Contents
15 found
Order:
  1. A framework for philosophical biology.Sepehr Ehsani - manuscript
    Advances in biology, at least over the past two centuries, have mostly relied on theories that were subsequently revised, expanded or eventually refuted using experimental and other means. The field of theoretical biology used to primarily provide a basis, similar to theoretical physics in the physical sciences, to rationally examine the frameworks within which biological experiments were carried out and to shed light on overlooked gaps in understanding. Today, however, theoretical biology has generally become synonymous with computational and mathematical biology. (...)
    Remove from this list   Download  
     
    Export citation  
     
    Bookmark   1 citation  
  2. Causal Specificity, Biological Possibility and Non-parity about Genetic Causes.Marcel Weber - manuscript
    Several authors have used the notion of causal specificity in order to defend non-parity about genetic causes (Waters 2007, Woodward 2010, Weber 2017, forthcoming). Non-parity in this context is the idea that DNA and some other biomolecules that are often described as information-bearers by biologists play a unique role in life processes, an idea that has been challenged by Developmental Systems Theory (e.g., Oyama 2000). Indeed, it has proven to be quite difficult to state clearly what the alleged special role (...)
    Remove from this list   Download  
     
    Export citation  
     
    Bookmark   1 citation  
  3. Causal Selection versus Causal Parity in Biology: Relevant Counterfactuals and Biologically Normal Interventions.Marcel Weber - forthcoming - In Waters C. Kenneth & Woodward James (eds.), Philosophical Perspectives on Causal Reasoning in Biology. Minnesota Studies in Philosophy of Science. Vol. XXI. University of Minnesota Press.
    Causal selection is the task of picking out, from a field of known causally relevant factors, some factors as elements of an explanation. The Causal Parity Thesis in the philosophy of biology challenges the usual ways of making such selections among different causes operating in a developing organism. The main target of this thesis is usually gene centrism, the doctrine that genes play some special role in ontogeny, which is often described in terms of information-bearing or programming. This paper is (...)
    Remove from this list   Download  
     
    Export citation  
     
    Bookmark   19 citations  
  4. Making sense of ‘genetic programs’: biomolecular Post–Newell production systems.Mihnea Capraru - 2024 - Biology and Philosophy 39 (2):1-12.
    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 (...)
    Remove from this list   Download  
     
    Export citation  
     
    Bookmark  
  5. A Third Way to the Selected Effect/Causal Role Distinction in the Great Encode Debate.Ehud Lamm & Sophie Veigl - 2023 - Theoretical Biology Forum 2023 (1-2):53-74.
    Since the ENCODE project published its final results in a series of articles in 2012, there is no consensus on what its implications are. ENCODE’s central and most controversial claim was that there is essentially no junk DNA: most sections of the human genome believed to be «junk» are functional. This claim was met with many reservations. If researchers disagree about whether there is junk DNA, they have first to agree on a concept of function and how function, given a (...)
    Remove from this list   Download  
     
    Export citation  
     
    Bookmark  
  6. Three overlooked key functional classes for building up minimal synthetic cells.Antoine Danchin - 2021 - Synthetic Biology 6 (1):ysab010.
    Assembly of minimal genomes revealed many genes encoding unknown functions. Three overlooked functional categories account for some of them. Cells are prone to make errors and age. As a first key function, discrimination between proper and changed entities is indispensable. Discrimination requires management of information, an authentic, yet abstract, cur- rency of reality. For example proteins age, sometimes very fast. The cell must identify, then get rid of old proteins without destroying young ones. Implementing discrimination in cells leads to the (...)
    Remove from this list   Download  
     
    Export citation  
     
    Bookmark   1 citation  
  7. The meaning of "cause" in genetics.Kate E. Lynch - 2021 - Combining Human Genetics and Causal Inference to Understand Human Disease and Development. Cold Spring Harbor Perspectives in Medicine.
    Causation has multiple distinct meanings in genetics. One reason for this is meaning slippage between two concepts of the gene: Mendelian and molecular. Another reason is that a variety of genetic methods address different kinds of causal relationships. Some genetic studies address causes of traits in individuals, which can only be assessed when single genes follow predictable inheritance patterns that reliably cause a trait. A second sense concerns the causes of trait differences within a population. Whereas some single genes can (...)
    Remove from this list   Download  
     
    Export citation  
     
    Bookmark  
  8. Genomic Stress Responses Drive Lymphocyte Evolvability: An Ancient and Ubiquitous Mechanism.Bartlomiej Swiatczak - 2020 - Bioessays 42 (10):2000032.
    Somatic diversification of antigen receptor genes depends on the activity of enzymes whose homologs participate in a mutagenic DNA repair in unicellular species. Indeed, by engaging error-prone polymerases, gap filling molecules and altered mismatch repair pathways, lymphocytes utilize conserved components of genomic stress response systems, which can already be found in bacteria and archaea. These ancient systems of mutagenesis and repair act to increase phenotypic diversity of microbial cell populations and operate to enhance their ability to produce fit variants during (...)
    Remove from this list   Download  
     
    Export citation  
     
    Bookmark   3 citations  
  9. Grounding knowledge and normative valuation in agent-based action and scientific commitment.Catherine Kendig - 2018 - In Hauke Riesch, Nathan Emmerich & Steven Wainwright (eds.), Philosophies and Sociologies of Bioethics: Crossing the Divides. Dordrecht, Netherlands: Springer. pp. 41-64.
    Philosophical investigation in synthetic biology has focused on the knowledge-seeking questions pursued, the kind of engineering techniques used, and on the ethical impact of the products produced. However, little work has been done to investigate the processes by which these epistemological, metaphysical, and ethical forms of inquiry arise in the course of synthetic biology research. An attempt at this work relying on a particular area of synthetic biology will be the aim of this chapter. I focus on the reengineering of (...)
    Remove from this list   Download  
     
    Export citation  
     
    Bookmark  
  10. Which Kind of Causal Specificity Matters Biologically?Marcel Weber - 2017 - Philosophy of Science 84 (3):574-585.
    Griffiths et al. (2015) have proposed a quantitative measure of causal specificity and used it to assess various attempts to single out genetic causes as being causally more specific than other cellular mechanisms, for example, alternative splicing. Focusing in particular on developmental processes, they have identified a number of important challenges for this project. In this discussion note, I would like to show how these challenges can be met.
    Remove from this list   Download  
     
    Export citation  
     
    Bookmark   12 citations  
  11. Metaanalysis of psychoanalysis.Andrej Poleev - 2016 - Enzymes.
    The perspective revolution of Sigmund Freud: An update.
    Remove from this list   Download  
     
    Export citation  
     
    Bookmark   22 citations  
  12. Re-examining the Gene in Personalized Genomics.Jordan Bartol - 2013 - Science & Education 22 (10):2529-2546.
    Personalized genomics companies (PG; also called ‘direct-to-consumer genetics’) are businesses marketing genetic testing to consumers over the Internet. While much has been written about these new businesses, little attention has been given to their roles in science communication. This paper provides an analysis of the gene concept presented to customers and the relation between the information given and the science behind PG. Two quite different gene concepts are present in company rhetoric, but only one features in the science. To explain (...)
    Remove from this list   Download  
     
    Export citation  
     
    Bookmark   5 citations  
  13. Distinguishing ecological from evolutionary approaches to transposable elements.Stefan Linquist, Brent Saylor, Karl Cottenie, Tyler A. Elliott, Stefan C. Kremer & T. Ryan Gregory - 2013 - Biological Reviews 88 (3):573- 584.
    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 (...)
    Remove from this list   Download  
     
    Export citation  
     
    Bookmark   3 citations  
  14. Structure and biological function of ribonucleic acid from Tobacco Mosaic Virus.Alfred Gierer - 1957 - Nature 179:1297-1299.
    Within the sedimentation diagram of infective RNA preparations isolated from Tobacco Mosaic Virus, undegraded molecules form a sharp peak with a molecular weight corresponding to the total RNA content of the virus particle. Degradation kinetics by ribonuclease is of the linear, single-target type, indicating that the RNA is single-stranded. The intact RNA of a virus particle thus forms one big single-stranded molecule. Quantitative evaluation of the effect degradation by RNA-ase on the infectivity of the RNA shows that the integrity of (...)
    Remove from this list   Download  
     
    Export citation  
     
    Bookmark  
  15. Infectivity of ribonucleic acid from Tobacco Mosaic Virus.Alfred Gierer & Gerhard Schramm - 1956 - Nature 177:702-703.
    Upon separation of the protein from the nucleic acid component of tobacco mosaic virus by phenol, using a fast and gentle procedure, the nucleic acid is infective in assays on tobacco leaves. A series of qualitative and quantitative control experiments demonstrates that the biological activity cannot depend on residual proteins in the preparation, but is a property of isolated nucleic acid which is thus the genetic material of the virus.
    Remove from this list   Download  
     
    Export citation  
     
    Bookmark   9 citations