2024-03-28T19:22:24Z
http:///cgi/oai2
oai:philsci-archive.pitt.edu:162
2010-10-07T15:10:06Z
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
7375626A656374733D67656E:6574686963616C2D697373756573
7375626A656374733D67656E:736369656E63652D706F6C696379
74797065733D706974747072657072696E74
https://philsci-archive.pitt.edu/162/
The Import of Uncertainty
Mitchell, Sandra D.
Ecology/Conservation
Ethical Issues
Science and Policy
In this paper I argue that two domains of uncertainty should inform our strategies for making social policy on new genetic technologies. The first is biological complexity, which includes both unknown consequences on known variables and unknown unknowns. The second is value pluralism, which includes both moral conflict and moral pluralism. This framework is used to investigate policy on genetically modified food and suggests that adaptive management is required to track changes in biological knowledge of these interventions and that less simplistic, polemic representations of scientific knowledge are required to permit democratic decision making.
2000-05
Preprint
NonPeerReviewed
doc
en
https://philsci-archive.pitt.edu/162/1/final_paper.doc
Mitchell, Sandra D. (2000) The Import of Uncertainty. [Preprint]
oai:philsci-archive.pitt.edu:269
2010-10-07T15:10:17Z
7375626A656374733D73706563:62696F6C6F6779
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
74797065733D706974747072657072696E74
https://philsci-archive.pitt.edu/269/
Defining 'Biodiversity'; Assessing Biodiversity
Sarkar, Sahotra
Biology
Ecology/Conservation
This paper analyzes the concept of biodiversity in conservation biology and assesses potential methods for its measurement.
2001-05
Preprint
NonPeerReviewed
application/pdf
en
https://philsci-archive.pitt.edu/269/1/Biodiversity.pdf
Sarkar, Sahotra (2001) Defining 'Biodiversity'; Assessing Biodiversity. [Preprint]
oai:philsci-archive.pitt.edu:1955
2010-10-07T15:12:52Z
7374617475733D696E7072657373
7375626A656374733D67656E:6D6F64656C732D616E642D696465616C697A6174696F6E
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
74797065733D636F6E666572656E63655F6974656D
https://philsci-archive.pitt.edu/1955/
Qualitative Scientific Modeling and Loop Analysis
Justus, James
Models and Idealization
Ecology/Conservation
Loop analysis is a method of qualitative modeling anticipated by Sewall Wright and systematically developed by Richard Levins. In Levins’ (1966) distinctions between modeling strategies, loop analysis sacrifices precision for generality and realism. Besides criticizing the clarity of these distinctions, Orzack and Sober (1993) argued qualitative modeling is conceptually and methodologically problematic. Loop analysis of the stability of ecological communities shows this criticism is unjustified. It presupposes an overly narrow view of qualitative modeling and underestimates the broad role models play in scientific research, especially in helping scientists represent and understand complex systems.
2004
Conference or Workshop Item
PeerReviewed
application/pdf
en
https://philsci-archive.pitt.edu/1955/1/PSA_2004_submission.pdf
Justus, James (2004) Qualitative Scientific Modeling and Loop Analysis. In: UNSPECIFIED. (In Press)
oai:philsci-archive.pitt.edu:1963
2010-10-07T15:12:53Z
7374617475733D696E7072657373
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
74797065733D636F6E666572656E63655F6974656D
https://philsci-archive.pitt.edu/1963/
Qualitative Scientific Modeling and Loop Analysis
Justus, James
Ecology/Conservation
Loop analysis is a method of qualitative modeling anticipated by Sewall Wright and systematically developed by Richard Levins. In Levins’ (1966) distinctions between modeling strategies, loop analysis sacrifices precision for generality and realism. Besides criticizing the clarity of these distinctions, Orzack and Sober (1993) argued qualitative modeling is conceptually and methodologically problematic. Loop analysis of the stability of ecological communities shows this criticism is unjustified. It presupposes an overly narrow view of qualitative modeling and underestimates the broad role models play in scientific research, especially in helping scientists represent and understand complex systems.
2004
Conference or Workshop Item
PeerReviewed
application/pdf
en
https://philsci-archive.pitt.edu/1963/1/PSA_2004_submission.pdf
Justus, James (2004) Qualitative Scientific Modeling and Loop Analysis. In: UNSPECIFIED. (In Press)
oai:philsci-archive.pitt.edu:2170
2010-10-07T15:21:03Z
oai:philsci-archive.pitt.edu:2987
2010-10-07T15:14:30Z
7375626A656374733D67656E:6D6F64656C732D616E642D696465616C697A6174696F6E
7375626A656374733D73706563:6D617468656D6174696373
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
74797065733D636F6E666572656E63655F6974656D
https://philsci-archive.pitt.edu/2987/
Ecological and Lyapunov Stability
Justus, James
Models and Idealization
Mathematics
Ecology/Conservation
Ecologists have proposed several incompatible definitions of ecological stability. Emulating physicists, mathematical ecologists commonly define it as Lyapunov stability. This formalizes the problematic concept by integrating it into a well-developed mathematical theory. The formalization also seems to capture the intuition that ecological stability depends on how ecological systems respond to perturbation. Despite these advantages, this definition is flawed. Although Lyapunov stability adequately characterizes perturbation responses of systems typically studied in physics, it does not for ecological systems. This failure reveals a limitation of its underlying mathematical theory, and an important difference between dynamic systems modeling in physics and biology.
2006
Conference or Workshop Item
NonPeerReviewed
application/pdf
en
https://philsci-archive.pitt.edu/2987/1/PSA_2006_Justus_10-15-06.pdf
Justus, James (2006) Ecological and Lyapunov Stability. In: UNSPECIFIED.
oai:philsci-archive.pitt.edu:4085
2013-02-28T22:33:11Z
7375626A656374733D67656E:6D6F64656C732D616E642D696465616C697A6174696F6E
7375626A656374733D73706563:62696F6C6F6779
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
74797065733D706974747072657072696E74
https://philsci-archive.pitt.edu/4085/
The Robust Volterra Principle
Weisberg, Michael
Reisman, Kenneth
Models and Idealization
Biology
Ecology/Conservation
Theorizing in ecology and evolution often proceeds via the construction of multiple idealized models. To determine whether a theoretical result actually depends on core features of the models and is not an artifact of simplifying assumptions, theorists have developed the technique of robustness analysis, the examination of multiple models looking for common predictions. A striking example of robustness analysis in ecology is the discovery of the Volterra Principle, which describes the effect of general biocides in predator-prey systems. This paper details the discovery of the Volterra Principle and the demonstration of its robustness. It considers the classical ecology literature on robustness and introduces two individual-based models of predation, which are used to further analyze the Volterra Principle. The paper also introduces a distinction between \emph{parameter robustness}, \emph{structural robustness}, and \emph{representational robustness}, and demonstrates that the Volterra Principle exhibits all three kinds of robustness.
2008-01
Preprint
NonPeerReviewed
application/pdf
en
https://philsci-archive.pitt.edu/4085/1/VolterraPrinciplefinal.pdf
text/plain
en
https://philsci-archive.pitt.edu/4085/2/Wolf_Sheep_Predation-biocide.nlogo
other
en
https://philsci-archive.pitt.edu/4085/5/stable-probabilistic-predation.nlogo
Weisberg, Michael and Reisman, Kenneth (2008) The Robust Volterra Principle. [Preprint]
oai:philsci-archive.pitt.edu:4509
2010-10-07T15:17:44Z
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
7375626A656374733D67656E:6D6F64656C732D616E642D696465616C697A6174696F6E
7375626A656374733D67656E:6C6177732D6F662D6E6174757265
74797065733D636F6E666572656E63655F6974656D
https://philsci-archive.pitt.edu/4509/
From Laws to Models and Mechanisms: Ecology in the Twentieth Century
Wilson, Brad
Ecology/Conservation
Models and Idealization
Laws of Nature
Philosophers, and to a lesser degree historians, have paid much less attention to the discipline of ecology than to other areas of science (e.g. physics, chemistry, biology) as a focus for addressing issues in the philosophy of science. In this paper, I hope to begin to address this imbalance. There is much to be learned from ecology about some of the current issues in the philosophy of science. Because ecology is a relatively young discipline, it is possible to trace significant changes in the relative importance of concepts such as laws, theories, models and mechanisms in historically short periods of time. To a large extent, the history of ecology serves as a microcosm of the larger history of science. My focus is on the origins of population ecology in the 1920’s and 30’s (see Kingsland, 1985, for a good overview). My thesis is that in this early period in the development of population ecology, for some ecologists (especially Pearl), the development of mathematics was integral to the search for laws in ecology. However, I will argue that while mathematical models continue to play a central role in ecology, the significance of generalizable ecological laws is much less prevalent today. In the early history of population ecology, emphasis was placed on the discovery of laws in the development of general theories. In contemporary ecological research, the emphasis is on modeling, with a corresponding search for underlying ecological mechanisms. Philosophers of science working in other areas have recognized a similar shift, from laws and theories to models and mechanisms. The context of ecology provides a new arena in which to examine this shift.
2009
Conference or Workshop Item
NonPeerReviewed
doc
en
https://philsci-archive.pitt.edu/4509/1/Laws_and_Models_in_Ecology%2C_%26HPS2.doc
Wilson, Brad (2009) From Laws to Models and Mechanisms: Ecology in the Twentieth Century. In: UNSPECIFIED.
oai:philsci-archive.pitt.edu:4810
2010-10-07T15:18:26Z
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65766F6C7574696F6E6172792D7468656F7279
7375626A656374733D67656E:6578706572696D656E746174696F6E
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
74797065733D636F6E666572656E63655F6974656D
https://philsci-archive.pitt.edu/4810/
Experiments in Ecology and Evolutionary Biology
Wilson, Brad
Evolutionary Theory
Experimentation
Ecology/Conservation
Most of the philosophical work done on experimentation has focused on the physical sciences, i.e., physics and chemistry. I consider to what extent this work is relevant to experimentation in ecology and evolutionary biology, and will identify some important differences between laboratory experiments and experiments in nature. I focus on the ontological and epistemological aspects of experiments in the physical sciences and the life sciences and argue that experiments in ecology and evolutionary biology provide knowledge of particular systems from which it is difficult to generalize.
2009
Conference or Workshop Item
NonPeerReviewed
application/pdf
en
https://philsci-archive.pitt.edu/4810/1/Nature_as_Laboratory_for_SPSP.docx
Wilson, Brad (2009) Experiments in Ecology and Evolutionary Biology. In: UNSPECIFIED.
oai:philsci-archive.pitt.edu:5234
2010-10-07T15:19:23Z
7375626A656374733D73706563:70737963686F6C6F67792D70737963686961747279
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
7375626A656374733D73706563:616E7468726F706F6C6F6779
74797065733D636F6E666572656E63655F6974656D
https://philsci-archive.pitt.edu/5234/
More than Designing an Ethogram, The Implications of Choosing a Methodology in Primatology
Botero, Maria
Psychology
Ecology/Conservation
Anthropology
All methodologies used to characterize mother-infant interaction includes mother, infant, and other social factors. The chief difference is how each methodology selects certain elements of this interaction as relevant. I will argue that in the context of the mother-infant interaction a methodology’s results depend on the model’s presuppositions on the nature of communication. These presupposition affects the kinds of questions asked, the kind of data obtained, and how these data are analyzed. I will show this by contrasting two different analysis of separation studies in infant primates: what I call the Ecological-Linear approach vs. Dynamic System Theory (DST) approach.
2009
Conference or Workshop Item
NonPeerReviewed
doc
en
https://philsci-archive.pitt.edu/5234/1/More_than_Designing_an_Ethogram-Botero.doc
Botero, Maria (2009) More than Designing an Ethogram, The Implications of Choosing a Methodology in Primatology. In: UNSPECIFIED.
oai:philsci-archive.pitt.edu:9226
2012-07-13T00:00:15Z
7375626A656374733D73706563:62696F6C6F6779
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65766F6C7574696F6E6172792D7468656F7279
74797065733D706974747072657072696E74
https://philsci-archive.pitt.edu/9226/
Exploring the Status of Population Genetics: The Role of Ecology
Millstein, Roberta L.
Biology
Ecology/Conservation
Evolutionary Theory
The status of population genetics has become hotly debated among biologists and philosophers of biology. Many seem to view population genetics as relatively unchanged since the Modern Synthesis and have argued that subjects such as development were left out of the Synthesis. Some have called for an extended evolutionary synthesis or for recognizing the insignificance of population genetics. Yet others such as Michael Lynch have defended population genetics, declaring "nothing in evolution makes sense except in the light of population genetics" (a twist on Dobzhansky's famous slogan that "nothing in biology makes sense except in the light of evolution"). Missing from this discussion is the use of population genetics to shed light on ecology and vice versa, beginning in the 1940s and continuing until the present day. I highlight some of that history through an overview of traditions such as ecological genetics and population biology, followed by a slightly more in-depth look at a contemporary study of the endangered California Tiger Salamander. I argue that population genetics is a powerful and useful tool that continues to be used and modified, even if it isn't required for all evolutionary explanations or doesn't incorporate all the causal factors of evolution.
2012-07-11
Preprint
NonPeerReviewed
application/pdf
en
https://philsci-archive.pitt.edu/9226/1/Millstein-PopGen-Ecology.pdf
Millstein, Roberta L. (2012) Exploring the Status of Population Genetics: The Role of Ecology. [Preprint]
oai:philsci-archive.pitt.edu:9434
2012-11-10T14:52:55Z
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65766F6C7574696F6E6172792D7468656F7279
7375626A656374733D67656E:6D6F64656C732D616E642D696465616C697A6174696F6E
74797065733D636F6E666572656E63655F6974656D
https://philsci-archive.pitt.edu/9434/
Individual Based Models in Ecology:
An Evaluation, or How Not to Ruin a Good Thing
Roughgarden, Joan
Ecology/Conservation
Evolutionary Theory
Models and Idealization
2012-11-09
Conference or Workshop Item
NonPeerReviewed
application/pdf
en
https://philsci-archive.pitt.edu/9434/1/RoughgardenPSA2012IBMLecture.pdf
Roughgarden, Joan (2012) Individual Based Models in Ecology: An Evaluation, or How Not to Ruin a Good Thing. In: UNSPECIFIED.
oai:philsci-archive.pitt.edu:9547
2013-02-01T15:29:07Z
7375626A656374733D73706563:62696F6C6F6779
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
74797065733D706974747072657072696E74
https://philsci-archive.pitt.edu/9547/
Environmental Ethics
Millstein, Roberta L.
Biology
Ecology/Conservation
A number of areas of biology raise questions about what is of value in the natural environment and how we ought to behave towards it: conservation biology, environmental science, and ecology, to name a few. Based on my experience teaching students from these and similar majors, I argue that the field of environmental ethics has much to teach these students. They come to me with pent-up questions and a feeling that more is needed to fully engage in their subjects, and I believe some exposure to environmental ethics can help focus their interests and goals. I identify three primary areas in which environmental ethics can con- tribute to their education. The first is an examination of who (or what) should be considered to be part of our moral community (i.e., the community to whom we owe direct duties). Is it humans only? Or does it include all sentient life? Or all life? Or ecosystems considered holistically? Often, readings implicitly assume one or more of these answers; the goal is to make the student more sensitive to these implicit claims and to get them to think about the different reasons that support them. The second area, related to the first, is the application of the different answers concerning the extent of the ethical community to real environmental issues and problems. Students need to be aware of how the different answers concerning the moral community can imply conflicting answers for how we should act in certain cases and to think about ways to move toward conflict resolution. The third area in which environmental ethics can contribute is a more conceptual one, focusing on central concepts such as biodiversity, sustainability, species, and ecosystems. Exploring and evaluating various meanings of these terms will make students more reflective and thoughtful citizens and biologists, sensitive to the implications that different conceptual choices make.
2013
Preprint
NonPeerReviewed
application/pdf
en
https://philsci-archive.pitt.edu/9547/1/Millstein2013-EnvironmentalEthics.pdf
Millstein, Roberta L. (2013) Environmental Ethics. [Preprint]
https://www.springer.com/philosophy/epistemology+and+philosophy+of+science/book/978-94-007-6536-8
oai:philsci-archive.pitt.edu:9552
2013-02-08T14:38:05Z
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
7375626A656374733D67656E:636175736174696F6E
7375626A656374733D67656E:636F6E6669726D6174696F6E2D696E64756374696F6E
7375626A656374733D73706563:65617274682D736369656E636573
7375626A656374733D67656E:6578706572696D656E746174696F6E
7375626A656374733D67656E:686973746F72792D6F662D736369656E63652D636173652D73747564696573
7375626A656374733D67656E:6D6F64656C732D616E642D696465616C697A6174696F6E
74797065733D7075626C69736865645F61727469636C65
https://philsci-archive.pitt.edu/9552/
Modeling causal structures: Volterra's struggle and Darwin's success
Scholl, Raphael
Räz, Tim
Ecology/Conservation
Causation
Confirmation/Induction
Earth Sciences
Experimentation
History of Science Case Studies
Models and Idealization
The Lotka-Volterra predator-prey-model is a widely known example of model-based science. Here we reexamine Vito Volterra's and Umberto D'Ancona's original publications on the model, and in particular their methodological reflections. On this basis we develop several ideas pertaining to the philosophical debate on the scientific practice of modeling. First, we show that Volterra and D'Ancona chose modeling because the problem in hand could not be approached by more direct methods such as causal inference. This suggests a philosophically insightful motivation for choosing the strategy of modeling. Second, we show that the development of the model follows a trajectory from a "how possibly" to a "how actually" model. We discuss how and to what extent Volterra and D'Ancona were able to advance their model along that trajectory. It turns out they were unable to establish that their model was fully applicable to any system. Third, we consider another instance of model-based science: Darwin's model of the origin and distribution of coral atolls in the Pacific Ocean. Darwin argued more successfully that his model faithfully represents the causal structure of the target system, and hence that it is a "how actually" model.
Springer
2013
Published Article or Volume
NonPeerReviewed
application/pdf
en
https://philsci-archive.pitt.edu/9552/1/scholl-raz-2013.pdf
Scholl, Raphael and Räz, Tim (2013) Modeling causal structures: Volterra's struggle and Darwin's success. European Journal for Philosophy of Science, 3 (1). pp. 115-132. ISSN 1879-4912
http://link.springer.com/article/10.1007/s13194-012-0060-z
10.1007/s13194-012-0060-z
oai:philsci-archive.pitt.edu:9805
2013-05-31T12:39:20Z
7375626A656374733D73706563:616E7468726F706F6C6F6779
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D646576656C6F706D656E74616C
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65766F6C7574696F6E6172792D7468656F7279
7375626A656374733D73706563:65636F6E6F6D696373
7375626A656374733D67656E:6D6F64656C732D616E642D696465616C697A6174696F6E
74797065733D636F6E666572656E63655F6974656D
https://philsci-archive.pitt.edu/9805/
Eco-phenotypic physiologies: a new kind of modeling for unifying evolution, ecology and cultural transmission
Panebianco, Fabrizio
Serrelli, Emanuele
Anthropology
Developmental Biology
Ecology/Conservation
Evolutionary Theory
Economics
Models and Idealization
Mathematical modeling can ground communication and reciprocal enrichment among fields of knowledge whose domains are very different. We propose a new mathematical model applicable in biology, specified into ecology and evolutionary biology, and in cultural transmission studies, considered as a branch of economics. Main inspiration for the model are some biological concepts we call “eco-phenotypic” such as development, plasticity, reaction norm, phenotypic heritability, epigenetics, and niche construction. “Physiology” is a core concept we introduce and translate differently in the biological and cultural domains. The model is ecological in that it aims at describing and studying organisms and populations that perform living, intended as a thermodynamic, matter-energy process concerning resources gathering, usage, and depletion in a spatiotemporal context with given characteristics, as well as with multiplication and space occupation. The model also supports evolution, intended as a dynamics including cumulative change in the features of unique organisms that are connected into breeding populations. The model is then applicable to the economics of cultural transmission in which individuals form their attitudes and patterns of behavior under a complex system of influences derived from their “cultural parents”, other members of the society, and the environment. On the side of biology, an innovative goal is to integrate in a single model all the eco-phenotypic concepts as well as both evolution and ecology. On the side of cultural transmission, eco-phenotypic modeling seems more appropriate in capturing some aspects of cultural systems which are modeled away in the earlier framework based on Mendelian population genetics.
2013-05-28
Conference or Workshop Item
NonPeerReviewed
application/pdf
en
cc_by_nc_nd
https://philsci-archive.pitt.edu/9805/1/Panebianco_Serrelli_-_Eco-phenotypic_physiologies_-_Evolutionary_Patterns_2013.pdf
Panebianco, Fabrizio and Serrelli, Emanuele (2013) Eco-phenotypic physiologies: a new kind of modeling for unifying evolution, ecology and cultural transmission. In: UNSPECIFIED.
http://evolutionarypatterns.fc.ul.pt
oai:philsci-archive.pitt.edu:10027
2013-10-01T12:53:00Z
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
7375626A656374733D67656E:6574686963616C2D697373756573
7375626A656374733D67656E:6D6F64656C732D616E642D696465616C697A6174696F6E
7375626A656374733D67656E:736369656E63652D616E642D736F6369657479
7375626A656374733D67656E:736369656E63652D706F6C696379
7375626A656374733D67656E:76616C7565732D696E2D736369656E6365
74797065733D706974747072657072696E74
https://philsci-archive.pitt.edu/10027/
Non-Epistemic Values and the Multiple Goals of Science
Elliott, Kevin
McKaughan, Daniel
Ecology/Conservation
Ethical Issues
Models and Idealization
Science and Society
Science and Policy
Values In Science
Recent efforts to argue that non-epistemic values have a legitimate role to play in assessing scientific models, theories, and hypotheses typically either reject the distinction between epistemic and non-epistemic values or incorporate non-epistemic values only as a secondary consideration for resolving epistemic uncertainty. Given that scientific representations can legitimately be evaluated not only based on their fit with the world but also with respect to their fit with the needs of their users, we show in two case studies that non-epistemic values can play a legitimate role as factors that override epistemic considerations in assessing scientific representations for practical purposes.
2013-09-30
Preprint
NonPeerReviewed
application/msword
en
https://philsci-archive.pitt.edu/10027/1/Epistemic_Values_and_Multiple_Goals_of_Science_PREPRINT_FOR_ARCHIVE.docx
Elliott, Kevin and McKaughan, Daniel (2013) Non-Epistemic Values and the Multiple Goals of Science. [Preprint]
oai:philsci-archive.pitt.edu:10244
2014-01-26T13:24:56Z
7375626A656374733D73706563:62696F6C6F6779
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65766F6C7574696F6E6172792D7468656F7279
74797065733D636F6E666572656E63655F6974656D
https://philsci-archive.pitt.edu/10244/
How the Concept of 'Population' Resolves Concepts of 'Environment'
Millstein, Roberta L.
Biology
Ecology/Conservation
Evolutionary Theory
Millstein (2009, 2010) defends the “causal interactionist population concept” (CIPC). Here I further defend the CIPC by showing how it clarifies another concept that biologists grapple with, namely, environment. Should we understand selection as ranging only over homogeneous environments or, alternatively, as ranging over any habitat area we choose to study? I argue instead that the boundaries of the population dictate the range of the environment, whether homogeneous or heterogeneous, over which selection operates. Thus, understanding the concept of “population” helps us to understand concepts of “selective environment,” exemplifying the importance of the CIPC to other concepts and debates.
2014
Conference or Workshop Item
NonPeerReviewed
application/pdf
en
https://philsci-archive.pitt.edu/10244/1/Millstein2014-population-environment-concepts.pdf
Millstein, Roberta L. (2014) How the Concept of 'Population' Resolves Concepts of 'Environment'. In: UNSPECIFIED.
oai:philsci-archive.pitt.edu:10608
2014-04-11T18:12:57Z
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
7375626A656374733D67656E:686973746F72792D6F662D736369656E63652D636173652D73747564696573
74797065733D6F74686572
https://philsci-archive.pitt.edu/10608/
The theory of the rise of sap in trees: some historical and conceptual remarks
Brown, Harvey R.
Ecology/Conservation
History of Science Case Studies
The ability of trees to suck water from roots to leaves, sometimes to heights of over a hundred meters, is remarkable given the absence of any mechanical pump. This study deals with a number of issues, of both an historical and conceptual nature, in the orthodox ``Cohesion-Tension'' theory of the ascent of sap in trees. The theory relies chiefly on the exceptional cohesive and adhesive properties of water, the structural properties of trees, and the role of evaporation (``transpiration'') from leaves. But it is not the whole story. Plant scientists have been aware since the inception of the theory in the late 19th century that further processes are at work in order to “prime” the trees, the main such process -- growth itself -- being so obvious to them that it is often omitted from the story. Other factors depend largely on the type of tree, and are not always fully understood. For physicists, in particular, it may be helpful to see the fuller picture, which is what this study attempts to provide in non-technical terms.
Springer
Other
NonPeerReviewed
application/pdf
en
https://philsci-archive.pitt.edu/10608/1/trees_final.pdf
Brown, Harvey R. The theory of the rise of sap in trees: some historical and conceptual remarks. Springer, Basel.
http://link.springer.com/journal/16
10.1007/s00016-013-0117-1
oai:philsci-archive.pitt.edu:10876
2014-07-14T18:29:16Z
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
7375626A656374733D67656E:64657465726D696E69736D2D696E64657465726D696E69736D
7375626A656374733D67656E:76616C7565732D696E2D736369656E6365
74797065733D636F6E666572656E63655F6974656D
https://philsci-archive.pitt.edu/10876/
You Can't Go Home Again - or Can you? 'Replication' Indeterminacy and 'Location' Incommensurability in Three Biological Re-Surveys
Shavit, Ayelet
Ecology/Conservation
Determinism/Indeterminism
Values In Science
Reproducing empirical results and repeating experimental processes is fundamental to science, but is of grave concern to scientists. Revisiting the same location is necessary for tracking biological processes, yet I argue that ‘location’ and ‘replication’ contain a basic ambiguity. The analysis of the practical meanings of ‘replication’ and ‘location’ will strip of incommensurability from its common conflation with empirical equivalence, underdetermination and indeterminacy of reference. In particular, I argue that three biodiversity re-surveys, conducted by the research institutions of Harvard, Berkeley, and Hamaarag, all reveal incommensurability without indeterminacy in the smallest spatial scale, and indeterminacy without incommensurability in higher scales.
2014-03-01
Conference or Workshop Item
NonPeerReviewed
application/pdf
en
https://philsci-archive.pitt.edu/10876/1/PSA2014_Archive.pdf
Shavit, Ayelet (2014) You Can't Go Home Again - or Can you? 'Replication' Indeterminacy and 'Location' Incommensurability in Three Biological Re-Surveys. In: UNSPECIFIED.
oai:philsci-archive.pitt.edu:10936
2016-01-02T13:22:18Z
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
7375626A656374733D67656E:6C6177732D6F662D6E6174757265
74797065733D636F6E666572656E63655F6974656D
https://philsci-archive.pitt.edu/10936/
Against Lawton’s contingency thesis, or, why the reported demise of community ecology is greatly exaggerated
Linquist, Stefan
Ecology/Conservation
Laws of Nature
Lawton’s contingency thesis (CT) states that there are no useful generalizations (“laws”) at the level of ecological communities because these systems are especially prone to contingent historical events. I argue that this influential thesis has been grounded on the wrong kind of evidence. CT is best understood in Woodward’s (2010) terms as a claim about the instability of certain causal dependencies across different background conditions. A recent distinction between evolution and ecology reveals what an adequate test of Lawton’s thesis would look like. To date, CT remains untested. But developments in genome and molecular ecology point in a promising direction.
2014-08-08
Conference or Workshop Item
NonPeerReviewed
application/pdf
en
https://philsci-archive.pitt.edu/10936/1/againstlawton%28PSA%29.pdf
Linquist, Stefan (2014) Against Lawton’s contingency thesis, or, why the reported demise of community ecology is greatly exaggerated. In: UNSPECIFIED.
oai:philsci-archive.pitt.edu:10941
2014-08-10T15:18:37Z
7375626A656374733D73706563:62696F6C6F6779
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
7375626A656374733D67656E:6C6177732D6F662D6E6174757265
7375626A656374733D67656E:6D6F64656C732D616E642D696465616C697A6174696F6E
7375626A656374733D73706563:70726F626162696C6974792D73746174697374696373
7375626A656374733D67656E:726564756374696F6E69736D2D686F6C69736D
7375626A656374733D73706563:70687973696373:737461746973746963616C2D6D656368616E6963732D746865726D6F64796E616D696373
74797065733D636F6E666572656E63655F6974656D
https://philsci-archive.pitt.edu/10941/
Ceteris Paribus Laws and Minutis Rectis Laws
Fenton-Glynn, Luke
Biology
Ecology/Conservation
Laws of Nature
Models and Idealization
Probability/Statistics
Reductionism/Holism
Statistical Mechanics/Thermodynamics
Special science generalizations admit of exceptions. Among the class of non-exceptionless special science generalizations, I distinguish (what I will call) minutis rectis (mr) generalizations from the more familiar category of ceteris paribus (cp) generalizations. I argue that the challenges involved in showing that mr generalizations can play the law role are underappreciated, and quite different from those involved in showing that cp generalizations can do so. I outline some potential strategies for meeting the challenges posed by mr generalizations.
2014-08-10
Conference or Workshop Item
NonPeerReviewed
application/pdf
en
https://philsci-archive.pitt.edu/10941/1/Ceteris_Paribus_Laws_and_Minutis_Rectis_Laws.pdf
Fenton-Glynn, Luke (2014) Ceteris Paribus Laws and Minutis Rectis Laws. In: UNSPECIFIED.
oai:philsci-archive.pitt.edu:11012
2014-09-07T19:35:26Z
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D646576656C6F706D656E74616C
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65766F6C7574696F6E6172792D7468656F7279
7375626A656374733D67656E:6578706572696D656E746174696F6E
7375626A656374733D67656E:6578706C616E6174696F6E
7375626A656374733D67656E:7374727563747572652D6F662D7468656F72696573
74797065733D636F6E666572656E63655F6974656D
https://philsci-archive.pitt.edu/11012/
Atrazine Research and Criteria of Characterizational Adequacy
Powers, Jack
Developmental Biology
Ecology/Conservation
Evolutionary Theory
Experimentation
Explanation
Structure of Theories
The effects of atrazine on amphibians has been the subject of much research, requiring the input of many disciplines. Theory reductive accounts of the relationships among scientific disciplines do not seem to characterize well the ways that diverse disciplines interact in the context of addressing such complex scientific problems. "Problem agenda" accounts of localized scientific integrations seem to fare better. However, problem agenda accounts have tended to focus rather narrowly on scientific explanation. Attention to the details of atrazine research reveals that characterization deserves the sort of attention that problem agenda theorists have thus far reserved for explanation.
2014-01-01
Conference or Workshop Item
NonPeerReviewed
application/pdf
en
https://philsci-archive.pitt.edu/11012/1/Powers_2014_Atrazine_and_CCA_PSA.pdf
Powers, Jack (2014) Atrazine Research and Criteria of Characterizational Adequacy. In: UNSPECIFIED.
oai:philsci-archive.pitt.edu:11283
2016-03-25T02:16:05Z
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
7375626A656374733D67656E:6574686963616C2D697373756573
7375626A656374733D67656E:686973746F72792D6F662D736369656E63652D636173652D73747564696573
74797065733D706974747072657072696E74
https://philsci-archive.pitt.edu/11283/
Re-examining the Darwinian Basis for Aldo Leopold’s Land Ethic
Millstein, Roberta L.
Ecology/Conservation
Ethical Issues
History of Science Case Studies
Many philosophers have become familiar with Leopold’s land ethic through the writings of J. Baird Callicott, who claims that Leopold bases his land ethic on a “protosociobiological” argument that Darwin gives in the Descent of Man. On this view, which has become the canonical interpretation, Leopold’s land ethic is based on extending our moral sentiments to ecosystems. I argue that the evidence weighs in favor of an alternative interpretation of Leopold; his reference to Darwin does not refer to the Descent, but rather to the Origin of Species, where Darwin discusses the interdependencies between organisms in the struggle for existence.
2015-01-29
Preprint
NonPeerReviewed
application/pdf
en
https://philsci-archive.pitt.edu/11283/1/Millstein-Darwin-Leopold-3-1.pdf
Millstein, Roberta L. (2015) Re-examining the Darwinian Basis for Aldo Leopold’s Land Ethic. [Preprint]
oai:philsci-archive.pitt.edu:11483
2015-05-28T13:21:24Z
7375626A656374733D73706563:62696F6C6F6779
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
7375626A656374733D67656E:6578706572696D656E746174696F6E
74797065733D636F6E666572656E63655F6974656D
https://philsci-archive.pitt.edu/11483/
Types of Experiments and Causal Process Tracing:
What Happened on the Kaibab Plateau in the 1920s?
Millstein, Roberta L.
Biology
Ecology/Conservation
Experimentation
I argue that Binkley et al. use causal process tracing in conjunction with a natural trajectory experiment and two natural snapshot experiments in their re-examination of the Kaibab. This shows that Aldo Leopold may have been right about trophic cascade in the Kaibab in the 1920s, i.e., that there are good (albeit defeasible) reasons to think that a loss of predators (together with fire suppression) led to a deer irruption which decreased aspen recruitment. Using the different cause-finding practices in combination can strengthen causal inferences and mitigate the shortcomings that each practice has.
2014-11
Conference or Workshop Item
NonPeerReviewed
application/pdf
en
https://philsci-archive.pitt.edu/11483/1/Millstein_-_Nat_Expts_and_CPT-Kaibab-draft.pdf
Millstein, Roberta L. (2014) Types of Experiments and Causal Process Tracing: What Happened on the Kaibab Plateau in the 1920s? In: UNSPECIFIED.
oai:philsci-archive.pitt.edu:11586
2015-07-22T15:10:52Z
7375626A656374733D73706563:62696F6C6F6779
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
7375626A656374733D67656E:6574686963616C2D697373756573
7375626A656374733D67656E:686973746F72792D6F662D736369656E63652D636173652D73747564696573
74797065733D636F6E666572656E63655F6974656D
https://philsci-archive.pitt.edu/11586/
Is Aldo Leopold's 'Land Community' an Individual?
Millstein, Roberta L.
Biology
Ecology/Conservation
Ethical Issues
History of Science Case Studies
Aldo Leopold’s Land Ethic has often been interpreted as ascribing intrinsic value to what he calls the biotic community. But what is the biotic community? Is it actually an entity at all, which might seem necessary (albeit not sufficient) for it to be intrinsically valuable; more precisely, is it an individual?
Some authors equate Leopold’s “biotic community” with “ecosystem.” It is true that Leopold’s concept of “biotic community” is similar to that of “ecosystem,” since like an ecosystem it includes abiotic components and like an ecosystem it is at least partially characterized in terms of energy flow. However, Leopold also emphasizes that a biotic community is composed of interdependent parts. By underscoring the interactions between species and the way in which changes in some species affect other species, his concept of “biotic community” sounds a bit more like the concept of “community” studied by community ecologists.
So, perhaps Leopold’s “biotic community” blends the concepts of “ecosystem” and “community” in some fashion. But this blending raises a complication, which is illuminated nicely by considering a recent essay by Jay Odenbaugh. Odenbaugh invokes a “causal relations” criterion of individuality; the relevant causal relations for communities are interactions between species whereas the relevant causal relations for ecosystems consist of nutrient and energy cycling. If this is right, what sense can be made, if any, of a blended community-ecosystem? Would it be an individual as well? I explore answers to these questions, considering, e.g., recent attempts to integrate community and ecosystem ecology. My goal is to shed light on what an integrated community-ecosystem might look like and how to make sense of the relationship between a community-individual, an ecosystem-individual, and a community-ecosystem-individual, helping to provide a solid basis for Leopold’s Land Ethic.
2015-07
Conference or Workshop Item
NonPeerReviewed
application/pdf
en
https://philsci-archive.pitt.edu/11586/1/Millstein_-_Land_Community_as_Individual_-_presented_draft.pdf
Millstein, Roberta L. (2015) Is Aldo Leopold's 'Land Community' an Individual? In: UNSPECIFIED.
oai:philsci-archive.pitt.edu:11635
2015-08-26T14:43:32Z
7375626A656374733D73706563:62696F6C6F6779
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65766F6C7574696F6E6172792D7468656F7279
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D6D6F6C6563756C61722D62696F6C6F67792D67656E6574696373
74797065733D706974747072657072696E74
https://philsci-archive.pitt.edu/11635/
Applying ecological models to communities of genetic elements: the case of neutral theory
Linquist, Stefan
Cottenie, Karl
Elliott, Tyler
Saylor, Brent
Kremer, Stefan
Gregory, T. Ryan
Biology
Ecology/Conservation
Evolutionary Theory
Molecular Biology/Genetics
A promising recent development in molecular biology involves viewing the genome as a miniecosystem, where genetic elements are compared to organisms and the surrounding cellular and genomic structures are regarded as the local environment. Here we critically evaluate the prospects of Ecological Neutral Theory (ENT), a popular model in ecology, as it applies at the genomic level. This assessment requires an overview of the controversy surrounding neutral models in community ecology. In particular, we discuss the limitations of using ENT both as an explanation of community dynamics and as a null hypothesis. We then analyze a case study in which ENT has been applied to genomic data. Our central finding is that genetic elements do not conform to the requirements of ENT once its assumptions and limitations are made explicit. We further compare this genome-level application of ENT to two other, more familiar approaches in genomics that rely on neutral mechanisms: Kimura’s Molecular Neutral Theory and Lynch’s Mutational Hazard Model. Interestingly, this comparison reveals that there are two distinct concepts of neutrality associated with these models which we dub ‘fitness-neutrality’ and ‘competitive neutrality’. This distinction helps to clarify the various roles for neutral models in genomics, for example, in explaining the evolution of genome size.
2015-07
Preprint
NonPeerReviewed
application/pdf
en
https://philsci-archive.pitt.edu/11635/1/neutral_models_of_genomic_communities_%28preprint_version%29.pdf
Linquist, Stefan and Cottenie, Karl and Elliott, Tyler and Saylor, Brent and Kremer, Stefan and Gregory, T. Ryan (2015) Applying ecological models to communities of genetic elements: the case of neutral theory. [Preprint]
http://onlinelibrary.wiley.com/doi/10.1111/mec.13219/abstract
10.1111/mec.13219
oai:philsci-archive.pitt.edu:11637
2015-08-26T14:49:19Z
7375626A656374733D73706563:62696F6C6F6779
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65766F6C7574696F6E6172792D7468656F7279
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D6D6F6C6563756C61722D62696F6C6F67792D67656E6574696373
74797065733D706974747072657072696E74
https://philsci-archive.pitt.edu/11637/
Distinguishing ecological from evolutionary approaches to transposable elements
Linquist, Stefan
Saylor, Brent
Cottenie, Karl
Elliott, Tyler A.
Kremer, Stefan C.
Gregory, T. Ryan
Biology
Ecology/Conservation
Evolutionary Theory
Molecular Biology/Genetics
Considerable variation exists not only in the kinds of transposable elements (TEs) occurring within the genomes of different species, but also in their abundance and distribution. Noting a similarity to the assortment of organisms among ecosystems, some researchers have called for an ecological approach to the study of transposon dynamics. However, there are several ways to adopt such an approach, and it is sometimes unclear what an ecological perspective will add to the existing co-evolutionary framework for explaining transposon-host interactions. This review aims to clarify the conceptual foundations of transposon ecology in order to evaluate its explanatory prospects. We begin by identifying three unanswered questions regarding the abundance and distribution of TEs that potentially call for an ecological explanation. We then offer an operational distinction between evolutionary and ecological approaches to these questions. By determining the amount of variance in transposon abundance and distribution that is explained by ecological and evolutionary factors, respectively, it is possible empirically to assess the prospects for each of these explanatory frameworks. To illustrate how this methodology applies to a concrete example, we analyzed whole-genome data for one set of distantly related mammals and another more closely related group of arthropods. Our expectation was that ecological factors are most informative for explaining differences among individual TE lineages, rather than TE families, and for explaining their distribution among closely related as opposed to distantly related host genomes. We found that, in these data sets, ecological factors do in fact explain most of the variation in TE abundance and distribution among TE lineages across less distantly related host organisms. Evolutionary factors were not significant at these levels. However, the explanatory roles of evolution and ecology become inverted at the level of TE families or among more distantly related genomes. Not only does this example demonstrate the utility of our distinction between ecological and evolutionary perspectives, it further suggests an appropriate explanatory domain for the burgeoning discipline of transposon ecology. The fact that ecological processes appear to be impacting TE lineages over relatively short time scales further raises the possibility that transposons might serve as useful model systems for testing more general hypotheses in ecology.
2013-08
Preprint
NonPeerReviewed
application/pdf
en
https://philsci-archive.pitt.edu/11637/1/Distinguishing_ecological_from_evolutionary_approaches_to_transposable_elements_%28preprint_version%29.pdf
Linquist, Stefan and Saylor, Brent and Cottenie, Karl and Elliott, Tyler A. and Kremer, Stefan C. and Gregory, T. Ryan (2013) Distinguishing ecological from evolutionary approaches to transposable elements. [Preprint]
http://onlinelibrary.wiley.com/doi/10.1111/brv.12017/abstract
10.1111/brv.12017
oai:philsci-archive.pitt.edu:11788
2015-12-03T15:20:02Z
7375626A656374733D73706563:62696F6C6F6779
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
7375626A656374733D67656E:686973746F72792D6F662D736369656E63652D636173652D73747564696573
7375626A656374733D73706563:6D65646963696E65
74797065733D706974747072657072696E74
https://philsci-archive.pitt.edu/11788/
Disease ecology and the concept of emerging infectious disease: its impact on the epidemiology of rabies virus, 1990s-2010s
Kostyrka, Gladys
Biology
Ecology/Conservation
History of Science Case Studies
Medicine
In the beginning of the 1990s, the concept of “emerging infectious disease” (EID) was elaborated in the United States in order to trigger institutional as well as conceptual changes in the fight against infectious diseases at national and international scales. For this reason it has been described as an “active concept” by sociologists Lorna Weir and Eric Mykhalovskiy (Weir & Mykhalovskiy 2010). The impact at the institutional level of the EID concept has been described in detail, but the concrete consequences of this concept at the level of research, on the agenda of researchers, remain poorly explored by historians, philosophers and sociologists of biology and medicine. One of the major consequences of the EID concept at the research level relies on the re-conceptualization of infectious disease emergence as a complex and multifactorial phenomenon, taking place inside a “dynamic and complex global ecology” (Satcher 1995, p.4). Taking rabies epidemiology as a case study, I illustrate how epidemiologists deal with the “global ecology” of this neglected old viral disease that is present everywhere on Earth except in Antarctica and still claims more than 55,000 lives annually. I further investigate the extent to which the complexity of rabies ecology is or is not perceived as an argument against the feasibility of rabies elimination or even eradication. Finally, this paper shows that (1) the EID concept, finding its roots in the tradition of disease ecology, significantly impacts rabies epidemiology and (2) despite its complexity, rabies ecology is not always perceived as an insurmountable obstacle to rabies elimination or eradication.
2015-11
Preprint
NonPeerReviewed
application/pdf
en
https://philsci-archive.pitt.edu/11788/1/KOSTYRKA_Emerging_infectious_disease_Rabies_ecology_and_elimination.pdf
Kostyrka, Gladys (2015) Disease ecology and the concept of emerging infectious disease: its impact on the epidemiology of rabies virus, 1990s-2010s. [Preprint]
oai:philsci-archive.pitt.edu:11789
2015-12-03T15:14:12Z
7375626A656374733D73706563:62696F6C6F6779
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
7375626A656374733D67656E:686973746F72792D6F662D736369656E63652D636173652D73747564696573
7375626A656374733D73706563:6D65646963696E65
74797065733D706974747072657072696E74
https://philsci-archive.pitt.edu/11789/
Interspecies transmission and viral epidemics: integration of molecular and ecological approaches in the epidemiology of two RNA viruses (1989-2010s)
Kostyrka, Gladys
Biology
Ecology/Conservation
History of Science Case Studies
Medicine
At a crossroads between biology and medicine, epidemiology is the study of infectious and non infectious diseases in populations. In particular, epidemiology of infectious diseases relies on the articulation between the biology of the germ(s) and the biology of the host population(s). Virus-host interactions are studied by epidemiologists at different levels and from different perspectives. The concept of emerging infectious disease, elaborated in the 1990s, emphasizes the need to investigate both the molecular and ecological aspects of virus-host interactions. Molecular approaches in epidemiology focus on the genetic, subcellular and cellular aspects of the host-germ relationship at the individual and population levels, while ecological approaches insist on the spatial distribution of host and germ populations, their relationships with their environment, and their interactions with other species. This paper describes integration processes at work between ecological and molecular approaches in the epidemiology of two RNA viruses since the advent of the concept of emerging infectious disease. Based on these two case studies, it further explores the meaning of integration, and aims at identifying the specific goals, challenges, expectations and issues associated with integration in these contexts.
2015-03
Preprint
NonPeerReviewed
application/pdf
en
https://philsci-archive.pitt.edu/11789/1/KOSTYRKA_JHB_2015_Interspecies_transmission_and_viral_epidemics.pdf
Kostyrka, Gladys (2015) Interspecies transmission and viral epidemics: integration of molecular and ecological approaches in the epidemiology of two RNA viruses (1989-2010s). [Preprint]
oai:philsci-archive.pitt.edu:11845
2016-01-02T13:22:18Z
7375626A656374733D73706563:62696F6C6F6779
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
7375626A656374733D67656E:6C6177732D6F662D6E6174757265
74797065733D636F6E666572656E63655F6974656D
https://philsci-archive.pitt.edu/11845/
Against Lawton’s contingency thesis, or, why the reported demise of community ecology is greatly exaggerated
Linquist, Stefan
Biology
Ecology/Conservation
Laws of Nature
Lawton’s contingency thesis (CT) states that there are no useful generalizations (“laws”) at the level of ecological communities because these systems are especially prone to contingent historical events. I argue that this influential thesis has been grounded on the wrong kind of evidence. CT is best understood in Woodward’s (2010) terms as a claim about the instability of certain causal dependencies across different background conditions. A recent distinction between evolution and ecology reveals what an adequate test of Lawton’s thesis would look like. To date, CT remains untested. But developments in genome and molecular ecology point in a promising direction.
2015-12-19
Conference or Workshop Item
NonPeerReviewed
application/pdf
en
https://philsci-archive.pitt.edu/11845/4/against_lawton_%28PSA_-_preprint%29.pdf
Linquist, Stefan (2015) Against Lawton’s contingency thesis, or, why the reported demise of community ecology is greatly exaggerated. In: UNSPECIFIED.
http://www.jstor.org.subzero.lib.uoguelph.ca/stable/10.1086/684024
10.1086/684024
oai:philsci-archive.pitt.edu:11990
2016-03-25T02:16:05Z
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
7375626A656374733D67656E:6574686963616C2D697373756573
7375626A656374733D67656E:686973746F72792D6F662D736369656E63652D636173652D73747564696573
74797065733D706974747072657072696E74
https://philsci-archive.pitt.edu/11990/
Re-examining the Darwinian Basis for Aldo Leopold’s Land Ethic
Millstein, Roberta L.
Ecology/Conservation
Ethical Issues
History of Science Case Studies
Many philosophers have become familiar with Leopold’s land ethic through the writings of J. Baird Callicott, who claims that Leopold bases his land ethic on a “protosociobiological” argument that Darwin gives in the Descent of Man. On this view, which has become the canonical interpretation, Leopold’s land ethic is based on extending our moral sentiments to ecosystems. I argue that the evidence weighs in favor of an alternative interpretation of Leopold; his reference to Darwin does not refer to the Descent, but rather to the Origin of Species, where Darwin discusses the interdependencies between organisms in the struggle for existence.
2015-08-01
Preprint
NonPeerReviewed
application/pdf
en
https://philsci-archive.pitt.edu/11990/1/Millstein-Darwin-Leopold-3-1.pdf
Millstein, Roberta L. (2015) Re-examining the Darwinian Basis for Aldo Leopold’s Land Ethic. [Preprint]
http://www.tandfonline.com/doi/full/10.1080/21550085.2015.1111617
10.1080/21550085.2015.1111617
oai:philsci-archive.pitt.edu:12088
2016-05-11T22:17:50Z
7375626A656374733D73706563:62696F6C6F6779
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
7375626A656374733D67656E:636175736174696F6E
7375626A656374733D67656E:6C6177732D6F662D6E6174757265
74797065733D7075626C69736865645F61727469636C65
https://philsci-archive.pitt.edu/12088/
Exclusions, Explanations, and Exceptions: On the Causal and Lawlike Status of the Competitive Exclusion Principle
Raerinne, Jani
Baedke, Jan
Biology
Ecology/Conservation
Causation
Laws of Nature
The lawlike and explanatory status of ecologists’ Competitive Exclusion Principle (CEP) is a debated topic. It has been argued that the CEP is a ceteris paribus law, a non-lawlike regularity riddled with exceptions, a tautology, a causal regularity, and so on. We argue that the CEP is an empirically respectful and testable strict law that is not riddled with genuine exceptions. Moreover, we argue that the CEP is not a causal explanans in explanations, because it is a coexistence law, not a causal law. Rather than being an explanans, the CEP acts as a contrastive principle sharpening causal explanations. These results contrast with previous analyses of the CEP by Eliot (2011) and Weber (1999), which are also discussed. As a more general conclusion, we suggest that accounts of causal explanation in biology have neglected some of the roles that non-causal laws play in restricting, sharpening, and facilitating causal explanations.
Michigan Publishing, University of Michigan Library
2015-06-28
Published Article or Volume
NonPeerReviewed
application/pdf
en
cc_by_nc_nd
https://philsci-archive.pitt.edu/12088/1/exclusions-explanations-and-exceptions-on-the-causal.pdf
Raerinne, Jani and Baedke, Jan (2015) Exclusions, Explanations, and Exceptions: On the Causal and Lawlike Status of the Competitive Exclusion Principle. Philosophy and Theory in Biology, 7. ISSN 1949-0739
http://dx.doi.org/10.3998/ptb.6959004.0007.002
10.3998/ptb.6959004.0007.002
oai:philsci-archive.pitt.edu:12105
2016-05-22T16:31:51Z
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D646576656C6F706D656E74616C
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7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D73797374656D6174696373
74797065733D7075626C69736865645F61727469636C65
https://philsci-archive.pitt.edu/12105/
Understanding viruses: Philosophical investigations.
Pradeu, Thomas
Kostyrka, Gladys
Dupré, John
Developmental Biology
Ecology/Conservation
Evolutionary Theory
Function/Teleology
Molecular Biology/Genetics
Systematics
Viruses have been virtually absent from philosophy of biology. In this editorial introduction, we explain why we think viruses are philosophically important. We focus on six issues (the definition of viruses, the individuality and diachronic identity of a virus, the possibility to classify viruses into species, the question of whether viruses are living, the question of whether viruses are organisms, and finally the biological roles of viruses in ecology and evolution), and we show how they relate to classic questions of philosophy of biology and even general philosophy.
2016
Published Article or Volume
NonPeerReviewed
application/pdf
en
https://philsci-archive.pitt.edu/12105/1/Pradeu_et_al_Introduction_Understanding_Virus_Final_draft.pdf
Pradeu, Thomas and Kostyrka, Gladys and Dupré, John (2016) Understanding viruses: Philosophical investigations. Studies in history and philosophy of biological and biomedical sciences. ISSN 1879-2499
oai:philsci-archive.pitt.edu:12182
2016-06-08T19:50:39Z
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
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7375626A656374733D67656E:736369656E63652D616E642D736F6369657479
74797065733D7075626C69736865645F61727469636C65
https://philsci-archive.pitt.edu/12182/
Immunity in Context: Science and Society in Dialogue
Tauber, Alfred I.
Ecology/Conservation
Medicine
Science and Society
Without disputing the richness of the original incarnation of the immune self – conceived in segregated terms and defended by immunity – this useful heuristic is undergoing transformation. A relational or dialectical orientation has supplemented this incarnation of selfhood from an exclusive focus on the defensive scenario to one that now accommodates more expansive ecological intercourse, one in which active tolerance allows for cooperative exchanges within both the internal and external environments. This revision that emphasizes communal relationships finds support in the social matrix. Just as the autonomous immune self found its own conceptual coordinates in modernist notions of personal identity, changing cultural values, revised notions of personal identity, and the vast growth of ecological awareness resonate with shifts in theorizing about immunity. Such correspondence highlights the ready movement of potent metaphors between the laboratory and its supporting culture.
Euskal Herriko Unibertsitatea / Universidad del País Vasco
2016-05
Published Article or Volume
NonPeerReviewed
text
en
cc_by_nc_nd
https://philsci-archive.pitt.edu/12182/1/14560-59982-1-PB.pdf
Tauber, Alfred I. (2016) Immunity in Context: Science and Society in Dialogue. THEORIA. An International Journal for Theory, History and Foundations of Science, 31 (2). pp. 207-224. ISSN 2171-679X
http://www.ehu.eus/ojs/index.php/THEORIA/article/view/14560
10.1387/theoria.14560
oai:philsci-archive.pitt.edu:12200
2016-06-16T12:30:44Z
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65766F6C7574696F6E6172792D7468656F7279
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D6D6F6C6563756C61722D62696F6C6F67792D67656E6574696373
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7375626A656374733D67656E:686973746F72792D6F662D736369656E63652D636173652D73747564696573
74797065733D706974747072657072696E74
https://philsci-archive.pitt.edu/12200/
Spot the difference: Causal contrasts in scientific diagrams
Scholl, Raphael
Ecology/Conservation
Evolutionary Theory
Molecular Biology/Genetics
Causation
Experimentation
History of Science Case Studies
An important function of scientific diagrams is to identify causal relationships. This commonly relies on contrasts that highlight the effects of specific difference-makers. However, causal contrast diagrams are not an obvious and easy to recognize category because they appear in many guises. In this paper, four case studies are presented to examine how causal contrast diagrams appear in a wide range of scientific reports, from experimental to observational and even purely theoretical studies. It is shown that causal contrasts can be expressed in starkly different formats, including photographs of complexly visualized macromolecules as well as line graphs, bar graphs, or plots of state spaces. Despite surface differences, however, there is a measure of conceptual unity among such diagrams. In empirical studies they generally serve not only to infer and communicate specific causal claims, but also as evidence for them. The key data of some studies is given nowhere except in the diagrams. Many diagrams show multiple causal contrasts in order to demonstrate both that an effect exists and that the effect is specific -- that is, to narrowly circumscribe the phenomenon to be explained. In a large range of scientific reports, causal contrast diagrams reflect the core epistemic claims of the researchers.
2016
Preprint
NonPeerReviewed
text
en
https://philsci-archive.pitt.edu/12200/1/Scholl%20MS%20Spot%20the%20difference.pdf
Scholl, Raphael (2016) Spot the difference: Causal contrasts in scientific diagrams. [Preprint]
oai:philsci-archive.pitt.edu:12219
2016-06-23T01:18:54Z
7375626A656374733D73706563:62696F6C6F6779
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65766F6C7574696F6E6172792D7468656F7279
7375626A656374733D67656E:636175736174696F6E
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7375626A656374733D67656E:6D6F64656C732D616E642D696465616C697A6174696F6E
74797065733D706974747072657072696E74
https://philsci-archive.pitt.edu/12219/
From the neutral theory to a comprehensive and multiscale theory of ecological equivalence
Munoz, François
huneman, philippe
Biology
Ecology/Conservation
Evolutionary Theory
Causation
Determinism/Indeterminism
Laws of Nature
Models and Idealization
The neutral theory of biodiversity assumes that coexisting organisms are equally able to survive, reproduce and disperse (ecological equivalence), but predicts that stochastic fluctuations of these abilities drive diversity dynamics. It predicts remarkably well many biodiversity patterns, although substantial evidence for the role of niche variation across organisms seems contradictory. Here, we discuss this apparent paradox by exploring the meaning and implications of ecological equivalence.
We address the question whether neutral theory provides an explanation for biodiversity patterns and acknowledges causal processes. We underline that ecological equivalence, although central to neutral theory, can emerge at local and regional scales from niche-based processes through equalizing and stabilizing mechanisms. Such emerging equivalence corresponds to a weak conception of neutral theory, as opposed to the assumption of strict equivalence at individual level in the strong conception. We show that this duality is related to diverging views on hypothesis-testing and modeling in ecology. In addition, the stochastic dynamics exposed in neutral theory are pervasive in ecological systems and, rather than a null hypothesis, ecological equivalence is best understood as a parsimonious baseline to address biodiversity dynamics at multiple scales.
2016-02
Preprint
NonPeerReviewed
text
en
https://philsci-archive.pitt.edu/12219/1/Munoz%20and%20Huneman_in%20press.pdf
Munoz, François and huneman, philippe (2016) From the neutral theory to a comprehensive and multiscale theory of ecological equivalence. [Preprint]
oai:philsci-archive.pitt.edu:12363
2016-08-13T19:03:14Z
7375626A656374733D67656E:536369656E74696669635F4D65746170687973696373
7375626A656374733D73706563:62696F6C6F6779
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
7375626A656374733D67656E:6574686963616C2D697373756573
74797065733D706974747072657072696E74
https://philsci-archive.pitt.edu/12363/
Is Aldo Leopold's ‘Land Community’ an Individual?
Millstein, Roberta L.
Scientific Metaphysics
Biology
Ecology/Conservation
Ethical Issues
The “land community” (or “biotic community”) that features centrally in Aldo Leopold’s Land Ethic has typically been equated with the concept of “ecosystem.” Moreover, some have challenged this central Leopoldean concept given the multitude of meanings of the term “ecosystem” and the changes the term has undergone since Leopold’s time (see, e.g., Shrader-Frechette 1996). Even one of Leopold’s primary defenders, J. Baird Callicott, asserts that there are difficulties in identifying the boundaries of ecosystems and suggests that we recognize that their boundaries are determined by scientific questions ecologists pose (Callicott 2013). I argue that we need to rethink Leopold’s concept of land community in the following ways. First, we should recognize that Leopold’s views are not identical to those of his contemporaries (e.g., Clements, Elton), although they resemble those of some subsequent ecologists, including some of our contemporaries (e.g., O’Neill 2001, Post et al. 2007, Hastings and Gross 2012). Second, the land community concept does not map cleanly onto the concept of “ecosystem”; it also incorporates elements of the “community” concept in community ecology by emphasizing the interactions between organisms and not just the matter/energy flow of the ecosystem concept. Third, the boundary question can be illuminated by considering some of the recent literature on the nature of biological individuals (in particular, Odenbaugh 2007; Hamilton, Smith, and Haber 2009; Millstein 2009), focusing on concentrations of causal relations as determinative of the boundaries of the land community qua individual. There are challenges to be worked out, particularly when the interactions of community members do not map cleanly onto matter/energy flows, but I argue that these challenges can be resolved. The result is a defensible land community concept that is ontologically robust enough to be a locus of moral obligation while being consistent with contemporary ecological theory and practice.
2016
Preprint
NonPeerReviewed
text
en
https://philsci-archive.pitt.edu/12363/1/Millstein%20-%20Land%20Community%20as%20Individual%20-%202-5.pdf
Millstein, Roberta L. (2016) Is Aldo Leopold's ‘Land Community’ an Individual? [Preprint]
oai:philsci-archive.pitt.edu:12428
2016-09-15T12:52:11Z
oai:philsci-archive.pitt.edu:12442
2016-09-17T12:50:14Z
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
7375626A656374733D67656E:6578706C616E6174696F6E
7375626A656374733D67656E:686973746F72792D6F662D736369656E63652D636173652D73747564696573
7375626A656374733D73706563:6D617468656D6174696373
7375626A656374733D67656E:6D6F64656C732D616E642D696465616C697A6174696F6E
74797065733D706974747072657072696E74
https://philsci-archive.pitt.edu/12442/
The Volterra Principle Generalized
Räz, Tim
Ecology/Conservation
Explanation
History of Science Case Studies
Mathematics
Models and Idealization
Michael Weisberg and Kenneth Reisman argue that the so-called Volterra Principle can be derived from a series of predator-prey models, and that, therefore, the Volterra Principle is a prime example for the practice of robustness analysis. In the present paper, I give new results regarding the Volterra Principle, extending Weisberg’s and Reisman’s work, and I discuss the consequences of these new results for robustness analysis. I argue that we do not end up with multiple, independent models, but rather with one general model. I identify the kind of situation in which this generalization approach may occur, I analyze the generalized Volterra Principle from an explanatory perspective, and I propose that cases in which the generalization approach may not apply are in fact cases of mathematical coincidences.
2016
Preprint
NonPeerReviewed
text
en
https://philsci-archive.pitt.edu/12442/1/raez_volterra.pdf
Räz, Tim (2016) The Volterra Principle Generalized. [Preprint]
oai:philsci-archive.pitt.edu:12552
2016-10-29T16:57:36Z
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
7375626A656374733D67656E:6578706C616E6174696F6E
74797065733D636F6E666572656E63655F6974656D
https://philsci-archive.pitt.edu/12552/
Indexically Structured Ecological Communities
Lean, Christopher
Ecology/Conservation
Explanation
Ecological communities are seldom, if ever, biological individuals. They lack causal boundaries as the populations that constitute communities are not congruent and rarely have persistent functional roles regulating the communities’ higher properties. Instead we should represent ecological communities indexically, by identifying ecological communities via the network of weak causal interactions between populations that unfurl from a starting set of populations. This precisification of ecological communities helps identify how community properties remain invariant, and why they have robust characteristics. This is a more general framework than individuality, respecting the diversity and aggregational nature of these complex systems while still vindicating them as units worthy of investigation.
2016
Conference or Workshop Item
NonPeerReviewed
text
en
https://philsci-archive.pitt.edu/12552/1/PSA%20Indexical%20Paper%20Send%20In.pdf
Lean, Christopher (2016) Indexically Structured Ecological Communities. In: UNSPECIFIED.
oai:philsci-archive.pitt.edu:12659
2016-11-27T20:23:21Z
7375626A656374733D67656E:536369656E74696669635F4D65746170687973696373
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7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D6D6F6C6563756C61722D62696F6C6F67792D67656E6574696373
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7375626A656374733D73706563:6E6575726F736369656E6365
74797065733D7075626C69736865645F61727469636C65
https://philsci-archive.pitt.edu/12659/
The many faces of biological individuality
Pradeu, Thomas
Scientific Metaphysics
Biology
Developmental Biology
Ecology/Conservation
Evolutionary Theory
Function/Teleology
Molecular Biology/Genetics
Causation
Neuroscience
Biological individuality is a major topic of discussion in biology and philosophy of biology. Recently, several objections have been raised against traditional accounts of biological individuality, including the objections of monism (the tendency to focus on a single individuality criterion and/or a single biological field), theory-centrism (the tendency to discuss only theory-based individuation), ahistoricity (the tendency to neglect what biologists of the past and historians of biology have said about biological individuality), disciplinary isolationism (the tendency to isolate biological individuality from other scientific and philosophical domains that have investigated individuality), and the multiplication of conceptual uncertainties (the lack of a precise definition of “biological individual” and related terms). In this introduction, I will examine the current philosophical landscape about biological individuality, and show how the contributions gathered in this special issue address these five objections. Overall, the aim of this issue is to offer a more diverse, unifying, and scientifically informed conception of what a biological individual is.
Springer
2016-11
Published Article or Volume
NonPeerReviewed
text
en
https://philsci-archive.pitt.edu/12659/1/Pradeu_Many%20faces%20biological%20individuality_Editorial%20introduction_Final%20draft.pdf
Pradeu, Thomas (2016) The many faces of biological individuality. Biology and Philosophy, 31 (6). pp. 761-773.
http://link.springer.com/journal/10539/31/6/page/1
10.1007/s10539-016-9553-z
oai:philsci-archive.pitt.edu:13411
2017-09-11T16:56:57Z
7375626A656374733D67656E:536369656E74696669635F4D65746170687973696373
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
74797065733D706974747072657072696E74
https://philsci-archive.pitt.edu/13411/
Preserving the Tree of Life
Lean, Christopher
Scientific Metaphysics
Ecology/Conservation
Biodiversity is a key concept in the biological sciences. While it has its origin in conservation biology, it has become useful across multiple biological disciplines as a means to describe biological variation. It remains, however, unclear what particular biological units the concept refers to. There are currently multiple accounts of which biological features constitute biodiversity and how these are to be measured. In this paper, I draw from the species concept debate to argue for a set of desiderata for the concept of “biodiversity” that is both principled and coheres with the concept’s use. Given these desiderata, this concept should be understood as referring to difference quantified in terms of the phylogenetic structure of lineages, also known as the ‘tree of life’.
2017
Preprint
NonPeerReviewed
text
en
https://philsci-archive.pitt.edu/13411/1/Biodiversity%20Realism%20%28Biology%20and%20Philosophy%29%20Final.docx
Lean, Christopher (2017) Preserving the Tree of Life. [Preprint]
oai:philsci-archive.pitt.edu:13435
2017-09-15T17:51:50Z
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
74797065733D706974747072657072696E74
https://philsci-archive.pitt.edu/13435/
Conceptualizing Communities as Natural Entities:
A Philosophical Argument with Basic and Applied Implications
Steen, David, A.
Barrett, Kyle
Clarke, Ellen
Guyer, Craig
Ecology/Conservation
Recent work has suggested that conservation efforts such as restoration ecology and invasive species eradication are largely value-driven pursuits. Concurrently, changes to global climate are forcing ecologists to consider if and how collections of species will migrate, and whether or not we should be assisting such movements. Herein, we propose a philosophical framework which addresses these issues by utilizing ecological and evolutionary interrelationships to delineate individual ecological communities. Specifically, our Evolutionary Community Concept (ECC) recognizes unique collections of species that interact and have co-evolved in a given geographic area. We argue this concept has implications for a number of contemporary global conservation issues. Specifically, our framework allows us to establish a biological and science-driven context for making decisions regarding the restoration of systems and the removal of exotic species. The ECC also has implications for how we view shifts in species assemblages due to climate change and it advances our understanding of various ecological concepts, such as resilience.
2017
Preprint
NonPeerReviewed
text
en
https://philsci-archive.pitt.edu/13435/1/Conceptualizing%20Communities%20as%20Natural%20Entities_accepteddraft.docx
Steen, David, A. and Barrett, Kyle and Clarke, Ellen and Guyer, Craig (2017) Conceptualizing Communities as Natural Entities: A Philosophical Argument with Basic and Applied Implications. [Preprint]
oai:philsci-archive.pitt.edu:13492
2017-09-29T14:26:58Z
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
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https://philsci-archive.pitt.edu/13492/
Differentiating and defusing theoretical Ecology's criticisms: A rejoinder to Sagoff's reply to Donhauser (2016)
Donhauser, Justin
Ecology/Conservation
Function/Teleology
Laws of Nature
Logical Positivism/Logical Empiricism
Models and Idealization
In a (2016) paper in this journal, I defuse allegations that theoretical ecological research is problematic because it relies on teleological metaphysical assumptions. Mark Sagoff offers a formal reply. In it, he concedes that I succeeded in establishing that ecologists abandoned robust teleological views long ago and that they use teleological characterizations as metaphors that aid in developing mechanistic explanations of ecological phenomena. Yet, he contends that I did not give enduring criticisms of theoretical ecology a fair shake in my paper. He says this is because enduring criticisms center on concerns about the nature of ecological networks and forces, the instrumentality of ecological laws and theoretical models, and the relation between theoretical and empirical methods in ecology that that paper does not broach. Below I set apart the distinct criticisms Sagoff presents in his commentary and respond to each in turn.
2017
Published Article or Volume
NonPeerReviewed
text
en
https://philsci-archive.pitt.edu/13492/1/DONHAUSER%20Rejoinder%20to%20Sagoff%20preprint.pdf
Donhauser, Justin (2017) Differentiating and defusing theoretical Ecology's criticisms: A rejoinder to Sagoff's reply to Donhauser (2016). Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences, 63 (Supple). 70 - 79.
http://www.sciencedirect.com/science/article/pii/S1369848617300481
oai:philsci-archive.pitt.edu:13493
2017-09-29T14:39:43Z
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7375626A656374733D67656E:686973746F72792D6F662D736369656E63652D636173652D73747564696573
74797065733D7075626C69736865645F61727469636C65
https://philsci-archive.pitt.edu/13493/
Theoretical ecology as etiological from the start
Donhauser, Justin
Ecology/Conservation
Function/Teleology
Complex Systems
Explanation
History of Science Case Studies
The world's leading environmental advisory institutions look to ecological theory and research as an objective guide for policy and resource management decision-making. In addition to the theoretical and broadly philosophical merits of doing so, it is therefore practically significant to clear up confusions about ecology's conceptual foundations and to clarify the basic workings of inferential methods used in the science. Through discussion of key moments in the genesis of the theoretical branch of ecology, this essay elucidates a general heuristic role of teleological metaphors in ecological research and defuses certain enduring confusions about work in ecology.
2016
Published Article or Volume
NonPeerReviewed
text
en
https://philsci-archive.pitt.edu/13493/1/DONHAUSER%20Ecology%20as%20Etiological%20PENULT%20PREPRINT.pdf
Donhauser, Justin (2016) Theoretical ecology as etiological from the start. Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences, 60. 67 - 76.
http://www.sciencedirect.com/science/article/pii/S1369848616300723
oai:philsci-archive.pitt.edu:13495
2017-09-29T14:41:25Z
7375626A656374733D73706563:62696F6C6F6779
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
7375626A656374733D67656E:6574686963616C2D697373756573
7375626A656374733D67656E:726564756374696F6E69736D2D686F6C69736D
7375626A656374733D67656E:736369656E63652D616E642D736F6369657479
7375626A656374733D67656E:736369656E63652D706F6C696379
74797065733D7075626C69736865645F61727469636C65
https://philsci-archive.pitt.edu/13495/
Making Ecological Values Make Sense: Toward More Operationalizable Ecological Legislation
Donhauser, Justin
Biology
Ecology/Conservation
Ethical Issues
Reductionism/Holism
Science and Society
Science and Policy
Value claims about ecological populations, communities, and systems appear everywhere in the literature put out by leading environmental advisory institutions. In this essay, I clarify the content of such normatively significant value claims in two main steps. I first outline the conception of ecological entities, functionality, and properties, operative in the background of modern ecology. I then assess the implications of that background theory for how the many policies and management strategy directives that refer to such entities, functionality, and properties, can be most reasonably interpreted and operationalized.
2016
Published Article or Volume
NonPeerReviewed
text
en
https://philsci-archive.pitt.edu/13495/1/DONMEV.1.pdf
Donhauser, Justin (2016) Making Ecological Values Make Sense: Toward More Operationalizable Ecological Legislation. Ethics and the Environment, 21 (2). pp. 1-25.
https://muse.jhu.edu/article/640859/summary
oai:philsci-archive.pitt.edu:14103
2017-11-10T02:21:08Z
7375626A656374733D73706563:62696F6C6F6779
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
74797065733D636F6E666572656E63655F6974656D
https://philsci-archive.pitt.edu/14103/
Understanding Leopold’s Concept of ‘Interdependence’
for Environmental Ethics and Conservation Biology
Millstein, Roberta L.
Biology
Ecology/Conservation
Aldo Leopold’s Land Ethic, an extremely influential view in environmental ethics and conservation biology, is committed to the claim that interdependence between humans, other species, and abiotic entities plays a central role in our ethical responsibilities. Thus, a robust understanding of “interdependence” is necessary for evaluating the viability of the Land Ethic and related views, including ecological ones. I characterize and defend a Leopoldian concept of “interdependence,” arguing that it ought to include both negative and positive causal relations. I also show that strength and type of interdependence can vary with time, space, and context.
2017-10-07
Conference or Workshop Item
NonPeerReviewed
text
en
https://philsci-archive.pitt.edu/14103/1/Millstein-Interdependence-PhilSci.pdf
Millstein, Roberta L. (2017) Understanding Leopold’s Concept of ‘Interdependence’ for Environmental Ethics and Conservation Biology. In: UNSPECIFIED.
oai:philsci-archive.pitt.edu:14147
2017-11-27T15:20:23Z
7375626A656374733D73706563:62696F6C6F6779
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
74797065733D706974747072657072696E74
https://philsci-archive.pitt.edu/14147/
Debunking Myths About Aldo Leopold’s Land Ethic
Millstein, Roberta L.
Biology
Ecology/Conservation
Aldo Leopold’s land ethic has been extremely influential among people working in conservation biology, environmental ethics, and related fields. Others have abandoned the land ethic for purportedly being outdated or ethically untenable. Yet, both acceptance of the land ethic and rejection of the land ethic are often based on misunderstandings of Leopold’s original meaning – misunderstandings that have become so entrenched as to have the status of myths. This essay seeks to identify and then debunk six myths that have grown up around the land ethic. These myths include misunderstandings about how we should understand key terms like “stability” and “biotic community” as well as the scope and main message of the land ethic. Properly understanding Leopold’s original meaning, a meaning derived from ideas he developed after a lifetime of scientific theorizing and hands-on practical knowledge, prevents hasty rejection and provides a sounder basis for conservation policy.
2017-11
Preprint
NonPeerReviewed
text
en
https://philsci-archive.pitt.edu/14147/1/Millstein-DebunkingMythsLeopold-3-0-shareable.pdf
Millstein, Roberta L. (2017) Debunking Myths About Aldo Leopold’s Land Ethic. [Preprint]
oai:philsci-archive.pitt.edu:14314
2018-01-24T00:10:22Z
7375626A656374733D73706563:62696F6C6F6779
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
7375626A656374733D67656E:6574686963616C2D697373756573
7375626A656374733D67656E:76616C7565732D696E2D736369656E6365
74797065733D7075626C69736865645F61727469636C65
https://philsci-archive.pitt.edu/14314/
Ecological Historicity, Functional Goals, and Novelty in the Anthropocene
Desjardins, Eric
Donhauser, Justin
Barker, Gillian
Biology
Ecology/Conservation
Ethical Issues
Values In Science
While many recognize that rigid historical and compositional goals are inadequate in a world where climate and other global systems are undergoing unprecedented changes, others contend that promoting ecosystem services and functions encourages practices that can ultimately lower the bar of ecological management. These worries are foregrounded in discussions about Novel Ecosystems (NEs); where some researchers and conservationists claim that NEs provide a license to trash nature as long as some ecosystem services are provided. This criticism arises from what we call the “anything goes” problem created by the release of historical conditions. After explaining the notion of NE, we identify numerous substantive motivations for worrying about the anything-goes-problem and then go on to show the problem can be solved by correcting two mistaken assumptions. In short, we argue that the problem is a product of adopting an overly sparse functional perspective and one that assumes an unrealistically high degree of convergence in the trajectories of natural processes. Our analysis illuminates why such assumptions are unwarranted. Finally, we further argue that adopting an appropriate ethical framework is essential to overcoming the anything-goes-problem and suggest that a certain virtue ethics conception of ecological management provides useful resources for framing and resolving the problem.
The White Horse press
2018
Published Article or Volume
NonPeerReviewed
text
en
https://philsci-archive.pitt.edu/14314/1/DesjarDonhausBarker%20%28forthcoming%29%20NovelEcosystems.pdf
Desjardins, Eric and Donhauser, Justin and Barker, Gillian (2018) Ecological Historicity, Functional Goals, and Novelty in the Anthropocene. Environmental Values.
http://www.whpress.co.uk/EV/papers/1539-Desjardins.pdf
oai:philsci-archive.pitt.edu:14346
2018-02-02T17:32:27Z
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
7375626A656374733D67656E:6D6F64656C732D616E642D696465616C697A6174696F6E
74797065733D706974747072657072696E74
https://philsci-archive.pitt.edu/14346/
¬¬¬¬Modeling: Neutral, Null, and Baseline
Bausman, William
Ecology/Conservation
Models and Idealization
This paper distinguishes two reasoning strategies for using a model as a “null”. Null modeling evaluates whether a process is causally responsible for a pattern by testing it against a null model. Baseline modeling measures the relative significance of various processes responsible for a pattern by detecting deviations from a baseline model. Scientists sometimes conflate these strategies because their formal similarities, but they must distinguish them lest they privilege null models as accepted until disproved. I illustrate this problem with the neutral theory of ecology and use this as a case study to draw general lessons. First, scientists cannot draw certain kinds of causal conclusions using null modeling. Second, scientists can draw these kinds of causal conclusions using baseline modeling, but this requires more evidence than does null modeling.
2018-02-02
Preprint
NonPeerReviewed
text
en
https://philsci-archive.pitt.edu/14346/1/Modeling%20NNB%20PhilSciArch.pdf
Bausman, William (2018) ¬¬¬¬Modeling: Neutral, Null, and Baseline. [Preprint]
oai:philsci-archive.pitt.edu:14432
2018-03-12T14:00:09Z
7375626A656374733D73706563:62696F6C6F6779
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D6D6F6C6563756C61722D62696F6C6F67792D67656E6574696373
7375626A656374733D67656E:636175736174696F6E
7375626A656374733D67656E:6578706C616E6174696F6E
7375626A656374733D73706563:6D65646963696E65
7375626A656374733D73706563:6E6575726F736369656E6365
74797065733D706974747072657072696E74
https://philsci-archive.pitt.edu/14432/
Causal concepts in biology: How pathways differ from mechanisms and why it matters
Ross, Lauren N.
Biology
Ecology/Conservation
Molecular Biology/Genetics
Causation
Explanation
Medicine
Neuroscience
In the last two decades few topics in philosophy of science have received as much attention as mechanistic explanation. A significant motivation for these accounts is that scientists frequently use the term “mechanism” in their explanations of biological phenomena. While scientists appeal to a variety of causal concepts in their explanations, many philosophers argue or assume that all of these concepts are well understood with the single notion of mechanism (Robins and Craver 2009; Craver 2007). This reveals a significant problem with mainstream mechanistic accounts– although philosophers use the term “mechanism” interchangeably with other causal concepts, this is not something that scientists always do. This paper analyses two causal concepts in biology–the notions of “mechanism” and “pathway”–and how they figure in biological explanation. I argue that these concepts have unique features, that they are associated with distinct strategies of causal investigation, and that they figure in importantly different types of explanation.
2018-03-05
Preprint
NonPeerReviewed
text
en
https://philsci-archive.pitt.edu/14432/1/Mech_Path_.pdf
Ross, Lauren N. (2018) Causal concepts in biology: How pathways differ from mechanisms and why it matters. [Preprint]
oai:philsci-archive.pitt.edu:14623
2018-04-30T01:04:04Z
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
7375626A656374733D67656E:6578706C616E6174696F6E
7375626A656374733D67656E:6D6F64656C732D616E642D696465616C697A6174696F6E
74797065733D706974747072657072696E74
https://philsci-archive.pitt.edu/14623/
Big Dragons on Small Islands: generality and particularity in science. (review of Angela Potochnik's Idealization and the Aims of Science)
Currie, Adrian
Ecology/Conservation
Explanation
Models and Idealization
Angela Potochnik’s Idealization and the Aims of Science (Chicago) defends an ambitious and
systematic account of scientific knowledge: ultimately science pursues human understanding rather
than truth. Potochnik argues that idealization is rampant and unchecked in science. Further, given
that idealizations involve departures from truth, this suggests science is not primarily about truth. I
explore the relationship between truths about causal patterns and scientific understanding in light of
this, and suggest that Potochnik underestimates the importance and power of highly particular
narrative explanations.
2018
Preprint
NonPeerReviewed
text
en
https://philsci-archive.pitt.edu/14623/1/Potochnik%20Review.pdf
Currie, Adrian (2018) Big Dragons on Small Islands: generality and particularity in science. (review of Angela Potochnik's Idealization and the Aims of Science). [Preprint]
oai:philsci-archive.pitt.edu:14671
2018-05-16T13:00:07Z
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
7375626A656374733D67656E:6578706572696D656E746174696F6E
74797065733D706974747072657072696E74
https://philsci-archive.pitt.edu/14671/
Bottled Understanding: the role of lab-work in ecology
Currie, Adrian
Ecology/Conservation
Experimentation
2018
Preprint
NonPeerReviewed
text
en
https://philsci-archive.pitt.edu/14671/1/Bottled%20Understanding.pdf
Currie, Adrian (2018) Bottled Understanding: the role of lab-work in ecology. [Preprint]
oai:philsci-archive.pitt.edu:14676
2018-05-17T18:58:20Z
7375626A656374733D73706563:62696F6C6F6779
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
7375626A656374733D67656E:636175736174696F6E
74797065733D706974747072657072696E74
https://philsci-archive.pitt.edu/14676/
Generality and Causal Interdependence in Ecology
Elliott-Graves, Alkistis
Biology
Ecology/Conservation
Causation
A hallmark of ecological research is dealing with complexity in the systems under investigation. One strategy is to diminish this complexity by constructing models and theories that are general. Alternatively, ecologists can constrain the scope of their generalisations to particular phenomena or types of systems. However, research employing the second strategy is often met with scathing criticism. I offer a theoretical argument in support of moderate generalisations in ecological research, based on the notions of interdependence and causal heterogeneity and their effect on the tradeoff between generality and realism
2018
Preprint
NonPeerReviewed
text
en
https://philsci-archive.pitt.edu/14676/1/Generality%20and%20Causal%20Interdependence%20in%20Ecology%20-%20Preprint.pdf
Elliott-Graves, Alkistis (2018) Generality and Causal Interdependence in Ecology. [Preprint]
oai:philsci-archive.pitt.edu:14864
2018-07-15T22:47:15Z
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65766F6C7574696F6E6172792D7468656F7279
7375626A656374733D67656E:686973746F72792D6F662D736369656E63652D636173652D73747564696573
7375626A656374733D67656E:6D6F64656C732D616E642D696465616C697A6174696F6E
74797065733D706974747072657072696E74
https://philsci-archive.pitt.edu/14864/
Microbes, mathematics, and models
O'Malley, Maureen A.
Parke, Emily C.
Ecology/Conservation
Evolutionary Theory
History of Science Case Studies
Models and Idealization
Microbial model systems have a long history of fruitful use in fields that include evolution and ecology. In order to develop further insight into modelling practice, we examine how the competitive exclusion and coexistence of competing species have been modelled mathematically and materially over the course of a long research history. In particular, we investigate how microbial models of these dynamics interact with mathematical or computational models of the same phenomena. Our cases illuminate the ways in which microbial systems and equations work as models, and what happens when they generate inconsistent findings about shared targets. We reveal an iterative strategy of comparative modelling in different media, and suggest reasons why microbial models have a special degree of epistemic tractability in multimodel inquiry.
2018
Preprint
NonPeerReviewed
text
en
https://philsci-archive.pitt.edu/14864/1/Microbes%20math%20models%20SHPS%20preprint.pdf
O'Malley, Maureen A. and Parke, Emily C. (2018) Microbes, mathematics, and models. [Preprint]
oai:philsci-archive.pitt.edu:14954
2018-08-20T16:27:36Z
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
7375626A656374733D67656E:636F6E6669726D6174696F6E2D696E64756374696F6E
7375626A656374733D73706563:70737963686F6C6F67792D70737963686961747279
7375626A656374733D67656E:726865746F7269632D6F662D736369656E6365
74797065733D706974747072657072696E74
https://philsci-archive.pitt.edu/14954/
Not Null Enough: Pseudo-Null Hypotheses in Community Ecology and Comparative Psychology
Bausman, William / C
Halina, Marta
Ecology/Conservation
Confirmation/Induction
Psychology
Rhetoric of Science
We evaluate a common reasoning strategy used in community ecology and comparative psychology for selecting between competing hypotheses. This strategy labels one hypothesis as a “null” on the grounds of its simplicity and epistemically privileges it as accepted until rejected. We argue that this strategy is unjustified. The asymmetrical treatment of statistical null hypotheses is justified through the experimental and mathematical contexts in which they are used, but these contexts are missing in the case of the “pseudo-null hypotheses” found in our case studies. Moreover, statistical nulls are often not epistemically privileged in practice over their alternatives because failing to reject the null is usually a negative result about the alternative, experimental hypothesis. Scientists should eschew the appeal to pseudo-nulls. It is a rhetorical strategy that glosses over a commitment to valuing simplicity over other epistemic virtues in the name of good scientific and statistical methodology.
2018
Preprint
NonPeerReviewed
text
en
https://philsci-archive.pitt.edu/14954/1/NNE%20B%26P%20R3%20PhilSci.pdf
Bausman, William / C and Halina, Marta (2018) Not Null Enough: Pseudo-Null Hypotheses in Community Ecology and Comparative Psychology. [Preprint]
oai:philsci-archive.pitt.edu:15288
2018-11-11T14:55:30Z
7375626A656374733D73706563:62696F6C6F6779
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
7375626A656374733D73706563:6368616F732D7468656F7279
7375626A656374733D73706563:636F676E69746976652D736369656E6365
7375626A656374733D67656E:736369656E63652D616E642D736F6369657479
7375626A656374733D67656E:76616C7565732D696E2D736369656E6365
74797065733D7075626C69736865645F61727469636C65
https://philsci-archive.pitt.edu/15288/
Does Cognition Still Matter in Ethnobiology?
Ludwig, David
Biology
Ecology/Conservation
Complex Systems
Cognitive Science
Science and Society
Values In Science
Ethnobiology has become increasingly concerned with applied and normative questions about biocultural diversity and the livelihoods of local communities. While this development has created new opportunities for connecting ethnobiological research with ecological and social sciences, it also raises questions about the role of cognitive perspectives in current ethnobiology. In fact, there are clear signs of institutional separation as research on folkbiological cognition has increasingly found its home in the cognitive science community, weakening its ties to institutionalized ethnobiology. Rather than accepting this separation as inevitable disciplinary specialization, this short perspective article argues for a systemic perspective that addresses mutual influences and causal entanglement of cognitive and non-cognitive factors in socio-ecological dynamics. Such an integrative perspective requires a new conversation about cognition in ethnobiology beyond traditional polarization around issues of cognitive universals and cultural relativity.
2018
Published Article or Volume
NonPeerReviewed
text
en
https://philsci-archive.pitt.edu/15288/1/2018%20Does%20Cognition%20Still%20Matter%20of%20Ethnobiology.pdf
Ludwig, David (2018) Does Cognition Still Matter in Ethnobiology? Ethnobiology Letters.
https://ojs.ethnobiology.org/index.php/ebl/article/view/1350
10.14237/ebl.9.2.2018.1350
oai:philsci-archive.pitt.edu:15351
2018-11-20T01:43:04Z
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
7375626A656374733D67656E:736369656E63652D706F6C696379
7375626A656374733D67656E:7468656F72792D6F62736572766174696F6E
74797065733D7075626C69736865645F61727469636C65
https://philsci-archive.pitt.edu/15351/
"Ecology and the Environment"
Plutynski, A
Ecology/Conservation
Science and Policy
Theory/Observation
Ecology is the study of the interactions of organisms and their environments. The methods of ecology fall roughly into three categories: descriptive surveys of patterns of species and resource distribution and abundance, theoretical modeling, and experimental manipulations. Ecological systems are “open” systems, and patterns and processes are products of a huge number of interacting forces. Ecology and the environmental sciences have made enormous advances since the mid-twentieth century in the understanding of ecological systems, as well as in the human impact on the environment. Theory in ecology usually centers on the development of models. Environmental outcomes are uncertain and when making decisions under uncertainty, there are a variety of options available. One option is to carry out a cost benefit analysis based upon expected utilities and other is to adopt the precautionary principle. Uncertainty and under determination of theory by evidence is a fact of life in science.
OUP
2008
Published Article or Volume
NonPeerReviewed
text
en
https://philsci-archive.pitt.edu/15351/1/oxfordhb22.2008.pdf
Plutynski, A (2008) "Ecology and the Environment". Oxford Handbook in Philosophy of Biology.
http://www.oxfordhandbooks.com/view/10.1093/oxfordhb/9780195182057.001.0001/oxfordhb-9780195182057-e-022
10.1093/oxfordhb/9780195182057.003.0022
oai:philsci-archive.pitt.edu:15364
2018-11-23T14:05:55Z
7375626A656374733D73706563:616E7468726F706F6C6F6779
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
7375626A656374733D67656E:6578706C616E6174696F6E
7375626A656374733D67656E:736369656E63652D616E642D736F6369657479
74797065733D7075626C69736865645F61727469636C65
https://philsci-archive.pitt.edu/15364/
Relating traditional and academic ecological knowledge: mechanistic and holistic epistemologies across cultures
Ludwig, David
Poliseli, Luana
Anthropology
Ecology/Conservation
Explanation
Science and Society
Current debates about the integration of traditional and academic ecological knowledge (TEK and AEK) struggle with a dilemma of division and assimilation. On the one hand, the emphasis on differences between traditional and academic perspectives has been criticized as creating an artificial divide that brands TEK as “nonscientific” and contributes to its marginalization. On the other hand, there has been increased concern about inadequate assimilation of Indigenous and other traditional perspectives into scientific practices that disregards the holistic nature and values of TEK. The aim of this article is to develop a practice-based account of the epistemic
relations between TEK and AEK that avoids both horns of the dilemma. While relations between TEK and AEK are often described in terms of the “holistic” nature of the former and the “mechanistic” character of the latter, we argue that a simple holism–mechanism divide misrepresents the epistemic resources of both TEK and AEK. Based on the literature on mechanistic explanations in philosophy of science, we argue that holders of TEK are perfectly capable of identifying mechanisms that underlie ecological phenomena while AEK often relies on non-mechanistic strategies of dealing with ecological complexity. Instead of generic characterizations of knowledge systems as either mechanistic or holistic, we propose to approach epistemic relations between knowledge systems by analyzing their (partly mechanistic and partly holistic) heuristics in practice.
Springer
2018
Published Article or Volume
NonPeerReviewed
text
en
https://philsci-archive.pitt.edu/15364/1/2018%20Relating%20Traditional%20and%20Academic%20Ecological%20Knowledge%20Biology%20and%20Philosophy.pdf
Ludwig, David and Poliseli, Luana (2018) Relating traditional and academic ecological knowledge: mechanistic and holistic epistemologies across cultures. Biology & Philosophy, 33 (43). ISSN 1572-8404
doi.org/10.1007/s10539-018-9655-x
oai:philsci-archive.pitt.edu:15459
2018-12-17T17:50:41Z
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
7375626A656374733D67656E:736369656E63652D616E642D736F6369657479
7375626A656374733D67656E:736369656E63652D706F6C696379
7375626A656374733D67656E:746563686E6F6C6F6779
74797065733D7075626C69736865645F61727469636C65
https://philsci-archive.pitt.edu/15459/
Wild or Farmed? Seeking Effective Science in a Controversial Environment
Bocking, Stephen
Ecology/Conservation
Science and Society
Science and Policy
Technology
Arguments implicating nature and science can arise in the most unlikely places. At the supermarket smoked salmon awaits shoppers: chinook salmon from British Columbia, and Atlantic salmon from B.C., New Brunswick, or Norway. They are priced the same, and look similar, but embedded in their diverse provenance is a controversy thirty years in the making. The “wild” chinook salmon were caught in the open ocean; the “farmed” Atlantic salmon were raised in pens in coastal inlets. The distinction has spawned an intense debate over salmon farming (also known as aquaculture)—nowhere more so than in British Columbia. In some ways this coastal controversy is unique, epitomizing the symbolic significance of all things marine to British Columbians. But it shares a crucial feature with other controversies, such as those involving genetically modified organisms, nanotechnology, or climate change. Since the debate began, science has played an essential role as a source of information and authority. Scientific knowledge and practice can be said to have contributed to creating the controversy, have added to its intractability, and, perhaps hold some keys to its resolution.
The University of Toronto
2007-12-08
Published Article or Volume
NonPeerReviewed
text
en
cc_by_nc_nd_4
https://philsci-archive.pitt.edu/15459/1/Bocking_Stephen-Wild_or_Farmed.pdf
Bocking, Stephen (2007) Wild or Farmed? Seeking Effective Science in a Controversial Environment. Spontaneous Generations: A Journal for the History and Philosophy of Science, 1 (1). pp. 48-57. ISSN 1913 0465
https://spontaneousgenerations.library.utoronto.ca/index.php/SpontaneousGenerations/article/view/2971
https://doi.org/10.4245/sponge.v1i1.2971
oai:philsci-archive.pitt.edu:15739
2019-02-14T13:50:53Z
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
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74797065733D706974747072657072696E74
https://philsci-archive.pitt.edu/15739/
In Defense of Living Fossils
Turner, Derek
Ecology/Conservation
Evolutionary Theory
Systematics
Earth Sciences
Lately there has been a wave of criticism of the concept of living fossils. First, recent research has challenged the status of paradigmatic living fossil taxa, such as coelacanths, cycads, and tuataras. Critics have also complained that the living fossil concept is vague and/or ambiguous, and that it is responsible for misconceptions about evolution. This paper defends a particular phylogenetic conception of living fossils, or taxa that (a) exhibit deep prehistoric morphological stability (b) contain few extant species; and (c) make a high contribution to phylogenetic diversity. The paper shows how this conception of living fossils can make sense of recent research on contested cases. The phylogenetic living fossil concept has both theoretical and practical importance: theoretical, because it picks out an important explanatory target for evolutionary theory; and practical, because it picks out taxa that we might wish to prioritize for conservation. The best way to defend the concept of living fossils is to get clearer about the reasons for defending living fossil taxa.
2019-02-13
Preprint
NonPeerReviewed
text
en
https://philsci-archive.pitt.edu/15739/1/In%20Defense%20of%20Living%20Fossils.Preprint.Turner.docx
image
en
https://philsci-archive.pitt.edu/15739/2/image1.jpeg
image
en
https://philsci-archive.pitt.edu/15739/3/image2.jpeg
Turner, Derek (2019) In Defense of Living Fossils. [Preprint]
oai:philsci-archive.pitt.edu:15751
2019-02-20T18:40:28Z
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
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7375626A656374733D67656E:76616C7565732D696E2D736369656E6365
74797065733D706974747072657072696E74
https://philsci-archive.pitt.edu/15751/
Let Me Tell You ‘Bout the Birds and the Bee-Mimicking Flies and Bambiraptor
Havstad, Joyce C
Ecology/Conservation
Systematics
Ethical Issues
History of Science Case Studies
Values In Science
Scientists have been arguing for more than twenty-five years about whether it is a good idea to collect voucher specimens from particularly vulnerable biological populations. Some think that, obviously, scientists should not be harvesting (read: killing) organisms from, for instance, critically endangered species. Others think that, obviously, it is the special job of scientists to collect precisely such information before any chance of retrieving it is forever lost. The character, extent, longevity, and span of the ongoing disagreement indicates that this is likely to be a hard problem to solve. Nonetheless, the aim of this paper is to help field biologists figure out what do to when collecting a voucher specimen risks extinction. Here I present and assess varying practices of specimen collection for both extant (i.e., neontological) and extinct (i.e., paleontological) species in order to compare and contrast cases where extinction risk both is and is not a problem. When it comes to taking vouchers from extant species at some risk of extinction, I determine that those advocating for conservative approaches to collection as well as those advocating for liberal information-gathering practices have good reasons to assess things in the way they each do. This means that there is unlikely to be a decisive, one-size-fits-all response to this problem. Still, progress can be made. We can acknowledge the risks of proceeding in either manner, as well as the uncertainty about how best to proceed (which will be deep in some cases). We can proceed as thoughtfully as possible, and be ready to articulate a rationale for whichever procedure is used in any particular case.
2019-02-19
Preprint
NonPeerReviewed
text
en
https://philsci-archive.pitt.edu/15751/1/Let%20Me%20Tell%20You%20%28Havstad%29.pdf
Havstad, Joyce C (2019) Let Me Tell You ‘Bout the Birds and the Bee-Mimicking Flies and Bambiraptor. [Preprint]
oai:philsci-archive.pitt.edu:15834
2019-03-20T15:30:21Z
7375626A656374733D73706563:62696F6C6F6779
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
7375626A656374733D67656E:636175736174696F6E
7375626A656374733D67656E:6578706572696D656E746174696F6E
7375626A656374733D67656E:686973746F72792D6F662D736369656E63652D636173652D73747564696573
74797065733D706974747072657072696E74
https://philsci-archive.pitt.edu/15834/
Types of Experiments and Causal Process Tracing: What Happened on the Kaibab Plateau in the 1920s
Millstein, Roberta L.
Biology
Ecology/Conservation
Causation
Experimentation
History of Science Case Studies
In a well-cited book chapter, ecologist Jared Diamond characterizes three main types of experiment performed in community ecology: laboratory experiment, field experiment, and natural experiment. Diamond argues that each form of experiment has strengths and weaknesses, with respect to, for example, realism or the ability to follow a causal trajectory. But does Diamond’s typology exhaust the available kinds of cause-finding practices? Some social scientists have characterized something they call “causal process tracing.” Is this a fourth type of experiment or something else? I examine Diamond’s typology and causal process tracing in the context of a case study concerning the dynamics of wolf and deer populations on the Kaibab Plateau in the 1920s, a case that has been used as a canonical example of a trophic cascade by ecologists but which has also been subject to controversy. I argue that ecologists have profitably deployed causal process tracing together with other types of experiment to help settle questions of causality in this case. It remains to be seen how widespread the use of causal process tracing outside of the social sciences is (or could be), but there are some potentially promising applications, particularly with respect to questions about specific causal sequences.
2019-03
Preprint
NonPeerReviewed
text
en
https://philsci-archive.pitt.edu/15834/1/Millstein-Nat%20Expts%20and%20CPT-Kaibab-manuscript-penultimate-toshare.pdf
Millstein, Roberta L. (2019) Types of Experiments and Causal Process Tracing: What Happened on the Kaibab Plateau in the 1920s. [Preprint]
oai:philsci-archive.pitt.edu:15838
2019-03-22T03:00:08Z
7375626A656374733D73706563:6D617468656D6174696373:504D6578706C616E6174696F6E
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
7375626A656374733D67656E:636175736174696F6E
7375626A656374733D67656E:6578706C616E6174696F6E
74797065733D706974747072657072696E74
https://philsci-archive.pitt.edu/15838/
Explaining the behaviour of random ecological networks. The stability of the microbiome as a case of integrative pluralism.
Deulofeu, Roger
Suárez, Javier
Pérez-Cervera, Alberrto
Explanation
Ecology/Conservation
Causation
Explanation
Explaining the behaviour of ecosystems is one of the key challenges for the biological sciences. Since 2000, new-mechanicism has been the main model to account for the nature of scientific explanation in biology. The universality of the new-mechanist view in biology has been however put into question due to the existence of explanations that account for some biological phenomena in terms of their mathematical properties (mathematical explanations). Supporters of mathematical explanation have argued that the explanation of the behaviour of ecosystems is usually provided in terms of their mathematical properties, and not in mechanistic terms. They have intensively studied the explanation of the properties of ecosystems that behave following the rules of a non-random network. However, no attention has been devoted to the study of the nature of the explanation in those that form a random network. In this paper, we cover that gap by analysing the explanation of the stability behaviour of the microbiome recently elaborated by Coyte and colleagues, to determine whether it fits with the model of explanation suggested by the new-mechanist or by the defenders of mathematical explanation. Our analysis of this case study supports three theses: (1) that the explanation is not given solely in terms of mechanisms, as the new-mechanists understand the concept; (2) that the mathematical properties that describe the system play an essential explanatory role, but they do not exhaust the explanation; (3) that a non-previously identified appeal to the type of interactions that the entities in the network can exhibit, as well as their abundance, is also necessary for Coyte and colleagues’ account to be fully explanatory. From the combination of these three theses we argue for the necessity of an integrative pluralist view of the nature of behaviour explanation when this is given by appealing to the existence of a random network.
2019
Preprint
NonPeerReviewed
text
en
https://philsci-archive.pitt.edu/15838/1/DEUETBv2.docx
Deulofeu, Roger and Suárez, Javier and Pérez-Cervera, Alberrto (2019) Explaining the behaviour of random ecological networks. The stability of the microbiome as a case of integrative pluralism. [Preprint]
oai:philsci-archive.pitt.edu:15839
2019-03-22T03:01:02Z
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65766F6C7574696F6E6172792D7468656F7279
7375626A656374733D67656E:6578706C616E6174696F6E
7375626A656374733D67656E:6C6177732D6F662D6E6174757265
74797065733D7075626C69736865645F61727469636C65
https://philsci-archive.pitt.edu/15839/
When Mechanisms Are Not Enough: The Origin of Eukaryotes and Scientific Explanation
Deulofeu, Roger
Suárez, Javier
Ecology/Conservation
Evolutionary Theory
Explanation
Laws of Nature
The appeal to mechanisms in scientific explanation is commonplace in contemporary philosophy of science. In short, mechanists argue that an explanation of a phenomenon consists of citing the mechanism that brings the phenomenon about. In this paper, we present an argument that challenges the universality of mechanistic explanation: in explanations of the contemporary features of the eukaryotic cell, biologists appeal to its symbiogenetic origin and therefore the notion of symbiogenesis plays the main explanatory role. We defend the notion that symbiogenesis is non-mechanistic in nature and that any attempt to explain some of the contemporary features of the eukaryotic cell mechanistically turns out to be at least insufficient and sometimes fails to address the question that is asked. Finally, we suggest that symbiogenesis is better understood as a pragmatic scientific law and present an alternative non-mechanistic model of scientific explanation. In the model we present, the use of scientific laws is supposed to be a minimal requirement of all scientific explanations, since the purpose of a scientific explanation is to make phenomena expectable. Therefore, this model would help to understand biologists’ appeal to the notion of symbiosis and thus is shown to be better, for the case under examination, than the mechanistic alternative.
Springer
2018
Published Article or Volume
NonPeerReviewed
text
en
https://philsci-archive.pitt.edu/15839/1/978-3-319-72577-2_6
Deulofeu, Roger and Suárez, Javier (2018) When Mechanisms Are Not Enough: The Origin of Eukaryotes and Scientific Explanation. Philosophy of Science, 9. pp. 95-115. ISSN 2365-4228
http://doi.org/10.1007/978-3-319-72577-2_6
doi:10.1007/978-3-319-72577-2_6
oai:philsci-archive.pitt.edu:15840
2019-03-22T03:01:43Z
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65766F6C7574696F6E6172792D7468656F7279
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D73797374656D6174696373
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7375626A656374733D67656E:7265616C69736D2D616E74692D7265616C69736D
74797065733D7075626C69736865645F61727469636C65
https://philsci-archive.pitt.edu/15840/
Bacterial species pluralism in the light of medicine and endosymbiosis
Suárez, Javier
Ecology/Conservation
Evolutionary Theory
Systematics
Medicine
Realism/Anti-realism
This paper offers a new argument in defence of bacterial species pluralism. To do this, initially I present particular issues derived from the conflict between the non-theoretical understanding of species as units of classification and the theoretical comprehension of them as units of evolution. Secondly, the necessity of the concept of species for the bacterial world is justified; I show how both medicine and endosymbiosis research make use of concepts of bacterial species linked to their distinctive purposes which do not conjoin with the other available concepts. Finally, I argue that these examples provide a new defence for the philosophical thesis of pluralism.
2016
Published Article or Volume
NonPeerReviewed
text
en
https://philsci-archive.pitt.edu/15840/1/13242-57498-1-PB.pdf
Suárez, Javier (2016) Bacterial species pluralism in the light of medicine and endosymbiosis. THEORIA. An International Journal for Theory, History and Foundations of Science, 31 (1). pp. 91-105. ISSN 0495-4548
http://doi.org/10.1387/theoria.13242
doi:10.1387/theoria.13242
oai:philsci-archive.pitt.edu:15841
2019-03-22T03:03:14Z
7375626A656374733D73706563:62696F6C6F6779
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65766F6C7574696F6E6172792D7468656F7279
7375626A656374733D67656E:686973746F72792D6F662D736369656E63652D636173652D73747564696573
74797065733D7075626C69736865645F61727469636C65
https://philsci-archive.pitt.edu/15841/
The importance of symbiosis in philosophy of biology: an analysis of the current debate on biological individuality and its historical roots
Suárez, Javier
Biology
Ecology/Conservation
Evolutionary Theory
History of Science Case Studies
Symbiosis plays a fundamental role in contemporary biology, as well as in recent thinking in philosophy of biology. The discovery of the importance and universality of symbiotic associations has brought new light to old debates in the field, including issues about the concept of biological individuality. An important aspect of these debates has been the formulation of the hologenome concept of evolution, the notion that holobionts are units of natural selection in evolution. This review examines the philosophical assumptions that underlie recent proposal of the hologenome concept of evolution, and traces those debates back in time to their historical origins, to the moment when the connection between the topics of symbiosis and biological individuality first caught the attention of biologists. The review is divided in two parts. The first part explores the historical origins of the connection between the notion of symbiosis and the concept of biological individuality, and emphasizes the role of A. de Bary, R. Pound, A. Schneider and C. Merezhkowsky in framing the debate. The second part examines the hologenome concept of evolution and explores four parallelisms between contemporary debates and the debates presented in the first part of the essay, arguing that the different debates raised by the hologenome concept were already present in the literature. I suggest that the novelty of the hologenome concept of evolution lies in the wider appreciation of the importance of symbiosis for maintaining life on Earth as we know it. Finally, I conclude by suggesting the importance of exploring the connections among contemporary biology, philosophy of biology and history of biology in order to gain a better understanding of contemporary biology.
Springer
2018
Published Article or Volume
NonPeerReviewed
text
en
https://philsci-archive.pitt.edu/15841/1/s13199-018-0556-1
Suárez, Javier (2018) The importance of symbiosis in philosophy of biology: an analysis of the current debate on biological individuality and its historical roots. Symbiosis, 76 (2). pp. 77-96.
https://link.springer.com/article/10.1007/s13199-018-0556-1
10.1007/s13199-018-0556-1
oai:philsci-archive.pitt.edu:15892
2019-04-10T04:09:37Z
7375626A656374733D73706563:62696F6C6F6779
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
7375626A656374733D67656E:6E61747572616C2D6B696E6473
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7375626A656374733D67656E:76616C7565732D696E2D736369656E6365
74797065733D706974747072657072696E74
https://philsci-archive.pitt.edu/15892/
Philosophy of Ethnobiology: Understanding Knowledge Integration and Its Limitations
Ludwig, David
El-Hani, Charbel
Biology
Ecology/Conservation
Natural Kinds
Social Epistemology of Science
Values In Science
Ethnobiology has become increasingly concerned with applied and normative issues such as climate change adaptation, forest management, and sustainable agriculture. Applied ethnobiology emphasizes the practical importance of local and traditional knowledge in tackling these issues but thereby also raises complex theoretical questions about the integration of heterogeneous knowledge systems. The aim of this article is to develop a framework for addressing questions of integration through four core domains of philosophy -
epistemology, ontology, value theory, and political theory. In each of these dimensions, we argue for a model of “partial overlaps” that acknowledges both substantial similarities and differences between knowledge systems. While overlaps can ground successful collaboration, their partiality requires reflectivity about the limitations of collaboration and co-creation. By outlining such a general and programmatic framework, the article aims to contribute to developing “philosophy of ethnobiology” as a field of interdisciplinary exchange that provides new resources for addressing foundational issues in ethnobiology and also expands the agenda of philosophy of biology.
2019
Preprint
NonPeerReviewed
text
en
https://philsci-archive.pitt.edu/15892/1/Philosophy-of-Ethnobiology%20JOE.pdf
Ludwig, David and El-Hani, Charbel (2019) Philosophy of Ethnobiology: Understanding Knowledge Integration and Its Limitations. [Preprint]
oai:philsci-archive.pitt.edu:15923
2019-04-22T13:37:00Z
7375626A656374733D73706563:62696F6C6F6779
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65766F6C7574696F6E6172792D7468656F7279
7375626A656374733D67656E:726564756374696F6E69736D2D686F6C69736D
74797065733D706974747072657072696E74
https://philsci-archive.pitt.edu/15923/
A metaphysical approach to holobiont individuality: Holobionts as emergent individuals
Suárez, Javier
Triviño, Vanessa
Biology
Ecology/Conservation
Evolutionary Theory
Reductionism/Holism
Holobionts are symbiotic assemblages composed by a host plus its microbiome. The status of holobionts as individuals has recently been a subject of continuous controversy, which has given rise to two main positions: on the one hand, holobiont advocates argue that holobionts are biological individuals; on the other, holobiont detractors argue that they are just mere chimeras or ecological communities, but not individuals. Both parties in the dispute develop their arguments from the framework of the philosophy of biology, in terms of what it takes for a “conglomerate” to be considered an interesting individual from a biological point of view. However, the debates about holobiont individuality have important ontological implications that have remained vaguely explored from a metaphysical framework. The purpose of this paper is to cover that gap by presenting a metaphysical approach to holobionts individuality. Drawing upon a conception of natural selection that puts the focus on the transgenerational recurrence of the traits and that supports the thesis that holobionts are units of selection, we argue that holobionts bear emergent traits and exert downward powers over the entities that compose them. In this vein, we argue, a reasonable argument can be made for conceiving holobionts as emergent biological individuals.
2019
Preprint
NonPeerReviewed
text
en
https://philsci-archive.pitt.edu/15923/1/Suarez%20and%20Trivino%20-%20Holobionts%20DC.docx
Suárez, Javier and Triviño, Vanessa (2019) A metaphysical approach to holobiont individuality: Holobionts as emergent individuals. [Preprint]
oai:philsci-archive.pitt.edu:15964
2019-05-01T13:38:39Z
7375626A656374733D73706563:6D617468656D6174696373:504D6578706C616E6174696F6E
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
7375626A656374733D67656E:636175736174696F6E
7375626A656374733D67656E:6578706C616E6174696F6E
74797065733D706974747072657072696E74
https://philsci-archive.pitt.edu/15964/
Explaining the behaviour of random ecological networks. The stability of the microbiome as a case of integrative pluralism.
Deulofeu, Roger
Suárez, Javier
Pérez-Cervera, Alberto
Explanation
Ecology/Conservation
Causation
Explanation
Explaining the behaviour of ecosystems is one of the key challenges for the biological sciences. Since 2000, new-mechanicism has been the main model to account for the nature of scientific explanation in biology. The universality of the new-mechanist view in biology has been however put into question due to the existence of explanations that account for some biological phenomena in terms of their mathematical properties (mathematical explanations). Supporters of mathematical explanation have argued that the explanation of the behaviour of ecosystems is usually provided in terms of their mathematical properties, and not in mechanistic terms. They have intensively studied the explanation of the properties of ecosystems that behave following the rules of a non-random network. However, no attention has been devoted to the study of the nature of the explanation in those that form a random network. In this paper, we cover that gap by analysing the explanation of the stability behaviour of the microbiome recently elaborated by Coyte and colleagues, to determine whether it fits with the model of explanation suggested by the new-mechanist or by the defenders of mathematical explanation. Our analysis of this case study supports three theses: (1) that the explanation is not given solely in terms of mechanisms, as the new-mechanists understand the concept; (2) that the mathematical properties that describe the system play an essential explanatory role, but they do not exhaust the explanation; (3) that a non-previously identified appeal to the type of interactions that the entities in the network can exhibit, as well as their abundance, is also necessary for Coyte and colleagues’ account to be fully explanatory. From the combination of these three theses we argue for the necessity of an integrative pluralist view of the nature of behaviour explanation when this is given by appealing to the existence of a random network.
2019
Preprint
NonPeerReviewed
text
en
https://philsci-archive.pitt.edu/15964/1/DEUETBv2.docx
Deulofeu, Roger and Suárez, Javier and Pérez-Cervera, Alberto (2019) Explaining the behaviour of random ecological networks. The stability of the microbiome as a case of integrative pluralism. [Preprint]
oai:philsci-archive.pitt.edu:15979
2019-05-05T00:37:27Z
7375626A656374733D73706563:6D617468656D6174696373:504D6578706C616E6174696F6E
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
7375626A656374733D67656E:636175736174696F6E
7375626A656374733D67656E:6578706C616E6174696F6E
74797065733D706974747072657072696E74
https://philsci-archive.pitt.edu/15979/
Explaining the behaviour of random ecological networks. The stability of the microbiome as a case of integrative pluralism.
Deulofeu, Roger
Suárez, Javier
Pérez-Cervera, Alberto
Explanation
Ecology/Conservation
Causation
Explanation
Explaining the behaviour of ecosystems is one of the key challenges for the biological sciences. Since 2000, new-mechanicism has been the main model to account for the nature of scientific explanation in biology. The universality of the new-mechanist view in biology has been however put into question due to the existence of explanations that account for some biological phenomena in terms of their mathematical properties (mathematical explanations). Supporters of mathematical explanation have argued that the explanation of the behaviour of ecosystems is usually provided in terms of their mathematical properties, and not in mechanistic terms. They have intensively studied the explanation of the properties of ecosystems that behave following the rules of a non-random network. However, no attention has been devoted to the study of the nature of the explanation in those that form a random network. In this paper, we cover that gap by analysing the explanation of the stability behaviour of the microbiome recently elaborated by Coyte and colleagues, to determine whether it fits with the model of explanation suggested by the new-mechanist or by the defenders of mathematical explanation. Our analysis of this case study supports three theses: (1) that the explanation is not given solely in terms of mechanisms, as the new-mechanists understand the concept; (2) that the mathematical properties that describe the system play an essential explanatory role, but they do not exhaust the explanation; (3) that a non-previously identified appeal to the type of interactions that the entities in the network can exhibit, as well as their abundance, is also necessary for Coyte and colleagues’ account to be fully explanatory. From the combination of these three theses we argue for the necessity of an integrative pluralist view of the nature of behaviour explanation when this is given by appealing to the existence of a random network.
2019
Preprint
NonPeerReviewed
text
en
https://philsci-archive.pitt.edu/15979/1/DEUETBv2.docx
Deulofeu, Roger and Suárez, Javier and Pérez-Cervera, Alberto (2019) Explaining the behaviour of random ecological networks. The stability of the microbiome as a case of integrative pluralism. [Preprint]
https://link.springer.com/article/10.1007%2Fs11229-019-02187-9
https://doi.org/10.1007/s11229-019-02187-9
oai:philsci-archive.pitt.edu:16046
2019-05-25T16:35:01Z
7375626A656374733D73706563:62696F6C6F6779
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65766F6C7574696F6E6172792D7468656F7279
7375626A656374733D67656E:726564756374696F6E69736D2D686F6C69736D
74797065733D7075626C69736865645F61727469636C65
https://philsci-archive.pitt.edu/16046/
A metaphysical approach to holobiont individuality: Holobionts as emergent individuals
Suárez, Javier
Triviño, Vanessa
Biology
Ecology/Conservation
Evolutionary Theory
Reductionism/Holism
Holobionts are symbiotic assemblages composed by a host plus its microbiome. The status of holobionts as individuals has recently been a subject of continuous controversy, which has given rise to two main positions: on the one hand, holobiont advocates argue that holobionts are biological individuals; on the other, holobiont detractors argue that they are just mere chimeras or ecological communities, but not individuals. Both parties in the dispute develop their arguments from the framework of the philosophy of biology, in terms of what it takes for a “conglomerate” to be considered an interesting individual from a biological point of view. However, the debates about holobiont individuality have important ontological implications that have remained vaguely explored from a metaphysical framework. The purpose of this paper is to cover that gap by presenting a metaphysical approach to holobionts individuality. Drawing upon a conception of natural selection that puts the focus on the transgenerational recurrence of the traits and that supports the thesis that holobionts are units of selection, we argue that holobionts bear emergent traits and exert downward powers over the entities that compose them. In this vein, we argue, a reasonable argument can be made for conceiving holobionts as emergent biological individuals.
University of Valencia
2019
Published Article or Volume
NonPeerReviewed
text
en
https://philsci-archive.pitt.edu/16046/1/Suarez%2C%20Trivino%202019%20-%20Emergent%20holobiont.pdf
Suárez, Javier and Triviño, Vanessa (2019) A metaphysical approach to holobiont individuality: Holobionts as emergent individuals. Quaderns de Filosofia, 6 (1). pp. 59-76.
https://ojs.uv.es/index.php/qfilosofia/article/view/14825
https://doi.org/10.7203/qfia.6.1.14825
oai:philsci-archive.pitt.edu:16311
2019-08-10T15:41:40Z
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https://philsci-archive.pitt.edu/16311/
Social evolution and the two elements of causation
Pernu, Tuomas K.
Helanterä, Heikki
Ecology/Conservation
Evolutionary Theory
Causation
Explanation
The kin selection theory has recently been criticised on the basis of claiming that genetic relatedness does not play a causal role in the social evolution among individuals of insect societies. We outline here a line of criticism of this view by demonstrating two things. First, there are strong conceptual, theoretical and empirical reasons to think that close genetic relatedness has been necessary for the rise of the helper castes of social insects. And second, once we understand how causal explanation itself results from an interplay of two logically distinct elements, necessity and sufficiency, we can also understand the scenarios in which relatedness does not seem to play a causal role for evolution of helper castes. The result of this analysis is that we should be more careful about the way we frame the empirical data on the evolution of social behaviour.
2019
Published Article or Volume
NonPeerReviewed
Pernu, Tuomas K. and Helanterä, Heikki (2019) Social evolution and the two elements of causation. Oikos, 128. pp. 905-911.
https://onlinelibrary.wiley.com/doi/full/10.1111/oik.05887
oai:philsci-archive.pitt.edu:16471
2019-10-01T18:08:23Z
7375626A656374733D73706563:62696F6C6F6779
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65766F6C7574696F6E6172792D7468656F7279
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74797065733D706974747072657072696E74
https://philsci-archive.pitt.edu/16471/
Functions and Functioning in Aldo Leopold’s Land Ethic and in Ecology
Millstein, Roberta L.
Biology
Ecology/Conservation
Evolutionary Theory
Function/Teleology
I examine the use of the term function in Aldo Leopold's land ethic, invoked as: 1) the healthy functioning of the land community, which is dependent on 2) the maintenance of the characteristic functions of populations that are parts of the land community. The latter can be understood as referring to interactions between species that are the products of coevolution (such as parasite-host, predator-prey, etc.), and thus, in terms of the “selected effect” account of function. The performance of these functions under certain conditions maintain what Leopold took to be the healthy functioning of a land community.
2019-09
Preprint
NonPeerReviewed
text
en
https://philsci-archive.pitt.edu/16471/1/Millstein-LeopoldFunctionsFunctioning-5-1-shareable.pdf
Millstein, Roberta L. (2019) Functions and Functioning in Aldo Leopold’s Land Ethic and in Ecology. [Preprint]
oai:philsci-archive.pitt.edu:16569
2019-10-24T02:23:47Z
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
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7375626A656374733D73706563:6D65646963696E65:6865616C74682D616E642D64697365617365
74797065733D706974747072657072696E74
https://philsci-archive.pitt.edu/16569/
Can Communities Cause?
Lean, Christopher
Ecology/Conservation
Causation
Experimentation
Health and Disease
Lynch et al. 2019 propose an extremely useful framework to assess microbiome research. By utilising advances in the causation literature, they argue that many of the claims in microbiome research are ‘weak or misleading’ as these claims lack stability, specificity, or proportionality. In the final paragraph before the conclusion they entertain and rapidly dismiss the ‘ecological version’ of microbiomes, in which microbiome properties are emergent from their constituent populations and can fulfil Koch’s postulates. I assess the possibility of microbiomes having emergent causal efficacy on host health and suggest they can.
2019
Preprint
NonPeerReviewed
text
en
https://philsci-archive.pitt.edu/16569/1/%5BBIPH%20LynchCommentary%5D%20Unblinded%20manuscript%20for%20Publication.docx
Lean, Christopher (2019) Can Communities Cause? [Preprint]
oai:philsci-archive.pitt.edu:16570
2019-10-24T02:25:35Z
7375626A656374733D67656E:536369656E74696669635F4D65746170687973696373
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
7375626A656374733D73706563:656E7669726F6E6D656E74616C2D736369656E6365
7375626A656374733D67656E:6E61747572616C2D6B696E6473
74797065733D706974747072657072696E74
https://philsci-archive.pitt.edu/16570/
Indexically Structured Ecological Communities (Phil sci Published)
Lean, Christopher
Scientific Metaphysics
Ecology/Conservation
Environmental Science
Natural Kinds
Ecological communities are seldom, if ever, biological individuals. They lack causal boundaries as the populations that constitute communities are not congruent and rarely have persistent functional roles regulating the communities’ higher-level properties. Instead we should represent ecological communities indexically, by identifying ecological communities via the network of weak causal interactions between populations that unfurl from a starting set of populations. This precisification of ecological communities helps identify how community properties remain invariant, and why they have robust characteristics. This is a more general framework than individuality, respecting the diversity and aggregational nature of these complex systems while still vindicating them as units worthy of investigation.
2018
Preprint
NonPeerReviewed
text
en
https://philsci-archive.pitt.edu/16570/1/Indexical%20Communities%20accepted%20paper%20december.docx
Lean, Christopher (2018) Indexically Structured Ecological Communities (Phil sci Published). [Preprint]
https://doi.org/10.1086/697746
oai:philsci-archive.pitt.edu:16673
2019-12-02T00:43:58Z
7375626A656374733D73706563:62696F6C6F6779
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
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74797065733D7075626C69736865645F61727469636C65
https://philsci-archive.pitt.edu/16673/
Research Problems
Elliott, Steve
Biology
Ecology/Conservation
Rhetoric of Science
Science and Society
Science and Policy
Values In Science
To identify and conceptualize research problems in science, philosophers and often scientists rely on classical accounts of problems that focus on intellectual problems often defined in relation to theories. Recently, philosophers have begun to study the structures and functions of research problems not defined in relation to theories. Furthermore, scientists have long pursued research problems often labeled as practical or applied. As yet, no account of problems specifies the description of both so-called intellectual problems and so-called applied problems. This paper proposes a new conceptual framework of problems that accounts both for intellectual aspects of problems and for their practical or applied aspects. I illustrate the account with an example of a recent research project from evolutionary biology, and I indicate further routes by which to develop the account, especially in connection to empirical studies of science.
2019-11
Published Article or Volume
NonPeerReviewed
text
en
https://philsci-archive.pitt.edu/16673/1/BJPSResearchProblemsPreTypeset.pdf
Elliott, Steve (2019) Research Problems. The British Journal for the Philosophy of Science. ISSN 0007-0882
https://doi.org/10.1093/bjps/axz052
oai:philsci-archive.pitt.edu:16718
2019-12-15T03:13:20Z
7375626A656374733D73706563:616E7468726F706F6C6F6779
7375626A656374733D73706563:62696F6C6F6779
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7375626A656374733D73706563:63756C747572616C2D65766F6C7574696F6E
74797065733D7075626C69736865645F61727469636C65
https://philsci-archive.pitt.edu/16718/
Three Kinds of Niche Construction
Aaby, Bendik
Ramsey, Grant
Anthropology
Biology
Developmental Biology
Ecology/Conservation
Evolutionary Theory
Function/Teleology
Cultural Evolution
Niche construction theory concerns how organisms can change selection pressures by altering the feature–factor relationship between themselves and their environment. These alterations are standardly understood to be brought about through two kinds of organism–environment interaction: perturbative and relocational niche construction. We argue that a reconceptualization is needed on the grounds that if a niche is understood as the feature–factor relationship, then there are three fundamental ways in which organisms can engage in niche construction: constitutive, relational, and external niche construction. We further motivate our reconceptualization by showing some examples of organismic activities which fall outside of the current categorization of niche construction, but nonetheless should be included. We end by discussing two objections to niche construction and show how our reconceptualization helps to undercut these objections.
2019-12-05
Published Article or Volume
NonPeerReviewed
text
en
https://philsci-archive.pitt.edu/16718/1/ThreeKindsOfNicheConstruction.pdf
Aaby, Bendik and Ramsey, Grant (2019) Three Kinds of Niche Construction. The British Journal for the Philosophy of Science. ISSN 1464-3537
https://doi.org/10.1093/bjps/axz054
https://doi.org/10.1093/bjps/axz054
oai:philsci-archive.pitt.edu:16810
2020-01-13T00:09:04Z
7375626A656374733D73706563:62696F6C6F6779
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
7375626A656374733D73706563:656E7669726F6E6D656E74616C2D736369656E6365
74797065733D7075626C69736865645F61727469636C65
https://philsci-archive.pitt.edu/16810/
Defending a Leopoldian basis for biodiversity: a response to Newman, Varner, and Linquist
Millstein, Roberta L.
Biology
Ecology/Conservation
Environmental Science
In their book, Defending Biodiversity, Newman, Varner, and Linquist (NVL) cast doubt on whether Leopoldian defenses of biodiversity, in their current form, have been successful. I argue that there is a more accurate interpretation of Leopold that is not subject to the criticisms made by NVL, and that Leopold’s body of work as a whole, including but not limited to the essay “The Land Ethic” in A Sand County Almanac, provides quite a bit of useful guidance and perspective. I begin with a brief summary of some of my own recent work on Leopold. This is intended to orient the reader who is more familiar with J. Baird Callicott’s influential interpretations of Leopold. I then discuss NVL’s Chapter 10 first followed by a discussion of their Chapter 9, responding to their critiques. I then conclude. On the revised interpretation that I have given, Leopold’s land ethic is defended by the method of reflective equilibrium, showing us that the land communities that we are interdependent with have intrinsic value, necessitating preserving their (land) health, which in turn necessitates preserving biodiversity.
Springer
2020-01
Published Article or Volume
NonPeerReviewed
text
en
https://philsci-archive.pitt.edu/16810/1/Millstein-on-Leopold-biodiversity-1-4-shareable.pdf
Millstein, Roberta L. (2020) Defending a Leopoldian basis for biodiversity: a response to Newman, Varner, and Linquist. Biology & Philosophy, 35 (12). ISSN 1572-8404
https://link.springer.com/article/10.1007/s10539-019-9724-9
https://doi.org/10.1007/s10539-019-9724-9
oai:philsci-archive.pitt.edu:16817
2020-01-14T23:56:50Z
7375626A656374733D67656E:44617461
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74797065733D706974747072657072696E74
https://philsci-archive.pitt.edu/16817/
Unifying the essential concepts of biological networks: biological insights and philosophical foundations
Kostic, Daniel
Hilgetag, Claus
Tittgemeyer, Marc
Data
Biology
Ecology/Conservation
Molecular Biology/Genetics
Complex Systems
Cognitive Neuroscience
Explanation
Models and Idealization
Systems Neuroscience
Over the last decades, network-based approaches have become highly popular in diverse fields of biology, including neuroscience, ecology, molecular biology and genetics. While these approaches continue to grow very rapidly, some of their conceptual and methodological aspects still require a programmatic foundation. This challenge particularly concerns the question of whether a generalized account of explanatory, organisational and descriptive levels of networks can be applied universally across biological sciences. To this end, this highly interdisciplinary theme issue focuses on the definition, motivation and application of key concepts in biological network science, such as explanatory power of distinctively network explanations, network levels, and network hierarchies.
2020
Preprint
NonPeerReviewed
text
en
https://philsci-archive.pitt.edu/16817/1/08%20january%202020%20FINAL%20Unifying%20the%20essential%20concepts%20of%20biological%20networks.pdf
Kostic, Daniel and Hilgetag, Claus and Tittgemeyer, Marc (2020) Unifying the essential concepts of biological networks: biological insights and philosophical foundations. [Preprint]
oai:philsci-archive.pitt.edu:16940
2020-02-29T05:55:33Z
7375626A656374733D73706563:62696F6C6F6779
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D646576656C6F706D656E74616C
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7375626A656374733D67656E:6E61747572616C2D6B696E6473
74797065733D7075626C69736865645F61727469636C65
https://philsci-archive.pitt.edu/16940/
The stability of traits conception of the hologenome: An evolutionary account of holobiont individuality
Suárez, Javier
Biology
Developmental Biology
Ecology/Conservation
Evolutionary Theory
Natural Kinds
Bourrat and Griffiths (HPLS 40(2): 33, 2018) have recently argued that most of the evidence presented by holobiont defenders to support the thesis that holobionts are evolutionary individuals is not to the point and is not even adequate to discriminate multispecies evolutionary individuals from other multispecies assemblages that would not be considered evolutionary individuals by most holobiont defenders. They further argue that an adequate criterion to distinguish the two categories rests on the existence of fitness alignment, presenting the notion of fitness boundedness as a criterion that allows divorcing true multispecies evolutionary individuals from other multispecies assemblages and provides an adequate criterion to single out genuine evolutionary multispecies assemblages. A consequence of their criterion is that holobionts, as conventionally defined by hologenome defenders, are not evolutionary individuals except in very rare cases, and for very specific host-symbiont associations. This paper is a critical response to Bourrat and Griffiths’ arguments and as such it constitutes a refinement and a defence of the arguments presented by holobiont defenders. Drawing upon the case of the hologenomic basis of the evolution of sanguivory in vampire bats (Nat. Ecol. Evol. 2: 659-668, 2018), I argue that Bourrat and Griffiths overlook some aspects of the biological nature of the microbiome that justifies the thesis that holobionts are evolutionarily different to other multispecies assemblages. I argue that the hologenome theory of evolution should not define the hologenome as a collection of genomes, but as the sum of the host genome plus some traits of the microbiome which together constitute an evolutionary individual, a conception I refer to as the stability of traits conception of the hologenome. Based on that conception I argue that the evidence presented by holobiont defenders, if adequately refined under the “stability of traits” framework I advocate here, is to the point, and supports the thesis that holobionts are evolutionary individuals. In this sense, the paper offers an account of the holobiont that aims to foster a dialogue between hologenome advocates and hologenome critics.
Springer
2020-02-24
Published Article or Volume
NonPeerReviewed
text
en
https://philsci-archive.pitt.edu/16940/1/Suarez%202020%20-%20MANUSCRIPT%20HPLS%2C%20clean.pdf
Suárez, Javier (2020) The stability of traits conception of the hologenome: An evolutionary account of holobiont individuality. History and Philosophy of the Life Sciences, 42 (11).
https://link.springer.com/article/10.1007%2Fs40656-020-00305-2
10.1007/s40656-020-00305-2
oai:philsci-archive.pitt.edu:16964
2020-03-04T03:27:54Z
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
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74797065733D706974747072657072696E74
https://philsci-archive.pitt.edu/16964/
What is a Target System?
Elliott-Graves, Alkistis
Ecology/Conservation
Models and Idealization
Many phenomena in the natural world are complex, so scientists study them through simplified and idealised models. Philosophers of science have sought to explain how these models relate to the world. On most accounts, models do not represent the world directly, but through target systems. However, our knowledge of target systems is incomplete. First, what is the process by which target systems come about? Second, what types of entity are they? I argue that the basic conception of target systems, on which other conceptions depend, is as parts of the world. I outline the process of target system specification and show that it is a crucial step in modelling. I also develop an account of target system evaluation, based on aptness. Paying close attention to target system specification and evaluation can help scientists minimise the frequency and extent of mistakes, when they are using models to investigate phenomena in complex real-world systems.
2020
Preprint
NonPeerReviewed
text
en
https://philsci-archive.pitt.edu/16964/1/WIATS%20-%20B%26P%20-%20Final.docx
Elliott-Graves, Alkistis (2020) What is a Target System? [Preprint]
oai:philsci-archive.pitt.edu:17005
2020-03-16T03:54:06Z
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74797065733D706974747072657072696E74
https://philsci-archive.pitt.edu/17005/
Invasive Species and Natural Function in Ecology
Lean, Christopher
Ecology/Conservation
Function/Teleology
If ecological systems are functionally organised, they can possess functions or malfunctions. Natural function would provide justification for conservationists to act for the protection of current ecological arrangements and control the presence of populations that create ecosystem malfunctions. Invasive species are often thought to be malfunctional for ecosystems, so functional arrangement would provide an objective reason for their control. Unfortunately for this prospect, I argue no theory of function, which can support such normative conclusions, can be applied to large scale ecosystems. Instead ecological systems have causal structure, with small clusters of populations achieving functional arrangement. This, however, does not leave us without reason to control invasive species. We can look at the causal arrangement of ecological systems for populations that support ecological features that we should preserve. Populations that play a causal role in reducing biodiversity should be controlled, because biodiversity is a good all prudent agents should want to preserve.
2020
Preprint
NonPeerReviewed
text
en
https://philsci-archive.pitt.edu/17005/1/Invasive%20Species%20and%20Natural%20Function%20in%20Ecology%20Pub.pdf
Lean, Christopher (2020) Invasive Species and Natural Function in Ecology. [Preprint]
oai:philsci-archive.pitt.edu:17114
2020-04-26T19:59:37Z
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
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74797065733D7075626C69736865645F61727469636C65
https://philsci-archive.pitt.edu/17114/
The use and limitations of null-model-based hypothesis testing
Zhang, Mingjun
Ecology/Conservation
Evidence
Explanation
Models and Idealization
In this article I give a critical evaluation of the use and limitations of null-model-based hypothesis testing as a research strategy in the biological sciences. According to this strategy, the null model based on a randomization procedure provides an appropriate null hypothesis stating that the existence of a pattern is the result of random processes or can be expected by chance alone, and proponents of other hypotheses should first try to reject this null hypothesis in order to demonstrate their own hypotheses. Using as an example the controversy over the use of null hypotheses and null models in species co-occurrence studies, I argue that null-model-based hypothesis testing fails to work as a proper analog to traditional statistical null-hypothesis testing as used in well-controlled experimental research, and that the random process hypothesis should not be privileged as a null hypothesis. Instead, the possible use of the null model resides in its role of providing a way to challenge scientists’ commonsense judgments about how a seemingly unusual pattern could have come to be. Despite this possible use, null-model-based hypothesis testing still carries certain limitations, and it should not be regarded as an obligation for biologists who are interested in explaining patterns in nature to first conduct such a test before pursuing their own hypotheses.
Springer
2020-04-23
Published Article or Volume
NonPeerReviewed
text
en
https://philsci-archive.pitt.edu/17114/1/The%20use%20and%20limitations%20of%20null-model-based%20hypothesis%20testing.pdf
Zhang, Mingjun (2020) The use and limitations of null-model-based hypothesis testing. Biology & Philosophy, 35 (2). pp. 1-22. ISSN 0169-3867
http://doi.org/10.1007/s10539-020-09748-0
doi:10.1007/s10539-020-09748-0
oai:philsci-archive.pitt.edu:17118
2020-04-27T01:33:53Z
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74797065733D706974747072657072696E74
https://philsci-archive.pitt.edu/17118/
General Unificatory Theories in Community Ecology
Lean, Christopher
Ecology/Conservation
Causation
Explanation
Laws of Nature
Structure of Theories
ABSTRACT. The question of whether there are laws of nature in ecology has developed substantially in the last 20 years. Many have attempted to rehabilitate ecology’s lawlike status through establishing that ecology possesses laws that robustly appear across many different ecological systems. I argue that there is still something missing, which explains why so many have been skeptical of ecology’s lawlike status. Community ecology has struggled to establish what I call a General Unificatory Theory (GUT). The lack of a GUT causes problems for explanation as there are no guidelines for how to integrate the lower-level mathematical and causal models into a larger theory of how ecological assemblages are formed. I turn to a promising modern attempt to provide a unified higher-level explanation in ecology, presented by ecologist Mark Vellend, and advocate for philosophical engagement with its prospects for aiding ecological explanation.
2020
Preprint
NonPeerReviewed
text
en
https://philsci-archive.pitt.edu/17118/1/GUTiCE%2027th%20of%20April.pdf
Lean, Christopher (2020) General Unificatory Theories in Community Ecology. [Preprint]
oai:philsci-archive.pitt.edu:17243
2020-05-26T23:10:07Z
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
7375626A656374733D67656E:6D6F64656C732D616E642D696465616C697A6174696F6E
74797065733D706974747072657072696E74
https://philsci-archive.pitt.edu/17243/
The Value of Imprecise Prediction
Elliott-Graves, Alkistis
Ecology/Conservation
Models and Idealization
The traditional philosophy of science approach to prediction leaves little room for appreciating the value and potential of imprecise predictions. At best, they are considered a stepping stone to more precise predictions, while at worst they are viewed as detracting from the scientific quality of a discipline. The aim of this paper is to show that imprecise predictions are undervalued in philosophy of science. I review the conceptions of imprecise predictions, and the main criticisms levelled against them: (i) that they cannot aid in model selection and improvement and (ii) that they cannot support effective interventions in practical decision making. I will argue against both criticisms, showing that imprecise predictions have a circumscribed but important and legitimate place in the study of complex heterogeneous systems. The argument is illustrated and supported by an example from conservation biology, where imprecise models were instrumental in saving the kōkako from extinction.
2020
Preprint
NonPeerReviewed
text
en
https://philsci-archive.pitt.edu/17243/1/The%20Value%20of%20Imprecise%20Prediction%20-%20Preprint.pdf
Elliott-Graves, Alkistis (2020) The Value of Imprecise Prediction. [Preprint]
oai:philsci-archive.pitt.edu:18039
2020-08-31T01:01:16Z
7375626A656374733D73706563:62696F6C6F6779
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
7375626A656374733D67656E:6578706C616E6174696F6E
7375626A656374733D67656E:6D6F64656C732D616E642D696465616C697A6174696F6E
7375626A656374733D67656E:726865746F7269632D6F662D736369656E6365
7375626A656374733D67656E:74686F756768742D6578706572696D656E7473
74797065733D706974747072657072696E74
https://philsci-archive.pitt.edu/18039/
The emergence of scientific understanding in current ecological research practice
Poliseli, Luana
Biology
Ecology/Conservation
Explanation
Models and Idealization
Rhetoric of Science
Thought Experiments
Scientific understanding as a subject of inquiry has become widely discussed in philosophy of science
and is often addressed through case studies from history of science. Even though these historical reconstructions
engage with details of scientific practice, they usually provide only limited information about the gradual
formation of understanding in ongoing processes of model and theory construction. Based on a qualitative
ethnographic study of an ecological research project, this article shifts attention from understanding in the
context of historical case studies to evidence of current case studies. By taking de Regt's (2017) contextual
theory of scientific understanding into the field, it confirms core tenets of the contextual theory (e.g. the crucial
role of visualization and visualizability) suggesting a normative character with respect to scientific activities.
However, the case study also shows the limitations of de Regt's latest version of this theory as an attempt to
explain the development of understanding in current practice. This article provides a model representing the
emergence of scientific understanding that exposes main features of scientific understanding such as its gradual
formation, its relation to skills and imagination, and its capacity for knowledge selectivity. The ethnographic
evidence presented here supports the claim that something unique can be learned by looking into ongoing
research practices that can’t be gained by studying historical case studies.
2020
Preprint
NonPeerReviewed
text
en
https://philsci-archive.pitt.edu/18039/1/HPLS%5Bpreprint%5D.pdf
Poliseli, Luana (2020) The emergence of scientific understanding in current ecological research practice. [Preprint]
10.1007/s40656-020-00338-7
oai:philsci-archive.pitt.edu:18198
2020-10-07T02:30:32Z
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
7375626A656374733D67656E:6578706572696D656E746174696F6E
7375626A656374733D67656E:6D6F64656C732D616E642D696465616C697A6174696F6E
74797065733D706974747072657072696E74
https://philsci-archive.pitt.edu/18198/
The Future of Predictive Ecology
Elliott-Graves, Alkistis
Ecology/Conservation
Experimentation
Models and Idealization
Prediction is an important aspect of scientific practice, because it helps us to confirm theories and effectively intervene on the systems we are investigating. In ecology, prediction is a controversial topic: even though the number of papers focusing on prediction is constantly increasing, many ecologists believe that the quality of ecological predictions is unacceptably low, in the sense that they are not sufficiently accurate sufficiently often. Moreover, ecologists disagree on how predictions can be improved. On one side are the ‘theory-driven’ ecologists, those who believe that ecology lacks a sufficiently strong theoretical framework. For them, more general theories will yield more accurate predictions. On the other are the ‘applied’ ecologists, whose research is focused on effective interventions on ecological systems. For them, deeper knowledge of the system in question is more important than background theory. The aim of this paper is to provide a philosophical examination of both sides of the debate: as there are strengths and weaknesses in both approaches to prediction, a pluralistic approach is best for the future of predictive ecology.
2020
Preprint
NonPeerReviewed
text
en
https://philsci-archive.pitt.edu/18198/1/Future%20of%20Predictive%20Ecology%20-%20Preprint.pdf
Elliott-Graves, Alkistis (2020) The Future of Predictive Ecology. [Preprint]
oai:philsci-archive.pitt.edu:18333
2020-11-11T05:03:14Z
7375626A656374733D67656E:536369656E74696669635F4D65746170687973696373
7375626A656374733D73706563:62696F6C6F6779
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D646576656C6F706D656E74616C
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65766F6C7574696F6E6172792D7468656F7279
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D73797374656D6174696373
74797065733D7075626C69736865645F61727469636C65
https://philsci-archive.pitt.edu/18333/
A part‐dependent account of biological individuality: why holobionts are individuals and ecosystems simultaneously
Suárez, Javier
Stencel, Adrian
Scientific Metaphysics
Biology
Developmental Biology
Ecology/Conservation
Evolutionary Theory
Systematics
Given one conception of biological individuality (evolutionary, physiological, etc.), can a holobiont – that is the host + its symbiotic (mutualistic, commensalist and parasitic) microbiome – be simultaneously a biological individual and an ecological community? Herein, we support this possibility by arguing that the notion of biological individuality is part‐dependent. In our account, the individuality of a biological ensemble should not only be determined by the conception of biological individuality in use, but also by the biological characteristics of the part of the ensemble under investigation. In the specific case of holobionts, evaluations of their individuality should be made either host‐relative or microbe‐relative. We support the claim that biological individuality is part‐dependent by drawing upon recent empirical evidence regarding the physiology of hosts and microbes, and the recent characterization of the ‘demibiont’. Our account shows that contemporary disagreements about the individuality of the holobiont derive from an incorrect understanding of the ontology of biological individuality. We show that collaboration between philosophers and biologists can be very fruitful in attempts to solve some contemporary biological debates.
Wiley Online Library
2020-05-13
Published Article or Volume
NonPeerReviewed
text
en
https://philsci-archive.pitt.edu/18333/1/Suarez%20Stencel%202020%20-%20Part%20Dependent.docx
Suárez, Javier and Stencel, Adrian (2020) A part‐dependent account of biological individuality: why holobionts are individuals and ecosystems simultaneously. Biological Reviews of the Cambridge Philosophical Society, 95. pp. 1308-1324.
https://onlinelibrary.wiley.com/doi/full/10.1111/brv.12610
10.1111/brv.12610
oai:philsci-archive.pitt.edu:18474
2020-12-01T18:56:39Z
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
7375626A656374733D67656E:6578706572696D656E746174696F6E
7375626A656374733D67656E:6D6F64656C732D616E642D696465616C697A6174696F6E
74797065733D706974747072657072696E74
https://philsci-archive.pitt.edu/18474/
The Future of Predictive Ecology
Elliott-Graves, Alkistis
Ecology/Conservation
Experimentation
Models and Idealization
Prediction is an important aspect of scientific practice, because it helps us to confirm theories and effectively intervene on the systems we are investigating. In ecology, prediction is a controversial topic: even though the number of papers focusing on prediction is constantly increasing, many ecologists believe that the quality of ecological predictions is unacceptably low, in the sense that they are not sufficiently accurate sufficiently often. Moreover, ecologists disagree on how predictions can be improved. On one side are the ‘theory-driven’ ecologists, those who believe that ecology lacks a sufficiently strong theoretical framework. For them, more general theories will yield more accurate predictions. On the other are the ‘applied’ ecologists, whose research is focused on effective interventions on ecological systems. For them, deeper knowledge of the system in question is more important than background theory. The aim of this paper is to provide a philosophical examination of both sides of the debate: as there are strengths and weaknesses in both approaches to prediction, a pluralistic approach is best for the future of predictive ecology.
2020
Preprint
NonPeerReviewed
text
en
https://philsci-archive.pitt.edu/18474/1/Elliott-Graves%20%282019%29%20Future%20of%20Predictive%20Ecology.pdf
Elliott-Graves, Alkistis (2020) The Future of Predictive Ecology. [Preprint]
oai:philsci-archive.pitt.edu:18629
2021-01-21T14:42:16Z
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
7375626A656374733D67656E:76616C7565732D696E2D736369656E6365
74797065733D706974747072657072696E74
https://philsci-archive.pitt.edu/18629/
Distinguishing regeneration from degradation in coral ecosystems: the role of value
Jones, Elis
Ecology/Conservation
Values In Science
In this paper I argue that the value attributed to coral reefs drives the characterisation of evidence for their regeneration or degradation. I observe that regeneration and degradation depend on an understanding of what an ecosystem looks like when undegraded (a baseline), and that many mutually exclusive baselines can be given for any single case. Consequently, facts about ecological processes are insufficient to usefully and non-arbitrarily characterise changes to ecosystems. By examining how baselines and the value of reefs interact in coral and algal reef examples, I argue that considering the value of an ecosystem is a necessity when describing processes like regeneration and degradation. This connects value as studied in socio-ecological and economic research with values as discussed in the philosophy of science literature. It also explains why such a broad range of processes may be considered regenerative, including those which introduce significant novelty, as well as pointing towards ways to mediate related debates, such as those surrounding novel and ‘pristine’ ecosystems.
2021-01-02
Preprint
NonPeerReviewed
text
en
https://philsci-archive.pitt.edu/18629/1/CoralRegenValue-Preprint.pdf
Jones, Elis (2021) Distinguishing regeneration from degradation in coral ecosystems: the role of value. [Preprint]
10.1007/s11229-021-03023-9
oai:philsci-archive.pitt.edu:18641
2021-02-06T21:10:29Z
7375626A656374733D73706563:62696F6C6F6779
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D646576656C6F706D656E74616C
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65766F6C7574696F6E6172792D7468656F7279
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D66756E6374696F6E2D74656C656F6C6F6779
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D6D6F6C6563756C61722D62696F6C6F67792D67656E6574696373
74797065733D7075626C69736865645F61727469636C65
https://philsci-archive.pitt.edu/18641/
Programmed cell death as a black queen in microbial communities
Ndhlovu, Andrew
Durand, Pierre
Ramsey, Grant
Biology
Developmental Biology
Ecology/Conservation
Evolutionary Theory
Function/Teleology
Molecular Biology/Genetics
Programmed cell death (PCD) in unicellular organisms is in some instances an altruistic trait. When the beneficiaries are clones or close kin, kin selection theory may be used to explain the evolution of the trait, and when the trait evolves in groups of distantly related individuals, group or multilevel selection theory is invoked. In mixed microbial communities, the benefits are also available to unrelated taxa. But the evolutionary ecology of PCD in communities is poorly understood. Few hypotheses have been offered concerning the community role of PCD despite its far-reaching effects. The hypothesis we consider here is that PCD is a black queen. The Black Queen Hypothesis (BQH) outlines how public goods arising from a leaky function are exploited by other taxa in the community. Black Queen (BQ) traits are essential for community survival, but only some members bear the cost of possessing them, while others lose the trait In addition, BQ traits have been defined in terms of adaptive gene loss, and it is unknown whether this has occurred for PCD. Our conclusion is that PCD fulfils the two most important criteria of a BQ (leakiness and costliness), but that more empirical data are needed for assessing the remaining two criteria. In addition, we hold that for viewing PCD as a BQ, the original BQH needs to include social traits. Thus, despite some empirical and conceptual shortcomings, the BQH provides a helpful avenue for investigating PCD in microbial communities.
Wiley
2020-11-25
Published Article or Volume
NonPeerReviewed
text
en
https://philsci-archive.pitt.edu/18641/1/PCD_As_Black_Queen.pdf
Ndhlovu, Andrew and Durand, Pierre and Ramsey, Grant (2020) Programmed cell death as a black queen in microbial communities. Molecular Ecology. pp. 1-10.
https://doi.org/10.1111/mec.15757
10.1111/mec.15757
oai:philsci-archive.pitt.edu:18812
2021-03-13T00:11:00Z
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65766F6C7574696F6E6172792D7468656F7279
7375626A656374733D67656E:686973746F72792D6F662D736369656E63652D636173652D73747564696573
74797065733D706974747072657072696E74
https://philsci-archive.pitt.edu/18812/
Darwin’s empirical claim and the janiform character of fitness proxies
Krohs, Ulrich
Ecology/Conservation
Evolutionary Theory
History of Science Case Studies
Darwin’s claim about natural selection is reconstructed as an empirical claim about the causal relevance of the match between the individual and its environment for the condition of the individual, and the consequence of this condition for leaving progeny. It is shown that many fitness proxies are mediating between these two steps. They are indicators of the match and predictors of reproductive success at once. Modern concepts of fitness, in contrast, are focusing exclusively on the latter. Assuming that Darwin wanted to explain selection in terms of a modern concept of fitness thus confounds his argument. Taking the janiform character of fitness proxies serious, in contrast, does not only allow for integrating Darwin’s argument into current evolutionary biology, but also helps reframing and alleviating the dispute between the Modern Synthesis and the Extended Evolutionary Synthesis.
2021-03-12
Preprint
NonPeerReviewed
text
en
https://philsci-archive.pitt.edu/18812/1/Krohs_Darwin%20and%20fitness%20proxies%2012032021.pdf
Krohs, Ulrich (2021) Darwin’s empirical claim and the janiform character of fitness proxies. [Preprint]
oai:philsci-archive.pitt.edu:18853
2021-03-26T03:22:12Z
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
7375626A656374733D67656E:6578706572696D656E746174696F6E
7375626A656374733D67656E:6D6F64656C732D616E642D696465616C697A6174696F6E
74797065733D706974747072657072696E74
https://philsci-archive.pitt.edu/18853/
The Aims and Structures of Ecological Research Programs
Bausman, William C
Ecology/Conservation
Experimentation
Models and Idealization
Neutral Theory is controversial in ecology. Ecologists and philosophers have diagnosed the source of the controversy as: its false assumption that individuals in different species within the same trophic level are ecologically equivalent, its conflict with Competition Theory and the adaptation of species, its role as a null hypothesis, and as a Lakatosian research programme. In this paper, I show why we should instead understand the conflict at the level of research programs which involve more than theory. The Neutralist and Competitionist research programs borrow and construct theories, models, and experiments for various aims and given their home ecological systems. I present a holistic and pragmatic view of the controversy that foregrounds the interrelation between many kinds of practices and decisions in ecological research.
2020-10
Preprint
NonPeerReviewed
text
en
https://philsci-archive.pitt.edu/18853/1/Bausman%202020%20Aims%20and%20Structures%20Phil%20Topics.pdf
Bausman, William C (2020) The Aims and Structures of Ecological Research Programs. [Preprint]
http://www.jstor.org/stable/26948089
oai:philsci-archive.pitt.edu:18880
2021-04-02T14:19:55Z
7375626A656374733D73706563:62696F6C6F6779
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D73797374656D6174696373
7375626A656374733D73706563:6D65646963696E65:6865616C74682D616E642D64697365617365
7375626A656374733D67656E:7068696C6F736F70686572732D6F662D736369656E6365
74797065733D7075626C69736865645F61727469636C65
https://philsci-archive.pitt.edu/18880/
"Microbiota, symbiosis and individuality summer school" meeting report
Ronai, Isobel
Greslehner, Gregor P.
Boem, Federico
Carlisle, Judith
Stencel, Adrian
Suárez, Javier
Bayir, Saliha
Bretting, Wiebke
Formosinho, Joana
Guerrero, Anna C.
Morgan, William H.
Prigot-Maurice, Cybèle
Rodeck, Salome
Vasse, Marie
Wallis, Jacqueline M.
Zacks, Oryan
Biology
Ecology/Conservation
Systematics
Health and Disease
Philosophers of Science
How does microbiota research impact our understanding of biological individuality? We summarize the interdisciplinary summer school on "Microbiota, Symbiosis and Individuality: Conceptual and Philosophical Issues" (July 2019), which was supported by a European Research Council starting grant project "Immunity, DEvelopment, and the Microbiota" (IDEM). The summer school centered around interdisciplinary group work on four facets of microbiota research: holobionts, individuality, causation, and human health. The conceptual discussion of cutting-edge empirical research provided new insights into microbiota and highlights the value of incorporating into meetings experts from other disciplines, such as philosophy and history of science.
2020
Published Article or Volume
NonPeerReviewed
text
en
https://philsci-archive.pitt.edu/18880/1/Microbiota_summer_school_report_resubmission_Archive.pdf
Ronai, Isobel and Greslehner, Gregor P. and Boem, Federico and Carlisle, Judith and Stencel, Adrian and Suárez, Javier and Bayir, Saliha and Bretting, Wiebke and Formosinho, Joana and Guerrero, Anna C. and Morgan, William H. and Prigot-Maurice, Cybèle and Rodeck, Salome and Vasse, Marie and Wallis, Jacqueline M. and Zacks, Oryan (2020) "Microbiota, symbiosis and individuality summer school" meeting report. Microbiome, 8. p. 117.
10.1186/s40168-020-00898-7
oai:philsci-archive.pitt.edu:18941
2021-04-25T03:55:11Z
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
7375626A656374733D67656E:736369656E63652D616E642D736F6369657479
74797065733D7075626C69736865645F61727469636C65
https://philsci-archive.pitt.edu/18941/
Biodiversity databanks and scientific exploration
Barberousse, Anouk
Ecology/Conservation
Science and Society
For several decades now, biologists have been developing digital databanks, which are remarkable scientific instruments allowing scientists to accelerate the development of biological knowledge. From the beginnings of the Human Genome Project (HGP) onwards, genetic databanks have been a major component of current biological knowledge, and biodiversity databanks have also been developed in the wake of the HGP. The purpose of this paper is to identify the specific features of biodiversity data and databanks, and to point out their contribution to biodiversity knowledge.
Société de philosophie des sciences
2021-04-06
Published Article or Volume
NonPeerReviewed
text
en
cc_by_nc_sa_4
https://philsci-archive.pitt.edu/18941/1/20573-Article%20Text-106093-2-10-20210406.pdf
Barberousse, Anouk (2021) Biodiversity databanks and scientific exploration. Lato Sensu, revue de la Société de philosophie des sciences, 8 (2). pp. 32-43. ISSN 2295-8029
https://ojs.uclouvain.be/index.php/latosensu/article/view/20573
10.20416/LSRSPS.V8I2.4
oai:philsci-archive.pitt.edu:19012
2021-05-12T03:07:47Z
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
7375626A656374733D67656E:636175736174696F6E
7375626A656374733D67656E:6578706C616E6174696F6E
74797065733D706974747072657072696E74
https://philsci-archive.pitt.edu/19012/
The Limitations of Hierarchical Organization
Potochnik, Angela
McGill, Brian
Ecology/Conservation
Causation
Explanation
The concept of hierarchical organization is commonplace in science. Subatomic particles compose atoms, which compose molecules; cells compose tissues, which compose organs, which compose organisms; etc. Hierarchical organization is particularly prominent in ecology, a field of research explicitly arranged around levels of ecological organization. The concept of levels of organization is also central to a variety of debates in philosophy of science. Yet many difficulties plague the concept of discrete hierarchical levels. In this paper, we show how these difficulties undermine various implications ascribed to hierarchical organization, and we suggest the concept of scale as a promising alternative to levels. Investigating causal processes at different scales offers a way to retain a notion of quasi-levels that avoids the difficulties inherent in the classic concept of hierarchical levels of organization. Throughout, our focus is on ecology, but the results generalize to other invocations of hierarchy in science and philosophy of science.
2012
Preprint
NonPeerReviewed
text
en
https://philsci-archive.pitt.edu/19012/1/POTTLO-2.1.pdf
Potochnik, Angela and McGill, Brian (2012) The Limitations of Hierarchical Organization. [Preprint]
10.1086/663237
oai:philsci-archive.pitt.edu:19041
2021-05-17T14:05:05Z
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65766F6C7574696F6E6172792D7468656F7279
74797065733D706974747072657072696E74
https://philsci-archive.pitt.edu/19041/
Defining the Niche for Niche Construction: Evolutionary and Ecological Niches
Trappes, Rose
Ecology/Conservation
Evolutionary Theory
Niche construction theory (NCT) aims to transform and unite evolutionary biology and ecology. Much of the debate about NCT has focused on construction. Less attention has been accorded to the niche: what is it, exactly, that organisms are constructing? In this paper I compare and contrast the definition of the niche used in NCT with ecological niche definitions. NCT’s concept of the evolutionary niche is defined as the sum of selection pressures affecting a population. So defined, the evolutionary niche is narrower than the ecological niche. Moreover, when contrasted with a more restricted ecological niche concept, it has a slightly different extension. I point out three kinds of cases in which the evolutionary niche does not coincide with realized ecological niches: extreme habitat degradation, commensalism, and non-limiting or super-abundant resources. These conceptual differences affect the role of NCT in unifying ecology and evolutionary biology.
2021-05
Preprint
NonPeerReviewed
text
en
https://philsci-archive.pitt.edu/19041/1/trappes_defining-the-niche-for-niche-construction_preprint.pdf
Trappes, Rose (2021) Defining the Niche for Niche Construction: Evolutionary and Ecological Niches. [Preprint]
oai:philsci-archive.pitt.edu:19076
2021-05-21T03:00:35Z
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65636F6C6F6779
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D65766F6C7574696F6E6172792D7468656F7279
7375626A656374733D73706563:62696F6C6F6779:62696F6C6F67792D66756E6374696F6E2D74656C656F6C6F6779
7375626A656374733D67656E:6C6177732D6F662D6E6174757265
74797065733D706974747072657072696E74
https://philsci-archive.pitt.edu/19076/
The Selectionist Rationale for Evolutionary Progress
Desmond, Hugh
Ecology/Conservation
Evolutionary Theory
Function/Teleology
Laws of Nature
The dominant view today on evolutionary progress is that it has been thoroughly debunked. Even value-neutral progress concepts are seen to lack important theoretical underpinnings: (1) natural selection provides no rationale for progress, and (2) natural selection need not even be invoked to explain large-scale evolutionary trends. In this paper I challenge this view by analysing how natural selection acts in heterogeneous environments. This not only undermines key debunking arguments, but also provides a selectionist rationale for a pattern of “evolutionary unfolding”, where life radiates across an increased range of exploitation of environmental heterogeneity.
2021-05-10
Preprint
NonPeerReviewed
text
en
https://philsci-archive.pitt.edu/19076/1/2021%20-%20The%20selectionist%20rationale%20for%20progress.pdf
Desmond, Hugh (2021) The Selectionist Rationale for Evolutionary Progress. [Preprint]
oai:philsci-archive.pitt.edu:19223
2023-02-05T14:10:48Z
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https://philsci-archive.pitt.edu/19223/
Extending animal welfare science to include wild animals
Veit, Walter
Browning, Heather
Biology
Ecology/Conservation
Evolutionary Psychology
Comparative Psychology and Ethology
Psychology
Science and Policy
Ng’s (2016) target article built on his earlier work advocating a science of welfare biology (Ng 1995). Although there were problems with the models proposed in Ng’s original paper regarding the balance of pleasure and suffering for wild animals, his call for a science of wild animal welfare was a sound one. This does not require a new discipline but just an extension of the existing frameworks and methods of animal welfare science to include wild animals.
2021
Preprint
NonPeerReviewed
text
en
https://philsci-archive.pitt.edu/19223/1/Extending%20animal%20welfare%20science%20VeitBrowning.pdf
Veit, Walter and Browning, Heather (2021) Extending animal welfare science to include wild animals. [Preprint]
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