Abstract
Scientific hypotheses may either predict particular unknown facts or accommodate previously-known data. Although affirmed predictions are intuitively more rewarding than accommodations of established facts, opinions divide whether predictive hypotheses are also epistemically superior to accommodation hypotheses. This paper examines the contribution of predictive hypotheses to discoveries of several bio-molecular systems. Having all the necessary elements of the system known beforehand, an abstract predictive hypothesis of semiconservative mode of DNA replication was successfully affirmed. However, in defining the genetic code whose biochemical basis was unclear, hypotheses were only partially effective and supplementary experimentation was required for its conclusive definition. Markedly, hypotheses were entirely inept in predicting workings of complex systems that included unknown elements. Thus, hypotheses did not predict the existence and function of mRNA, the multiple unidentified components of the protein biosynthesis machinery, or the manifold unknown constituents of the ubiquitin–proteasome system of protein breakdown. Consequently, because of their inability to envision unknown entities, predictive hypotheses did not contribute to the elucidation of complex systems. As data-based accommodation theories remained the sole instrument to explain complex bio-molecular systems, the philosophical question of alleged advantage of predictive over accommodative hypotheses became inconsequential.
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Notes
Watson (1953), a March 12, 1953 letter to Delbrück: http://osulibrary.orst.edu/specialcollections/coll/pauling/dna/corr/corr432.1-watson-delbruck-19530312-03.html.
Untitled and undated typescript of a talk that was probably delivered in 1957: Wellcome Library Archives; Closed stores Arch. & MSS PP/CRI/H2/24: Box 79; Ref. no. ebaf293b-7f02-46c8-a16f-c45333219e28.
Gamow's July 8, 1953 handwritten letter to Watson and Crick; facsimile 1 in Watson (2001).
Facsimile of Gamow’s October 22, 1953 letter to Linus Pauling; OSU Linus Pauling Web archive: http://osulibrary.orst.edu/specialcollections/coll/pauling/dna/corr/sci9.001.43-gamow-lp-19531022-01.html.
An even earlier version of the Central Dogma was submitted by Boivin (1947): "We may at the most, catch a glimpse of a series of catalytic actions, which set out from primary directing centers (the desoxyribonucleic genes), proceed through secondary directing centers (the ribonucleic microsome-plasma-genes), and thence through tertiary directing centers (the enzymes), to determine finally the nature of the metabolic chains involved, and to condition, by this very means, all the characters of the cell in consideration."
In: “A career begins at the National Institute of Health”; the second of six oral history interviews that Ruth Harris conducted with Nirenberg between September 1995 and January 1996: http://history.nih.gov/archives/downloads/Nirenberg%20oral%20history%20Chap%202%20-NIH%201957_1959.pdf.
Facsimile of Watson’s December 11, 1954 letter to Crick in the NIH Profiles in Science Web site: http://profiles.nlm.nih.gov/ps/retrieve/ResourceMetadata/SCBBJN.
Crick’s unpublished communication to the RNA Tie Club (1955): “On degenerate templates and the adaptor hypothesis”. Facsimile in the NIH Profiles in Science Web site: http://profiles.nlm.nih.gov/SC/B/B/G/F/_/scbbgf.pdf.
According to Judson (1996, p. 323), Crick did not attend Volkin’s talk and only a year later he read its published form (Volkin and Astrachan, 1957). Judson also claimed that Crick and Brenner were familiar with the Volkin and Astrachan results when they came up with the idea of mRNA. Asked whether he was aware of the Oak Ridge findings, Jacob had said, “The question is what you mean, to be aware? To be aware is to have it on the front of consciousness, and clearly we were not, at this level, even if we knew” (Judson 1996, p. 414).
The other ‘bombshell’ was Arthur Kornberg’s report of DNA synthesis in E. coli extracts.
Brenner referred here to Volkin and Astrachan’s (1956, 1957) original notion that the unstable RNA was a precursor of phage DNA. Notably, however, he did not recall their later conclusion that the different kinetics of accumulation of radioactivity in phage RNA and DNA discounted precursor-product relationship between the two. He was also unaware of their later suggestion that the short-lived phage RNA molecules were templates for viral proteins (Volkin et al. 1958).
Facsimile of Crick’s handwritten note, dated May 1960 in the NIH Profiles in Science Web site: http://profiles.nlm.nih.gov/ps/retrieve/ResourceMetadata/SCBBFZ.
Facsimile of Crick’s May 10, 1960 letter to Kornberg, in the NIH Profiles in Science Web site: http://profiles.nlm.nih.gov/ps/retrieve/ResourceMetadata/SCBBGZ.
Meselson’s videotaped testament: http://www.dnalc.org/view/15330-Messenger-RNA-Matthew-Meselson.html.
References
Achinstein, P. (1994). Explanation v. prediction: Which carries more weight? Proceedings of the Biennial Meeting of the Philosophy of Science Association, 1994, 156–164.
Appelmans, F., Wattiaux, R., & De Duve, C. (1955). Tissue fractionation studies. 5. The association of acid phosphatase with a special class of cytoplasmic granules in rat liver. Biochemical Journal, 59(3), 438–445.
Avery, O. T., Macleod, C. M., & McCarty, M. (1944). Studies on the chemical nature of the substance inducing transformation of pneumococcal types: Induction of transformation by a desoxyribonucleic acid fraction isolated from pneumococcus type III. The Journal of Experimental Medicine, 79(2), 137–158.
Baker, A. (2003). Quantitative parsimony and explanatory power. The British Journal for the Philosophy of Science, 54(2), 245–259.
Baker, A. (2007). Occam’s razor in science: A case study from biogeography. Biology and Philosophy, 22(2), 193–215.
Baker, A. (2016). Simplicity. In E. N. Zalta (Ed.), Stanford encyclopedia of philosophy. Stanford: Stanford University Center for the Study of Language and Information. https://plato.stanford.edu/entries/simplicity/.
Barnes, E. (1996). Thoughts on Maher’s predictivism. Philosophy of Science, 63(3), 401–410.
Barnes, E. (2005). On Mendeleev’s predictions: Comment on Scerri and Worrall. Studies in History and Philosophy of Science Part A, 36(4), 801–812.
Beadle, G. W., & Tatum, E. L. (1941). Genetic control of biochemical reactions in Neurospora. Proceedings of the National Academy of Sciences of the United States of America, 27(11), 499–506.
Belozersky, A. N., & Spirin, A. S. (1958). A correlation between the compositions of deoxyribonucleic and ribonucleic acids. Nature, 182(4628), 111–112.
Benzer, S. (1955). Fine structure of a genetic region in bacteriophage. Proceedings of the National Academy of Sciences of the United States of America, 41(6), 344–354.
Benzer, S. (1961). On the topography of the genetic fine structure. Proceedings of the National Academy of Sciences of the United States of America, 47(3), 403–415.
Bergmann, M. (1942). A classification of proteolytic enzymes. Advances in Enzymology, 2, 49–68.
Bergmann, M., & Fraenkel-Conrat, H. (1937). The rôle of specificity in the enzymatic synthesis of proteins: Synthesis with intracellular enzymes. The Journal of Biological Chemistry, 119(2), 707–720.
Bergmann, M., & Fruton, J. S. (1938). Some synthetic and hydrolytic experiments with chymotrypsin. The Journal of Biological Chemistry, 124(1), 321–329.
Bergmann, M., & Fruton, J. S. (1941). The specificity of proteinases. Advances in Enzymology, 1, 63–98.
Beynon, R. J., & Bond, J. S. (1986). Catabolism of intracellular protein: Molecular aspects. American Journal of Physiology—Cell Physiology, 251(2), C141–C152.
Bhattacharyya, S., Yu, H., Mim, C., & Matouschek, A. (2014). Regulated protein turnover: Snapshots of the proteasome in action. Nature Reviews Molecular Cell Biology, 15(2), 122–133.
Bloch, D. P. (1955). A possible mechanism for the replication of the helical structure of desoxyribonucleic acid. Proceedings of the National Academy of Sciences of the United States of America, 41(12), 1058–1064.
Boivin, A. (1947). Directed mutation in colon bacilli, by inducing principle of desoxynucleic acid nature: Its meaning for the general biochemistry of heredity. Cold Spring Harbor Symposia on Quantitative Biology, 12, 7–17.
Borsook, H., & Dubnoff, J. W. (1940). The biological synthesis of hippouric acid in vitro. The Journal of Biological Chemistry, 132(1), 307–324.
Borsook, H., & Huffman, H. H. (1938). Some thermodynamical considerations of amino acids, peptides and related substances. In C. L. A. Schmidt (Ed.), Chemistry of the amino acids and proteins (p. 865). Springfield, IL: Thomas Publishing Co.
Brachet, J. (1947). The metabolism of nucleic acids during embryonic development. Cold Spring Harbor Symposia on Quantitative Biology, 12, 18–27.
Brachet, J. (1950). The localization and the role of ribonucleic acid in the cell. Annals of the New York Academy of Sciences, 50(8), 861–869.
Brachet, J. (1955). Recherches sur les interactions biochimiques entre le noyau et le cytoplasme chez les organismes unicellulaires. I. Amoeba proteus. Biochimica et Biophysica Acta, 18(2), 247–268.
Brenner, S. (1957). On the impossibility of all overlapping triplet codes in information transfer from nucleic acid to proteins. Proceedings of the National Academy of Sciences of the United States of America, 43(8), 687–694.
Brenner, S., Barnett, L., Crick, F. H. C., & Orgel, A. (1961a). The theory of mutagenesis. Journal of Molecular Biology, 3(1), 121–124.
Brenner, S., Jacob, F., & Meselson, M. (1961b). An unstable intermediate carrying information from genes to ribosomes for protein synthesis. Nature, 190(4776), 576–581.
Brush, S. G. (1989). Prediction and theory evaluation: The case of light bending. Science, 246(4934), 1124–1129.
Brush, S. G. (1990). Prediction and theory evaluation: Alfven on space plasma phenomena. EOS. Transactions of the American Geophysical Union, 71(2), 19–33.
Brush, S. G. (1993). Prediction and theory evaluation: Cosmic microwaves and the revival of the Big Bang. Perspectives on Science, 1(4), 565–602.
Brush, S. G. (1994). Dynamics of theory change: The role of predictions. Proceedings of the Biennial Meeting of the Philosophy of Science Association, 1994, 133–145.
Brush, S. G. (1996). The reception of Mendeleev’s periodic law in America and Britain. Isis, 87(4), 595–628.
Butler, J. A. (1956). The action of ionizing radiations on biological materials; facts and theories. Radiation Research, 4(1), 20–32.
Caldwell, P. C., & Hinshelwood, C. (1950). Some considerations on autosynthesis in bacteria. Journal of the Chemical Society, 4, 3156–3159.
Caspersson, T. (1947). The relations between nucleic acid and protein synthesis. Symposium of the Society for Experimental Biology, 1, 127–151.
Caspersson, T., & Schultz, J. (1938). Nucleic acid metabolism of the chromosomes in relation to gene reproduction. Nature, 142(3589), 294–295.
Caspersson, T., & Schultz, J. (1939). Pentose nucleotides in the cytoplasm of growing tissues. Nature, 143(3623), 602–603.
Cavalieri, L. F., Rosenberg, B. H., & Deutsch, J. F. (1959). The subunit of deoxyribonucleic acid. Biochemical and Biophysical Research Communications, 1(3), 124–128.
Chapeville, F., Lipmann, F., Von Ehrenstein, G., Weisblum, B., Ray, W. J., Jr., & Benzer, S. (1962). On the role of soluble ribonucleic acid in coding for amino acids. Proceedings of the National Academy of Sciences of the United States of America, 48(6), 1086–1092.
Ciechanover, A. (2005). Intracellular protein degradation: From a vague idea thru the lysosome and the ubiquitin–proteasome system and onto human diseases and drug targeting[ast]. Cell Death and Differentiation, 12(9), 1178–1190.
Ciechanover, A., Heller, H., Elias, S., Haas, A. L., & Hershko, A. (1980). ATP-dependent conjugation of reticulocyte proteins with the polypeptide required for protein degradation. Proceedings of the National Academy of Sciences of the United States of America, 77(3), 1365–1368.
Ciechanover, A., Heller, H., Katz-Etzion, R., & Hershko, A. (1981). Activation of the heat-stable polypeptide of the ATP-dependent proteolytic system. Proceedings of the National Academy of Sciences of the United States of America, 78(2), 761–765.
Ciehanover, A., Hod, Y., & Hershko, A. (1978). A heat-stable polypeptide component of an ATP-dependent proteolytic system from reticulocytes. Biochemical and Biophysical Research Communications, 81(4), 1100–1105.
Claude, A. (1943). The constitution of protoplasm. Science, 97(2525), 451–456.
Collins, R. (1994). Against the epistemic value of prediction over accommodation. Noûs, 28(2), 210–224.
Coux, O., Tanaka, K., & Goldberg, A. L. (1996). Structure and functions of the 20S and 26S proteasomes. Annual Review of Biochemistry, 65(1), 801–847.
Creager, A. N., & Morgan, G. J. (2008). After the double helix: Rosalind Franklin’s research on Tobacco Mosaic Virus. Isis, 99(2), 239–272.
Crick, F. H. (1958). On protein synthesis. Symposium of the Society for Experimental Biology, 12, 138–163.
Crick, F. H. (1959). Biochemical activities of nucleic acids. The present position of the coding problem. Brookhaven Symposia in Biology, 12, 35–39.
Crick, F. H., Barnett, L., Brenner, S., & Watts-Tobin, R. J. (1961). General nature of the genetic code for proteins. Nature, 192(4809), 1227–1232.
Crick, F. H., Griffith, J. S., & Orgel, L. E. (1957). Codes without commas. Proceedings of the National Academy of Sciences of the United States of America, 43(5), 416–421.
Crick, F. H., & Watson, J. D. (1956a). Structure of small viruses. Nature, 177(4506), 473–475.
Crick, F. H., & Watson, J. D. (1956b). Virus structure: General principles. In G. E. Wolstenholme & E. C. P. Millar (Eds.), Ciba foundation symposium—The nature of viruses. New York: Wiley.
Darden, L. (2006). Reasoning in biological discoveries: Assays on mechanisms, interfield relations, and anomaly resolution. Cambridge: Cambridge University Press.
Davern, C. I., & Meselson, M. (1960). The molecular conservation of ribonucleic acid during bacterial growth. Journal of Molecular Biology, 2(3), 153–160.
Delbruck, M. (1954). On the replication of desoxyribonucleic acid (DNA). Proceedings of the National Academy of Sciences of the United States of America, 40(9), 783–788.
Delbruck, M., & Stent, G. S. (1957). On the mechanism of DNA replication. In W. D. McElroy & B. Glass (Eds.), A symposium on the chemical basis of heredity (pp. 699–736). Baltimore: The John Hopkins Press.
Doty, P., Marmur, J., Eigner, J., & Schildkraut, C. (1960). Strand separation and specific recombination in deoxyribonucleic acids: Physical chemical studies. Proceedings of the National Academy of Sciences of the United States of America, 46(4), 461–476.
Douglas, H., & Magnus, P. D. (2013). State of the field: Why novel prediction matters. Studies in History and Philosophy of Science Part A, 44(4), 580–589.
Dounce, A. L. (1952). Duplicating mechanism for peptide chain and nucleic acid synthesis. Enzymologia, 15(5), 251–258.
Dounce, A. L. (1953). Nucleic acid template hypotheses. Nature, 172(4377), 541.
Duhem, P. (1962). The aim and structure of physical theory (Trans. Weiner, P. W.). New York: Atheneum.
Earman, J., & Glymour, C. (1978). Einstein and Hilbert: Two months in the history of general relativity. Archives for History of Exact Sciences, 19(3), 291–308.
Etlinger, J. D., & Goldberg, A. L. (1977). A soluble ATP-dependent proteolytic system responsible for the degradation of abnormal proteins in reticulocytes. Proceedings of the National Academy of Sciences of the United States of America, 74(1), 54–58.
Finley, D. (2009). Recognition and processing of ubiquitin-protein conjugates by the proteasome. Annual Review of Biochemistry, 78(1), 477–513.
Fisher, S. (2015). Not just “a clever way to detect whether DNA really made RNA”: The invention of DNA–RNA hybridization and its outcome. Studies in History and Philosophy of Science Part C, 53, 40–52.
Fraenkel-Conrat, H., & Williams, R. C. (1955). Reconstitution of active Tobacco Mosaic Virus from its inactive protein and nucleic acid components. Proceedings of the National Academy of Sciences of the United States of America, 41(10), 690–698.
Fruton, J. S. (1950). The role of proteolytic enzymes in the biosynthesis of peptide bonds. Yale Journal of Biology and Medicine, 22(3), 263–271.
Fruton, J. S., Johnston, R. B., & Fried, M. (1951). Elongation of peptide chains in enzyme-catalyzed transamidation reactions. The Journal of Biological Chemistry, 190(1), 39–53.
Fry, M. (2016a). Dissolution of hypotheses in biochemistry: Three case studies. History and Philosophy of Life Sciences, 38(4), 17. https://doi.org/10.1007/s40656-016-0118-x.
Fry, M. (2016b). Landmark experiments in molecular biology. Amsterdam: Elsevier.
Fuerst, C. R., & Stent, G. S. (1956). Inactivation of bacteria by decay of incorporated radioactive phosphorus. Journal of General Physiology, 40(1), 73–90.
Gamow, G. (1954a). Possible mathematical relation between deoxyribonucleic acid and proteins. Biologiske Meddelelser udviket af Det Kongelige Danske Videnskabernes Selskab, 22(3), 1–11.
Gamow, G. (1954b). Possible relation between deoxyribonucleic acid and protein structures. Nature, 173(4398), 318.
Gamow, G., Rich, A., & Ycas, M. (1956). The problem of information transfer from the nucleic acids to proteins. Advances in Biological and Medical Physics, 4, 23–68.
Gamow, G., & Ycas, M. (1955). Statistical correlation of protein and ribonucleic acid composition. Proceedings of the National Academy of Sciences of the United States of America, 41(12), 1011–1019.
Gardner, M. R. (1982). Predicting novel facts. The British Journal for the Philosophy of Science, 33(1), 1–15.
Gianetto, R., & De Duve, C. (1955). Tissue fractionation studies. 4. Comparative study of the binding of acid phosphatase, β-glucuronidase and cathepsin by rat-liver particles. Biochemical Journal, 59(3), 433–438.
Gierer, A., & Schramm, G. (1956). Infectivity of ribonucleic acid from tobacco mosaic virus. Nature, 177(4511), 702–703.
Gros, F., Hiatt, H., Gilbert, W., Kurland, C. G., Risebrough, R. W., & Watson, J. D. (1961). Unstable ribonucleic acid revealed by pulse labelling of Escherichia coli. Nature, 190(4776), 581–585.
Hall, B. D., & Spiegelman, S. (1961). Sequence complementarity of T2-DNA and T2-specific RNA. Proceedings of the National Academy of Sciences of the United States of America, 47(2), 137–146.
Harker, D. (2008). On the predilections for predictions. The British Journal for the Philosophy of Science, 59(3), 429–453.
Hayashi, M., & Spiegelman, S. (1961). The selective synthesis of informational RNA in bacteria. Proceedings of the National Academy of Sciences of the United States of America, 47(10), 1564–1580.
Hempel, C. G. (1966). Philosophy of natural science. Upper Saddle River: Prentice-Hall.
Hershey, A. D. (1953). Nucleic acid economy in bacteria infected with bacteriophage T2. The Journal of General Physiology, 37(1), 1–23.
Hershko, A. (2005). The ubiquitin system for protein degradation and some of its roles in the control of the cell division cycle[ast]. Cell Death and Differentaition, 12(9), 1191–1197.
Hershko, A., & Ciechanover, A. (1998). The ubiquitin system. Annual Review of Biochemistry, 67, 425–479.
Hitchcock, C., & Sober, E. (2004). Prediction versus accommodation and the risk of overfitting. The British Journal for the Philosophy of Science, 55(1), 1–34.
Hoagland, M. (1955). An enzymic mechanism for amino acid activation in animal tissues. Biochimica et Biophysica Acta, 16(2), 288–289.
Hoagland, M. (2004). Enter transfer RNA. Nature, 431(7006), 249.
Hoagland, M., Keller, E. B., & Zamecnik, P. C. (1956). Enzymatic carboxyl activation of amino acids. The Journal of Biological Chemistry, 218(1), 345–358.
Hoagland, M., Stephenson, M. L., Scott, J. F., Hecht, L. I., & Zamecnik, P. C. (1958). A soluble ribonucleic acid intermediate in protein synthesis. The Journal of Biological Chemistry, 231(1), 241–257.
Hoagland, M., Zamecnik, P. C., & Stephenson, M. L. (1957). Intermediate reactions in protein biosynthesis. Biochimica et Biophysica Acta, 24(1), 215–216.
Holmes, F. L. (2001). Meselson, Stahl and the replication of DNA: A history of “the most beautiful experiment in biology”. New Haven & London: Yale University Press.
Howson, C. (1988). Accommodation, prediction and Bayesian confirmation theory. Proceedings of the Biennial Meeting of the Philosophy of Science Association, 1988, 381–392.
Howson, C., & Franklin, A. (1991). Maher, Mendeleev and Bayesianism. Philosophy of Science, 58(4), 574–585.
Hultin, T. (1950). Incorporation in vivo of 15N-labeled glycine into liver fractions of newly hatched chicks. Experimental Cell Research, 1(3), 376–381.
Jacob, F., & Monod, J. (1961). Genetic regulatory mechanisms in the synthesis of proteins. Journal of Molecular Biology, 3(3), 318–356.
Jacob, F., & Wollman, E. L. (1956). Sur les processus de conjugaison et de recombinaison chez Escherichia coli. I. L’induction par conjugaison ou induction zygotique. Annales de l’Institut Pasteur (Paris), 91(4), 486–510.
Jansson, L., & Tallant, J. (2017). Quantitative parsimony: Probably for the better. The British Journal for the Philosophy of Science, 68(3), 781–803.
Judson, H. F. (1996). The eighth day of creation (Expanded ed.). New York: Cold Spring Harbor Laboratory Press.
Kahn, J. A., Landsburg, S. E., & Stockman, A. C. (1992). On novel confirmation. The British Journal for the Philosophy of Science, 43(4), 503–516.
Kalckar, H. M. (1941). The nature of energetic coupling in biological synthesis. Chemical Reviews, 28, 71–178.
Kay, L. E. (2000). Who wrote the book of life? A history of the genetic code. Stanford, CA: Stanford University Press.
Keller, E. G. (1951). Turnover of proteins of cell fractions of adult rat liver in vivo. Federation Proceedings, 10, 206.
Keynes, J. M. (1921). A treatise of probability. London: Macmillan.
Khorana, H. G. (1968). Synthetic nucleic acids and the genetic code. JAMA, the Journal of the American Medical Association, 206(9), 1978–1982.
Khorana, H. G. (Ed.). (1972). Nucleic acid synthesis in the study of the genetic code. Nobel Nobel lecture December 12, 1968. Amsterdam: Elsevier Publishing Company.
Kurland, C. G. (1960). Molecular characterization of ribonucleic acid from Escherichia coli ribosomes: I. Isolation and molecular weights. Journal of Molecular Biology, 2(2), 83–91.
Lakatos, I. (1978). The methodology of scientific research programmes (Vol. 1). Cambridge: Cambridge University Press.
Lange, M. (2001). The apparent superiority of prediction to accommodation as a side effect: A reply to Maher. The British Journal for the Philosophy of Science, 52(3), 575–588.
Levinthal, C. (1956). The mechanism of DNA replication and genetic recombination in phage. Proceedings of the National Academy of Sciences of the United States of America, 42(7), 394–404.
Levinthal, C., & Crane, H. R. (1956). On the unwinding of DNA. Proceedings of the National Academy of Sciences of the United States of America, 42(7), 436–438.
Lipmann, F. (1941). Metabolic generation and utilization of phosphate bond energy. In F. F. Nord & J. S. Fruton (Eds.), Advances in enzymology (Vol. 1, pp. 99–162). New York: Interscience Publishers.
Lipton, P. (2004). Inference to the best explanation (2nd ed.). London: Routledge.
Lipton, P. (2005). Testing hypotheses: Prediction and prejudice. Science, 307(5707), 219–221.
Livesey, G., Williams, K. E., Knowles, S. E., & Ballard, F. J. (1980). Effects of weak bases on the degradation of endogenous and exogenous proteins by rat yolk sacs. Biochemical Journal, 188(3), 895–903.
Loftfield, R. B., Grover, J. W., & Stephenson, M. L. (1953). Possible role of proteolytic enzymes in protein synthesis. Nature, 171(4362), 1024–1025.
Maher, P. (1988). Prediction, accommodation, and the logic of discovery. Proceedings of the Biennial Meeting of the Philosophy of Science Association, 1988(1), 273–285.
Maher, P. (1993). Howson and Franklin on prediction. Philosophy of Science, 60(2), 329–340.
Marmur, J., & Lane, D. (1960). Strand separation and specific recombination in deoxyribonucleic acids: Biological studies. Proceedings of the National Academy of Sciences of the United States of America, 46(4), 453–461.
McIntyre, L. (2001). Accommodation, prediction, and confirmation. Perspectives on Science, 9(3), 308–323.
Menninger, J. R. (1964). A determination of the mass per length of DNA using X-ray diffraction. Ph.D. thesis, Harvard University. http://books.google.co.il/books?id=9kg8twAACAAJ.
Meselson, M., & Stahl, F. W. (1958). The replication of DNA in Escherichia coli. Proceedings of the National Academy of Sciences of the United States of America, 44(7), 671–682.
Mill, J. S. (1843). A system of logic, ratiocinative and inductive (8th ed., Vol. 2). New York: Harper & Brothers.
Monod, J., Pappenheimer, A. M., Jr., & Cohen-Bazire, G. (1952). The kinetics of the biosynthesis of beta-galactosidase in Escherichia coli as a function of growth. Biochimica et Biophysica Acta, 9(6), 648–660.
Musgrave, A. (1974). Logical versus historical theories of confirmation. The British Journal for the Philosophy of Science, 25(1), 1–23.
Naono, S., & Gros, F. (1960). Synthese par E. coli d’une phosphatase modifiee en presence d’une analogue pyrimidique. Comptes Rendus de l’Académie des Sciences (Paris), 250(6), 3889–3891.
Nirenberg, M. (1972). The genetic code. Nobel lecture. Amsterdam: Elsevier.
Nirenberg, M., Caskey, T., Marshall, R., Brimacombe, R., Kellogg, D., Doctor, B., et al. (1966). The RNA code and protein synthesis. Cold Spring Harbor Symposia on Quantitative Biology, 31, 11–24.
Nolan, D. (1997). Quantitative parsimony. The British Journal for the Philosophy of Science, 48(3), 329–343.
Nomura, M., Hall, B. D., & Spiegelman, S. (1960). Characterization of RNA synthesized in Escherichia coli after bacteriophage T2 infection. Journal of Molecular Biology, 2(5), 306–326.
Orczy, E. (2000). The Scarlet Pimpernel [Reissue edition]. New York: Signet.
Pardee, A. B., Jacob, F., & Monod, J. (1959). The genetic control and cytoplasmic expression of “Inducibility” in the synthesis of β-galactosidase by E. coli. Journal of Molecular Biology, 1(2), 165–178.
Poole, B., Ohkuma, S., & Warburton, M. J. (1977). The accumulation of weakly basic substances in lysosomes and the inhibition of intracellular protein degradation. Acda Biologica et Medica Germanica, 36(11–12), 1777–1788.
Popper, K. (1963). Conjectures and refutations. New York and London: Basic Books.
Ratner, S., Rittenberg, D., Keston, A. S., & Schoenheimer, R. (1940). Studies in protein metabolism XIV. The chemical interaction of dietary glycine and body proteins in rats. The Journal of Biological Chemistry, 134(2), 665–676.
Rheinberger, H. J. (1993). Experiment and orientation: Early systems of in vitro protein synthesis. Journal of the History of Biology, 26(3), 443–471.
Rheinberger, H. J. (1995). From microsomes to ribosomes: “strategies” of “representation”. Journal of the History of Biology, 28(1), 49–89.
Rheinberger, H. J. (1997). Toward a history of epistemic things: Synthesizing proteins in the test tube (Vol. 32). Stanford: Stanford University Press.
Rheinberger, H. J. (2006). A history of protein biosynthesis and ribosome research. In K. H. Nierhaus & D. Wilson (Eds.), Protein synthesis and ribosome structure: Translating the genome (pp. 1–51). Weinheim: Wiley-VCH Verlag.
Rheinberger, H. J. (2016). A brief history of protein biosynthesis and ribosome research. Paper presented at the Lindau Nobel Laureate Meetings, Lindau, Germany. http://hdl.handle.net/11858/00-001M-0000-002B-A873-F.
Rich, A. (1960). A hybrid helix containing both deoxyribose and ribose polynucleotides and its relation to the transfer of information between the nucleic acids. Proceedings of the National Academy of Sciences of the United States of America, 46(8), 1044–1053.
Rich, A., & Davies, D. R. (1956). A new two stranded helical structure: Polyadenylic acid and polyuridylic acid. Journal of the American Chemical Society, 78(14), 3548–3549.
Rich, A., & Watson, J. D. (1954a). Physical studies on ribonucleic acid. Nature, 173(4412), 995–996.
Rich, A., & Watson, J. D. (1954b). Some relations between DNA and RNA. Proceedings of the National Academy of Sciences of the United States of America, 40(8), 759–764.
Riley, M., Pardee, A. B., Jacob, F., & Monod, J. (1960). On the expression of a structural gene. Journal of Molecular Biology, 2(4), 216–225.
Rolfe, R. (1962). The molecular arrangement of the conserved subunits of DNA. Journal of Molecular Biology, 4(1), 22–30.
Scerri, E. R. (2005). Response to Barnes’s critique of Scerri and Worrall. Studies in History and Philosophy of Science Part A, 36(4), 813–816.
Scerri, E. R., & Worrall, J. (2001). Prediction and the periodic table. Studies in History and Philosophy of Science Part A, 32(3), 407–452.
Schimke, R. T., & Doyle, D. (1970). Control of enzyme levels in animal tissues. Annual Review of Biochemistry, 39(1), 929–976.
Schindler, S. (2014). Novelty, coherence, and Mendeleev’s periodic table. Studies in History and Philosophy of Science Part A, 45(Supplement C), 62–69.
Schoenheimer, R., Ratner, S., & Rittenberg, D. (1939). Studies in protein metabolism: X. The metabolic activity of body proteins investigated with l(-)-leucine containing two isotopes. The Journal of Biological Chemistry, 130(2), 703–732.
Segal, H. L., & Doyle, D. (1978). Introduction. Protein turnover and lysosome function (pp. 1–6). New York: Academic Press.
Segal, H. L., Winkler, J. R., & Miyagi, M. P. (1974). Relationship between degradation rates of proteins in vivo and their susceptibility to lysosomal proteases. The Journal of Biological Chemistry, 249(19), 6364–6365.
Siekevitz, P. (1952). Uptake of radioactive alanine in vitro into the proteins of rat liver fractions. The Journal of Biological Chemistry, 195(2), 549–565.
Siekevitz, P., & Zamecnik, P. C. (1951). In vitro incorporation of 1-C14-DL-alanine into proteins of rat liver granular fractions. Federation Proceedings, 10, 246–247.
Smart, J. J. C. (1984). Ockham’s razor. In J. H. Fetzer (Ed.), Principles of philosophical reasoning (pp. 118–218). Totowa, NJ: Rowman & Allanheld.
Sober, E. (2006). Parsimony. In J. Pfeifer & S. Sarkar (Eds.), The philosophy of science: An encyclopedia (Vol. 2, pp. 531–538). New York: Routledge.
Sober, E. (2015). Ockham’s razors: A user’s manual. Cambridge: Cambridge University Press.
Spirin, A. S. (1961). The “temperature effect” and macromolecular structure of high-polymer ribonucleic acids of various origin. Biokhimiia, 26, 454–463.
Stent, G. S., & Jerne, N. K. (1955). The distribution of parental phosphorus atoms among bacteriophage progeny. Proceedings of the National Academy of Sciences of the United States of America, 41(10), 704–709.
Taylor, J. H., Woods, P. S., & Hughes, W. L. (1957). The organization and duplication of chromosomes as revealed by autoradiographic studies using tritium-labeled thymidine. Proceedings of the National Academy of Sciences of the United States of America, 43(1), 122–128.
Tissieres, A., & Watson, J. D. (1958). Ribonucleoprotein particles from Escherichia coli. Nature, 182(4638), 778–780.
Ts’o, P. O. P., & Squires, R. (1959). Quatitative isolation of intact RNA from microsomal particles of pea seedlings and rabbit reticulocytes. Federation Proceedings, 18, 341.
Tsugita, A., & Fraenkel-Conrat, H. (1960). The amino acid composition and C-terminal sequence of a chemically evoked mutant of TMV. Proceedings of the National Academy of Sciences of the United States of America, 46(5), 636–642.
Volkin, E., & Astrachan, L. (1956). Phosphorus incorporation in Escherichia coli ribo-nucleic acid after infection with bacteriophage T2. Virology, 2(2), 149–161.
Volkin, E., & Astrachan, L. (1957). RNA metabolism in T2-infected Escherichia coli. In W. D. McElroy & B. Glass (Eds.), A symposium on the chemical basis of heredity (pp. 686–695). Baltimore, MD: The Johns Hopkins Press.
Volkin, E., Astrachan, L., & Countryman, J. L. (1958). Metabolism of RNA phosphorus in Escherichia coli infected with bacteriophage T7. Virology, 6(2), 545–555.
Watson, J. D. (1954). The structure of tobacco mosaic virus. I. X-ray evidence of a helical arrangement of sub-units around the longitudinal axis. Biochimica et Biophysica Acta, 13(1), 10–19.
Watson, J. D. (1964). The involvement of RNA in the synthesis of proteins. In Nobel Lectures (Ed.), Physiology or medicine 1942–1962 (pp. 785–808). Amsterdam: Elsevier Publishing Company.
Watson, J. D. (2001). Genes, girls, and gamow: After the double helix. New York: Vintage Books.
Watson, J. D. (2012). The annotated and illustrated double helix. New York: Simon & Schuster.
Watson, J. D., & Crick, F. H. (1953a). Genetical implications of the structure of deoxyribonucleic acid. Nature, 171(4361), 964–967.
Watson, J. D., & Crick, F. H. (1953b). Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature, 171(4356), 737–738.
Weber, M. (2009). The crux of crucial experiments: Duhem’s problems and inference to the best explanation. The British Journal for the Philosophy of Science, 60(1), 19–49.
Whewell, W. (1860). On the philosophy of discovery, chapters historical and critical. London: John W. Parker and Son.
White, R. (2003). The epistemic advantage of prediction over accommodation. Mind, 112(448), 653–683.
Wilkinson, K. D., Urban, M. K., & Haas, A. L. (1980). Ubiquitin is the ATP-dependent proteolysis factor I of rabbit reticulocytes. The Journal of Biological Chemistry, 255(16), 7529–7532.
Wittmann, H. G. (1960a). Comparison of the tryptic peptides of chemically induced and spontaneous mutants of tobacco mosaic virus. Virology, 12(4), 609–612.
Wittmann, H. G. (1960b). Comparison of the tryptic peptides of wild strains of tobacco mosaic virus. Virology, 12(4), 613–616.
Worrall, J. (2005). Prediction and the ‘periodic law’: A rejoinder to Barnes. Studies in History and Philosophy of Science Part A, 36(4), 817–826.
Worrall, J. (2014). Prediction and accommodation revisited. Studies in History and Philosophy of Science Part A, 45(Supplement C), 54–61.
Ycas, M., & Vincent, W. S. (1960). A ribonucleic acid fraction from yeast related in composition to desoxyribonucleic acid. Proceedings of the National Academy of Sciences of the United States of America, 46(6), 804–811.
Zahar, E. (1973). Why did Einstein’s programme supersede Lorentz’s? (II). The British Journal for the Philosophy of Science, 24(3), 223–262.
Zamecnik, P. C. (1979). Historical aspects of protein synthesis. Annals of the New York Academy of Sciences, 325(1), 269–302.
Zamecnik, P. C., & Keller, E. B. (1954). Relation between phosphate energy donors and incorporation of labeled amino acids into proteins. The Journal of Biological Chemistry, 209(1), 337–354.
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Fry, M. Predictive hypotheses are ineffectual in resolving complex biochemical systems. HPLS 40, 25 (2018). https://doi.org/10.1007/s40656-018-0192-3
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DOI: https://doi.org/10.1007/s40656-018-0192-3