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Fry M. Ontologically simple theories do not indicate the true nature of complex biological systems: three test cases. HISTORY AND PHILOSOPHY OF THE LIFE SCIENCES 2020; 42:17. [PMID: 32346811 DOI: 10.1007/s40656-020-00310-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 04/13/2020] [Indexed: 06/11/2023]
Abstract
A longstanding philosophical premise perceives simplicity as a desirable attribute of scientific theories. One of several raised justifications for this notion is that simple theories are more likely to indicate the true makeup of natural systems. Qualitatively parsimonious hypotheses and theories keep to a minimum the number of different postulated entities within a system. Formulation of such ontologically simple working hypotheses proved to be useful in the experimental probing of narrowly defined bio systems. It is less certain, however, whether qualitatively parsimonious theories are effective indicators of the true nature of complex biological systems. This paper assesses the success of ontologically simple theories in envisaging the makeup of three complex systems in bacteriology, immunology, and molecular biology. Evidence shows that parsimonious theories completely misconstrued the actual ontologically complex constitutions of the three examined systems. Since evolution and selective pressures typically produce ontologically intricate rather than simple bio systems, qualitatively parsimonious theories are mostly inapt indicators of the true nature of complex biological systems.
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Affiliation(s)
- Michael Fry
- Department of Biochemistry, Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, POB 9649, 31096, Bat Galim, Haifa, Israel.
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Bogdanovic J, Colon J, Baker C, Huo Q. A label-free nanoparticle aggregation assay for protein complex/aggregate detection and study. Anal Biochem 2010; 405:96-102. [DOI: 10.1016/j.ab.2010.06.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2010] [Revised: 06/03/2010] [Accepted: 06/03/2010] [Indexed: 11/26/2022]
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Heidelberger M, Kendall FE. THE PRECIPITIN REACTION BETWEEN TYPE III PNEUMOCOCCUS POLYSACCHARIDE AND HOMOLOGOUS ANTIBODY : III. A QUANTITATIVE STUDY AND A THEORY OF THE REACTION MECHANISM. ACTA ACUST UNITED AC 2010; 61:563-91. [PMID: 19870380 PMCID: PMC2133233 DOI: 10.1084/jem.61.4.563] [Citation(s) in RCA: 183] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
The precipitin reaction between the specific polysaccharide of Type III pneumococcus and homologous antibody formed in the horse can be accounted for quantitatively by assuming the chemical combination of the components in a bimolecular reaction, followed by a series of competing bimolecular reactions which depend upon the relative proportions of the components. These reactions would lead to the formation of larger and larger aggregates until precipitation ultimately occurred. The mathematical formulation of this theory on the basis of the mass law is described. The derived expressions are shown to be in accord with the experimental findings and the constants used in these expressions are shown to have definite significance. In spite of the wide variation in the properties of individual sera these expressions permit the complete description of the behavior of an unknown serum with S III without an unduly burdensome number of analyses. The quantitative theory presented has been found applicable to other instances of the precipitin reaction, as will be shown in subsequent papers.
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Affiliation(s)
- M Heidelberger
- Department of Medicine, College of Physicians and Surgeons, Columbia University, and the Presbyterian Hospital, New York
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Boyd WC, Hooker SB. THE INFLUENCE OF THE MOLECULAR WEIGHT ANTIGEN ON THE PROPORTION OF ANTIBODY TO ANTIGEN IN PRECIPITATES. ACTA ACUST UNITED AC 2010; 17:341-8. [PMID: 19872783 PMCID: PMC2141298 DOI: 10.1085/jgp.17.3.341] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The assumption that, at the equivalence point in specific precipitin reactions, the antigen molecule is completely covered with a single layer of antibody-globulin molecules has been shown to account fairly well for the antibody-antigen ratios of some representative native single proteins, and the pneumococcus S III hapten.
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Affiliation(s)
- W C Boyd
- Evans Memorial, Massachusetts Memorial Hospitals, Boston
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Smithburn KC, Sabin FR. THE CELLULAR REACTIONS TO LIPOID FRACTIONS FROM ACID-FAST BACILLI. ACTA ACUST UNITED AC 2010; 56:867-91. [PMID: 19870109 PMCID: PMC2132207 DOI: 10.1084/jem.56.6.867] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
1. A comparative study has been made of the cellular reactions induced by phosphatides from five strains of acid-fast bacilli. Each of these reactions is characterized principally by epithelioid cells and giant cells. 2. The phosphatides are first phagocytized by young connective tissue cells or monocytes. The lipoid is then dispersed into fine particles with the formation of classical epithelioid cells. 3. A comparison has been made of the reactions induced by heat-killed and defatted tubercle bacilli with those induced by tuberculophosphatide. 4. Further studies have been made to determine whether or not the phosphatide causes sensitization to tuberculin. It does not do so. 5. The life cycle of the epithelioid cell has been observed in all its stages.
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Affiliation(s)
- K C Smithburn
- Laboratories of The Rockefeller Institute for Medical Research
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Malkiel S, Boyd WC. THE COMPOSITION OF SPECIFIC PRECIPITATES IN THE REGION OF ANTIGEN EXCESS. ACTA ACUST UNITED AC 2010; 66:383-96. [PMID: 19870670 PMCID: PMC2133613 DOI: 10.1084/jem.66.3.383] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Data are given, for seven different antisera, for the composition of the specific precipitate as a function of the relative proportions of antiserum and antigen used. In the region of antigen excess, a linear relation is found between the ratio of antibody to antigen in the precipitate and the amount of antiserum used. The significance of these results, particularly in their bearing on theories of the precipitin reaction, is discussed.
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Affiliation(s)
- S Malkiel
- Boston University School of Medicine, and Evans Memorial, Massachusetts Memorial Hospitals, Boston
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Smith F, Rous P. THE GRADIENT OF VASCULAR PERMEABILITY : IV. THE PERMEABILITY OF THE CUTANEOUS VENULES AND ITS FUNCTIONAL SIGNIFICANCE. ACTA ACUST UNITED AC 2010; 54:499-514. [PMID: 19869936 PMCID: PMC2132026 DOI: 10.1084/jem.54.4.499] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
The permeability of the venules of the skin of the mouse greatly exceeds that of the capillaries. A mounting gradient of permeability exists along the further portion of the latter. The significance of these facts is discussed with relation to conditions in human skin. The cutaneous venules are differentiated for several functions besides those ordinarily attributed to them, and must be considered as specialized organs.
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Affiliation(s)
- F Smith
- Laboratories of The Rockefeller Institute for Medical Research
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Heidelberger M, Kendall FE. QUANTITATIVE STUDIES ON THE PRECIPITIN REACTION : THE ROLE OF MULTIPLE REACTIVE GROUPS IN ANTIGEN-ANTIBODY UNION AS ILLUSTRATED BY AN INSTANCE OF CROSS-PRECIPITATION. ACTA ACUST UNITED AC 2010; 59:519-28. [PMID: 19870263 PMCID: PMC2132333 DOI: 10.1084/jem.59.4.519] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
1. Antisera to R-salt-azo-benzidine-azo-crystalline egg albumin give precipitates with crystalline egg albumin by virtue of their antidye content. 2. The quantitative course of the reactions with increasing amounts of antigen is very similar for the dye-antidye and egg albumin-anti-egg albumin systems, but differs markedly for the cross reaction between egg albumin and antidye. 3. A possible explanation for the occurrence of this one-sided crossreaction is given in terms of reactive groupings on the antigen and antibody. 4. A qualitative expression of the course of the cross-reaction is given in terms of the laws of classical chemistry.
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Affiliation(s)
- M Heidelberger
- Department of Medicine, College of Physicians and Surgeons, Columbia University, and the Presbyterian Hospital, New York
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Heidelberger M, Kendall FE. A QUANTITATIVE THEORY OF THE PRECIPITIN REACTION : II. A STUDY OF AN AZOPROTEIN-ANTIBODY SYSTEM. ACTA ACUST UNITED AC 2010; 62:467-83. [PMID: 19870428 PMCID: PMC2133297 DOI: 10.1084/jem.62.4.467] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
1. A quantitative theory of the precipitin reaction based on the laws of classical chemistry has been tested on an azoprotein-antiprotein system and found to apply. 2. With its aid relationships may be deduced which permit the calculation of the behavior of an antidye serum over its entire range after a few quantitative chemical analyses have been made for antigen and antibody in the precipitate. 3. An empirical relation is also presented which further reduces the number of analyses necessary. 4. A study of supernatants in the inhibition zone has shown that the entire amount of dissolved antigen-antibody compound present is precipitated when supernatants are analyzed for antigen by the precipitin method.
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Affiliation(s)
- M Heidelberger
- Department of Medicine, College of Physicians and Surgeons, Columbia University, and the Presbyterian Hospital, New York
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Heidelberger M, Kendall FE. QUANTITATIVE STUDIES ON THE PRECIPITIN REACTION : THE DETERMINATION OF SMALL AMOUNTS OF A SPECIFIC POLYSACCHARIDE. ACTA ACUST UNITED AC 2010; 55:555-61. [PMID: 19870012 PMCID: PMC2132119 DOI: 10.1084/jem.55.4.555] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
A method, based on the precipitin reaction, is given for the micro determination of the specific polysaccharide of Type III pneumococcus. As little as 0.01 mg. of S III can be determined. The method should be applicable to any specific polysaccharide upon standardization of an homologous antibody solution or antiserum in the region of excess antibody.
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Affiliation(s)
- M Heidelberger
- Department of Medicine, Presbyterian Hospital, and the College of Physicians and Surgeons, Columbia University, New York
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Sabin FR. CELLULAR REACTIONS TO A DYE-PROTEIN WITH A CONCEPT OF THE MECHANISM OF ANTIBODY FORMATION. ACTA ACUST UNITED AC 2010; 70:67-82. [PMID: 19870891 PMCID: PMC2133783 DOI: 10.1084/jem.70.1.67] [Citation(s) in RCA: 141] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
1. The use of an antigen which can be seen within cells demonstrates that one may stimulate the phagocytic cells either of the liver and spleen or of the tissues and lymph nodes to produce antibodies. 2. The appearance of antibodies in the serum correlates with the time when the dye-protein is no longer visible within the cells and with the phenomenon of a partial shedding of their surface films. 3. It is thus inferred that the cells of the reticulo-endothelial system normally produce globulin and that antibody globulin represents the synthesis of a new kind of protein under the influence of an antigen. 4. An antigen is a substance which can specifically modify the synthesis of the cytoplasm of the cells of the reticulo-endothelial system.
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Affiliation(s)
- F R Sabin
- Laboratories of The Rockefeller Institute for Medical Research
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Heidelberger M, Kendall FE, Soo Hoo CM. QUANTITATIVE STUDIES ON THE PRECIPITIN REACTION : ANTIBODY PRODUCTION IN RABBITS INJECTED WITH AN AZO PROTEIN. ACTA ACUST UNITED AC 2010; 58:137-52. [PMID: 19870185 PMCID: PMC2132290 DOI: 10.1084/jem.58.2.137] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
1. The preparation is described of a deep red protein dye, R-salt-azo-benzidine-azo-crystalline egg albumen, which contains no more than traces of protein with the original egg albumen specificity. 2. Based on previous publications of the writers, a quantitative method is given for the micro estimation of precipitin in the antisera to the dye. The method gives the actual weight of precipitin and may be applied to the determination of the maximum amount of precipitable antibody in any antiserum. 3. Data are given (1) on the influence of the period between the final injection and the bleeding on the precipitin content of rabbit antisera to the azo protein; (2) on the magnitude of the antibody response following the injection of multiple doses of the antigen varying within wide limits; (3) on the variations in the precipitin content of the sera of rabbits given successive courses of antigen injections; and (4) on the stability of antisera stored in the cold. 4. Four antisera were obtained in which over 100 times as much precipitin was recovered as the amount of antigen injected. This supplements the growing mass of evidence against the theory that specific antigen fragments are actually incorporated into the antibody molecule.
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Affiliation(s)
- M Heidelberger
- Department of Medicine, College of Physicians and Surgeons, Columbia University, and the Presbyterian Hospital, New York
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Rothbard S. BACTERIOSTATIC EFFECT OF HUMAN SERA ON GROUP A STREPTOCOCCI : III. INTERFERENCE WITH BACTERIOSTATIC ACTIVITY BY BLOCKAGE OF THE LEUKOCYTES. ACTA ACUST UNITED AC 2010; 82:119-32. [PMID: 19871487 PMCID: PMC2135544 DOI: 10.1084/jem.82.2.119] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
1. Type-specific M extracts and group-specific C carbohydrate of group A streptococci inhibited bacteriostasis of these microorganisms in the presence of normal whole blood and of sera from patients convalescent from streptococcal infections. The inhibition was not specific with respect to streptococcal types and depended merely on the formation of precipitates in the system. The extracts had no antagonistic action in themselves. 2. Preformed precipitates derived from the interaction of an antigen and its homologous antibody or from finely divided coagulated particles of human plasma or ascitic fluid also interfered with the bacteriostasis. The supernatant fluid in which one of these precipitates was formed did not inhibit bacteriostatic activity; therefore, it seems that other possible products of the antigen-antibody reaction were not inhibitory. The relative size of the precipitate particles was a conditioning factor since small particles of one precipitate inhibited bacteriostasis, but large ones of the same precipitate failed to do so. 3. Stained films of blood cells treated with antigen-antibody mixtures which formed a precipitate revealed large cytoplasmic vacuoles containing precipitates in the polymorphonuclear leukocytes and monocytes; such engorged cells subsequently failed to phagocytize streptococci in homologous serum. Blood cells treated in the same manner, except that the antigen-antibody mixtures formed no precipitate, contained no vacuoles, and these cells were able to phagocytize the streptococci. 4. Leukocytes studied in the living state in the presence of colored precipitate and streptococci sensitized by convalescent human serum showed unselective phagocytosis of both precipitate and bacteria. The capacity of these leukocytes to ingest material however was limited. 5. As a result of non-selective saturation of their phagocytic capacity in the bacteriostatic systems containing both streptococci and precipitate, the limited number of leukocytes phagocytized only a fraction of the streptococci; consequently the remainder were able to multiply.
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Affiliation(s)
- S Rothbard
- Hospital of The Rockefeller Institute for Medical Research
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Liu X, Huo Q. A washing-free and amplification-free one-step homogeneous assay for protein detection using gold nanoparticle probes and dynamic light scattering. J Immunol Methods 2009; 349:38-44. [DOI: 10.1016/j.jim.2009.07.015] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2009] [Revised: 07/23/2009] [Accepted: 07/28/2009] [Indexed: 12/15/2022]
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KRUSE H, McMASTER PD. The distribution and storage of blue antigenic azoproteins in the tissues of mice. ACTA ACUST UNITED AC 2007; 90:425-46. [PMID: 18143587 PMCID: PMC2135922 DOI: 10.1084/jem.90.5.425] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Intensely blue dye-azoproteins have been prepared by diazotization and coupling of the highly indiffusible blue dye T-1824, Evans blue, with various serum proteins and egg albumin. The products, whether purified by precipitation with alcohol or by chromatography, have a constant dye-to-protein ratio and tests have shown them to be essentially free from unlinked dye. An extremely diffusible dye, echt-säure-blau, has also been coupled to bovine gamma-globulin. These materials are adapted to physiological experimentation. They seem to behave in the bodies of mice like other proteins; they fail to appear in either the bile or urine of normal animals, and they are strongly antigenic. When these soluble antigenic azoproteins are injected into the blood stream of mice for the first time they enter reticulo-endothelial cells in almost every organ of the body; the final distribution is like that of intravenously injected, finely divided particulate matter. The azoproteins appear in the cells which classical immunological studies have shown to be active in removing particulate antigenic materials or bacteria from the blood or body fluids. The Kupffer cells of the liver and sinus and reticular cells in lymph nodes, especially the great mesenteric node, are particularly active in the removal of the blue antigens from the blood, but many other R-E cells are active to a lesser degree. The storage of the antigenic material is in the cytoplasm only; it has not been seen within nuclei, nor has it been seen within cells of the brain. Serological methods disclose that the blue material seen within Kupffer cells of the liver after as long a period as 2 days is still antigenic in its reactions. The blue azoproteins, therefore, serve excellently as tracer antigens, especially since they can be seen directly in fresh and fixed tissue preparations and in the body fluids.
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Heidelberger M. QUANTITATIVE ABSOLUTE METHODS IN THE STUDY OF ANTIGEN-ANTIBODY REACTIONS. BACTERIOLOGICAL REVIEWS 2006; 3:49-95. [PMID: 16350055 PMCID: PMC440832 DOI: 10.1128/br.3.1.49-95.1939] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- M Heidelberger
- Department of Medicine, College of Physicians and Surgeons, Columbia University, New York City
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BOURSNELL* JC, DEWEY HM, FRANCIS GE, WORMALL A. Use of Radioactive Isotopes in Immunological Investigations. Nature 1947; 160:339. [DOI: 10.1038/160339a0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Sur la Production d'Anticorps au Moyen d'Un Antigène Enrobé dans la Lanoline-Vaseline. Antonie van Leeuwenhoek 1943. [DOI: 10.1007/bf02293059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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