Complex, multigenic biological traits are shaped by the emergent interaction of proteins being the main functional units at the molecular scale. Based on a phenomenological approach, algorithms for quantifying two different aspects of emergence were introduced (Wegner and Hao in Progr Biophys Mol Biol 161:54–61, 2021) describing: (i) pairwise reciprocal interactions of proteins mutually modifying their contribution to a complex trait (denoted as weak emergence), and (ii) formation of a new, complex trait by a set of n ‘constitutive’ proteins at (...) concentrations exceeding individual threshold values (strong emergence). The latter algorithm is modified here to take account of protein redundancy with respect to a complex trait (‘full redundancy’). Irreducibility is considered a necessary and sufficient criterion for strong biological emergence; if one constitutive protein is missing, or its concentration drops below the threshold the trait is lost. A definition based on ‘unpredictability’ is dismissed, because this criterion is irrelevant for the evolution of a complex trait, and apparent unpredictability may rather reflect our basic deficits in understanding unless we can provide an unequivocal proof for it. The phenomenological approach advocated here allows to identify hidden rules according to which strongly emergent traits may be organized. This is of high value for understanding the evolution of complex traits which seems to require the saltational advent of all constitutive proteins ‘in one turn’ to arrive at a functional trait providing for an improved fitness of the organism. Rather than being a purely random process, it may be guided by fundamental structural principles. (shrink)

In recent years, many philosophers of science have attempted to articulate a theory of non-epistemic emergence that is compatible with mechanistic explanation and incompatible with reductionism. The 2005 account of Fred C. Boogerd et al. has been particularly influential. They argued that a systemic property was emergent if it could not be predicted from the behaviour of less complex systems. Here, I argue that Boogerd et al.'s attempt to ground emergence in complexity guarantees that we will see emergence, but at (...) the cost of rendering it either trivial or epistemic. There are three basic problems. First, neither the measures of complexity explicitly mentioned by Boogerd et al. nor the most popular measures in the literature can do the practical and theoretical work that they assign to complexity. Second, I argue that while the success of their view depends on restricting the base of information available to the reductionist, this cannot be done in a way that is metaphysically neutral with respect to emer.. (shrink)

This paper argues that the difference between contemporary software intensive scientific practice and more traditional non-software intensive varieties results from the characteristically high conditionality of software. We explain why the path complexity of programs with high conditionality imposes limits on standard error correction techniques and why this matters. While it is possible, in general, to characterize the error distribution in inquiry that does not involve high conditionality, we cannot characterize the error distribution in inquiry that depends on software. Software intensive (...) science presents distinctive error and uncertainty modalities that pose new challenges for the epistemology of science. (shrink)

We address some of the epistemological challenges highlighted by the Critical Data Studies literature by reference to some of the key debates in the philosophy of science concerning computational modeling and simulation. We provide a brief overview of these debates focusing particularly on what Paul Humphreys calls epistemic opacity. We argue that debates in Critical Data Studies and philosophy of science have neglected the problem of error management and error detection. This is an especially important feature of the epistemology of (...) Big Data. In “Error” section we explain the main characteristics of error detection and correction along with the relationship between error and path complexity in software. In this section we provide an overview of conventional statistical methods for error detection and review their limitations when faced with the high degree of conditionality inherent to modern software systems. (shrink)

What does it mean to trust the results of a computer simulation? This paper argues that trust in simulations should be grounded in empirical evidence, good engineering practice, and established theoretical principles. Without these constraints, computer simulation risks becoming little more than speculation. We argue against two prominent positions in the epistemology of computer simulation and defend a conservative view that emphasizes the difference between the norms governing scientific investigation and those governing ordinary epistemic practices.

Artefacts do not always do what they are supposed to, due to a variety of reasons, including manufacturing problems, poor maintenance, and normal wear-and-tear. Since software is an artefact, it should be subject to malfunctioning in the same sense in which other artefacts can malfunction. Yet, whether software is on a par with other artefacts when it comes to malfunctioning crucially depends on the abstraction used in the analysis. We distinguish between “negative” and “positive” notions of malfunction. A negative malfunction, (...) or dysfunction, occurs when an artefact token either does not or cannot do what it is supposed to. A positive malfunction, or misfunction, occurs when an artefact token may do what is supposed to but, at least occasionally, it also yields some unintended and undesirable effects. We argue that software, understood as type, may misfunction in some limited sense, but cannot dysfunction. Accordingly, one should distinguish software from other technical artefacts, in view of their design that makes dysfunction impossible for the former, while possible for the latter. (shrink)

A model is “any representation or concept that helps us to understand the world whenever common sense or direct observations are inadequate.” Common sense and direct observation often prove inadequate to the complexities of the twenty-first-century cities. Thus, models abound in urban life and governance. However, a model is not only a tool for control but a way of defining a situation. Framing the city so as to render it susceptible to interpretation and intervention is an exercise not merely with (...) scientific or technological value but with rhetorical power. The tradition of comprehensive urban models, beginning with the advent of computers and culminating in the self-analyzing “smart city,” I argue, sidelines this rhetorical power in favor of a tone of scientific authority that, while justifiable in technical domains, does not legitimately scale to the level of a political community. Making good on the civic potential of Big Data thus requires recontextualizing properly scientific enterprises within an adequate political philosophy of the city, allowing for the construction of cultural urban models that set human freedom at the core of its inner workings. (shrink)

Modelos representacionais são usados na prática científica para representar diferentes fenômenos. O propósito deste trabalho é examinar o uso de autômatos celulares para representar fenômenos emergentes, isto é, fenômenos com aspectos globais que não podem ser preditos apenas a partir de seus aspectos locais, procurando entender como se dá a representação nesse processo de modelagem. Uma abordagem sugerida é a acepção DEKI desenvolvida por Roman Frigg e James Nguyen, no qual o processo de representação envolve quatro aspectos: denotação do sistema-alvo (...) pelo modelo sob uma interpretação, exemplificação das propriedades relevantes no modelo, formulação de uma legenda que relaciona propriedades do modelo com propriedades do alvo e imputação das propriedades dadas pela chave ao alvo. Nessa acepção, AC representariam os sistemas-alvo denotados como sistemas complexos que podem ser interpretados em nível local e global, de modo que propriedades emergentes são exemplificadas em nível global. (shrink)