Philosophy of biology

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The philosophy of biology is a subfield of philosophy of science, which deals with epistemological, metaphysical, and ethical issues in the biological and biomedical sciences. Although philosophers of science and philosophers generally have long been interested in biology (e.g., Aristotle, Descartes, and even Kant), philosophy of biology only emerged as an independent field of philosophy in the 1960s and 1970s. Philosophers of science then began paying increasing attention to biology, from the rise of Neodarwinism in the 1930s and 1940s to the discovery of the structure of DNA in 1953 to more recent advances in genetic engineering. Other key ideas include the reduction of all life processes to biochemical reactions, and the incorporation of psychology into a broader neuroscience.

Philosophy of science is a sub-field of philosophy concerned with the foundations, methods, and implications of science. The central questions of this study concern what qualifies as science, the reliability of scientific theories, and the ultimate purpose of science. This discipline overlaps with metaphysics, ontology, and epistemology, for example, when it explores the relationship between science and truth.

Epistemology A branch of philosophy concerned with the nature and scope of knowledge

Epistemology is the branch of philosophy concerned with the theory of knowledge.

Metaphysics Branch of philosophy dealing with the nature of reality

Metaphysics is the branch of philosophy that examines the fundamental nature of reality, including the relationship between mind and matter, between substance and attribute, and between possibility and actuality. The word "metaphysics" comes from two Greek words that, together, literally mean "after or behind or among [the study of] the natural". It has been suggested that the term might have been coined by a first century CE editor who assembled various small selections of Aristotle’s works into the treatise we now know by the name Metaphysics.

Contents

Overview

Philosophers of biology examine the practices, theories, and concepts of biologists with a view toward better understanding biology as a scientific discipline (or group of scientific fields). Scientific ideas are philosophically analyzed and their consequences are explored. Philosophers of biology have also explored how our understanding of biology relates to epistemology, ethics, aesthetics, and metaphysics and whether progress in biology should compel modern societies to rethink traditional values concerning all aspects of human life. It is sometimes difficult to separate philosophy of biology from theoretical biology.

In biology, a species ( ) is the basic unit of classification and a taxonomic rank of an organism, as well as a unit of biodiversity. A species is often defined as the largest group of organisms in which any two individuals of the appropriate sexes or mating types can produce fertile offspring, typically by sexual reproduction. Other ways of defining species include their karyotype, DNA sequence, morphology, behaviour or ecological niche. In addition, paleontologists use the concept of the chronospecies since fossil reproduction cannot be examined. While these definitions may seem adequate, when looked at more closely they represent problematic species concepts. For example, the boundaries between closely related species become unclear with hybridisation, in a species complex of hundreds of similar microspecies, and in a ring species. Also, among organisms that reproduce only asexually, the concept of a reproductive species breaks down, and each clone is potentially a microspecies.

Natural selection Mechanism of evolution by differential survival and reproduction of individuals

Natural selection is the differential survival and reproduction of individuals due to differences in phenotype. It is a key mechanism of evolution, the change in the heritable traits characteristic of a population over generations. Charles Darwin popularised the term "natural selection", contrasting it with artificial selection, which in his view is intentional, whereas natural selection is not.

Disease abnormal condition negatively affecting organisms

A disease is a particular abnormal condition that negatively affects the structure or function of part or all of an organism, and that is not due to any external injury. Diseases are often construed as medical conditions that are associated with specific symptoms and signs. A disease may be caused by external factors such as pathogens or by internal dysfunctions. For example, internal dysfunctions of the immune system can produce a variety of different diseases, including various forms of immunodeficiency, hypersensitivity, allergies and autoimmune disorders.

Christianity is an Abrahamic religion based on the life and teachings of Jesus of Nazareth, as described in the New Testament. Its adherents, known as Christians, believe that Jesus Christ is the Son of God and savior of all people, whose coming as the Messiah was prophesied in the Old Testament.

Religion is a cultural system of designated behaviors and practices, morals, worldviews, texts, sanctified places, prophecies, ethics, or organizations, that relates humanity to supernatural, transcendental, or spiritual elements. However, there is no scholarly consensus over what precisely constitutes a religion.

Increasingly, ideas drawn from philosophical ontology and logic are being used by biologists in the domain of bioinformatics. Ontologies such as the Gene Ontology [3] are being used to annotate the results of biological experiments in a variety of model organisms in order to create logically tractable bodies of data available for reasoning and search. The Gene Ontology itself is a species-neutral graph-theoretical representation of biological types joined together by formally defined relations. [4]

Ontology study of the nature of being, becoming, existence or reality, as well as the basic categories of being and their relations

Ontology is the philosophical study of being. More broadly, it studies concepts that directly relate to being, in particular becoming, existence, reality, as well as the basic categories of being and their relations. Traditionally listed as a part of the major branch of philosophy known as metaphysics, ontology often deals with questions concerning what entities exist or may be said to exist and how such entities may be grouped, related within a hierarchy, and subdivided according to similarities and differences.

Bioinformatics Software tools for understanding biological data

Bioinformatics is an interdisciplinary field that develops methods and software tools for understanding biological data. As an interdisciplinary field of science, bioinformatics combines biology, computer science, information engineering, mathematics and statistics to analyze and interpret biological data. Bioinformatics has been used for in silico analyses of biological queries using mathematical and statistical techniques.

Philosophy of biology today has become a visible, well-organized discipline - with its own journals, conferences, and professional organizations. The largest of the latter is the International Society for the History, Philosophy, and Social Studies of Biology (ISHPSSB). [5]

Biological Laws and Autonomy of Biology

A prominent question in the philosophy of biology is whether or not there can be distinct biological laws in the way there are distinct physical laws. [6]

Scientific reductionism is the view that higher-level biological processes reduce to physical and chemical processes. For example, the biological process of respiration is explained as a biochemical process involving oxygen and carbon dioxide. Some philosophers of biology have attempted to answer the question of whether all biological processes reduce to physical or chemical ones. On the reductionist view, there would be no distinctly biological laws.[ citation needed ]

Holism is the view that emphasizes higher-level processes, phenomena at a larger level that occur due to the pattern of interactions between the elements of a system over time. For example, to explain why one species of finch survives a drought while others die out, the holistic method looks at the entire ecosystem. Reducing an ecosystem to its parts in this case would be less effective at explaining overall behavior (in this case, the decrease in biodiversity). As individual organisms must be understood in the context of their ecosystems, holists argue, so must lower-level biological processes be understood in the broader context of the living organism in which they take part. Proponents of this view cite our growing understanding of the multidirectional and multilayered nature of gene modulation (including epigenetic changes) as an area where a reductionist view is inadequate for full explanatory power. [7] (See also Holism in science.)

All processes in organisms obey physical laws, but some argue that the difference between inanimate and biological processes is that the organisation of biological properties is subject to control by coded information. This has led some biologists and philosophers (for example, Ernst Mayr and David Hull) to return to the strictly philosophical reflections of Charles Darwin to resolve some of the problems which confronted them when they tried to employ a philosophy of science derived from classical physics. The positivist approach used in physics emphasised a strict determinism (as opposed to high probability) and led to the discovery of universally applicable laws, testable in the course of experiment. It was difficult for biology, beyond a basic microbiological level, to use this approach. [8] Standard philosophy of science seemed to leave out a lot of what characterised living organisms - namely, a historical component in the form of an inherited genotype.

Philosophers of biology have also examined the notion of “teleology.” Some have argued that scientists have had no need for a notion of cosmic teleology that can explain and predict evolution, since one was provided by Darwin. But teleological explanations relating to purpose or function have remained useful in biology, for example, in explaining the structural configuration of macromolecules and the study of co-operation in social systems. By clarifying and restricting the use of the term “teleology” to describe and explain systems controlled strictly by genetic programmes or other physical systems, teleological questions can be framed and investigated while remaining committed to the physical nature of all underlying organic processes. While some philosophers claim that the ideas of Charles Darwin ended the last remainders of teleology in biology, the matter continues to be debated. Debates in these areas of philosophy of biology turn on how one views reductionism more generally. [9] [10] [11] [12]

Ethical Implications of Biology

Sharon Street claims that contemporary evolutionary biological theory creates what she calls a “Darwinian Dilemma” for realists. She argues that this is because it is unlikely that our evaluative judgements about morality are tracking anything true about the world. Rather, she says, it is likely that moral judgements and intuitions that promote our reproductive fitness[link] were selected for, and there is no reason to think “true” moral intuitions would be selected for as well. She notes that a moral intuition most people share, that someone being a close family member is a prima facie good reason to help them, happens to an intuition likely to increase reproductive fitness, while a moral intuition almost no one has, that someone being a close family member is a reason not to help them, is likely to decrease reproductive fitness. [13]

David Copp responded to Street by arguing that realists can avoid this so-called dilemma by accepting what he calls a “quasi-tracking” position. Copp explains that what he means by quasi tracking is that it is likely that moral positions in a given society would have evolved to be at least somewhat close to the truth. He justifies this by appealing to the claim that the purpose of morality is to allow a society to meet certain basic needs, such as social stability, and a society with a successful moral codes would be better at doing this. [14]

Other perspectives

While the overwhelming majority of English-speaking scholars operating under the banner of "philosophy of biology" work within the Anglo-American tradition of analytical philosophy, there is a stream of philosophic work in continental philosophy which seeks to deal with issues deriving from biological science. The communication difficulties involved between these two traditions are well known, not helped by differences in language. Gerhard Vollmer is often thought of as a bridge but, despite his education and residence in Germany, he largely works in the Anglo-American tradition, particularly pragmatism, and is famous for his development of Konrad Lorenz's and Willard Van Orman Quine's idea of evolutionary epistemology. On the other hand, one scholar who has attempted to give a more continental account of the philosophy of biology is Hans Jonas. His "The Phenomenon of Life" (New York, 1966) sets out boldly to offer an " existential interpretation of biological facts", starting with the organism's response to stimulus and ending with man confronting the Universe, and drawing upon a detailed reading of phenomenology. This is unlikely to have much influence on mainstream philosophy of biology, but indicates, as does Vollmer's work, the current powerful influence of biological thought on philosophy. Another account is given by the late Virginia Tech philosopher Marjorie Grene.[ citation needed ]

Philosophy of biology was historically associated very closely with theoretical evolutionary biology, however more recently there have been more diverse movements within philosophy of biology including movements to examine for instance molecular biology. [15]

Scientific discovery process

Research in biology continues to be less guided by theory than it is in other sciences. [16] This is especially the case where the availability of high throughput screening techniques for the different "-omics" fields such as genomics, whose complexity makes them predominantly data-driven. Such data-intensive scientific discovery is by some considered to be the fourth paradigm, after empiricism, theory and computer simulation. [17] Others reject the idea that data driven research is about to replace theory. [18] [19] As Krakauer et al. put it: "machine learning is a powerful means of preprocessing data in preparation for mechanistic theory building, but should not be considered the final goal of a scientific inquiry." [20] In regard to cancer biology, Raspe et al. state: "A better understanding of tumor biology is fundamental for extracting the relevant information from any high throughput data." [21] The journal Science chose cancer immunotherapy as the breakthrough of 2013. According to their explanation a lesson to be learned from the successes of cancer immunotherapy is that they emerged from decoding of basic biology. [22]

Theory in biology is to some extent less strictly formalized than in physics. Besides 1) classic mathematical-analytical theory, as in physics, there is 2) statistics-based, 3) computer simulation and 4) conceptual/verbal analysis. [23] Dougherty and Bittner argue that for biology to progress as a science, it has to move to more rigorous mathematical modeling, or otherwise risk to be "empty talk". [24]

In tumor biology research, the characterization of cellular signaling processes has largely focused on identifying the function of individual genes and proteins. Janes [25] showed however the context-dependent nature of signaling driving cell decisions demonstrating the need for a more system based approach. [26] The lack of attention for context dependency in preclinical research is also illustrated by the observation that preclinical testing rarely includes predictive biomarkers that, when advanced to clinical trials, will help to distinguish those patients who are likely to benefit from a drug. [27]

See also

Related Research Articles

Ernst Mayr German-American evolutionary biologist

Ernst Walter Mayr was one of the 20th century's leading evolutionary biologists. He was also a renowned taxonomist, tropical explorer, ornithologist, philosopher of biology, and historian of science. His work contributed to the conceptual revolution that led to the modern evolutionary synthesis of Mendelian genetics, systematics, and Darwinian evolution, and to the development of the biological species concept.

Sociobiology

Sociobiology is a field of biology that aims to examine and explain social behavior in terms of evolution. It draws from disciplines including ethology, anthropology, evolution, zoology, archaeology, and population genetics. Within the study of human societies, sociobiology is closely allied to Darwinian anthropology, human behavioral ecology and evolutionary psychology.

<i>The Selfish Gene</i> Book by Richard Dawkins

The Selfish Gene is a 1976 book on evolution by Richard Dawkins, in which the author builds upon the principal theory of George C. Williams's Adaptation and Natural Selection (1966). Dawkins uses the term "selfish gene" as a way of expressing the gene-centred view of evolution, popularising ideas developed during the 1960s by W. D. Hamilton and others. From the gene-centred view, it follows that the more two individuals are genetically related, the more sense it makes for them to behave selflessly with each other.

Reductionism Philosophical view explaining systems in terms of smaller parts

Reductionism is any of several related philosophical ideas regarding the associations between phenomena which can be described in terms of other simpler or more fundamental phenomena.

Teleology Philosophical study of nature by attempting to describe things in terms of their apparent purpose, directive principle, or goal

Teleology or finality is a reason or explanation for something as a function of its end, purpose, or goal. It is derived from two Greek words: telos and logos. A purpose that is imposed by a human use, such as that of a fork, is called extrinsic. Natural teleology, common in classical philosophy but controversial today, contends that natural entities also have intrinsic purposes, irrespective of human use or opinion. For instance, Aristotle claimed that an acorn's intrinsic telos is to become a fully grown oak tree.

History of biology History of the study of life from ancient to modern times

The history of biology traces the study of the living world from ancient to modern times. Although the concept of biology as a single coherent field arose in the 19th century, the biological sciences emerged from traditions of medicine and natural history reaching back to ayurveda, ancient Egyptian medicine and the works of Aristotle and Galen in the ancient Greco-Roman world. This ancient work was further developed in the Middle Ages by Muslim physicians and scholars such as Avicenna. During the European Renaissance and early modern period, biological thought was revolutionized in Europe by a renewed interest in empiricism and the discovery of many novel organisms. Prominent in this movement were Vesalius and Harvey, who used experimentation and careful observation in physiology, and naturalists such as Linnaeus and Buffon who began to classify the diversity of life and the fossil record, as well as the development and behavior of organisms. Antonie van Leeuwenhoek revealed by means of microscopy the previously unknown world of microorganisms, laying the groundwork for cell theory. The growing importance of natural theology, partly a response to the rise of mechanical philosophy, encouraged the growth of natural history.

Evolutionary biology Study of the processes that produced the diversity of life

Evolutionary biology is the subfield of biology that studies the evolutionary processes that produced the diversity of life on Earth, starting from a single common ancestor. These processes include natural selection, common descent, and speciation.

Teleonomy is the quality of apparent purposefulness and goal-directedness of structures and functions in living organisms brought about by the exercise, augmentation, and, improvement of reasoning. The term derives from two Greek words, τέλος telos and νόμος nomos ("law"), and means "end-directed". Teleonomy is sometimes contrasted with teleology, where the latter is understood as a purposeful goal-directedness brought about through human or divine intention. Teleonomy is thought to derive from evolutionary history, adaptation for reproductive success, and/or the operation of a program. Teleonomy is related to programmatic or computational aspects of purpose.

Gene-centered view of evolution Reasoning that since heritable information is passed from generation to generation almost exclusively by DNA, natural selection and evolution are best considered from the perspective of genes

The gene-centered view of evolution, gene's eye view, gene selection theory, or selfish gene theory holds that adaptive evolution occurs through the differential survival of competing genes, increasing the allele frequency of those alleles whose phenotypic trait effects successfully promote their own propagation, with gene defined as "not just one single physical bit of DNA [but] all replicas of a particular bit of DNA distributed throughout the world". The proponents of this viewpoint argue that, since heritable information is passed from generation to generation almost exclusively by DNA, natural selection and evolution are best considered from the perspective of genes.

Evolutionary ethics Field of inquiry that explores how evolutionary theory might bear on our understanding of ethics or morality.

Evolutionary ethics is a field of inquiry that explores how evolutionary theory might bear on our understanding of ethics or morality. The range of issues investigated by evolutionary ethics is quite broad. Supporters of evolutionary ethics have claimed that it has important implications in the fields of descriptive ethics, normative ethics, and metaethics.

Structuralism (biology) school of biological thought that objects to an exclusively Darwinian or adaptationist explanation of natural selection, arguing that other mechanisms also guide evolution, and sometimes implying that these supersede selection altogether

Biological or process structuralism is a school of biological thought that objects to an exclusively Darwinian or adaptationist explanation of natural selection such as is described in the 20th century's modern synthesis. It proposes instead that evolution is guided differently, basically by more or less physical forces which shape the development of an animal's body, and sometimes implies that these forces supersede selection altogether.

Developmental systems theory (DST) is an overarching theoretical perspective on biological development, heredity, and evolution. It emphasizes the shared contributions of genes, environment, and epigenetic factors on developmental processes. DST, unlike conventional scientific theories, is not directly used to help make predictions for testing experimental results; instead, it is seen as a collection of philosophical, psychological, and scientific models of development and evolution. As a whole, these models argue the inadequacy of the modern evolutionary synthesis on the roles of genes and natural selection as the principle explanation of living structures. Developmental systems theory embraces a large range of positions that expand biological explanations of organismal development and hold modern evolutionary theory as a misconception of the nature of living processes.

Evolution as fact and theory A discussion of the meaning and usage of the terms evolution, fact and theory

Many scientists and philosophers of science have described evolution as fact and theory, a phrase which was used as the title of an article by paleontologist Stephen Jay Gould in 1981. He describes fact in science as meaning data, not absolute certainty but "confirmed to such a degree that it would be perverse to withhold provisional assent". A scientific theory is a well-substantiated explanation of such facts. The facts of evolution come from observational evidence of current processes, from imperfections in organisms recording historical common descent, and from transitions in the fossil record. Theories of evolution provide a provisional explanation for these facts.

Biology is the natural science that studies life and living organisms, including their physical structure, chemical processes, molecular interactions, physiological mechanisms, development and evolution. Despite the complexity of the science, there are certain unifying concepts that consolidate it into a single, coherent field. Biology recognizes the cell as the basic unit of life, genes as the basic unit of heredity, and evolution as the engine that propels the creation and extinction of species. Living organisms are open systems that survive by transforming energy and decreasing their local entropy to maintain a stable and vital condition defined as homeostasis.

In biology, function has been defined in many ways. In physiology, it is simply what an organ, tissue, cell or molecule does. In evolutionary biology, it is the reason some object or process occurred in a system that evolved through natural selection. That reason is typically that it achieves some result, such as that chlorophyll helps to capture the energy of sunlight in photosynthesis. Hence, the organism that contains it is more likely to survive and reproduce, in other words the function increases the organism's fitness. A characteristic that assists in evolution is called an adaptation; other characteristics may be non-functional spandrels, though these in turn may later be co-opted by evolution to serve new functions.

Evolutionary psychology has generated substantial controversy and criticism. The criticism includes but is not limited to: disputes about the testability of evolutionary hypotheses, alternatives to some of the cognitive assumptions frequently employed in evolutionary psychology, alleged vagueness stemming from evolutionary assumptions, differing stress on the importance of non-genetic and non-adaptive explanations, and political and ethical issues.

Complex systems biology branch or subfield of mathematical and theoretical biology

Complex systems biology (CSB) is a branch or subfield of mathematical and theoretical biology concerned with complexity of both structure and function in biological organisms, as well as the emergence and evolution of organisms and species, with emphasis being placed on the complex interactions of, and within, bionetworks, and on the fundamental relations and relational patterns that are essential to life. CSB is thus a field of theoretical sciences aimed at discovering and modeling the relational patterns essential to life that has only a partial overlap with complex systems theory, and also with the systems approach to biology called systems biology; this is because the latter is restricted primarily to simplified models of biological organization and organisms, as well as to only a general consideration of philosophical or semantic questions related to complexity in biology. Moreover, a wide range of abstract theoretical complex systems are studied as a field of applied mathematics, with or without relevance to biology, chemistry or physics.

Robert Arp Philosopher/ontologist/technical writer

Robert Arp is an American philosopher known for his work in ethics, modern philosophy, ontology, philosophy of biology, cognitive science, evolutionary psychology, religious studies, and philosophy and popular culture. He currently works as an adjunct professor teaching philosophy courses in the classroom and online at numerous schools in the Kansas City, Missouri area and other areas of the United States.

The philosophy of archaeology seeks to investigate the foundations, methods and implications of the discipline of archaeology in order to further understanding of the human past and present.

Teleology in biology The use of language of goal-directedness in the context of evolutionary adaptation

Teleology in biology is the use of the language of goal-directedness in accounts of evolutionary adaptation, which some biologists and philosophers of science find problematic. The term teleonomy has also been proposed. Before Darwin, organisms were seen as existing because God had designed and created them; their features such as eyes were taken by natural theology to have been made to enable them to carry out their functions, such as seeing. Evolutionary biologists often use similar teleological formulations that invoke purpose, but these imply natural selection rather than actual goals, whether conscious or not. Dissenting biologists and religious thinkers held that evolution itself was somehow goal-directed (orthogenesis), and in vitalist versions, driven by a purposeful life force. Since such views are now discredited, with evolution working by natural selection acting on inherited variation, the use of teleology in biology has attracted criticism, and attempts have been made to teach students to avoid teleological language.

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