Performing abstraction: two ways of modelling<Emphasis Type="Italic"> Arabidopsis thaliana</Emphasis>

What is the best way to analyse abstraction in scientific modelling? I propose to focus on abstracting as an epistemic activity, which is achieved in different ways and for different purposes depending on the actual circumstances of modelling and the features of the models in question. This is in contrast to a more conventional use of the term ‘abstract’ as an attribute of models, which I characterise as black-boxing the ways in which abstraction is performed and to which epistemological advantage. I exemplify my claims through a detailed reconstruction of the practices involved in creating two types of models of the flowering plant Arabidopsis thaliana, currently the best-known model organism in plant biology. This leads me to distinguish between two types of abstraction processes: the ‘material abstracting’ required in the production of Arabidopsis specimens and the ‘intellectual abstracting’ characterising the elaboration of visual models of Arabidopsis genomics. Reflecting on the differences between these types of abstracting helps to pin down the epistemic skills and research commitments used by researchers to produce each model, thus clarifying how models are handled by researchers and with which epistemological implications.     

Extending, changing, and explaining the brain

This paper addresses concerns raised recently by Datteri (Biol Philos 24:301–324, 2009) and Craver (Philos Sci 77(5):840–851, 2010) about the use of brain-extending prosthetics in experimental neuroscience. Since the operation of the implant induces plastic changes in neural circuits, it is reasonable to worry that operational knowledge of the hybrid system will not be an accurate basis for generalisation when modelling the unextended brain. I argue, however, that Datteri’s no-plasticity constraint unwittingly rules out numerous experimental paradigms in behavioural and systems neuroscience which also elicit neural plasticity. Furthermore, I propose that Datteri and Craver’s arguments concerning the limitations of prosthetic modelling in basic neuroscience, as opposed to neuroengineering, rests on too narrow a view of the ways models in neuroscience should be evaluated, and that a more pluralist approach is needed. I distinguish organisational validity of models from mechanistic validity. I argue that while prosthetic models may be deficient in the latter of these explanatory virtues because of neuroplasticity, they excel in the former since organisational validity tracks the extent to which a model captures coding principles that are invariant with plasticity. Changing the brain, I conclude, is one viable route towards explaining the brain.     

Possibility,legitimacy, and the new ontologies of choice: a comment on Brubaker

In Trans, Rogers Brubaker makes a major argument about the contentious politics of the contemporary self. In this commentary, I first lay out what is think is the solidity of the book’s contrasting tableau of the functioning of race and gender in American society and beyond. I then point to Brubaker’s bundling together of issues of legitimacy and issues of ontology and begin to imagine what alternative analyses can come out of their unbundling – suggesting that race and gender are perhaps more analogous social formations than Trans argues. Finally, I bring attention to the role of ontological hierarchy in the formulation and policing of identity claims and conclude that the return of biology and the new empire of choice may not be two parallel, independent developments but one and the same process. Theoretically, I amplify one of the book’s epistemological contributions by calling for a reflexive turn in social-constructionist thought.     

Evolutionary arguments against moral realism: Why the empirical details matter (and which ones do)

The aim of this article is to identify the strongest evolutionary debunking argument (EDA) against moral realism and to assess on which empirical assumptions it relies. In the recent metaethical literature, several authors have de-emphasized the evolutionary component of EDAs against moral realism: presumably, the success or failure of these arguments is largely orthogonal to empirical issues. I argue that this claim is mistaken. First, I point out that Sharon Street’s and Michael Ruse’s EDAs both involve substantive claims about the evolution of our moral judgments. Next, I argue that combining their respective evolutionary claims can help debunkers to make the best empirical case against moral realism. Some realists have argued that the very attempt to explain the contents of our endorsed moral judgments in evolutionary terms is misguided, and have sought to escape EDAs by denying their evolutionary premise. But realists who pursue this reply can still be challenged on empirical grounds: debunkers may argue that the best, scientifically informed historical explanations of our moral endorsements do not involve an appeal to mind-independent truths. I conclude, therefore, that the empirical considerations relevant for the strongest empirically driven argument against moral realism go beyond the strictly evolutionary realm; debunkers are best advised to draw upon other sources of genealogical knowledge as well.     

Objects on the loose

What happens to the relations involved in ownership when faced with new claims and challenges? This article looks at three examples of the way in which Mongolians are managing claims to resources and responding to new regimes of ownership. In each case, recourse to models of ownership based on masters and custodians are marshalled and extended to suit new contexts. I suggest that these should not be viewed as modern responses to the inequalities of current economic and social life [cf. Comaroff and Comaroff. 1999, May. Occult Economies and the Violence of Abstraction: Notes from the South African Postcolony. American Ethnologist, 26(2): 279–303], nor should they be viewed as a historical remnant from some previous social life. Rather, and here I follow Tsing [2004. Friction: An Ethnography of Global Connection. Princeton: Princeton University Press; 2015a. The Mushroom at the End of the World: On the Possibility of Life in Capitalist Ruins. Princeton: Princeton University Press; 2015b. Salvage Accumulation, or the Structural Effects of Capitalist Generativity. In Theorizing the Contemporary, Cultural Anthropology Website, March 30, 2015. https://culanth.org/fieldsights/656-salvage-accumulation-or-the-structural-effects-of-capitalist-generativity], they may be viewed as an outcome of an innovative ‘friction’, or ‘salvage economy’, between global and local realities that gives rise to what Gibson-Graham [2006. A Postcapitalist Politics. Minnesota: Minnesota University Press] argues is a heterogeneous capitalist landscape, here manifested in Mongolia’s dramatically rising and falling mineral economy.     

Modelling the spatial distribution of wildlife animals using presence and absence data

This study was conducted to analyze the habitat preference of six major mammals for various environmental factors based on 100 random points within a mountain area in South Korea. In-situ presence and absence data for the mammals were surveyed and collected, and twelve explanatory variables related to topography, water, greenness, and anthropogenic influence were applied to create a habitat distribution model. The best combination of variables was determined using Moran’s I coefficients and Akaike criteria information, and applied to estimate the habitat preference for each species using GRASP v.3.0. The predictive map showed that wildlife animals in this study were mainly categorized into two groups: Group I (Korean squirrel, Sciurus vulgaris, mole, Talpa micrura and water deer, Hydropotes inermis), showed equal preference for all mountainous areas; Group II (weasel, Mustela sibirica, leopard cat, Felis bengalensis and raccoon dog, Nyctereutes procyonoides) showed different preferences in a mountain.     

It is better to be ignorant of our moral enhancement: A reply to Zambrano

In a recent issue of Bioethics, I argued that compulsory moral bioenhancement should be administered covertly. Alexander Zambrano has criticized this argument on two fronts. First, contrary to my claim, Zambrano claims that the prevention of ultimate harm by covert moral bioenhancement fails to meet conditions for permissible liberty-restricting public health interventions. Second, contrary to my claim, Zambrano claims that covert moral bioenhancement undermines autonomy to a greater degree than does overt moral bioenhancement. In this paper, I rebut both of these arguments, then finish by noting important avenues of research that Zambrano’s arguments motivate.     

Violinists,demandingness, and the impairment argument against abortion

The ‘impairment argument’ against abortion developed by Perry Hendricks aims to derive the wrongness of abortion from the wrongness of causing foetal alcohol syndrome (FAS). Hendricks endorses an ‘impairment principle’, which states that, if it is wrong to inflict an impairment of a certain degree on an organism, then, ceteris paribus, it is also wrong to inflict a more severe impairment on that organism. Causing FAS is wrong in virtue of the impairment it inflicts. But abortion inflicts an even more severe impairment (death), and so, ceteris paribus, is also wrong. Notably, Hendricks thinks that this argument does not require the claim that the foetus is a person. Here, I respond to Hendricks by arguing that the ceteris paribus clause of the impairment principle is not met in ordinary cases of pregnancy. Carrying an unwanted pregnancy to term is much more burdensome than is refraining from excessive drinking for nine months. This provides a pro tanto justification for obtaining an abortion that does not apply to causing FAS. If the foetus is not a person, it seems fairly clear to me that this justification is strong enough to render abortion permissible. Hendricks is therefore incorrect in claiming that the impairment argument can go without claims concerning foetal personhood. If the foetus is a person, then whether burdensomeness justifies abortion depends on certain questions relating to Thomson’s famous violinist argument. I will not attempt to answer those. But anyone who is otherwise sympathetic to Thomson’s argument should not be moved by the impairment argument.     

Dynamical crises,multistability and the influence of the duration of immunity in a seasonally-forced model of disease transmission

Background

Highly successful strategies to make populations more resilient to infectious diseases, such as childhood vaccinations programs, may nonetheless lead to unpredictable outcomes due to the interplay between seasonal variations in transmission and a population’s immune status.

Methods

Motivated by the study of diseases such as pertussis we introduce a seasonally-forced susceptible-infectious-recovered model of disease transmission with waning and boosting of immunity. We study the system’s dynamical properties using a combination of numerical simulations and bifurcation techniques, paying particular attention to the properties of the initial condition space.

Results

We find that highly unpredictable behaviour can be triggered by changes in biologically relevant model parameters such as the duration of immunity. In the particular system we analyse — previously used in the literature to study pertussis dynamics — we identify the presence of an initial-condition landscape containing three coexisting attractors. The system’s response to interventions which perturb population immunity (e.g. vaccination "catch-up" campaigns) is therefore difficult to predict.

Conclusion

Given the increasing use of models to inform policy decisions regarding vaccine introduction and scheduling and infectious diseases intervention policy more generally, our findings highlight the importance of thoroughly investigating the dynamical properties of those models to identify key areas of uncertainty. Our findings suggest that the often stated tension between capturing biological complexity and utilising mathematically simple models is perhaps more nuanced than generally suggested. Simple dynamical models, particularly those which include forcing terms, can give rise to incredibly complex behaviour.

     

Geometric service life modelling and discounting,a practical method for parametrised life cycle assessment

Purpose

To evaluate the long-term advantage of reusing building elements, including reduced material consumption and waste production, life cycle assessments are purposeful. To translate these assessments in relevant design advices, it is necessary to model accurately the service life of the considered elements and acknowledge the related uncertainties. Practical methods to do this are nevertheless lacking. In reaction, this paper proposes a new assessment method: geometric service life modelling and discounting.

Methods

The developed method is extensively parametric. Its formulas express an element’s service life in terms of a limited number of variables. This facilitates the evaluation of large series of elements as well as the automation of uncertainty analyses. Further, the method tackles different modelling complexities such as the interaction between replacements and refurbishments. Taking into account these complexities aligns the assessments with realistic service lives. For the presentation of the developed method, a focus on life cycle costing is chosen.

Results and discussion

In this paper, the outcomes of the newly developed method are compared to those of an existing calculation method and benchmarked with the manual modelling and assessment of 390 simplified building elements. This comparison is based on three indicators characterising the methods’ accuracy: the number of interventions, their individual impact and their resulting net present value. For each indicator, geometric discounting led to a considerable increase of accuracy compared to the existing method.

Conclusions

From this comparison, it is concluded that geometric service life modelling and discounting offers not only a well-defined procedure for parametrised life cycle assessment studies, this method is also more accurate than the existing one. Moreover, the uncertainty analyses it facilitates illustrate how detailed assessment outcomes and relevant design advices about the effectiveness of element reuse can be obtained. Nevertheless, further research about the method’s practical implementation is required.

     

Calls during agonistic interactions vary with arousal and raise audience attention in ravens

Background

Acoustic properties of vocalizations can vary with the internal state of the caller, and may serve as reliable indicators for a caller’s emotional state, for example to prevent conflicts. Thus, individuals may associate distinct characteristics in acoustic signals of conspecifics with specific social contexts, and adjust their behaviour accordingly to prevent escalation of conflicts. Common ravens (Corvus corax) crowd-forage with individuals of different age classes, sex, and rank, assemble at feeding sites, and engage in agonistic interactions of varying intensity. Attacked individuals frequently utter defensive calls in order to appease the aggressor. Here, we investigated if acoustic properties of defensive calls change with varying levels of aggression, and if bystanders respond to these changes.

Results

Individuals were more likely to utter defensive calls when the attack involved contact aggression, and when the attacker was higher in rank than the victim. Defensive calls produced during intense conflicts were longer and uttered at higher rates, and showed higher fundamental frequency- and amplitude-related measures than calls uttered during low-intensity aggression, indicating arousal-based changes in defensive calls. Playback experiments showed that ravens were more likely to react in response to defensive calls with higher fundamental frequency by orientating towards the speakers as compared to original calls and calls manipulated in duration.

Conclusions

Arousal-based changes are encoded in acoustic parameters of defensive calls in attacked ravens, and bystanders in the audience pay attention to the degree of arousal in attacked conspecifics. Our findings imply that common ravens can regulate conflicts with conspecifics by means of vocalizations, and are able to gather social knowledge from conspecific calls.

     

The distribution of an invasive fish species is highly affected by the presence of native fish species: evidence based on species distribution modelling

Topmouth gudgeon (Pseudorasbora parva) is one of the most invasive aquatic fish species in Europe and causes adverse effects to ecosystem structure and functioning. Knowledge and understanding of the species’ interactions with the environment and with native fish are important to stop and prevent the further spread of the species. Creating species distribution models is a useful technique to determine which factors influence the occurrence and abundance of a species. We applied three different modelling techniques: general additive models, random forests and fuzzy habitat suitability modelling (FHSM) to assess the habitat suitability of topmouth gudgeon. The former two techniques indicated that the abundance of native fish (i.e. biotic variables) was more important than environmental variables when determining the abundance of topmouth gudgeon in Flanders (Belgium). Bitterling (Rhodeus amarus), stone loach (Barbatula barbatula), three-spined stickleback (Gasterosteus aculeatus) and predator abundance were selected as the most important biotic variables and implemented in the FHSM to investigate species interactions. Depending on the preferred food source and spawning behaviour, either coexistence or interspecific competition can occur with bitterling, stone loach and three-spined stickleback. In contrast, the presence of predators clearly had a top down effect on topmouth gudgeon abundance. These findings could be applied as a biological control measure and implemented in conservation strategies in order to reduce the abundance of earlier established populations of topmouth gudgeon.     

Mirror self-recognition and symbol-mindedness

The view that mirror self-recognition (MSR) is a definitive demonstration of self-awareness is far from universally accepted, and those who do support the view need a more robust argument than the mere assumption that self-recognition implies a self-concept (e.g. Gallup in Socioecology and Psychology of Primates, Mouton, Hague, 1975; Gallup and Suarez in Psychological Perspectives on the Self, vol 3, Erlbaum, Hillsdale, 1986). In this paper I offer a new argument in favour of the view that MSR shows self-awareness by examining the nature of the mirror image itself. I argue, using the results of ‘symbol-mindedness’ experiments by Deloache (Trends Cogn Sci 8(2):66–70, 2004), that where self-recognition exists, the mirror image must be functioning as a symbol from the perspective of the subject and the subject must therefore be ‘symbol-minded’ and hence concept possessing. Further to this, according to the Concept Possession Hypothesis of Self-Consciousness (Savanah in Conscious Cogn 2011), concept possession alone is sufficient to demonstrate the existence of self-awareness. Thus MSR as a demonstration of symbol-mindedness implies the existence of self-awareness. I begin by defending the ‘mark test’ protocol as a robust methodology for determining self-recognition. Then follows a critical examination of the extreme views both for and against the interpretation of MSR as an indication of self-awareness: although the non-mentalistic interpretation of MSR is unconvincing, the argument presented by Gallup is also inadequate. I then present the symbol-mindedness argument to fill in the gaps in the Gallup approach.     

Autonomy,Natality and Freedom: A Liberal Re‐examination of Habermas in the Enhancement Debate

Jurgen Habermas has argued that carrying out pre‐natal germline enhancements would be inimical to the future child's autonomy. In this article, I suggest that many of the objections that have been made against Habermas' arguments by liberals in the enhancement debate misconstrue his claims. To explain why, I begin by explaining how Habermas' view of personal autonomy confers particular importance to the agent's embodiment and social environment. In view of this, I explain that it is possible to draw two arguments against germline enhancements from Habermas' thought. I call these arguments ‘the argument from negative freedom’ and ‘the argument from natality’. Although I argue that many of the common liberal objections to Habermas are not applicable when his arguments are properly understood, I go on to suggest ways in which supporters of enhancement might appropriately respond to Habermas' arguments.     

Nature protection as moral duty: The ethical trend in the Russian conservation movement

Conclusion Shortly after the October Revolution, Semenov-Tian-Shanskii prophetically remarked that voices in defense of nature in Russia under the new regime might be nothing more than miserable voices crying in the wilderness.⁵² Alas, this turned out to be all too true: by the end of the 1930s the voices of the aestheticethical approach had become silent in the wilderness of socialist construction.Nevertheless, I would not like to conclude my talk on this mournful note. Instead I would like to emphasize that, although the history of Russian environmental ethics turned out to be tragically brief, its basic ideas seem to me to be still relevant and important today. What I consider perhaps most important is the idea that is best expressed in Semenov-Tian-Shanskii's words: freedom is necessary for nature as it is necessary for humans.⁵³ This outlook calls us to surrender our pretensions to ontological superiority over the rest of nature. It calls us to recognize that nature is valuable in itself, and to live in harmonious cooperation with nature. *** DIRECT SUPPORT *** A8402064 00008     

Cost-Effectiveness of HBV and HCV Screening Strategies – A Systematic Review of Existing Modelling Techniques

Introduction

Studies evaluating the cost-effectiveness of screening for Hepatitis B Virus (HBV) and Hepatitis C Virus (HCV) are generally heterogeneous in terms of risk groups, settings, screening intervention, outcomes and the economic modelling framework. It is therefore difficult to compare cost-effectiveness results between studies. This systematic review aims to summarise and critically assess existing economic models for HBV and HCV in order to identify the main methodological differences in modelling approaches.

Methods

A structured search strategy was developed and a systematic review carried out. A critical assessment of the decision-analytic models was carried out according to the guidelines and framework developed for assessment of decision-analytic models in Health Technology Assessment of health care interventions.

Results

The overall approach to analysing the cost-effectiveness of screening strategies was found to be broadly consistent for HBV and HCV. However, modelling parameters and related structure differed between models, producing different results. More recent publications performed better against a performance matrix, evaluating model components and methodology.

Conclusion

When assessing screening strategies for HBV and HCV infection, the focus should be on more recent studies, which applied the latest treatment regimes, test methods and had better and more complete data on which to base their models. In addition to parameter selection and associated assumptions, careful consideration of dynamic versus static modelling is recommended. Future research may want to focus on these methodological issues. In addition, the ability to evaluate screening strategies for multiple infectious diseases, (HCV and HIV at the same time) might prove important for decision makers.     

Life cycle assessment of construction materials: the influence of assumptions in end-of-life modelling

Purpose

The nature of end-of-life (EoL) processes is highly uncertain for constructions built today. This uncertainty is often neglected in life cycle assessments (LCAs) of construction materials. This paper tests how EoL assumptions influence LCA comparisons of two alternative roof construction elements: glue-laminated wooden beams and steel frames. The assumptions tested include the type of technology and the use of attributional or consequential modelling approaches.

Methods

The study covers impact categories often considered in the construction industry: total and non-renewable primary energy demand, water depletion, global warming, eutrophication and photo-chemical oxidant creation. The following elements of the EoL processes are tested: energy source used in demolition, fuel type used for transportation to the disposal site, means of disposal and method for handling allocation problems of the EoL modelling. Two assumptions regarding technology development are tested: no development from today’s technologies and that today’s low-impact technologies have become representative for the average future technologies. For allocating environmental impacts of the waste handling to by-products (heat or recycled material), an attributional cut-off approach is compared with a consequential substitution approach. A scenario excluding all EoL processes is also considered.

Results and discussion

In all comparable scenarios, glulam beams have clear environmental benefits compared to steel frames, except for in a scenario in which steel frames are recycled and today’s average steel production is substituted, in which impacts are similar. The choice of methodological approach (attributional, consequential or fully disregarding EoL processes) does not seem to influence the relative performance of the compared construction elements. In absolute terms, four factors are shown to be critical for the results: whether EoL phases are considered at all, whether recycling or incineration is assumed in the disposal of glulam beams, whether a consequential or attributional approach is used in modelling the disposal processes and whether today’s average technology or a low-impact technology is assumed for the substituted technology.

Conclusions

The results suggest that EoL assumptions can be highly important for LCA comparisons of construction materials, particularly in absolute terms. Therefore, we recommend that EoL uncertainties are taken into consideration in any LCA of long-lived products. For the studied product type, LCA practitioners should particularly consider EoL assumptions regarding the means of disposal, the expected technology development of disposal processes and any substituted technology and the choice between attributional and consequential approaches.     

At the Margins of Moral Personhood

In this article I examine the proposition that severe cognitive disability is an impediment to moral personhood. Moral personhood, as I understand it here, is articulated in the work of Jeff McMahan as that which confers a special moral status on a person. I rehearse the metaphysical arguments about the nature of personhood that ground McMahan’s claims regarding the moral status of the “congenitally severely mentally retarded” (CSMR for short). These claims, I argue, rest on the view that only intrinsic psychological capacities are relevant to moral personhood: that is, that relational properties are generally not relevant. In addition, McMahan depends on an argument that species membership is irrelevant for moral consideration and a contention that privileging species membership is equivalent to a virulent nationalism (these will be discussed below). In consequence, the CSMR are excluded from moral personhood and their deaths are less significant as their killing is less wrong than that of persons. To throw doubt on McMahan’s conclusions about the moral status and wrongness of killing the CSMR I question the exclusive use of intrinsic properties in the metaphysics of personhood, the dismissal of the moral importance of species membership, and the example of virulent nationalism as an apt analogy. I also have a lot to say about McMahan’s empirical assumptions about the CSMR.     

Differences in preference for species-specific female calls between acoustically experienced and acoustically naive maleRibautodelphax planthoppers (Homoptera: Delphacidae)

Males of the planthopper Ribautodelphax imitanswere exposed to playbacks of either conspecific or heterospecific (R. imitantoides)female calls during their development from egg to adult, and thereafter these, as well as naive males,were offered a two- way choice between these calls. Males of all treatments approached the conspecific call significantly more often. However, males primed by the conspecific call chose the heterospecific call almost four times less often than did males primed by heterospecific calls or naive males, thus showing that the preference for conspecific calls can be partly learned. Males primed by heterospecific calls performed very similarly to completely naive males, suggesting that the signal recognition mechanism is much less sensitive to heterospecific calls than to conspecific calls. Males with experience of the conspecific female call tended to take more time to reach the call source in the trials than both other types of males. The evolutionary implications of these findings are discussed.