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Ontologically simple theories do not indicate the true nature of complex biological systems: three test cases

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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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Notes

  1. Carroll, Sean. “The physicist who made sense of the universe” (obituary to Murray Gell-Mann). New York Times, May 28, 2019 https://www.nytimes.com/2019/05/28/opinion/gell-mann-physics.html?searchResultPosition=2.

  2. This strategy was gainfully used in experiments that led to discoveries of many individual components of biomolecular machineries such as the ubiquitin–proteasome protein breakdown system, various signal transduction pathways, or the protein biosynthesis machinery.

  3. The term "bacterium", meaning “cane” in Latinized Greek, was coined by Christian Gottfried Ehrenberg in 1828, more than 150 years after Leeuwenhoek’s original observations. The bacterium that Ehrenberg described was a rod-like non-spore-forming microorganism.

  4. English translation: (Lagerkvist 2003, pp. 63–64).

  5. English translation: (Bergstrand 1920, p. 22).

  6. Bizio’s letter ‘to the most eminent priest, Angelo Bellani concerning the phenomenon of the red-colored polenta’. Translation into English by (Merlino 1924).

  7. English translation: (Brock 1999, pp. 210–215).

  8. English translation: (Bary 1887a, p. 473).

  9. English translation: (Carter 1987, p. 84).

  10. Attendance was restricted, however, to males only as was documented in an unsigned Lancet editorial (Anon 1881, p. 290): “Early in the course of the arrangements made for the recent meeting the Executive Committee decided to limit the invitations to be present to men only. It has been reported by some of our lay contemporaries that this decision was not that of the majority of the Committee, who "were over-ruled by Sir WILLIAM JENNER, who declared that he was empowered to remove the name of the QUEEN as patron of the Congress if lady doctors were admitted to the medical meetings." We have-the highest authority for stating that this report is entirely and totally without foundation, that no such statement was ever made by Sir WILLIAM JENNER, and that the decision arrived at was the deliberate conviction of the large majority of the Committee. We regret to see that this wise resolve has been protested against " by forty-three duly qualified medical women." It is well to bear in mind that the Congress is a voluntary assemblage of medical men for a certain purpose, and that those who are not asked to join suffer no infringement of their rights.”

  11. English translation and commentary by Thomas D. Brock: https://lib.guides.umbc.edu/ld.php?content_id=46751829.

  12. Within just 7 years after Koch isolated Mycobacterium tuberculosis, investigators identified the glanders causing Burkholderia mallei (Löffler and Schütz, 1882); Vibrio cholera, (Koch, 1884); Corynebacterium diphtheria, (Löffler, 1884); typhoid fever causing Salmonella, (Gaffky, 1884); Streptococcus and Staphylococcus from infected wounds, (Rosenbach, 1884); Neisseria gonorrhea, (Bumm, 1885; Neisser, 1879; Sinclair, 1888); Escherichia coli, (Escherich, 1885); Streptococcus pneumonia (pneumococcus), (Fränkel, 1884, 1886); Malta fever causing Brucella, (Bruce, 1887); Meningitis causing Neisseria meningitides, (Meningococcus) (Weichselbaum, 1887); plague causing Yersinia pestis, (Kitasato, 1894) and tetanus causing Clostridium tetani, (Kitasato, 1889). This string of discoveries of new bacterial species continued into the early twentieth century.

  13. This obvious collision between syntactic and ontological simplicities in competing theories on one system is indicative of the paradoxically complex nature of the very concept of simplicity itself. Discussion of this point is beyond the scope of this paper.

  14. The Ava Helen and Linus Pauling Papers Archive: http://scarc.library.oregonstate.edu/coll/pauling/proteins/narrative/page20.html.

  15. The Ava Helen and Linus Pauling Papers Archive: http://scarc.library.oregonstate.edu/coll/pauling/proteins/notes/sci14.038.9-ts-19410318.html.

  16. Online immunology system databases are listed in: https://omictools.com/immunology-databases-category.

  17. See for instance databases of immune epitopes (Sathiamurthy et al. 2005): http://www.iedb.org/home_v3.php; of haptens and anti-hapten antibodies (Singh et al. 2006): http://crdd.osdd.net/raghava/haptendb/; and gene ontology annotations, (Diehl et al. 2007; Lovering et al. 2008) of genes involved in humoral immune response: http://www.informatics.jax.org/go/term/GO:0006959 and in abnormal humoral immune response: https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=MP:0001800.

  18. Facsimile of Gamow’s July 8, 1953 letter to Watson and Crick, under “Gamow memorabilia” in Watson (2001).

  19. Autograph of the October 22, 1953 letter in the Oregon State University Linus Pauling Online Archive: http://scarc.library.oregonstate.edu/coll/pauling/dna/corr/sci9.001.43-gamow-lp-19531022.html.

  20. Facsimile of the handwritten manuscript is at the Wellcome Library Web site: https://wellcomelibrary.org/item/b18186300 and a typewritten version is in the NIH ‘Profiles in Science’ online archive: https://profiles.nlm.nih.gov/spotlight/sc/catalog/nlm:nlmuid-101584582X73-doc.

  21. Gamow’s assembled a virtual think tank of leading biologists, physicists and mathematicians who searched for solutions to the coding and translation problem (Fry 2016b, pp. 288–289).

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    Michael Fry

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Fry, M. Ontologically simple theories do not indicate the true nature of complex biological systems: three test cases. HPLS 42, 17 (2020). https://doi.org/10.1007/s40656-020-00310-5

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