Biology & Philosophy最新文献_第3页

Does nature learn? Information integration and rare events in systems of increasing complexity 大自然会学习吗？复杂性不断增加的系统中的信息整合和罕见事件

IF 2.5 1区哲学

Biology & Philosophy Pub Date : 2024-03-13 DOI: 10.1007/s10539-024-09942-4

Juan Carlos Jaimes-Martínez, Leandro Lopes Loguercio

{"title":"Does nature learn? Information integration and rare events in systems of increasing complexity","authors":"Juan Carlos Jaimes-Martínez, Leandro Lopes Loguercio","doi":"10.1007/s10539-024-09942-4","DOIUrl":"https://doi.org/10.1007/s10539-024-09942-4","url":null,"abstract":"The environment is a continuous source of matter and energy, which dynamizes the adaptive processes of biological systems, so that these systems emerge, persist or are extinguished as a consequence of their reactions to the environment. This perspective, forged from classical physics, gives way to multiple ecological theories, with evolution being the most prominent one. In all these cases, information would be both dependent and subsequent to matter and energy. Thus, the emergence and dynamics of genetic material or ecological attributes such as abundance, richness or diversity depend mainly on the interaction of these two fundamental states. However, recent approaches from quantum physics and complexity views put forward the notion that information can be independent and prior to matter and energy, which allows us to see ecological processes from another perspective, i.e., as including complex biological systems as capable of showing emergent properties such as cognition. We proposed here a set of postulates and ideas that suggests how the ability to manipulate (internalize, integrate, store and generate) information can be developed by those systems, which would directly and non-randomly influence ecological attributes and their dynamics; i.e., how this property can possibly help replacing the notion of the environment as the ultimate cause of changes. Besides fully detailing the sources of knowledge and our rationale in this sense, we have also discussed how these thoughts and possibilities can be employed in devising better and more comprehensive approaches for biological conservation strategies.","PeriodicalId":55368,"journal":{"name":"Biology & Philosophy","volume":"31 1","pages":""},"PeriodicalIF":2.5,"publicationDate":"2024-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140126741","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"哲学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Making sense of ‘genetic programs’: biomolecular Post–Newell production systems 理解 "基因程序"：生物分子后纽厄尔生产系统

IF 2.5 1区哲学

Biology & Philosophy Pub Date : 2024-03-11 DOI: 10.1007/s10539-024-09943-3

Mihnea Capraru

{"title":"Making sense of ‘genetic programs’: biomolecular Post–Newell production systems","authors":"Mihnea Capraru","doi":"10.1007/s10539-024-09943-3","DOIUrl":"https://doi.org/10.1007/s10539-024-09943-3","url":null,"abstract":"The biomedical literature makes extensive use of the concept of a genetic program. So far, however, the nature of genetic programs has received no satisfactory elucidation from the standpoint of computer science. This unsettling omission has led to doubts about the very existence of genetic programs, on the grounds that gene regulatory networks lack a predetermined schedule of execution, which may seem to contradict the very idea of a program. I show, however, that we can make perfect sense of genetic programs, if only we abandon the preconception that all computers have a von Neumann architecture. Instead, genetic programs instantiate the computational architecture of Post–Newell Production Systems. That is, genetic programs are unordered sets of conditional instructions, instructions that fire independently when their conditions are matched. For illustration I present a paradigm Production System that regulates the functioning of the well-known lac operon of E. coli. On close reflection it turns out that not only genes, but also proteins encode instructions. I propose, therefore, to rename genetic programs to biomolecular programs. Biomolecular and/or genetic programs, and the cellular computers than run them, are to be understood not as von Neumann computers, but as Post–Newell production systems.","PeriodicalId":55368,"journal":{"name":"Biology & Philosophy","volume":"67 1","pages":""},"PeriodicalIF":2.5,"publicationDate":"2024-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140097961","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"哲学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Commitment: From Hunting to Promising 承诺：从狩猎到承诺

IF 2.5 1区哲学

Biology & Philosophy Pub Date : 2024-02-14 DOI: 10.1007/s10539-024-09940-6

Saira Khan

引用次数: 0

What is foraging? 什么是觅食？

IF 2.5 1区哲学

Biology & Philosophy Pub Date : 2024-02-12 DOI: 10.1007/s10539-024-09939-z

{"title":"What is foraging?","authors":"","doi":"10.1007/s10539-024-09939-z","DOIUrl":"https://doi.org/10.1007/s10539-024-09939-z","url":null,"abstract":"<h3>Abstract</h3> Foraging is a central competence of all mobile organisms. Models and concepts from foraging theory have been applied widely throughout biology to the search for many kinds of external resources, including food, sexual encounters, minerals, water, and the like. In cognitive science and neuroscience, the tools of foraging theory are increasingly applied to a wide range of other types of search, including for abstract resources like information or for internal resources like memories, concepts, and strategies for problem solving. Despite its importance in ecology and increasing relevance for the study of cognition, the concept of foraging is rarely analyzed. Here, I aim to rectify this situation. I outline three desiderata: first, an analysis should differentiate foraging from search and decision making more generally; second, an analysis should unify different types of foraging; and third, an analysis should help ground predictions. I present an analysis of foraging as the serial search for general resources in accept-or-reject, exclusive, persistent decision contexts. Not all search is serial and not all decision making is exclusive, differentiating foraging from search and decision making generally. With the aid of Markov decision processes and directed cyclical models, I show how the analysis implies a cyclical graph. This cyclical graph is embedded in the description of many types of foraging, unifying the different instances. Finally, I argue that the cyclical graph is also embedded in representations of novel task contexts that have not previously been viewed as foraging. I illustrate this novel application of the concept of foraging by arguing that reasoning is a type of foraging.","PeriodicalId":55368,"journal":{"name":"Biology & Philosophy","volume":"144 1","pages":""},"PeriodicalIF":2.5,"publicationDate":"2024-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139773679","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"哲学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Neutral and niche theory in community ecology: a framework for comparing model realism 群落生态学中的中性理论和生态位理论：比较模型现实性的框架

IF 2.5 1区哲学

Biology & Philosophy Pub Date : 2024-02-12 DOI: 10.1007/s10539-024-09941-5

Katie H. Morrow

引用次数: 0

Evolvability: filling the explanatory gap between adaptedness and the long-term mathematical conception of fitness. 可进化性：填补适应性与长期适应性数学概念之间的解释空白。

IF 1.7 1区哲学

Biology & Philosophy Pub Date : 2024-01-01 Epub Date: 2024-07-16 DOI: 10.1007/s10539-024-09951-3

Pierrick Bourrat, Katie Deaven, Cristina Villegas

{"title":"Evolvability: filling the explanatory gap between adaptedness and the long-term mathematical conception of fitness.","authors":"Pierrick Bourrat, Katie Deaven, Cristina Villegas","doi":"10.1007/s10539-024-09951-3","DOIUrl":"10.1007/s10539-024-09951-3","url":null,"abstract":"The new foundation for the propensity interpretation of fitness (PIF), developed by Pence and Ramsey (Br J Philos Sci 64:851-881, 2013), describes fitness as a probability distribution that encompasses all possible daughter populations to which the organism may give rise, including daughter populations in which traits might change and the possible environments that members of the daughter populations might encounter. This long-term definition of fitness is general enough to avoid counterexamples faced by previous mathematical conceptions of PIF. However, there seem to be downsides to its generality: the ecological role of fitness involves describing the degree of adaptedness between an organism and the specific environment it inhabits. When all possible changes in traits and all possible environments that a daughter population may encounter are included in the concept, it becomes difficult to see how fitness can fulfill this role. In this paper, we argue that this is a feature of Pence and Ramsey's view rather than a bug: long-term fitness accommodates evolvability considerations, which concern the role that variation plays in evolutionary processes. Building on the foundations, we show that Pence and Ramsey's fitness-F-can be partitioned into fourths: adaptedness, robustness of adaptedness, and two facets of evolvability. Conceptualizing these last three components forces us to consider the role played by grains of description of both organisms and the environment when thinking about long-term fitness. They track the possibility that there could be a change in type in a daughter population as a way of responding to environmental challenges, or that the type persists in the face of novel environments. We argue that these components are just as salient as adaptedness for long-term fitness. Together, this decomposition of F provides a more accurate picture of the factors involved in long-term evolutionary success.","PeriodicalId":55368,"journal":{"name":"Biology & Philosophy","volume":"39 4","pages":"15"},"PeriodicalIF":1.7,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11249714/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141635870","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"哲学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Phylogenetically distant animals sleep: why do sleep researchers care? 系统发育遥远的动物睡眠：睡眠研究人员为何关心这个问题？

IF 2.5 1区哲学

Biology & Philosophy Pub Date : 2023-12-29 DOI: 10.1007/s10539-023-09938-6

William Bechtel

{"title":"Phylogenetically distant animals sleep: why do sleep researchers care?","authors":"William Bechtel","doi":"10.1007/s10539-023-09938-6","DOIUrl":"https://doi.org/10.1007/s10539-023-09938-6","url":null,"abstract":"<h3>Abstract</h3> Philosophers examining mechanistic explanations in biology have identified heuristic strategies scientists use in discovering mechanisms. This paper examines the heuristic strategy of investigating phylogenetically distant model organisms, using research on sleep in fruit flies as an example. At the time sleep was discovered in flies in 2000 next to nothing was known about mechanisms regulating sleep in flies and what they could reveal about those in us. One relatively straightforward line of research focused on homologous genes in flies and humans, using those in flies to understand what roles their homologs played in controlling sleep in us. But other research focused on a higher level of organization—the neural networks involved in homeostatic and circadian control of sleep. This raises a puzzle—given that fly and vertebrate brains are organized very differently, how could sleep regulation in flies serve as an informative model of vertebrate sleep? I argue that the basic design of mechanisms such as those regulating sleep can be conserved even as the composition of the mechanism changes and that researchers can hope to use the designs deciphered in flies as heuristic models for understanding sleep in humans.","PeriodicalId":55368,"journal":{"name":"Biology & Philosophy","volume":"20 1","pages":""},"PeriodicalIF":2.5,"publicationDate":"2023-12-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139071653","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"哲学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Epistemic enhancement, pastism, and fossil anomalies in paleontology and ichnology 古生物学和昆虫学中的认识论强化、过去论和化石异常现象

IF 2.5 1区哲学

Biology & Philosophy Pub Date : 2023-12-19 DOI: 10.1007/s10539-023-09937-7

Ali Mirza

{"title":"Epistemic enhancement, pastism, and fossil anomalies in paleontology and ichnology","authors":"Ali Mirza","doi":"10.1007/s10539-023-09937-7","DOIUrl":"https://doi.org/10.1007/s10539-023-09937-7","url":null,"abstract":"This paper presents explication on how paleontologists reconstruct the past using fossils when good modern analogues are not available. I call these pastist methods to differentiate them from presentist methods in which such analogues are available. I do so by presenting two fossil cases: the problematica and graphoglyptids. I describe a forgotten heuristic, “analogue chaining,” that involves jumping from fossil anomaly to fossil anomaly using one to make sense of the other in successive fashion, using the relations between fossils to guide reconstruction. I relate this to the philosophy of historical sciences in four ways. First, that methods like analogue chaining have a “linearity” meaning that there are limited ways in which to learn about specimens using analogues. Second, that they are intrinsically difficult to notice, i.e. invisible. Third, that linearity and invisibility put pressure on some accounts of optimism about historical sciences. Fourth, our cases provide novel forms of optimism based on epistemic enhancement: the phenomena that some questions regarding an event are better answered millions of years after its occurrence.","PeriodicalId":55368,"journal":{"name":"Biology & Philosophy","volume":"82 1","pages":""},"PeriodicalIF":2.5,"publicationDate":"2023-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138742683","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"哲学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Molecular-biological machines: a defense 分子生物学机器：防御

IF 2.5 1区哲学

Biology & Philosophy Pub Date : 2023-09-09 DOI: 10.1007/s10539-023-09915-z

Arnon Levy

引用次数: 0

Humans, the Norm-Breakers 人类，打破常规的人

IF 2.5 1区哲学

Biology & Philosophy Pub Date : 2023-08-29 DOI: 10.1007/s10539-023-09918-w

Kristin Andrews

引用次数: 0