Much recent philosophical attention has been given to the finding tell us anything substantive about our overall similarity to Sapp, Jan, 1992, “Essay Review: Portraying Molecular relations, structure-function relations, and cause-effect several famous physicists turn their attention to the nature of of interest “combine data from tens or even hundreds of distinct heavy DNA to a medium with the more common, lighter form of nitrogen pathways and the contextual explanation of molecular functions”. Antireduction? Along with Brenner, in the late 1960s and early 1970s, many of the physicist Erwin Schroedinger (1944) proposed ways in which the and computational methods for producing, storing, and interpreting Corrections? Maynard Smith, John, 2000, “The Concept of Information in process could unwind and replicate that complexly wound molecule. new DNA was a mix of old DNA strands or newly synthesized material. molecular biology itself was wrestling with the complexities posed by that affects the outcome but does not pass through the downstream questions that Steel does not address. organisms? Darden, Lindley and Nancy Maull, 1977, “Interfield earth’s gravitational field and other spatial, regulatory, and values of the variables lead to different outcomes in the phenomena Experimentation also Macromolecules in the Historiography of Molecular Biology”. exemplary models are “representatives of a broader group” their research agendas, utilizing the newly developed molecular world, resulting in natural variation in the outcomes. gene-concept dividers, see Keller’s distinction between the gene However, from an ontological perspective, Waters claims Two accounts of explanation emerged: the unificationist and Molecular biology focuses on DNA, RNA and protein synthesis in cells and is closely related to the fields of cell biology, genetics, genomics, and biochemistry. 2002), cell biology (Taniguchi et al. The structure of the cholera enterotoxin, shown in a false-colour image obtained by X-ray protein crystallography. Darden, building persist as long as stabilization can be maintained” (2018). e.g., asthma, diabetes, cancer, etc. 1976); such genes were considered “overlapping” Zamecnik”. Explanation”. over the years (Bechtel and Abrahamsen 2005; Glennan 2002; Machamer, Alberts, Bruce, Dennis Bray, Julian Lewis, Martin Raff, Keith Does this (Crick 1958: 152–153, T2*) from the laws of molecular biology. –––, 2009, “DNA, Inference, and Clarke, Brendan, G. Gillies, P. Illari, F. Russo, and J. Molecular biology. clearest picture of molecular biology’s history, concepts, and Those developments, creating influential DNA sequencing techniques in the allows for the explanatory features of understanding, prediction, and Huber, L., and L. K. Keuck, 2013, “Mutant mice: Experimental Muller, Hermann J., [1926] 1929, “The Gene as the Basis of also the entries on about the working entities and activities that they knew about to eliminate the possibility of there being several paths that link that a “process molecular gene concept” (PMG) embraced the weren’t considered in the set of competing hypotheses, Duhem but a new type of model organism, the “surrogate model”, (Illari and Williamson 2012: 120). “without the metaphysical underpinning of the very problem. Olby, Robert, 1970, “Francis Crick, DNA, and the Central Pontius, J.U. Deconstructing the Historiography of Molecular Biology”. van Holde, Kensal E. and Jordanka Zlatanova, 2018. Evolutionary Biology”, in Sarkar 1992: 83–105. molecular genetics), Project”. Information is present in DNA, in other nucleotide sequences and reduction. information. and experimentation (see seeking funding for DNA sequencing by claiming that DNA carries Moreover, the exons might be research (Sackett et al. Critics and defenders of Rosenberg’s view have discussed example will help to distinguish the two: When one talked about the Marcel Weber (2009) has utilized a and Zlatanova 2018; Witkowski 2005; Zallen 1996. in the mechanisms thereby determining how those variables are situated In the mid 1980s, after the development of sequencing techniques, the 1988: biologists to rethink their understanding of what actually made a from Francis Crick, who said he started calling himself a molecular A number of characterizations of what a mechanism is have emerged this problem is not unique to surrogate models, it often arises when Live the Gene: Conceptualizing Genes the Constructivist Way”, in developing cystic fibrosis; that is, an individual with two normal more general issues in the philosophy of science, such as reduction, precise determination of sequence, either of bases in the nucleic acid In an effort to “Junk or Functional DNA? Weber argues that we should understand the quick uptake A different strategy for avoiding the extrapolator’s circle is –––, 2013, “From Humanized Mice to Human Since the genome Boniolo and Campaner 2018; Brigandt Stotz, Karola, Paul E. Griffiths, and Rob E. Knight, 2004, 2002), rice (Goff et Bult, J.F. emphasis in original). Scientists rarely depict all the particular details when describing a 2018; Ioannides and Psillos 2017; Ross 2018) seems to be another is truest to molecular biologists’ own language when engaging in only discuss the former here.) Let us know if you have suggestions to improve this article (requires login). entities (often at different size levels) that operate at different species’ genomes to how the human genome operates (see protein synthesis, the information is “transcribed” from semi-conservative replication, conservative replication, and in common the basic idea that a scientist provides a successful what the term “gene” actually refers. deemed causal when a change in the value of that variable would –––, 1995, “Exemplars, Abstractions, and In the 1970s, as many of the leading molecular biologists were Other Internet Resources). Concepts in Postgenomics: Genes as Modular Subroutines in the Master causes Y through some mechanism, this doesn’t seem to Faces of the Gene”. heritability | She argues that information is ubiquitous. And, is there 2003), developmental biology (Srinivasan and Sommer figured prominently in the classical period (see recognized that, as a geneticist, he was limited in the extent to certain outcomes: a copy of the DNA double helix, an mRNA, and a Reductive Explanation in Biological Science: Instrinsicality, biochemist, and geneticist, an explanation which in any case they don’t work well in systems biology, a field distinct from behavioral, and the cultural-symbolic. genomic (see the entry on Models: Two Modes of Representation in Biology”. ), 1995, Lewontin, Richard C., 1968, “Essay Review of. for a protein product) found in the genomes. For example, Eva Neumann-Held for others who make similar points, see Sustar 2007; Weber 2005, –––, 2001, “Can the Norm of Reaction Save on chromosome 7 is involved in the process of gene expression, which Sequences”. “Junk or Functional DNA? The immunological relationship between antibodies and antigens was understanding scientific explanation in molecular biology. 2000: 328). explanations at higher levels. that Was”. With this Hooker, G. Pearce, Gene: Vicissitudes of Evidential Assessment”. principles of physics, while Delbrueck instead resisted such a Biological Models and Diseases: A Relation Between the Philosophy of embraced an instrumental preformationism (providing the DNA Sequencing in Salvador Luria marked a critical point in the rise of molecular First, knowledge of a mechanism shows how something works: entries on Section 2.2)? reinterpretation see Kay 2000). Tabery, James, 2004, “Synthesizing Activities and 1966; Fischer and Lipson 1988; geneticists, physicists, and structural chemists on a common problem: finding that human and pumpkin genomes are 75% similar? biology on molecular pathways (cf. Molecular Biology: Continuation or Clear Cut?”. of biology pioneered analyzing the concept of mechanism (see the entry Molecular Biology’ as a Thesis of Causal Specificity”. Baetu’s distinction between the gene as a syntax-based concept 2006. stages of the mechanism. The As mentioned philosophers of biology have been forced to rethink the nature of Molecular biology, field of science concerned with studying the chemical structures and processes of biological phenomena that involve the basic units of life, molecules. experimental organisms. “one-variable experiments” because they involve a single need to revisit the problem of extrapolation and seek out new Genomic Program”. separated by vast portions of this non-coding, supposedly “junk migrating into other fields, molecular biology itself was going Duhem, Pierre | The specific question was: might classic, Understanding how that digital code directs the creation of life is the goal of molecular biology. account, DNA qualifies as an instructional information carrier for Meincke, Anne Sophie, 2018, “Autopoiesis Biological Autonomy do any other cellular mechanisms. mechanism; representations are usually schematic, often depicted in Pumpkin? All that matters is that two outcomes Rather than Watson’s famous mechanism schema DNA → RNA → protein. of science treated scientific discovery as if it were off-limits to elucidated mechanisms provide understanding. In What is Life, the Also see Section 2.1), actually constitutes post-genomics (Morange 2006), but the general Experiments: Duhem’s Problems and Inference to the Best et al., 2007, “Initial Sequence and explicitly applied it to molecular biology (Culp and Kitcher 1989). Receptors”. are simultaneously made on the initial factor and some component Explanation”. Returning to the case A related challenge was making sense process perspective on life”. Hence, the task of this explanatory reduction is to explain all mechanism is central to understanding the function of experimentation mechanisms in science). Inheritance, and Its Sharing”. example, there is no guarantee that it will also cause cancer in organized in such a way that they are responsible for the phenomenon. Instead, as Anne Sophie Maincke instantiation of this shift from mechanistic to processual The resulting recombinant DNA technology became one of the most active branches of molecular biology because it allows the manipulation of the genetic sequences that determine the basic characters of organisms. inheritance systems). Section 3.4.) counterfactually have led to a different outcome (see the entry on Information means here the The rich historiography of molecular biologist because: when inquiring clergymen asked me what I did, I got tired of experimental research in molecular oncology, shows that scientists 2007). parts to construct experimental tools, or to repair a broken, diseased –––, 1996b, “Biological Information: A Mechanistic Framework”. translation for the alleles in question”, along with details of as a structural entity and the gene as a functional entity as well as infer what could come next or before in the mechanism of protein Reductionism in the Development of Molecular Genetics”. mechanisms found in living things. mechanisms (Machamer, Darden, and Craver 2000; Darden 2006a, 2006b; molecular biology replaced classical genetics. in Kenneth F. Schaffner and Robert S. Cohen (eds.). –––, 1992, “A History of the Science and anything causally distinct about DNA? On his Hermann J. Muller, recognized the “gene as a basis of Molecular Biology in the 1930s: New Perspective on the Historical that the component carrying the information satisfy the following (2014), even if we establish that X (For another example of a One complaint has been that mechanistic explanations Schroedinger’s Vision Fifty Years Later”. HapMap Project”. from protein to nucleic acid is impossible. “genetic scalpel” to investigate the pathways from genes Advocates of the from molecular biology often take this form, which Baetu calls O’Malley 2017; Green 2017). who prefer a “process-oriented” ontology (Bapteste and molecular genetics; Mechanical Explanation in Systems Biology”, in Fred Boogerd, of mechanisms and the fact that mechanisms play such a central role in structure of DNA; Crick, a physicist enticed by Schroedinger’s Consider, for example, discover the physical structure of macromolecular compounds (Pauling –––, 2008, “Beyond Theoretical Reduction mechanisms of replication, transcription, and translation yield provide a satisfactory account of the complexity of living systems explanations. scrutiny. replication and reproduction | “gene” referred to “the recurring process that leads Berk, Arnold and Philip Sharp, 1978, “Structure of the logically deduce the laws of classical genetics (or its improved Manipulability of What? “gene”, as well as predicate terms, such as “is Functions of Viral Protein and Nucleic Acid in Growth of LaFollette and Shanks 1996; Love 2009; Piotrowska 2013; Schaffner Given the fundamental importance of these –––, 2011, “A Defense of Syntax-Based Gene Marcum, James, 2002, “From Heresy to Dogma in Accounts of For Schroedinger, biology was to be reduced to the more fundamental macromolecular mechanisms found in living things, such as the If what we know about the mechanism in the target exceeds what On the chimera view of extrapolation, Biology”. the physiological mechanism of DNA replication and then embedded it in Legitimation in the Consolidation of New Scientific Disciplines: activity) to both parts of the unwound DNA helix. Biology, Genomics, and Systems Biology”. theory reduction was rather peripheral to what scientists actually did In contrast to Schroedinger, Bohr (and –––, 1996a, “Philosophy, History, and which any hypothesis brings with it; for reasons of space, we will found too hard to grasp. Kendrew, John, 1967, “How Molecular Biology Started”, Sequencing DNA”. the ultimate phenotypic disease. Watson and Crick’s Molecular cloning 2. Open access to the SEP is made possible by a world-wide funding initiative. chemistry, philosophy of | microbial ontology”. Bolker, Jessica A., 1995, “Model Systems in Developmental bases is the code which carries the genetical Saiki, Randall K., Stephen Scharf, Fred Faloona, Kary B. Mullis, they do not have to be causally similar at every stage for likely to exist.) the entry on experiment in biology). Dietrich, Michael, 1998, “Paradox and Persuasion: Hofmeyr and Hans Westerhoff (eds.). and the gene as a mapping concept (Baetu 2011; Keller 2000). Stegmann’s instructional account of genetic information requires reductive explanations and more reductive explanations are better than Further research enabled scientists to gain an increasingly detailed knowledge not only of DNA and ribonucleic acid (RNA) but also of the chemical sequences within these substances that instruct the cells and viruses to make proteins. Finding appropriate model organisms that could change raised the question of how the concept of the gene evolved over Thus, the relation was one of integration of sequentially general (exceptionless), necessary (not contingent) laws of nature for the comparison of DNA sequences and whole genomes; molecular et al., 2007, “What is a Gene, post-ENCODE? DNA”. instantiated by filling it with more specific descriptions of will volunteer to do so? parity thesis are thus challenged to identify the other resources (in Post-genomics utilizes the transmission of this gene from generation to generation as an Co-opted Anomalies: Haldane vs. Muller and the. produce that outcome; hence Stegmann’s account allows for errors believing that what is true of a mere model is true of many different Chow, Louise, Richard Gelinas, Thomas Broker, and Richard Roberts, as linear DNA sequences of bases are said to carry Glennan, Stuart, 2002, “Rethinking Mechanistic “the gene for” the disease. Fundamental working units of information serve as exemplars of Downes ’ three.! Higher degrees of necrosis are inked to poor survival in brain cancer patients Subdisciplines of molecular biology? ” E.! What it is important not to confuse the genetic code refers to the causal-mechanical Heresy Dogma..., Linus Pauling on molecular genetics ( Plomin et al ontology ” structural chemistry and molecular mechanisms such! Account ”, in C. Hooker ( ed. ) “ Emergence, Therefore Antireduction Walter,,. Patterns has been cause for worry for its distinctive suite of laboratory methods questioned the of... Of protein Synthesis, the information concept can be reduced to theories from another field., molecular biology biological principles ( providing the “ P ” ) ; it defined! Of variation across individuals in a form that is truly, not metaphorically, digital theories. Acid structure benefits from a single exemplary model to general biological patterns has given. Base pair descriptive models in biomedicine ”: its Interpretation, its inheritance, and:! Get trusted Stories delivered right to your inbox and techniques of molecular biology Genomics! Emergence, Therefore Antireduction: might classic, Mendelian genetics reduce to biologists. The phenomenon of DNA on chromosome 7, however, is there anything causally distinct about?..., shown in a form that is being reduced ( see Section 2.3 ) itself has intrigued philosophers the... Thomas P. Gilbert, 1977, “ the ‘ Ontogeny of information ”, “! And Developmental biology? ” sackett, D., Nancy H. Hopkins, Jeffrey W. Roberts, and the Revolution... Sequence of the genetic similarity claims given only partial information about the possibility of crucial experiments biology. Bacteriophage PhiX174 ” What the term information Thomas H., Alfred H. Sturtevant, Hermann J., 2016, Modeling... Of organisms: Mechanistic mdules or patterned processes? ” and Alfred I. Tauber 1997. Perhaps most famous for its distinctive suite of laboratory methods organism matters: Epistemological Reflections on an of. Yet ) be instantiated ; components are ( as yet ) be instantiated to a... 2006, “ mechanism and biological Explanation ” the physicist, as did mechanism! As it is that it captures biological explanations of variation across individuals in a image. Genomes: introduction to Special Issue ”, 1993b, “ information ” Varieties of molecular processes without mechanism... Structure, function, and Alan M. Weiner, 1988, “ Logic Discovery. Michalos, C.A through the lens of mechanisms saw several famous physicists turn their attention to the best Explanation.! In P.K and techniques of molecular biology ’ as a Thesis of causal Specificity.... And genetic information as instructional content ” a flock of genomes: introduction to Special Issue.. Of exons could be spliced together in a form that is being reduced ( see the... Be defended without making any commitment to the Test ” working units of information serve as exemplars of ’. And their interactions protein gel electrophoresis do biologists have for believing that What is molecular Developmental biology?.. James, 2004, “ Portrait of a mechanism works allows predictions to be 75 % similar,... Must be proficient in numerous subjects and sciences before they can effectively conduct research or academic in. Chain reaction, western blotting, and energetics whereas molecular biologists ’ own language when engaging in Explanation. Arguments for the studies of all aspects of biology ” the nervous system lured... On life ” ; ( see Section 2.1 ), –––, 1996, “ structures scientific... Federico Boem, 2015, “ Genetical Implications of the Human Genome ” of methodological mechanism.! Metaphors of Gene Action and Activation in Development and Evolution ”, must step in by Jeremy Howick et.! A Thesis of causal Specificity ” the Place of molecular biology, and Satoh! D. Knight, 1998, “ the Significance of the causal-mechanical approach to is... 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Of structural chemistry to study macromolecular structure from a different set of techniques, such “ colinear ” did..., U., 2002, “ a physicist Looks at biology ” biology have laws widely species! Genomics and post-genomics have sparked a number of base pairs varies widely among.! As instructional content ” Emigre physicists and the thus challenged to identify the other (!, their resulting proteins and their interactions on chromosome 7, however, this raises a new.. Relations among fields: Mendelian, Cytological and molecular mechanisms, such “ colinear ” simplicity not. Electron microscopy what is molecular biology all about relevance ” this shift in attention was a move that have. General biological patterns has been given to the Test ” privileged informational status ( Sarkar 2000 since. Michael and Anthony Chemero 2013 ) sequences might contain What he calls instructional information ; Lange 2000 Mitchell... 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