrink)

Focusing on computational studies of pericyclic reactions from the late twentieth century into the twenty-first century, this paper argues that computational diagnostics is a key methodological development that characterize the management and coordination of plural approximation methods in computational organic chemistry. Predictive divergence between semi-empirical and ab initio approximation methods in the study of pericyclic reactions has issued in epistemic dissent. This has resulted in the use of diagnostics to unpack computational greyboxes in order to (...) critically assess the effect of specific misrepresentations on predictive accuracy given that approximations and idealizations must be made to render computational models tractable. Furthermore, benchmarking is used to determine the applicability of approximation methods depending on how accurate the results need to be in a given research context. The epistemology of benchmarking consists of the co-generation of data sets in a hybrid computational–experimental form used to standardize computational methods but does not determine a unique quantitative method to be used across computational organic chemistry. (shrink)

This paper discusses how computational modeling combines the autonomy of models with the automation of computational procedures. In particular, the case of ab-initio methods in quantum chemistry will be investigated to draw two lessons from the analysis of computational modeling. The first belongs to general philosophy of science: Computational modeling faces a trade-off and enlarges predictive force at the cost of explanatory force. The other lesson is about the philosophy of chemistry: The methodology of (...) computational modeling puts into doubt claims about the reduction of chemistry to physics. (shrink)

In 1965, John A. Pope presented a paper entitled 'Two-Dimensional Chart of Quantum Chemistry' to illustrate the inverse relationship between the sophistication of computational methods and the size of molecules under study. This chart, later called the 'hyperbola of quantum chemistry', succinctly summarized the growing tension between the proponents of two different approaches to computation–the ab initio method and semiempirical method–in the early years of electronic digital computers. Examining the development of quantum chemistry after World War (...) II, I focus on the role of computers in shaping disciplinary identity. The availability of high-speed computers in the early 1950s attracted much attention from quantum chemists, and their community took shape through a series of conferences and personal networking. However, this emerging community soon encountered the problem of communication between groups that differed in the degree of reliance they placed on computers. I show the complexity of interactions between computing technology and a scientific discipline, in terms of both forming and splitting the community of quantum chemistry. (shrink)

The drastically increasing availability ofmodern computers coupled with the equally drasticallylower cost of a given amount of computer power inrecent years has resulted in the evolution of thetraditional experimental/theoretical dichotomy inchemistry into anexperimental/theoretical/computational trichotomy. This trichotomy can be schematically represented by atriangle with experimental,theoretical, and computational chemistry at the threevertices. The ET and EC edges of the ETC triangledepict the uses of theoretical and computationalchemistry, respectively, to predict and interpretexperimental results. The TC edge depicts therelationship between theoretical (...) and computationalchemistry. Mathematics plays an increasing role in allaspects of chemistry, particularly theoreticalchemistry, and has led to the evolution of thediscipline of mathematical chemistry. Research inmathematical chemistry can be considered to lie on achemistry-mathematics continuum depending on therelative depths of the underlying chemistry andmathematics. Examples of the author's own researchlying near each end of the chemistry-mathematicscontinuum include his work on applications of graphtheory and topology in inorganic coordination andcluster chemistry lying near the chemistry end and hiswork on chirality algebra lying near the mathematicsend. The general points in this essay are illustratedby an analysis of the roles of computational andtheoretical chemistry in developing an understandingof structure and bonding in deltahedral boranes andrelated carboranes. This work has allowed extensionof the concept of aromaticity from two dimensions asin benzene and other planar hydrocarbons to the thirddimension in deltahedral boranes. (shrink)

Usually within the context of computer simulations in quantum chemistry practices, there is a distinction between ab initio and semi-empirical methods. Related to this, a controversy within the scientific and philosophical communities came about regarding the superiority of the ab initio methods due to their theoretical rigor. In this article we re-evaluate the condition of the semi-empirical simulations in this area of research. We examine some of the aspects of this debate that have been considered in philosophy and provide (...) additional elements to the analysis. (shrink)

This book reflects on the significant and highly original scientific contributions of Hans Primas. A professor of chemistry at ETH Zurich from 1962 to 1995, Primas continued his research activities until his death in 2014. Over these 50 years and more, he worked on the foundations of nuclear magnetic resonance spectroscopy, contributed to a number of significant issues in theoretical chemistry, helped to clarify central topics in quantum theory and the philosophy of physics, suggested innovative ways of addressing (...) interlevel relations in the philosophy of science, and introduced cutting-edge approaches in the flourishing young field of scientific studies of consciousness. His work in these areas of research and its continuing impact is described by noted experts, colleagues, and collaborators of Primas. All authors contextualize their contributions to facilitate the mutual dialog between these fields. (shrink)

It is my pleasure to open this special issue with which we like to celebrate the fifth birthday of our journal. What was originally conceived as one special issue of HYLE that has rapidly grown to a considerable number of high quality papers for which we need at least two issues. We received a total of 19 paper submissions, some of which are still under review. The manuscripts cover nearly every aspect of models outlined in the Call for Paper (HYLE (...) 4, pp. 171f.), and much more. As far as the review procedure allows, we are going to divide the topic roughly into three topical sections, each with about four contributions. The following four papers of the present volume make up the first section that is devoted to models in quantum and computational chemistry. The second section, to be published in the next issue, is more specifically on a very peculiar type of models in chemistry: molecular models. The third and last section will be on models of complex systems, in particular in biochemistry, geochemistry, and chemical engineering. (shrink)

Algorithmic chemistries are often based on a fixed formalism which limits the fragment of chemistry expressible in the domain of the models. This results in limited applicability of the models in contemporary mathematical chemistry and is due to the poor fit between the logic used for model construction and the system being modeled. In this paper, I propose a system-oriented methodology which selects a formalism through a mapping of chemical transformation rules to proof-theoretic structural rules. Using a formal (...) specification framework from the field of artificial chemistry, expressive adequacy is ensured by the choice of logic being based on the system properties to be modeled. To illustrate the methodology, a case study is provided that shows how the proposed approach selects linear logic for modeling resource sensitivity and the proof-theoretic interpretation facilitates translation to a programming language. Since the method results in a plurality of models, I conclude with a discussion on how the proposal contributes to multi-model paradigms in computational pharmacology. (shrink)

The book starts with the assumption that vagueness is a fundamental property of this world. From a philosophical account of vagueness via the presentation of alternative mathematics of vagueness, the subsequent chapters explore how vagueness manifests itself in the various exact sciences: physics, chemistry, biology, medicine, computer science, and engineering.

The ideas of quantum simulation and advances in quantum algorithms to solve quantum chemistry problems have been discussed. Theoretical proposals and experimental investigations both have been studied to gauge the extent to which quantum computation has been applied to solve quantum chemical problems till date. The distinctive features and limitations of the application of quantum simulation on chemical systems and current approaches to define and improve upon standard quantum algorithms have been studied in detail. The possibility and consequences of (...) designing an efficient quantum computer that can address chemical problems have been assessed. The experimental realization of quantum supremacy defies the conventional belief of chemists, that millions of qubits would be required to solve fundamental chemistry problems. It is predicted that quantum simulation of quantum chemistry problems will radically revolutionize this field. (shrink)

The prediction of protein–protein interactions based on independently obtained structural information for each interacting partner remains an important challenge in computational chemistry. Procedures where hypothetical interaction models (or decoys) are generated, then ranked using a biochemically relevant scoring function have been garnering interest as an avenue for addressing such challenges. The program PatchDock has been shown to produce reasonable decoys for modeling the association between pig alpha-amylase and the VH-domains of camelide antibody raised against it. We designed a (...) biochemically relevant method by which PatchDock decoys could be ranked in order to separate near-native structures from false positives. Several thousand steps of energy minimization were used to simulate induced fit within the otherwise rigid decoys and to rank them. We applied a partial free energy function to rank each of the binding modes, improving discrimination between near-native structures and false positives. Sorting decoys according to strain energy increased the proportion of near-native decoys near the bottom of the ranked list. Additionally, we propose a novel method which utilizes regression analysis for the selection of minimization convergence criteria and provides approximation of the partial free energy function as the number of algorithmic steps approaches infinity. (shrink)

I propose that a sociological and historical examination of nanotechnologists can contribute more to an understanding of nanotechnology than an ontological definition. Nanotechnology emerged from the convergent evolution of numerous "technical knowledge communities"-networks of tightly-interconnected people who operate between disciplines and individual research groups. I demonstrate this proposition by sketching the co-evolution of computational chemistry and computational nanotechnology. Computational chemistry arose in the 1950s but eventually segregated into an ab initio, basic research, physics-oriented flavor and (...) an industry-oriented, molecular modeling and visualization, biochemical flavor. Computational nanotechnology arose in the 1990s as a synthesis of these two subgroups, infused by people and practices from computational materials science, engineering, computer science, and elsewhere. I show that to understand the aims and outcomes of computational nanotechnology-and nanotechnology more generally-we need to understand relationships between different, but related, nano knowledge communities and their dependence on particular practices, artifacts, and theories. (shrink)

This article provides a survey of some of the reasons why computational approaches have become a permanent addition to the set of scientific methods. The reasons for this require us to represent the relation between theories and their applications in a different way than do the traditional logical accounts extant in the philosophical literature. A working definition of computer simulations is provided and some properties of simulations are explored by considering an example from quantum chemistry.

Computational reproducibility possesses its own dynamics and narratives of crisis. Alongside the difficulties of computing as an ubiquitous yet complex scientific activity, computational reproducibility suffers from a naive expectancy of total reproducibility and a moral imperative to embrace the principles of free software as a non-negotiable epistemic virtue. We argue that the epistemic issues at stake in actual practices of computational reproducibility are best unveiled by focusing on software as a pivotal concept, one that is surprisingly often (...) overlooked in accounts of reproducibility issues. Software is not only about designing and coding but also about maintaining, supporting, distributing, licensing, and governance; it is not only about developers but also about users. We focus on openness debates among computational chemists involved in molecular modeling software packages as empirical grounding for our argument. We then identify and analyse four epistemic characteristics as key to the role of software in computational reproducibility. (shrink)

A personal account is presented for the present status of mathematical chemistry, with emphasis on non-numerical applications. These use mainly graph-theoretical concepts. Most computational chemical applications involve quantum chemistry and are therefore largely reducible to physics, while discrete mathematical applications often do not. A survey is provided for opinions and definitions of mathematical chemistry, and then for journals, books and book series, as well as symposia of mathematical chemistry.

Scientific discovery is often regarded as romantic and creative - and hence unanalyzable - whereas the everyday process of verifying discoveries is sober and more suited to analysis. Yet this fascinating exploration of how scientific work proceeds argues that however sudden the moment of discovery may seem, the discovery process can be described and modeled. Using the methods and concepts of contemporary information-processing psychology (or cognitive science) the authors develop a series of artificial-intelligence programs that can simulate the human thought (...) processes used to discover scientific laws. The programs - BACON, DALTON, GLAUBER, and STAHL - are all largely data-driven, that is, when presented with series of chemical or physical measurements they search for uniformities and linking elements, generating and checking hypotheses and creating new concepts as they go along. "Scientific Discovery examines the nature of scientific research and reviews the arguments for and against a normative theory of discovery; describes the evolution of the BACON programs, which discover quantitative empirical laws and invent new concepts; presents programs that discover laws in qualitative and quantitative data; and ties the results together, suggesting how a combined and extended program might find research problems, invent new instruments, and invent appropriate problem representations. Numerous prominent historical examples of discoveries from physics and chemistry are used as tests for the programs and anchor the discussion concretely in the history of science. Pat Langley is an Associate Professor in the Department of Information and Computer Science at the University of California, Irvine.Herbert Simon is a Professor in the Departments of Psychology, Computer Science, and Philosophy at Carnegie-Mellon University. Gary L. Bradshaw is an Assistant Professor in the Department of Psychology and Institute of Cognitive Science at the University of Colorado, Boulder. Jan M. Zytkow is an Associate Professor in the Computer Science Department at Wichita State University. (shrink)

Scientific practices have been changed by the increasing use of computer simulations. A central question for philosophers is how to characterize computer simulations. In this paper, we address this question by analyzing simulations in biochemistry. We propose that simulations have been used in biochemistry long before computers arrived. Simulation can be described as a surrogate relationship between models. Moreover, a simulative aspect is implicit in the classical dichotomy between in vivo–in vitro conditions. Based on a discussion about how to characterize (...) a simulative aspect in this dichotomy, we will argue that an adequate understanding of computer simulations in biochemistry requires a previous understanding of simulations in experimental contexts. (shrink)

In this paper we investigate with a case study from chemistry under what conditions a simulation can serve as a surrogate for an experiment. The case-study concerns a simulation of H2-formation in outer space. We find that in this case the simulation can act as a surrogate for an experiment, because there exists comprehensive theoretical background knowledge in form of quantum mechanics about the range of phenomena to which the investigated process belongs and because any particular modelling assumptions as (...) can be justified. If these requirements are met then direct empirical validation may even be dispensable. We conjecture that this is not the case in the absence of comprehensive theoretical background knowledge. (shrink)

According to physicalism, everything is physical or metaphysically connected to the physical. If physicalism were true, it seems that we should – in principle – be able to reduce the descriptions and explanations of special sciences to physical ones, for example, explaining biological regularities, via chemistry, by the laws of particle physics. The multiple realization of the property types of the special sciences is often seen to be an obstacle to such epistemic reductions. Here, we introduce another, new argument (...) against epistemic reduction. Based on mathematical complexity, we show that, under certain conditions, there can be “complexity barriers” that make epistemic reduction – in principle – unachievable even if physicalism were true. (shrink)

Attempts to formalize the diagnostic process are by no means a recent undertaking; what is new is the availability of an engine to process these formalizations. The digital computer has therefore been increasingly turned to in the expectation of developing systems which will assist or replace the physician in diagnosis. Such efforts involve a number of assumptions regarding the nature of the diagnostic process: e.g. where it begins, and where it ends. ‘Diagnosis’ appears to include a number of quite different (...) cognitive processes, some of which seem more subject to formalization than others. Underlying the difficulties inherent in these efforts at formalization, is the hierarchical structure of medical knowledge including that of diseases. (By ‘hierarchical structure’, I mean no more than that our descriptions of clinical objects necessarily refer to different levels of organization; atomic, molecular, cellular, physiological system, entire patient.) Since diagnosis is in part a form of classification, measures of similarity between the clinical findings of a particular patient and a potential disease, are needed. This is complicated by the fact that some diseases are described using the vocabularies of physics and chemistry, others with the vocabulary of psychology, and most, with terms taken from a number of different hierarchical levels. The differences between the descriptions made using these vocabularies will be seen to exert systematic (if not uniform) influences upon the diagnostic process. CiteULike Connotea Del.icio.us What's this? (shrink)

Molecules have more or less symmetric and complex structures which can be defined in the mathematical framework of topology, group theory, dynamical systems theory, and quantum mechanics. But symmetry and complexity are by no means only theoretical concepts of research. Modern computer aided visualizations show real forms of matter which nevertheless depend on the technical standards of observation, computation, and representation. Furthermore, symmetry and complexity are fundamental interdisciplinary concepts of research inspiring the natural sciences since the antiquity.

A commonly held background assumption about the sciences is that they connect along borders characterized by ontological or explanatory relationships, usually given in the order of mathematics, physics, chemistry, biology, psychology, and the social sciences. Interdisciplinary work, in this picture, arises in the connecting regions of adjacent disciplines. Philosophical research into interdisciplinary model transfer has increasingly complicated this picture by highlighting additional connections orthogonal to it. But most of these works have been done through case studies, which due to (...) their strong focus struggle to provide foundations for claims about large-scale relations between multiple scientific disciplines. As a supplement, in this contribution, we propose to philosophers of science the use of modern science mapping techniques to trace connections between modeling techniques in large literature samples. We explain in detail how these techniques work, and apply them to a large, contemporary, and multidisciplinary data set (n=383.961 articles). Through the comparison of textual to mathematical representations, we suggest formulaic structures that are particularly common among different disciplines and produce first results indicating the general strength and commonality of such relationships. (shrink)

Climatology is a paradigmatic complex systems science. Understanding the global climate involves tackling problems in physics, chemistry, economics, and many other disciplines. I argue that complex systems like the global climate are characterized by certain dynamical features that explain how those systems change over time. A complex system's dynamics are shaped by the interaction of many different components operating at many different temporal and spatial scales. Examining the multidisciplinary and holistic methods of climatology can help us better understand the (...) nature of complex systems in general. -/- Questions surrounding climate science can be divided into three rough categories: foundational, methodological, and evaluative questions. "How do we know that we can trust science?" is a paradigmatic foundational question (and a surprisingly difficult one to answer). Because the global climate is so complex, questions like "what makes a system complex?" also fall into this category. There are a number of existing definitions of `complexity,' and while all of them capture some aspects of what makes intuitively complex systems distinctive, none is entirely satisfactory. Most existing accounts of complexity have been developed to work with information-theoretic objects (signals, for instance) rather than the physical and social systems studied by scientists. -/- Dynamical complexity, a concept articulated in detail in the first third of the dissertation, is designed to bridge the gap between the mathematics of contemporary complexity theory (in particular the formalism of "effective complexity" developed by Gell-Mann and Lloyd [2003]) and a more general account of the structure of science generally. Dynamical complexity provides a physical interpretation of the formal tools of mathematical complexity theory, and thus can be used as a framework for thinking about general problems in the philosophy of science, including theories, explanation, and lawhood. -/- Methodological questions include questions about how climate science constructs its models, on what basis we trust those models, and how we might improve those models. In order to answer questions about climate modeling, it's important to understand what climate models look like and how they are constructed. Climate model families are significantly more diverse than are the model families of most other sciences (even sciences that study other complex systems). Existing climate models range from basic models that can be solved on paper to staggeringly complicated models that can only be analyzed using the most advanced supercomputers in the world. I introduce some of the central concepts in climatology by demonstrating how one of the most basic climate models might be constructed. I begin with the assumption that the Earth is a simple featureless blackbody which receives energy from the sun and releases it into space, and show how to model that assumption formally. I then gradually add other factors (e.g. albedo and the greenhouse effect) to the model, and show how each addition brings the model's prediction closer to agreement with observation. After constructing this basic model, I describe the so-called "complexity hierarchy" of the rest of climate models, and argue that the sense of "complexity" used in the climate modeling community is related to dynamical complexity. -/- With a clear understanding of the basics of climate modeling in hand, I then argue that foundational issues discussed early in the dissertation suggest that computation plays an irrevocably central role in climate modeling. "Science by simulation" is essential given the complexity of the global climate, but features of the climate system--the presence of non-linearities, feedback loops, and chaotic dynamics--put principled limits on the effectiveness of computational models. This tension is at the root of the staggering pluralism of the climate model hierarchy, and suggests that such pluralism is here to stay, rather than an artifact of our ignorance. Rather than attempting to converge on a single "best fit" climate model, we ought to embrace the diversity of climate models, and view each as a specialized tool designed to predict and explain a rather narrow range of phenomena. Understanding the climate system as a whole requires examining a number of different models, and correlating their outputs. This is the most significant methodological challenge of climatology. -/- Climatology's role contemporary political discourse raises an unusually high number of evaluative questions for a physical science. The two leading approaches to crafting policy surrounding climate change center on mitigation (i.e. stopping the changes from occurring) and adaptation (making post hoc changes to ameliorate the harm caused by those changes). Crafting an effective socio-political response to the threat of anthropogenic climate change, however, requires us to integrate multiple perspectives and values: the proper response will be just as diverse and pluralistic as the climate models themselves, and will incorporate aspects of both approaches. I conclude by offering some concrete recommendations about how to integrate this value pluralism into our socio-political decision making framework. (shrink)

Information Theory, Evolution and The Origin ofLife: The Origin and Evolution of Life as a Digital Message: How Life Resembles a Computer, Second Edition. Hu- bert P. Yockey, 2005, Cambridge University Press, Cambridge: 400 pages, index; hardcover, US $60.00; ISBN: 0-521-80293-8. The reason that there are principles of biology that cannot be derived from the laws of physics and chemistry lies simply in the fact that the genetic information content of the genome for constructing even the simplest organisms is (...) much larger than the information content of these laws. Yockey in his previous book (1992, 335) In this new book, Information Theory, Evolution and The Origin ofLife, Hubert Yockey points out that the digital, segregated, and linear character of the genetic information system has a fundamental significance. If inheritance would blend and not segregate, Darwinian evolution would not occur. If inheritance would be analog, instead of digital, evolution would be also impossible, because it would be impossible to remove the effect of noise. In this way, life is guided by information, and so information is a central concept in molecular biology. The author presents a picture of how the main concepts of the genetic code were developed. He was able to show that despite Francis Crick's belief that the Central Dogma is only a hypothesis, the Central Dogma of Francis Crick is a mathematical consequence of the redundant nature of the genetic code. The redundancy arises from the fact that the DNA and mRNA alphabet is formed by triplets of 4 nucleotides, and so the number of letters (triplets) is 64, whereas the proteome alphabet has only 20 letters (20 amino acids), and so the translation from the larger alphabet to the smaller one is necessarily redundant. Except for Tryptohan and Methionine, all amino acids are coded by more than one triplet, therefore, it is undecidable which source code letter was actually sent from mRNA. This proof has a corollary telling that there are no such mathematical constraints for protein-protein communication. With this clarification, Yockey contributes to diminishing the widespread confusion related to such a central concept like the Central Dogma. Thus the Central Dogma prohibits the origin of life "proteins first." Proteins can not be generated by "self-organization." Understanding this property of the Central Dogma will have a serious impact on research on the origin of life. (shrink)

This book addresses a wide range of topics relating to the properties and behavior of condensed matter under extreme conditions such as intense magnetic and electric fields, high pressures, heat and cold, and mechanical stresses. It is divided into four sections devoted to condensed matter theory, molecular chemistry, theoretical physics, and the philosophy and history of science. The main themes include electronic correlations in material systems under extreme pressure and temperature conditions, surface physics, the transport properties of low-dimensional electronic (...) systems, applications of the density functional theory in molecular systems, and graphene. The book is the outcome of a workshop held at the University of Catania, Italy, in honor of Professor Renato Pucci on the occasion of his 70th birthday. It includes selected invited contributions from collaborators and co-authors of Professor Pucci during his long and successful career, as well as from other distinguished guest authors. (shrink)

Drawing on the work of Bernadette Bensaude-Vincent and Isabelle Stengers on the history of chemistry, this article develops the idea that drug molecules can be understood as ‘informed materials’. This study argues that molecules should not be viewed as discrete objects, but as constituted in their relations to complex informational and material environments. Through a case study of commercial pharmaceutical R&D, the article examines the role of combinatorial and computational chemistry in enriching the informational and material environment (...) of potential drug molecules. Within the contemporary pharmaceutical laboratory, experiments on molecules can be conducted not just in vitro and in vivo but also, according to researchers, in silico. Molecules come to exist not just as physical reagents but also as elements of arrays, libraries and databases of other molecules, and in a virtual form in computer simulations and virtual libraries. Molecules are also understood by researchers to exist in a ‘chemical space’ of other different molecules, where the notion of chemical space is used both to refer to differences in molecular structure and to territories owned or occupied by particular firms. The article argues that pharmaceutical companies do not merely discover molecular structures that potentially could exist, but also invent novel forms of chemical entity. (shrink)

The systems view on life and its emergence from complex chemistry has remarkably increased the scientific attention on metabolism in the last two decades. However, during this time there has not been much theoretical discussion on what constitutes a metabolism and what role it actually played in biogenesis. A critical and updated review on the topic is here offered, including some references to classical models from last century, but focusing more on current and future research. Metabolism is considered as (...) intrinsically related to the living but not necessarily equivalent to it. More precisely, the idea of “minimal metabolism”, in contrast to previous, top‐down conceptions, is formulated as a heuristic construct, halfway between chemistry and biology. Thus, rather than providing a complete or final characterization of metabolism, our aim is to encourage further investigations on it, particularly in the context of life's origin, for which some concrete methodological suggestions are provided. Also see the video abstract here:https://youtu.be/DP7VMKk2qpA. (shrink)

Scientific knowledge production is a domain of human excellence, but recently this position became progressively challenged by machine intelligence. Some human tasks will be conquered sooner; others, which include design, may still require human intuition. Would the automated knowledge production truly challenge the human, or is one just an extension – a prosthetic – of the other? What could be the place of art in such environment? Mess and messy scientific models have the potential to provide paradigm shifts in molecular (...) modelling, cancer research and systems biology where not only living humans but also machine learning algorithms craft knowledge. Together with art they have the potential for different reading and re-framing, which are the qualities scientists are looking for when engaging works of art within their molecular modelling process. In my opinion, these are the same qualities scientists are also looking for in the outputs of machine learning and computational chemistry modelling. (shrink)

This paper combines naturalized metaphysics and a philosophical reflection on a recently evolving interdisciplinary branch of quantum chemistry, ab initio molecular dynamics. Bridging the gaps among chemistry, physics, and computer science, this cutting-edge research field explores the structure and dynamics of complex molecular many-body systems through computer simulations. These simulations are allegedly crafted solely by the laws of fundamental physics, and are explicitly designed to capture nature as closely as possible. The models and algorithms employed, however, involve many (...) approximations and significant degrees of idealization of their target systems. Therefore, for philosophers of science the pivotal question of whether relying only on the fundamental laws of physics supports a reductionist or realist stance arises. One conceivable answer to this question is that the irreducible approximations and idealizations support rather anti-realist positions. After reviewing an influential attitude in the philosophy of computer simulations and the debate concerning scientific realism, I offer a fair interpretation of such ab initio modelling in quantum chemistry within a naturalistic metaphysical framework that gives rise to a specific type of ontic structural realism. (shrink)

Although the electron density can be calculated with the formal resources of quantum mechanics, in physics it does not play the leading role that the quantum state does. In contrast, the concept of electron density is central in quantum chemistry. There is no doubt about how the electron density is computed in terms of the wave function of an atom or molecule. However, when the interpretation of the concept is at stake, there is no general agreement. In this article (...) we will analyze the two main interpretations of the concept of electron density: the Born-style probability density interpretation and the Schrödinger-style charge density interpretation. In particular, we will examine their differences, their relations with quantum mechanics and the consequences that each of them entails from a strictly quantum point of view. (shrink)

The theory of nonlinear complex systems has become a successful and widely used problem-solving approach in the natural sciences - from laser physics, quantum chaos and meteorology to molecular modeling in chemistry and computer simulations of cell growth in biology. In recent times it has been recognized that many of the social, ecological and political problems of mankind are also of a global, complex and nonlinear nature. And one of the most exciting topics of present scientific and public interest (...) is the idea that even the human mind is governed largely by the nonlinear dynamics of complex systems. In this wide-ranging but concise treatment Prof. Mainzer discusses, in nontechnical language, the common framework behind these endeavours. Special emphasis is given to the evolution of new structures in natural and cultural systems and it is seen clearly how the new integrative approach of complexity theory can give new insights that were not available using traditional reductionistic methods. (shrink)

This paper examines a looming reproducibility crisis in the core of the hard sciences. Namely, it concentrates on molecular modeling and simulation (MMS), a family of methods that predict properties of substances through computing interactions on a molecular level and that is widely popular in physics, chemistry, materials science, and engineering. The paper argues that in order to make quantitative predictions, sophisticated models are needed which have to be evaluated with complex simulation procedures that amalgamate theoretical, technological, and social (...) factors – leading to problems with reproducibility. Thus, for methodological reasons, the predictive success causes a reproducibility problem. (shrink)

structure of a laboratory report (generalized from Italian, Chinese and US sources), we distill a fifth flavor, the givens, whose flip side is the freedoms or tangibles of an experiment. (Stated in terms of computer science, we are trying to find inputs and outputs, but these turn out to be surprisingly vague in chemistry.) Then, in the service of a white-boxing ethos (which sounds less severe than ‘anti black-boxing’), we establish a movable boundary between givens and tangibles, with implications (...) for ‘ontological attitudes’ and for the future of chemistry. Next, in revisiting a 2002 exchange between Schummer and Laszlo, which might be paraphrased as the chemist-as-philosopher versus chemist-as-artisan, we apply a second kind of sliding scale which seems to harmonize the discussion. Finally, on a possibly quixotic note, we look briefly at a third kind of sliding scale, now aimed squarely at ontology itself. For illustrative purposes, we adopt an atomocentric viewpoint (as distinct from atomistic), and assign it the provisional name ‘Fuzzy CH4 Ontology’. (shrink)

Epistemologists have debated at length whether scientific discovery is a rational and logical process. If it is, according to the Artificial Intelligence hypothesis, it should be possible to write computer programs able to discover laws or theories; and if such programs were written, this would definitely prove the existence of a logic of discovery. Attempts in this direction, however, have been unsuccessful: the programs written by Simon's group, indeed, infer famous laws of physics and chemistry; but having found no (...) new law, they cannot properly be considered discovery machines. The programs written in the Turing tradition, instead, produced new and useful empirical generalization, but no theoretical discovery, thus failing to prove the logical character of the most significant kind of discoveries. A new cognitivist and connectionist approach by Holland, Holyoak, Nisbett and Thagard, looks more promising. Reflection on their proposals helps to understand the complex character of discovery processes, the abandonment of belief in the logic of discovery by logical positivists, and the necessity of a realist interpretation of scientific research. (shrink)

Intra-molecular connectivity (that is, chemical structure) does not emerge from computations based on fundamental quantum-mechanical principles. In order to compute molecular electronic energies (of C 3 H 4 hydrocarbons, for instance) quantum chemists must insert intra-molecular connectivity “by hand.” Some take this as an indication that chemistry cannot be reduced to physics: others consider it as evidence that quantum chemistry needs new logical foundations. Such discussions are generally synchronic rather than diachronic —that is, they neglect ‘historical’ aspects. However, (...) systems of interest to chemists generally are metastable . In many cases chemical systems of a given elemental composition may exist in any one of several different metastable states depending on the history of the system. Molecular structure generally depends on contingent historical circumstances of synthesis and separation, rather than solely or mainly on relative energies of alternative stable states, those energies in turn determined by relationships among components. Chemical structure is usually ‘kinetically-determined’ rather than ‘thermodynamically-determined.’ For instance, cyclical hydrocarbon ring-systems (as in cyclopropene) are produced only in special circumstances. Adequate theoretical treatments must take account of the persistent effects of such contingent historical events whenever they are relevant—as they generally are in chemistry. (shrink)

Why are computers so smart these days? And why are humans apparently still a bit smarter? Does this have something to do with the difference between data and meaning? Does this in turn mean that at least some abstract entities, such as numbers, exist independently of human thought? Wouldn’t that require an expansion of our scientific world view? And would that at all be compatible with what we know about our world from physics and chemistry, philosophy, psychology, neuroscience and (...) the theory of evolution? Finally, what would this tell us about ethical and aesthetic value theories? These and related questions will be discussed in this book. We will find that the difference between data and meaning, i.e. quantitative and qualitative information, does indeed appear to be of central importance for understanding both artificial and natural intelligence. And then the independent existence of abstract entities not only appears to be a particularly promising hypothesis, but also one that is entirely compatible with the sum of our scientific knowledge, especially with regard to value theories. The book thus arrives at the exploration of a scientifically tenable, panpsychistically inspired, objective idealism that can be derived from our most fundamental intuitions as subjects that perceive qualities, but that can also take into account the structuring of the world already at the micro-scale, found in the modern natural sciences. The result is a Platonic, but in a second step also a scientific realism and a naturalism in the sense that it is informed by the natural sciences in terms of an inductive metaphysics. An objective idealism, not in a rationalistic maximum form, but in a pragmatic minimum form; without eternal truths, but dependent on the continued philosophical-scientific and also philosophicalsocial dialog. The proposed model could offer interesting solutions to a number of problems at and near the mind/matter boundary: Proposals are being considered for the interpretation of quantum mechanics, the problem of molecular symmetry, the neuronal code and the binding problem in neuroscience, mental causation, a more holistic understanding of mental processes, and so on and so forth. However, the extent to which the model threatens to promise far too much is also being discussed. In sum, the core question is how we can imagine human thinking beyond physically conceived information processing. An alternative model of human thinking is then put up for discussion, for which not only machine-like cognitive performance, but above all the intentional perception of qualitative information, i.e. of abstract entities, would be central, as well as the free, ultimately creative linking of patterns of quantitative information (signals, data) with such qualities (meanings). (shrink)

This book provides a short, hands-on introduction to the science of complexity using simple computational models of natural complex systems--with models and exercises drawn from physics, chemistry, geology, and biology. By working through the models and engaging in additional computational explorations suggested at the end of each chapter, readers very quickly develop an understanding of how complex structures and behaviors can emerge in natural phenomena as diverse as avalanches, forest fires, earthquakes, chemical reactions, animal flocks, and epidemic (...) diseases. Natural Complexity provides the necessary topical background, complete source codes in Python, and detailed explanations for all computational models. (shrink)

In the last years there has been a great improvement in the development of computational methods for combinatorial chemistry applied to drug discovery. This approach to drug discovery is sometimes called a “rational way” to manage a well known phenomenon in chemistry: serendipity discoveries. Traditionally, serendipity discoveries are understood as accidental findings made when the discoverer is in quest for something else. This ‘traditional’ pattern of serendipity appears to be a good characterization of discoveries where “luck” plays (...) a key role. In this sense, some initial failures in combinatorial chemistry are frequently attributed to a naïf appropriation of a “serendipity model” for discovery (a “serendipity mistake”). In this paper we try to evaluate this statement by criticizing its foundations. It will be suggested that the notion of serendipity has different aspects and that the criticism to the first attempts could be understood as a “serendipity mistake.” We will suggest that “serendipity” strategies, a kind of blind search, can be seen sometimes as a “genuine part” of scientific practice. A discussion will ensue about how this characterization can give us a better understanding of some aspects of serendipity discoveries. (shrink)

This paper explores the use of chemical symbolism in works by the new media artist Sonya Rapoport, with a focus on the pivotal Cobalt series from the late 1970s. These works, drawings on computer printouts generated by research at the Lawrence Berkeley Laboratory, respond to experiments in nuclear chemistry. They mark the beginning of three productive decades in which Rapoport produced a variety of images related to chemistry in her work. She states, “I looked for authentic research projects (...) that were interesting to me, preferably with captivating pictorial subject matter. Then came the creative chaotic process of resolving a cohesive product that combined scientific research with art concept.” Rapoport had an unusual degree of access to scientific materials through her husband, organic chemist Henry Rapoport, a faculty member at the University of California, Berkeley. At the time of production, these works were outside mainstream art world interests and they have received little critical attention. This paper examines the development of Rapoport’s images and places her use of chemical references in context in her lifetime of work. (shrink)

The INBIOSA project brings together a group of experts across many disciplines who believe that science requires a revolutionary transformative step in order to address many of the vexing challenges presented by the world. It is INBIOSA’s purpose to enable the focused collaboration of an interdisciplinary community of original thinkers. This paper sets out the case for support for this effort. The focus of the transformative research program proposal is biology-centric. We admit that biology to date has been more fact-oriented (...) and less theoretical than physics. However, the key leverageable idea is that careful extension of the science of living systems can be more effectively applied to some of our most vexing modern problems than the prevailing scheme, derived from abstractions in physics. While these have some universal application and demonstrate computational advantages, they are not theoretically mandated for the living. A new set of mathematical abstractions derived from biology can now be similarly extended. This is made possible by leveraging new formal tools to understand abstraction and enable computability. [The latter has a much expanded meaning in our context from the one known and used in computer science and biology today, that is "by rote algorithmic means", since it is not known if a living system is computable in this sense (Mossio et al., 2009).] Two major challenges constitute the effort. The first challenge is to design an original general system of abstractions within the biological domain. The initial issue is descriptive leading to the explanatory. There has not yet been a serious formal examination of the abstractions of the biological domain. What is used today is an amalgam; much is inherited from physics (via the bridging abstractions of chemistry) and there are many new abstractions from advances in mathematics (incentivized by the need for more capable computational analyses). Interspersed are abstractions, concepts and underlying assumptions “native” to biology and distinct from the mechanical language of physics and computation as we know them. A pressing agenda should be to single out the most concrete and at the same time the most fundamental process-units in biology and to recruit them into the descriptive domain. Therefore, the first challenge is to build a coherent formal system of abstractions and operations that is truly native to living systems. Nothing will be thrown away, but many common methods will be philosophically recast, just as in physics relativity subsumed and reinterpreted Newtonian mechanics. -/- This step is required because we need a comprehensible, formal system to apply in many domains. Emphasis should be placed on the distinction between multi-perspective analysis and synthesis and on what could be the basic terms or tools needed. The second challenge is relatively simple: the actual application of this set of biology-centric ways and means to cross-disciplinary problems. In its early stages, this will seem to be a “new science”. This White Paper sets out the case of continuing support of Information and Communication Technology (ICT) for transformative research in biology and information processing centered on paradigm changes in the epistemological, ontological, mathematical and computational bases of the science of living systems. Today, curiously, living systems cannot be said to be anything more than dissipative structures organized internally by genetic information. There is not anything substantially different from abiotic systems other than the empirical nature of their robustness. We believe that there are other new and unique properties and patterns comprehensible at this bio-logical level. The report lays out a fundamental set of approaches to articulate these properties and patterns, and is composed as follows. -/- Sections 1 through 4 (preamble, introduction, motivation and major biomathematical problems) are incipient. Section 5 describes the issues affecting Integral Biomathics and Section 6 -- the aspects of the Grand Challenge we face with this project. Section 7 contemplates the effort to formalize a General Theory of Living Systems (GTLS) from what we have today. The goal is to have a formal system, equivalent to that which exists in the physics community. Here we define how to perceive the role of time in biology. Section 8 describes the initial efforts to apply this general theory of living systems in many domains, with special emphasis on crossdisciplinary problems and multiple domains spanning both “hard” and “soft” sciences. The expected result is a coherent collection of integrated mathematical techniques. Section 9 discusses the first two test cases, project proposals, of our approach. They are designed to demonstrate the ability of our approach to address “wicked problems” which span across physics, chemistry, biology, societies and societal dynamics. The solutions require integrated measurable results at multiple levels known as “grand challenges” to existing methods. Finally, Section 10 adheres to an appeal for action, advocating the necessity for further long-term support of the INBIOSA program. -/- The report is concluded with preliminary non-exclusive list of challenging research themes to address, as well as required administrative actions. The efforts described in the ten sections of this White Paper will proceed concurrently. Collectively, they describe a program that can be managed and measured as it progresses. (shrink)

Physics and chemistry underlie the nature of all the world around us, including human brains. Consequently some suggest that in causal terms, physics is all there is. However, we live in an environment dominated by objects embodying the outcomes of intentional design (buildings, computers, teaspoons). The present day subject of physics has nothing to say about the intentionality resulting in existence of such objects, even though this intentionality is clearly causally effective. This paper examines the claim that the underlying (...) physics uniquely causally determines what happens, even though we cannot predict the outcome. It suggests that what occurs is the contextual emergence of complexity: the higher levels in the hierarchy of complexity have autonomous causal powers, functionally independent of lower level processes. This is possible because top-down causation takes place as well as bottom-up action, with higher level contexts determining the outcome of lower level functioning and even modifying the nature of lower level constituents. Stored information plays a key role, resulting in non-linear dynamics that is non-local in space and time. Brain functioning is causally affected by abstractions such as the value of money and the theory of the laser. These are realised as brain states in individuals, but are not equivalent to them. Consequently physics per se cannot causally determine the outcome of human creativity, rather it creates the possibility space allowing human intelligence to function autonomously. The challenge to physics is to develop a realistic description of causality in truly complex hierarchical structures, with top-down causation and memory effects allowing autonomous higher levels of order to emerge with genuine causal powers. (shrink)

The INBIOSA project brings together a group of experts across many disciplines who believe that science requires a revolutionary transformative step in order to address many of the vexing challenges presented by the world. It is INBIOSA’s purpose to enable the focused collaboration of an interdisciplinary community of original thinkers. This paper sets out the case for support for this effort. The focus of the transformative research program proposal is biology-centric. We admit that biology to date has been more fact-oriented (...) and less theoretical than physics. However, the key leverageable idea is that careful extension of the science of living systems can be more effectively applied to some of our most vexing modern problems than the prevailing scheme, derived from abstractions in physics. While these have some universal application and demonstrate computational advantages, they are not theoretically mandated for the living. A new set of mathematical abstractions derived from biology can now be similarly extended. This is made possible by leveraging new formal tools to understand abstraction and enable computability. [The latter has a much expanded meaning in our context from the one known and used in computer science and biology today, that is "by rote algorithmic means", since it is not known if a living system is computable in this sense (Mossio et al., 2009).] Two major challenges constitute the effort. The first challenge is to design an original general system of abstractions within the biological domain. The initial issue is descriptive leading to the explanatory. There has not yet been a serious formal examination of the abstractions of the biological domain. What is used today is an amalgam; much is inherited from physics (via the bridging abstractions of chemistry) and there are many new abstractions from advances in mathematics (incentivized by the need for more capable computational analyses). Interspersed are abstractions, concepts and underlying assumptions “native” to biology and distinct from the mechanical language of physics and computation as we know them. A pressing agenda should be to single out the most concrete and at the same time the most fundamental process-units in biology and to recruit them into the descriptive domain. Therefore, the first challenge is to build a coherent formal system of abstractions and operations that is truly native to living systems. Nothing will be thrown away, but many common methods will be philosophically recast, just as in physics relativity subsumed and reinterpreted Newtonian mechanics. -/- This step is required because we need a comprehensible, formal system to apply in many domains. Emphasis should be placed on the distinction between multi-perspective analysis and synthesis and on what could be the basic terms or tools needed. The second challenge is relatively simple: the actual application of this set of biology-centric ways and means to cross-disciplinary problems. In its early stages, this will seem to be a “new science”. This White Paper sets out the case of continuing support of Information and Communication Technology (ICT) for transformative research in biology and information processing centered on paradigm changes in the epistemological, ontological, mathematical and computational bases of the science of living systems. Today, curiously, living systems cannot be said to be anything more than dissipative structures organized internally by genetic information. There is not anything substantially different from abiotic systems other than the empirical nature of their robustness. We believe that there are other new and unique properties and patterns comprehensible at this bio-logical level. The report lays out a fundamental set of approaches to articulate these properties and patterns, and is composed as follows. -/- Sections 1 through 4 (preamble, introduction, motivation and major biomathematical problems) are incipient. Section 5 describes the issues affecting Integral Biomathics and Section 6 -- the aspects of the Grand Challenge we face with this project. Section 7 contemplates the effort to formalize a General Theory of Living Systems (GTLS) from what we have today. The goal is to have a formal system, equivalent to that which exists in the physics community. Here we define how to perceive the role of time in biology. Section 8 describes the initial efforts to apply this general theory of living systems in many domains, with special emphasis on crossdisciplinary problems and multiple domains spanning both “hard” and “soft” sciences. The expected result is a coherent collection of integrated mathematical techniques. Section 9 discusses the first two test cases, project proposals, of our approach. They are designed to demonstrate the ability of our approach to address “wicked problems” which span across physics, chemistry, biology, societies and societal dynamics. The solutions require integrated measurable results at multiple levels known as “grand challenges” to existing methods. Finally, Section 10 adheres to an appeal for action, advocating the necessity for further long-term support of the INBIOSA program. -/- The report is concluded with preliminary non-exclusive list of challenging research themes to address, as well as required administrative actions. The efforts described in the ten sections of this White Paper will proceed concurrently. Collectively, they describe a program that can be managed and measured as it progresses. (shrink)

Students are using file sharing sites to breach academic integrity in light of the Covid-19 pandemic. This paper analyses the use of one such site, Chegg, which offers “homework help” and other academic services to students. Chegg is often presented as a file sharing site in the academic literature, but that is just one of many ways in which it can be used. As this paper demonstrates, Chegg can and is used for contract cheating This is despite the apparent existence (...) of an Honour Code on Chegg which asks students not to breach academic integrity. With pandemic led safety considerations leading to increased online teaching and assessment, the paper analyses data relating to how Chegg is used by students in five STEM subjects, namely Computer Science, Mechanical Engineering, Electrical Engineering, Physics and Chemistry. The results show that students are using Chegg to request exam style questions. They demonstrate that contract cheating requests can be put live and answered within the short duration of an examination. The number of student requests posted for these five subjects increased by 196.25% comparing the time period April 2019 to August 2019 with the period April 2020 to August 2020. This increase corresponds with the time when many courses moved to be delivered and assessed online. The growing number of requests indicates that students are using Chegg for assessment and exam help frequently and in a way that is not considered permissible by universities. The paper concludes by recommending that academic institutions put interventions in place to minimise the risk to educational standards posed by sites such as Chegg, particularly since increased online teaching and assessment may continue after the pandemic. (shrink)

Despite its long history, there is no agreed-upon conception of emergence. One might claim that a common idea of emergence seems to be that something termed a "system" gives rise to, or possesses, characteristics termed "properties," which latter are absent or unmanifested in whatever individual components the system consists and are thus "emergent" from the system itself. However, types of systems discussed run a gamut from purely mental entities to simple tools . "Properties" is similarly unconstrained . The so-called special (...) sciences, such as biology, psychology, sociology, and even chemistry have all claimed some properties as emergent. However, the enormous literature dealing with various types of systems characterized as emergent can be divided, roughly speaking, into two classes of descriptions of emergence. One might be termed "structural" and the other "functional." The first characterizes emergent systems in terms of their components and their interrelationships , while the second characterizes them in terms of their effects on other systems or elements . There is generally no mention of possible internal structures of the system in the latter, and if there is, it is in vague and/or abstract terms, while the former emphasizes internal structures over clear characterizations of the effects of emergence. Thus, a conception of emergence like Kim's is functional, while explicit descriptions of small-world networks, chaotic systems, or other types of complex internal organizations in mathematics, physics, and computer science are structural. The structuralfunctional distinction will play a part in the analysis of emergence later in this paper. (shrink)

In the twenty-first century, there has been a resurgence of ecologically conscious art among artists using new technologies. Like Eco-art, this recent movement, which might be called Eco-media, is interdisciplinary. Eco-media is heavily influenced by developments in environmental science, in particular developments in remote imaging and other kinds of remote Earth sensing (for example, the widespread use of satellite imaging and GPS) and developments in computer modelling (for example, detailed global models of climate that not only model the physics of (...) the Earth and solar system, but also explore the chemistry and biology of the Earth). This article will discuss developments in media art related to the computerized interpretation of complex data sets describing and modelling the natural world. It will explore work that has historically straddled artistic and scientific development, specifically Marey's work in the nineteenth century in photography and motion pictures and give examples of artists who are working in the area in-between art and science today. It will also discuss connections between this work and the historical Romantic sublime and the political dimension of this work as advocating for the preservation of the natural world, and give examples of some of the author's artworks in this area. (shrink)