Philosophy of Biology

Edited by Manolo Martínez (Universitat de Barcelona)
Assistant editor: Wiseley Wong (University of Western Ontario)
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  1. BioEssays 8∕2019.Bérénice A. Benayoun & Changhan Lee - 2019 - Bioessays 41 (9):1970091.
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    Developmental Biology
     Developmental Constraints
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     Epigenetic Inheritance
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  2. Habituation Is More Than Learning to Ignore: Multiple Mechanisms Serve to Facilitate Shifts in Behavioral Strategy.Troy A. McDiarmid, Alex J. Yu & Catharine H. Rankin - 2019 - Bioessays 41 (9):1900077.
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    Developmental Biology
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    Teleology and Function
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  3. At the Intersection of Microbiota and Circadian Clock: Are Sexual Dimorphism and Growth Hormones the Missing Link to Pathology?Benjamin D. Weger, Oliver Rawashdeh & Frédéric Gachon - 2019 - Bioessays 41 (9):1900059.
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    Developmental Biology
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  4. DNA G‐Quadruplexes Modulate Epigenetic Programming and Chromatin Remodeling.Anna Varizhuk, Ekaterina Isaakova & Galina Pozmogova - 2019 - Bioessays 41 (9):1900091.
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    Developmental Biology
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    Teleology and Function
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  5. MOTS‐C: A Mitochondrial‐Encoded Regulator of the Nucleus.Bérénice A. Benayoun & Changhan Lee - 2019 - Bioessays 41 (9):1900046.
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    Developmental Biology
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    Teleology and Function
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  6. Half‐Intercalation Stabilizes Slipped Mispairing and Explains Genome Vulnerability to Frameshift Mutagenesis by Endogenous “Molecular Bookmarks”.Andrei Kuzminov - 2019 - Bioessays 41 (9):1900062.
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    Developmental Biology
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  7. Heat Shock Proteins in the “Hot” Mitochondrion: Identity and Putative Roles.Mohamed A. Nasr, Galina I. Dovbeshko, Stephen L. Bearne, Nagwa El‐Badri & Chérif F. Matta - 2019 - Bioessays 41 (9):1900055.
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    Developmental Biology
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  8. Interdisciplinary Communication Needs to Become a Core Scientific Skill.Ralf Dahm, Jonathan Byrne & Michael A. Wride - 2019 - Bioessays 41 (9):1900101.
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    Developmental Biology
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  9. Immune Regulation in Eutherian Pregnancy: Live Birth Coevolved with Novel Immune Genes and Gene Regulation.Jiyun M. Moon, John A. Capra, Patrick Abbot & Antonis Rokas - 2019 - Bioessays 41 (9):1900072.
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    Developmental Biology
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  10. We Should Not Use the Term “Lamarckian” as It Is Often Used in Opposition to “Darwinian”.Dave Speijer - 2019 - Bioessays 41 (9):1900092.
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    Developmental Biology
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  11. Chromatin Architecture in the Fly: Living Without CTCF/Cohesin Loop Extrusion?Nicholas E. Matthews & Rob White - 2019 - Bioessays 41 (9):1900048.
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    Developmental Biology
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  12. Memes: Food for Attitudes and Behavior Crucial for Our Survival.Sven Kurbel & Beatrica Kurbel - 2019 - Bioessays 41 (9):1900075.
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  13. On the Likelihood of Life Originating.Dave Speijer - 2019 - Bioessays 41 (9):1900085.
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  14. Viral Detection: Past, Present, and Future.Konstantina Katsarou, Eirini Bardani, Paraskevi Kallemi & Kriton Kalantidis - forthcoming - Bioessays.
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  15. The Bio-Evolutionary Anthropocene Hypothesis: Rethinking the Role of Human-Induced Novel Organisms in Evolution.Pablo José Francisco Pena Rodrigues & Catarina Fonseca Lira - 2019 - Biological Theory 14 (3):141-150.
    Anthropogenic changes in the biosphere, driven mainly by human cultural habits and technological advances, are altering the direction of evolution on Earth, with ongoing and permanent changes modifying uncountable interactions between organisms, the environment, and humankind itself. While numerous species may go extinct, others will be favored due to strong human influences. The Bio-Evolutionary Anthropocene hypothesizes that directly or indirectly human-driven organisms, including alien species, hybrids, and genetically modified organisms, will have major roles in the evolution of life on Earth, (...)
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  16. Reflections on a Biometrics of Organismal Form.Fred L. Bookstein - 2019 - Biological Theory 14 (3):177-211.
    Back in 1987 the physicist/theoretical biologist Walter Elsasser reviewed a range of philosophical issues at the foundation of organismal biology above the molecular level. Two of these are particularly relevant to quantifications of form: the concept of ordered heterogeneity and the principle of nonstructural memory, the truism that typically the forms of organisms substantially resemble the forms of their ancestors. This essay attempts to weave Elsasser’s principles together with morphometrics for one prominent data type, the representation of animal forms by (...)
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  17. Are Verbal-Narrative Models More Suitable Than Mathematical Models as Information Processing Devices for Some Behavioral Problems?Gabriel Francescoli - 2019 - Biological Theory 14 (3):171-176.
    This article argues that many, if not most, behavior descriptions and sequencing are in essence an interpretation of signs, and are evaluated as sequences of signs by researchers. Thus, narrative analysis, as developed by Barthes and others, seems best suited to be used in behavioral/biosemiotic studies rather than mathematical modeling, and is very similar to some classic ethology methods. As our brain interprets behaviors as signs and attributes meaning to them, narrative analysis seems more suitable than mathematical modeling to describe (...)
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  18. Criteria for Holobionts From Community Genetics.Elisabeth A. Lloyd & Michael J. Wade - 2019 - Biological Theory 14 (3):151-170.
    We address the controversy in the literature concerning the definition of holobionts and the apparent constraints on their evolution using concepts from community population genetics. The genetics of holobionts, consisting of a host and diverse microbial symbionts, has been neglected in many discussions of the topic, and, where it has been discussed, a gene-centric, species-centric view, based in genomic conflict, has been predominant. Because coevolution takes place between traits or genes in two or more species and not, strictly speaking, between (...)
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  19. Prominent Inhibitory Projections Guide Sensorimotor Computation: An Invertebrate Perspective.Samantha Hughes & Tansu Celikel - forthcoming - Bioessays:1900088.
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  20. Species in the Age of Discordance.Matthew H. Haber - 2019 - Philosophy, Theory, and Practice in Biology 11.
    When I was a graduate student, the entomologist Phil Ward posed the following question in a seminar on species and phylogenetics: “Are the branches of phylogenetic trees too thin?” This question struck me then, and it has continued to resonate as I think about contemporary phylogenetics. Ward was pressing us to think about what, if anything, was lost in the way we idealize phylogenetic relationships and ignore the internal structure of those lineages. Though the term ‘genealogical discordance’ had not quite (...)
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  21. The Adaptive Continuum and How Species Succeed and Fail.Jason P. Sexton - 2019 - Philosophy, Theory, and Practice in Biology 11.
    Why do species fail to adapt? This has been a long-standing question since Darwin posed it, and is still often asked. How should we evaluate the adaptive success of an organism, and what is the relevant timescale to evaluate adaptation? Over a generation? Across the time span of a species? Here, I frame a perspective on the adaptive process and discuss how adaptation occurs and what factors affect adaptive potential. To provide a broad context for adaptation, I describe generalized species (...)
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  22. Castes and Trees: Tracing the Link Between European and Mexican Representations of Human Taxonomy.Erica Torrens & Ana Barahona - 2019 - Philosophy, Theory, and Practice in Biology 11.
    Twenty-two years after Charles Darwin began to think of character divergence from a common ancestor in his Notebook B, the now famous and iconic branching diagram appeared in the fourth chapter of On the Origin of Species.
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  23. The Foundations of Concordance Views of Phylogeny.Joel D. Velasco - 2019 - Philosophy, Theory, and Practice in Biology 11.
    Despite the enormous importance and widespread use of the term, it is unclear exactly what a phylogeny represents. It is important to define phylogeny precisely since other central terms like “clade” and “monophyletic” are often defined relative to phylogenetic trees and on some views in taxonomy, taxa must be clades. Edwards presents the common picture in contemporary systematics as depending on the existence of a “species tree” in which phylogeny “records the branching pattern of evolving lineages through time”. But what, (...)
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  24. Speciation Without Species: A Final Word.W. Ford Doolittle - 2019 - Philosophy, Theory, and Practice in Biology 11.
    This paper, like many before it, aims to solve the “species problem” by declaring it a non-problem. It borrows its title from an earlier article by Jeff Lawrence and its philosophical concepts from Marc Ereshefsky, John Dupré, Peter Godfrey-Smith, Ken Waters, and Jody Hey. The emphasis is on bacteria, but my pragmatic species anti-realist conclusion may be a general one.
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  25. Pluralism is the Answer! What is the Question?Marco J. Nathan - 2019 - Philosophy, Theory, and Practice in Biology 11.
    The ‘species problem’ can be characterized, to a first approximation, as the task of providing a viable species concept —that is, a functional analysis that picks out the ‘right’ kind of biological entities. After decades of debate and centuries of taxonomic practice, no overarching consensus has been reached. The individuation and definition of the units of evolution and classification, species included, remains controversial. If anything, there now seems to be more disagreement than ever before.
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  26. Forming Lineages by Sticking Together.Makmiller Pedroso - 2019 - Philosophy, Theory, and Practice in Biology 11.
    Nature is replete with borderline cases that fall somewhere between organisms and communities, such as lichens, biofilms, and the Portuguese Man-of-War. At first glance, the existence of such borderline cases might suggest that the concept of what constitutes an organism is too fuzzy to be useful in evolutionary biology. Yet, the notion of organisms is entrenched within central debates in evolution, including discussions over how fitness should be measured, what the bearers of adaptations and fitness are, and the status of (...)
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  27. Diagnosing Discordance: Signal in Data, Conflict in Paradigms.Aleta Quinn - 2019 - Philosophy, Theory, and Practice in Biology 11.
    Sterner and Lidgard urge that philosophers of phylogenetics move beyond the “systematics wars”, referring to the 1960s–80s debates between numerical taxonomists, evolutionary taxonomists, and phylogenetic systematists. Indeed, philosophers would do well to move beyond those wars, and to focus even more recently than the parsimony versus likelihood debates of the 1980s–90s. In this paper I use integrated historical-philosophical analysis of those debates to clarify a contemporary dispute between proponents of coalescence-based methods and proponents of concatenation. My intent is to illuminate (...)
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  28. Species and Other Evolving Lineages as Feedback Systems.Matthew J. Barker - 2019 - Philosophy, Theory, and Practice in Biology 11.
    Memorably in Nature, Jerry Coyne likened recalcitrant debates between species experts to barnacles on a whale, saying they “retard slightly the progress of the field”. However, experts have been happy to agree on at least this: species are evolving lineages. The importance of that putative fact, and of agreement about it, have been emphasized for over twenty years. Recent review works reaffirm both. But this lends some urgency to the unhappy fact that the exact nature of the implicated evolving lineages (...)
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  29. Species in the Age of Discordance: Meeting Report and Introduction.Matthew H. Haber & Daniel J. Molter - 2019 - Philosophy, Theory, and Practice in Biology 11.
    The papers included in this special issue were selected from a series of three interdisciplinary workshops titled Species in the Age of Discordance. Participants including philosophers, phylogeneticists, systematists, population geneticists, invasion biologists, historians, social scientists, botanists, herpetologists, ichthyologists, and microbiologists, among others, were asked to consider species in the context of discordance. The sense of “discordance” was left intentionally ambiguous in the call for abstracts, as our goal was to examine this question from many different perspectives, to seek out connections (...)
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  30. The galaxy of the non-Linnaean nomenclature.Alessandro Minelli - 2019 - History and Philosophy of the Life Sciences 41 (3):31.
    Contrary to the traditional claim that needs for unambiguous communication about animal and plant species are best served by a single set of names ruled by international Codes, I suggest that a more diversified system is required, especially to cope with problems emerging from aggregation of biodiversity data in large databases. Departures from Linnaean nomenclature are sometimes intentional, but there are also other, less obvious but widespread forms of not Code-compliant grey nomenclature. A first problem is due to the circumstance (...)
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  31. Are Emotional States Based in the Brain? A Critique of Affective Brainocentrism From a Physiological Perspective.Giovanna Colombetti & Eder Zavala - 2019 - Biology and Philosophy 34 (5):45.
    We call affective brainocentrism the tendency to privilege the brain over other parts of the organism when defining or explaining emotions. We distinguish two versions of this tendency. According to brain-sufficient, emotional states are entirely realized by brain processes. According to brain-master, emotional states are realized by both brain and bodily processes, but the latter are entirely driven by the brain: the brain is the master regulator of bodily processes. We argue that both these claims are problematic, and we draw (...)
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  32. Crossover Interference, Crossover Maturation, and Human Aneuploidy.Shunxin Wang, Yanlei Liu, Yongliang Shang, Binyuan Zhai, Xiao Yang, Nancy Kleckner & Liangran Zhang - forthcoming - Bioessays.
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  33. Investigating Macrophages Plasticity Following Tumour–Immune Interactions During Oncolytic Therapies.R. Eftimie & G. Eftimie - forthcoming - Acta Biotheoretica.
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  34. Publisher Correction to: O Organism, Where Art Thou? Old and New Challenges for Organism-Centered Biology.Jan Baedke - forthcoming - Journal of the History of Biology:1-1.
    Please note that this article belongs to the Special Issue on “New Styles of Thought and Practices: Biology in the Interwar Period,” guest editors Jan Baedke and Christina Brandt, but was included in volume 52, issue 2, Summer 2019 by mistake. It should be regarded as part of this special issue collection of articles.
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  35. A Combinatorial Exploration of Boolean Dynamics Generated by Isolated and Chorded Circuits.B. Mossé & É Remy - forthcoming - Acta Biotheoretica.
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  36. Out of the Sludge: How Vertebrates Came to Have Subjective Experience. [REVIEW]Dylan Black & Colin Allen - 2017 - BioScience 67:1004-1007.
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  37. The Uroboros Theory of Life’s Origin: 22-Nucleotide Theoretical Minimal RNA Rings Reflect Evolution of Genetic Code and tRNA-rRNA Translation Machineries.Jacques Demongeot & Hervé Seligmann - forthcoming - Acta Biotheoretica.
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  38. Psychoneural Reduction: A Perspective From Neural Circuits.David Parker - 2019 - Biology and Philosophy 34 (4):44.
    Psychoneural reduction has been debated extensively in the philosophy of neuroscience. In this article I will evaluate metascientific approaches that claim direct molecular and cellular explanations of cognitive functions. I will initially consider the issues involved in linking cellular properties to behaviour from the general perspective of neural circuits. These circuits that integrate the molecular and cellular components underlying cognition and behaviour, making consideration of circuit properties relevant to reductionist debates. I will then apply this general perspective to specific systems (...)
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  39. The Evolution of Cooperation in Finite Populations with Synergistic Payoffs.Rafael Ventura - 2019 - Biology and Philosophy 34 (4):43.
    In a series of papers, Forber and Smead :151–166, 2014, Biol Philos 30:405–421, 2015) and Smead and Forber :698–707, 2013) make a valuable contribution to the study of cooperation in finite populations by analyzing an understudied model: the prisoner’s delight. It always pays to cooperate in the one-shot prisoner’s delight, so this model presents a best-case scenario for the evolution of cooperation. Yet, what Forber and Smead find is highly counterintuitive. In finite populations playing the prisoner’s delight, increasing the benefit (...)
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  40. When Cultures Meet: The Landscape of “Social” Interactions Between the Host and Its Indigenous Microbes.Naama Geva‐Zatorsky, Eran Elinav & Sven Pettersson - forthcoming - Bioessays:1900002.
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  41. Are Homologies Really Natural Kinds?Christopher H. Pearson - 2019 - Biology and Philosophy 34 (4):42.
    The metaphysical nature of homologies has been variously characterized as natural kind, individualist, and pluralist-pragmatic. In this essay, I aim to build on the work of proponents of a natural kinds ontology for homologies using Richard Boyd’s influential HPC account of natural kinds. I aim to advance this position by showing the unique fit of extending the HPC account to homologies, deflecting individualist critiques, as well as the pluralist-pragmatic alternative, showing that homologies have a determinate metaphysical character as kinds. As (...)
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