Reductive Explanation and Mechanistic Explanation

2014 ◽  
pp. 53-81
Author(s):  
Raphael van Riel
Keyword(s):  
Mechanistic Explanation ◽  
Reductive Explanation

Counter culture: Causes, extent and solutions of systematic bias in the analysis of behavioural counts

2019 ◽  
Author(s):  
Joel L Pick ◽  
Nyil Khwaja ◽  
Michael A. Spence ◽  
Malika Ihle ◽  
Shinichi Nakagawa
Keyword(s):  
Recent Literature ◽  
Null Model ◽  
Mechanistic Explanation ◽  
Effect Sizes ◽  
Systematic Bias ◽  
Intra Class Correlation ◽  
Counter Culture ◽  
Provisioning Rate ◽  
Parental Provisioning ◽  
Observation Period

We often quantify a behaviour by counting the number of times it occurs within a specific, short observation period. Measuring behaviour in such a way is typically unavoidable but induces error. This error acts to systematically reduce effect sizes, including metrics of particular interest to behavioural and evolutionary ecologists such as R2, repeatability (intra-class correlation, ICC) and heritability. Through introducing a null model, the Poisson process, for modelling the frequency of behaviour, we give a mechanistic explanation of how this problem arises and demonstrate how it makes comparisons between studies and species problematic, because the magnitude of the error depends on how frequently the behaviour has been observed (e.g. as a function of the observation period) as well as how biologically variable the behaviour is. Importantly, the degree of error is predictable and so can be corrected for. Using the example of parental provisioning rate in birds, we assess the applicability of our null model for modelling the frequency of behaviour. We then review recent literature and demonstrate that the error is rarely accounted for in current analyses. We highlight the problems that arise from this and provide solutions. We further discuss the biological implications of deviations from our null model, and highlight the new avenues of research that they may provide. Adopting our recommendations into analyses of behavioural counts will improve the accuracy of estimated effect sizes and allow meaningful comparisons to be made between studies.

Sobre el concepto de función en biología. Historia y problemas recientes

2010 ◽  
Vol 16 ◽  
Author(s):  
Andrés L. Jaume
Keyword(s):  
Biological Function ◽  
Mechanistic Explanation ◽  
Functional Explanation ◽  
Function Concept ◽  
Philosophical Thinking ◽  
Systemic Theory ◽  
Points Of View

RESUMENEl presente artículo analiza las diferentes teorías que sobre el concepto de función se han vertido en los últimos cuarenta años y sus problemas. Respecto de los dos grandes enfoques (histórico-etiológico y sistémico) se sostiene que el primero, pese a su hegemonía histórica, presenta considerables dificultades y que la reflexión actual se centra cada vez más en la perspectiva sistémica. Esta última puede enfrentarse mejor a los diversos problemas que genera el concepto de función biológica y es siempre preferible.PALABRAS CLAVEFUNCIÓN BIOLÓGICA, FUNCIÓN SISTéMICA, EXPLICACIÓN FUNCIONAL, EXPLICACIÓN BASADA EN MECANISMOS, TELEOLOGíAABSTRACTThis paper analyzes the different theories on biological function and the problems they brought up over the last forty years. Concerning the two most important points of view on functions (aetiological theory and systemic theory) I hold that the aetiological theory, despite its historical hegemony, presents substantial difficulties and that the present philosophical thinking is centred on systemic theories. Systemic theories are capable of solving the various problems generated by the biological function concept which is preferable.KEYWORDSBIOLOGICAL FUNCTION, SySTEMIC FUNCTION, FUNCTIONAL EXPLANATION, MECHANISTIC EXPLANATION TELEOLOGY

The face value of feedback: Facial behavior is shaped by goals and punishments during interaction with dynamic faces

2020 ◽  
Author(s):  
Jonathan Yi ◽  
Philip Pärnamets ◽  
Andreas Olsson
Keyword(s):  
Decision Making ◽  
Facial Expression ◽  
Facial Expressions ◽  
Large Body ◽  
Mechanistic Explanation ◽  
Experimental Manipulation ◽  
Corrugator Supercilii ◽  
Dynamic Faces ◽  
Facial Behavior ◽  
Reinforcement Learning Models

Responding appropriately to others’ facial expressions is key to successful social functioning. Despite the large body of work on face perception and spontaneous responses to static faces, little is known about responses to faces in dynamic, naturalistic situations, and no study has investigated how goal directed responses to faces are influenced by learning during dyadic interactions. To experimentally model such situations, we developed a novel method based on online integration of electromyography (EMG) signals from the participants’ face (corrugator supercilii and zygomaticus major) during facial expression exchange with dynamic faces displaying happy and angry facial expressions. Fifty-eight participants learned by trial-and-error to avoid receiving aversive stimulation by either reciprocate (congruently) or respond opposite (incongruently) to the expression of the target face. Our results validated our method, showing that participants learned to optimize their facial behavior, and replicated earlier findings of faster and more accurate responses in congruent vs. incongruent conditions. Moreover, participants performed better on trials when confronted with smiling, as compared to frowning, faces, suggesting it might be easier to adapt facial responses to positively associated expressions. Finally, we applied drift diffusion and reinforcement learning models to provide a mechanistic explanation for our findings which helped clarifying the underlying decision-making processes of our experimental manipulation. Our results introduce a new method to study learning and decision-making in facial expression exchange, in which there is a need to gradually adapt facial expression selection to both social and non-social reinforcements.

Evo-Devo and the Structure(s) of Evolutionary Theory

2017 ◽  
Author(s):  
Alan C. Love
Keyword(s):  
Developmental Biology ◽  
Evolutionary Theory ◽  
Mechanistic Explanation ◽  
Evolutionary Developmental Biology ◽  
Primary Concern ◽  
Adaptive Function ◽  
Specific Content ◽  
Central Location ◽  
Developmental Form ◽  
Evo Devo

Many researchers have argued that evolutionary developmental biology (evo-devo) constitutes a challenge to standard evolutionary theory, requiring the explicit inclusion of developmental processes that generate variation and attention to organismal form (rather than adaptive function). An analysis of these developmental-form challenges indicates that the primary concern is not the inclusion of specific content but the epistemic organization or structure of evolutionary theory. Proponents of developmental-form challenges favor moving their considerations to a more central location in evolutionary theorizing, in part because of a commitment to the value of mechanistic explanation. This chapter argues there are multiple legitimate structures for evolutionary theory, instead of a single, overarching or canonical organization, and different theory presentations can be understood as idealizations that serve different investigative and explanatory goals in evolutionary inquiry.

scholarly journals Landscape heterogeneity buffers biodiversity of simulated meta-food-webs under global change through rescue and drainage effects

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Remo Ryser ◽  
Myriam R. Hirt ◽  
Johanna Häussler ◽  
Dominique Gravel ◽  
Ulrich Brose
Keyword(s):  
Habitat Fragmentation ◽  
Food Web ◽  
Food Webs ◽  
Landscape Heterogeneity ◽  
Landscape Connectivity ◽  
Biodiversity Loss ◽  
Mechanistic Explanation ◽  
Population Densities ◽  
Rescue Effect ◽  
Drainage Effect

AbstractHabitat fragmentation and eutrophication have strong impacts on biodiversity. Metacommunity research demonstrated that reduction in landscape connectivity may cause biodiversity loss in fragmented landscapes. Food-web research addressed how eutrophication can cause local biodiversity declines. However, there is very limited understanding of their cumulative impacts as they could amplify or cancel each other. Our simulations of meta-food-webs show that dispersal and trophic processes interact through two complementary mechanisms. First, the ‘rescue effect’ maintains local biodiversity by rapid recolonization after a local crash in population densities. Second, the ‘drainage effect’ stabilizes biodiversity by preventing overshooting of population densities on eutrophic patches. In complex food webs on large spatial networks of habitat patches, these effects yield systematically higher biodiversity in heterogeneous than in homogeneous landscapes. Our meta-food-web approach reveals a strong interaction between habitat fragmentation and eutrophication and provides a mechanistic explanation of how landscape heterogeneity promotes biodiversity.

Acute O2 sensing through HIF2α-dependent expression of atypical cytochrome oxidase subunits in arterial chemoreceptors

2019 ◽  
Vol 13 (615) ◽  
pp. eaay9452 ◽  
Author(s):  
Alejandro Moreno-Domínguez ◽  
Patricia Ortega-Sáenz ◽  
Lin Gao ◽  
Olalla Colinas ◽  
Paula García-Flores ◽  
...  
Keyword(s):  
Ion Channels ◽  
Carotid Body ◽  
Acute Hypoxia ◽  
Mechanistic Explanation ◽  
Nerve Fibers ◽  
Adaptive Responses ◽  
Glomus Cells ◽  
Adult Mice ◽  
Genes Encoding ◽  
Regulation Of Breathing

Acute cardiorespiratory responses to O2 deficiency are essential for physiological homeostasis. The prototypical acute O2-sensing organ is the carotid body, which contains glomus cells expressing K+ channels whose inhibition by hypoxia leads to transmitter release and activation of nerve fibers terminating in the brainstem respiratory center. The mechanism by which changes in O2 tension modulate ion channels has remained elusive. Glomus cells express genes encoding HIF2α (Epas1) and atypical mitochondrial subunits at high levels, and mitochondrial NADH and reactive oxygen species (ROS) accumulation during hypoxia provides the signal that regulates ion channels. We report that inactivation of Epas1 in adult mice resulted in selective abolition of glomus cell responsiveness to acute hypoxia and the hypoxic ventilatory response. Epas1 deficiency led to the decreased expression of atypical mitochondrial subunits in the carotid body, and genetic deletion of Cox4i2 mimicked the defective hypoxic responses of Epas1-null mice. These findings provide a mechanistic explanation for the acute O2 regulation of breathing, reveal an unanticipated role of HIF2α, and link acute and chronic adaptive responses to hypoxia.

scholarly journals Antibiotics-induced intestinal dysbacteriosis caused behavioral alternations and neuronal activation in different brain regions in mice

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Pan Wang ◽  
Ke Tu ◽  
Peng Cao ◽  
Yuefan Yang ◽  
Hao Zhang ◽  
...  
Keyword(s):  
Mechanical Allodynia ◽  
Neuroprotective Effect ◽  
Memory Performance ◽  
Mechanistic Explanation ◽  
Brain Regions ◽  
Basic Knowledge ◽  
Spontaneous Pain ◽  
Oral Antibiotic ◽  
Microbial Composition ◽  
Intestinal Dysbacteriosis

AbstractAntibiotics affect gut microbial composition, leading to Gut–Brain-Axis imbalance and neurobehavioral changes. However, the intestinal dysbacteriosis associated behavior changes are not consistently reported. It is not clear whether these changes are transient or permanent. The neuroprotective effect of probiotics against intestinal dysbacteriosis induced alternations needs to be determined either. In the present study, oral antibiotic mixture including Ampicillin, Streptomycin, and Clindamycin was utilized to induce intestinal dysbacteriosis in mice. Antibiotics application triggered mechanical allodynia in von frey test and spontaneous pain in open field test. It also resulted in increased anxiety and depressive-like behaviors and damaged spatial memory performance. After application of probiotics, the mechanical allodynia and spontaneous pain were alleviated significantly. The anxiety behaviors, depressive-like behaviors and recognitive performance were ameliorative as well. By using Fos protein as a marker, it is found that the sensory, emotion and memory related brain regions were activated in mice with intestinal dysbacteriosis. Our study is not only helpful for enriching our basic knowledge for understanding the changed pain responses and related brain disorders in antibiotics-induced dysbacteriosis mice, but also beneficial for providing a more comprehensive mechanistic explanation for the regulation of antibiotics and probiotics on gut microbiota and relevant alternations in animal neurological behaviors.

scholarly journals Foliar endophytes in trees varying greatly in age

2021 ◽  
Author(s):  
Zhongdong Yu ◽  
Hongru Ding ◽  
Kuocheng Shen ◽  
Fangfang Bu ◽  
George Newcombe ◽  
...  
Keyword(s):  
Exploratory Study ◽  
Leaf Age ◽  
Mechanistic Explanation ◽  
Tree Age ◽  
Botryosphaeria Dothidea ◽  
Platycladus Orientalis ◽  
Age Diversity ◽  
Components Analysis ◽  
Endophyte Community ◽  
Latent Pathogens

AbstractTemple trees, including the gymnosperm Platycladus orientalis and the angiosperm Styphnolobium japonicum, have been planted in China for thousands of years. Tree age thus varies widely from young to ancient trees. Foliar endophytes of P. orientalis and S. japonicum were surveyed in this exploratory study that was based on isolation into culture and sequencing of fungi from trees varying in age from 10 to 5000 years (P. orientalis) and from 10 to 1700 years (S. japonicum). Sequenced endophytes of P. orientalis and S. japonicum belonged to 24 and 16 fungal genera, respectively. Principal components analysis showed that 14 components were necessary to explain 90% of the variance in endophyte community structure in P. orientalis. In S. japonicum eight components were needed for 90%. It is against that backdrop of complex etiology in community structuring, that the relative frequencies (abundances) of 17 of the 24 endophytes from P. orientalis and 9 of the 16 from S. japonicum were significantly correlated with tree age. There were two major trends. Abundant fungal genera [Fusarium + Alternaria = 74.57% (P. orientalis) and 81.24% (S. japonicum)] tended to decline linearly with tree age. Most of the rare fungal genera, in contrast, increased in relative abundance linearly with tree age. Diversity (H′) and richness (Margalef) of endophyte communities in foliage thus increased as the trees aged. Relative abundances of pathogenic endophytes, or latent pathogens, (Pestalotiopsis funerea and Amyloporia subxantha in P. orientalis; Collectotrichum gloeosporioides and Botryosphaeria dothidea in S. japonicum) also increased linearly as the trees aged.Since leaf age does not vary with tree age in the deciduous S. japonicum, nor in the evergreen P. orientalis, ‘tree age’ currently lacks a mechanistic explanation for its apparent importance among common foliar endophytes.

scholarly journals Pore constrictions in intervessel pit membranes provide a mechanistic explanation for xylem embolism resistance in angiosperms

2021 ◽  
Vol 230 (5) ◽  
pp. 1829-1843 ◽  
Author(s):  
Lucian Kaack ◽  
Matthias Weber ◽  
Emilie Isasa ◽  
Zohreh Karimi ◽  
Shan Li ◽  
...  
Keyword(s):  
Mechanistic Explanation ◽  
Xylem Embolism ◽  
Embolism Resistance

scholarly journals Stress-Inducible Gene Atf3 Dictates a Dichotomous Macrophage Activity in Chemotherapy-Enhanced Lung Colonization

2021 ◽  
Vol 22 (14) ◽  
pp. 7356
Author(s):  
Justin D. Middleton ◽  
Jared Fehlman ◽  
Subhakeertana Sivakumar ◽  
Daniel G. Stover ◽  
Tsonwin Hai
Keyword(s):  
Cancer Cells ◽  
Cancer Cell ◽  
Early Stage ◽  
Mechanistic Explanation ◽  
Host Cells ◽  
Secondary Site ◽  
Initial Increase ◽  
Cell Retention ◽  
Lung Colonization ◽  
Inducible Gene

Previously, we showed that chemotherapy paradoxically exacerbated cancer cell colonization at the secondary site in a manner dependent on Atf3, a stress-inducible gene, in the non-cancer host cells. Here, we present evidence that this phenotype is established at an early stage of colonization within days of cancer cell arrival. Using mouse breast cancer models, we showed that, in the wild-type (WT) lung, cyclophosphamide (CTX) increased the ability of the lung to retain cancer cells in the vascular bed. Although CTX did not change the WT lung to affect cancer cell extravasation or proliferation, it changed the lung macrophage to be pro-cancer, protecting cancer cells from death. This, combined with the initial increase in cell retention, resulted in higher lung colonization in CTX-treated than control-treated mice. In the Atf3 knockout (KO) lung, CTX also increased the ability of lung to retain cancer cells. However, the CTX-treated KO macrophage was highly cytotoxic to cancer cells, resulting in no increase in lung colonization—despite the initial increase in cell retention. In summary, the status of Atf3 dictates the dichotomous activity of macrophage: pro-cancer for CTX-treated WT macrophage but anti-cancer for the KO counterpart. This dichotomy provides a mechanistic explanation for CTX to exacerbate lung colonization in the WT but not Atf3 KO lung.

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