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Methods and problems in biophysics

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La Rivista del Nuovo Cimento (1978-1999) Aims and scope

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Bibliography and Notes

  1. C. R. Woese:The Genetic Code (Harper and Row, New York, N.Y., 1967), Chapt. 2;M. Yčas:The Biological Code (North Holland, Amsterdam and London, 1969), Chapts. 2 and 3.

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  7. During the last few decades, the relationship between genes and characters has been the subject of a very lively controversy for and against the so-called biological determinism (more correctly, genetic determinism), an ideology that has been historically presented in subsequent times in various forms, but that one can characterize in general saying that, according to it, in the human species the genes completely determine the behaviour of the individual in the environment in which it lives, while the caracteristic of human society would be nothing but the result of the independent individual behaviours and of the tendencies and attitudes of the individual men who make up the society. The flexibility of the phenotypes is not denied, but the adaptation that results from them is still a single-valued function of the genes and of the environmental conditions. Because of this, the essentially deterministic character of this conception does not become attenuated. A systematic treatment of the various aspects of biological determinism, with a declared refutation intent, is offered from the volume:S. Rose, R. Lewontin andL. Kamin:Il gene e la sua mente (Mondadori, Milano, 1983). Which is, however, a wasted opportunity, inasmuch as it contrasts ideology with ideology, rather than demonstrating (which is very possible) the scientific groundlessness of biological determinism. Many of the theses that the authors defend are certainly correct, but surely not based on their arguments which risk, in fact, to convince many readers of the opposite opinion. In reality, the unpredictability of the genotype of any organism (also known that they are the genotypes of parents), the great flexibility of phenotypes and the absolute chance of single environmental events capable of exerting a permanent influence on the matter, usually assure a multiplicity of possible alternatives for internal processes, all compatible with the boundary conditions, and fully contradict biological determinism.

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  9. This is a system made up of three substances,A, B, C, in solution, each one of which can transform itself into the other two. Under irradiation with photons of such an energy as to be able to be absorbed only by substanceA, which thus transforms itself intoB, that in its turn retransforms itself intoA, either directly or by way ofC (losing the surplus energy in two stages), in the system a continuous flow of materials takes place that follows the cycleA→B→C→A.L. Onsager:Reciprocal relations in irreversible processes, I, Phys. Rev.,37, 405 (1931);Reciprocal relations in irreversible processes, II,38, 2265 (1931) For a discussion of the system, see:M. Ageno:Programmi di Biofisica (Boringhieri, Torino, 1979), pp. 26–29.M. Ageno:La Biofisica (Laterza, Roma-Bari, 1987), pp. 88–89.

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  10. The most known and studied of the so-called instabilities of hydrodynamics. For an elementary discussion of the system, see:M. Ageno:Lezioni di Biofisica, Vol. 1–3 (Zanichelli, Bologna, 1980), pp. 486–500.

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  13. The concepts of feedback or negative reaction, borrowed from the theory of servomechanisms, is extended here to the case of a chain of chemical reactions catalyzed by enzymes, whose final product is requested, for example, with an assigned concentration. If the final concentration is not the requested one, an error signal is generated that acts on the activity of the enzymatic system (including one or more allosteric enzymes), in such a way as to reduce the signal itself.

  14. The experimentally demonstrated fact that a large number of small mutations in a population are neutral or nearly neutral, that is they have no appreciable influence on the phenotype, and that therefore natural selection does not have any effect on the mutated organisms, suggested the so-called neutralistic theories of biological evolution, that were developed during the 1970s, especially by Kimura and Ohta. See:M. Kimura:The Neutral Theory of Molecular Evolution (Cambridge University Press, Cambridge and London, 1983). It seems now that such theories should not only be reinterpreted (inasmuch as the mutations that they deal with are not at all, usually, neutral, but neutralized in the majority of genotypes by the general control system at the biochemical level), but they should also be reformulated, in as much as the alleles in question, if conveniently associated with certain alleles of other genes, do not appear at all neutral with regard to natural selection.

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  15. For the current ideas on cell division, see:W. D. Donachie andA. C. Robinson:Cell division: parameter values and the process, in:F. C. Neidhardt (Editor): cited in note [23], pp. 1578–1593.

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  17. For the particular circuits making up the general control system of the cell, one can see the volumes of the collection:R. F. Goldberger (Editor):Biological Regulation and Development (Plenum Press, New York and London, 1979).

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  18. M. Ageno:La crescita batterica.—I:La legge di crescita della numerosità batterica, inRend. Accad. Naz. Lincei,82, 371–376 (1988).M. Ageno:La crescita batterica.—II:Il processo di desincronizzazione di una coltura, inRend. Accad. Naz. Lincei,82, 595–602 (1988).

  19. One of the first unfortunate attempts in such a sense was that of Goodwin. See:B. C. Goodwin:Temporal Organization in Cells (Academic Press, London and New York, 1963)B. C. Goodwin:Analytical Physiology of Cells and Developing Organisms (Academic Press, London, 1976).

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  20. For a mechanico-statistical theory of the hourglass, see together:B. Touschek andG. Rossi:Meccanica Statistica (Boringhieri, Torino, 1970), pp. 210–214.M. Ageno:Le origine della irreversibilità macroscopica, in private distribution, § 2.6.

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  21. J. D. Watson et al.: cited in note [5]. pp. 341–342.

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  22. M. Ageno:La macchina batterica, being printed.

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  24. This is rather long series of published notes, or notes in the process of being published, inRend. Accad. Naz. Lincei, from 1986 onward. For a general presentation, critically organized, of the results, see the volume «La macchina batterica», cited in note [22].

  25. M. Ageno:La crescita batterica.—III:La legge di crescita del batterio singolo, inRend. Accad. Naz. Lincei (1989). In press.M. Ageno:La crescita batterica.—IV:La legge di crescita del materiale biologico di una coltura, inRend. Accad. Naz. Lincei (1989). In press.

  26. M. Ageno, A. Battistini, E. Liberati andA. M. F. Valli:Verifiche sperimentali della teoria della crescita batterica.—I, inRend. Fis. Accad. Lincei, (9) 1, 63 (1990).

  27. The concept of balanced growth was introduced by Campbell in 1957. Revived by Maaløe. and Kjeldgaard, it has today become part of the currently accepted paradigm.A. Campbell:Synchronization of cell division, inBacteriol. Rev.,21, 263 (1957).O. Maaløe andN. O. Kjeldgaard:Control of Macromolecular Synthesis (Benjamin, New York and Amsterdam, 1966), pp. 63–64.L. J. Ingraham, O. Maaløe andF. C. Neidhardt:Growth of the Bacterial Cell (Sinauer, Sunderland, Mass., 1983), p. 5. and p. 268.

  28. B. A. Haddock andC. W. Jones:Bacterial respiration, inBacteriol. Rev.,41, 47 (1977).J. L. Ingraham et al.: cited in note [27],Growth of the Bacterial Cell (Sinauer, Sunderland, Mass., 1983), p. 5 and p. 268. p. 147.

  29. The datum is drawn from the comparison of the values of bacterial numerosity at saturation after totally aerobic growth, and the mass of carbon incorporated on the average per bacterium gotten from the literature. See:J. L. Ingraham et al.: cited in note [27], p. 2.

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  32. A. I. Oparin:Proishoždenie Žizni (The origin of Life) (Izatel’stvo Moskovkij rabocij, Moscow, 1924). The model of a protocell, as a small drop of coacervate, is developed in the successive editions of the book. Editons that become less and less interesting, being more and more inflationed with randomly collected materials, and that in the end are nothing but mediocre popularized compilations. See especially the English translation of the second edition (1936):A. I. Oparin:The Origin of the Life (MacMillan, New York, N.Y., 1938; reprinted: Dover, New York, N.Y., 1959).

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  33. The list of paper by S. Fox and coworkers on the microspheres as a model of protocells, and their presumed properties, is endless. See for the essential information:S. W. Fox andK. Dose:Molecular Evolution and the Origin of Life, rev. ed. (Dekker, New York and Basel, 1977).

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  42. The idea of a prebiotic broth is already present in the first papers on the origin of life by Oparin (1924) and by Haldane (1929). See Appendix 1 of the volume:J. D. Bernal:The Origin of Life (Weidenfeld and Nicolson, London, 1967). Which includes the English translation of Oparin’s little book (see note [32]) and the reprint of the famous article by Haldane in «The Rationalist Annual».

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  66. After that the solar wind, at the moment of the ignition of the Sun, dispersed the rest of the primordial nebula, with the fall to the surface of the Earth of the last planetesimals, ammonia and methane were surely brought to the Earth and vaporizing they contribued, together with the gases emitted by the volcanoes, to the formation of a new atmosphere. However, the solar ultraviolet radiation must have rapidly decomposed the ammonia and produced the polymerization of methane, with the formation of various organic compounds, depositing on the surface of the planet.

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  91. We allude in particular toF. Hoyle andN. C. Wickramasinge:Disease from Space (Dent, London, 1979).

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  92. The innovative ideas of Oparin did not in reality just spring from nothing. Between the end (around 1875) of the polemic on spontaneous generation and the issue in 1924 of Oparin’s little book, there appeared a whole series of papers, for the most part in Russian and German, in which the idea of a spontaneous generation, not instantaneous but the final outcome of a long evolutionary process, is often at least hinted at. For a reconstruction of this particular episode of the history of science, such papers, today forgetten by the historians, should be re-examined and compared to Oparin’s booklet.

  93. The scientific contribution of Haldane was that of having launched the idea of a resemblance between those that must have been the first entities capable of reproducing themselves to have appeared on the Earth, and a viral particle, that the American εneticist Muller had already compared with a free gene. A really surprising idea (even in its evident fortuity), if one notices the year in which it was proposed: 1929.

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  96. A vast comprehensive volume on the state of our knowledge of the primitive biosphere is:J. W. Schon (Editor):Earth’s Earliest Biosphere: Its Origin and Evolution (Princeton University Press, Princeton, N.J., 1983). See in particular chap. 4: «Prebiotic organic syntheses and the origin of life».

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Translated from the Italian by Jean M. Scanlan.

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Ageno, M. Methods and problems in biophysics. Riv. Nuovo Cim. 14, 1–71 (1991). https://doi.org/10.1007/BF02810146

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