Through the comparison between two major, long-lasting theoretical frameworks – geocentrism and genocentrism – we discuss the different epistemological role played by metaphors in physics and biology. Throughout its history, physics developed theories and mathematical formalisms, which either do not seem to rely on metaphors at all (as geocentrism) or have absorbed initial thrusting metaphors into original theoretical frameworks. When considering genocentrism, in turn, the situation looks different. For some authors, genocentric theories are not metaphorical, but for opposite reasons with respect to geocentrism: pivotal concepts of information theories are straightforwardly imported as theoretical ones into biology. For others, the reference to information in genocentrism is indeed metaphorical, although the similarities and dissimilarities are not spelt out. Some problematic consequences of the application of genocentrism to biology are discussed.
AcetoL., LongoG., and VictorB., eds. 2003. “The Difference between Concurrent and Sequential Computations. ” In Special Issue, Mathematical Structures in Computer Science , vol.
13, 4–5. Cambridge: Cambridge University Press.
2.
AdlemanL. M.1994. “Molecular Computation of Solutions to Combinatorial Problems. ” Science 266 (5187): 1021–1024.
3.
AspectA., GrangierP., and RogerG.. 1982. “New York. Experimental Realization of the Einstein-Podolsky-Rosen-Bohm Gedanken experiment: A New Violation of Bell's Inequalities. ” Physical Review Letters 49: 91–94.
4.
AudétatM., ed. 2015. Sciences et technologies émergentes: Pourquoi tant de promesses? Paris: Hermann.
5.
AyduzS., KalinI., and DagliC.. 2014. The Oxford Encyclopedia of Philosophy, Science, and Technology in Islam . Oxford: Oxford University Press. p. 64. ISBN 9780199812578.
6.
BakerS.2014. “Recognizing Paradigm Instability in Theories of Carcinogenesis. ” British Journal of Medicine and Medical Research 4 (5): 1149–1163.
7.
BaillyF., and LongoG.. 2011. Mathematics and the Natural Sciences: The Physical Singularity of Life . London: Imperial College Press.
8.
BarabasiA., and OltvaiZ. N.. 2004. “Network Biology: Understanding the Cells’ Functional Organization. ” Nature Reviews Genetics 5 (2): 101–113.
9.
BarendregtH.1984. The Lambda-Calculus: Its Syntax, Its Semantics . Amsterdam: North-Holland.
10.
BernardC.
((1865) 1984. Introduction à l’étude de la médecine expérimentale . Paris: Baillière.
11.
BezemM., KlopJ. W., and Roelde VrijerR.. 2013. Term Rewriting Systems . Cambridge MA: Cambridge University Press.
12.
BraviB., and LongoG.. 2015. “The Unconventionality of Nature: Biology, from Noise to Functional Randomness. ” In Unconventional Computation and Natural Computation , edited by CaludeDinneen, 3–34. Cham: Springer LNCS 9252.
13.
BrettD., PospisilH., ValcárcelJ., ReichL., and BorkP.. 2001. “Alternative Splicing and Genome Complexity. ” Nature Genetics 30: 29–30.
14.
BuiattiM., and LongoG.. 2013. “Randomness and Multi-level Interactions in Biology. ” Theory in Biosciences 132 (3): 139–158.
15.
CaludeC.2002. Information and Randomness . Berlin: Springer-Verlag.
16.
CaludeC., and LongoG.. 2016. “Classical, Quantum and Biological Randomness as Relative Unpredictability. ” Special Issue of Natural Computing 15 (2): 263–278.
17.
CardelliL., and ShihW.. 2011. “
A Programming Language for Composable DNA Circuits . ”
Proceedings of the 17th International Conference, DNA 17, Pasadena, CA, USA.
18.
CardelliL., KwiatkowskaM., and LaurentiL.. 2016. “Stochastic Analysis of Chemical Reaction Networks Using Linear Noise Approximation. ” Biosystems 149: 26–33.
19.
ChaitinG.2012. Proving Darwin: Making Biology Mathematical . New York: Pantheon.
20.
ChibbaroS., RondoniL., and VulpianiA.. 2015. Reductionism, Emergence and Levels of Reality: The Importance of Being Borderline . Berlin: Springer.
21.
CortiniR., BarbiM., CaréB., LavelleC., LesneA., MozziconacciJ., and VictorJ. M.. 2016. “The Physics of Epigenetics. ” Reviews of Modern Physics 88: 025002.
22.
CrickF. H.1958. “On Protein Synthesis. ” Symposia of the Society for Experimental Biology 12: 138–163. PMID 1358086.
23.
DanchinA.2003. The Delphic Boat. What Genomes Tell Us . Cambridge: Harvard University Press.
24.
DanchinA.2009. “Bacteria as Computers Making Computers. ” Microbiology Review 33: 3–26.
25.
DanosV.2009. “Agile Modelling of Cellular Signalling. ” Electronic Notes in Theoretical Computer Science 229: 3–10.
26.
DarwinC.1859. On the Origin of Species . London: John Murray.
27.
DawkinsR.1986. The Blind Watchmaker . London: Longmans.
28.
DevaneyR. L.1989. An Introduction to Chaotic Dynamical Systems . Redwood: Addison-Wesley.
29.
DurrantA.1962. “The Environmental Induction of Heritable Change in Linum. ” Heredity 17 (1): 27–61.
30.
ElowitzM. B., LevineA. J., SiggiaE., and SwainP. S.. 2002. “Stochastic Gene Expression in a Single Cell. ” Science 297: 1183–6.
31.
FromionV., LeonciniE., and RobertP.. 2013. “Stochastic Gene Expression in Cells: A Point Process Approach. ” SIAM Journal on Applied Mathematics 73 (1): 195–211.
32.
GatenbyR. A.2017. “Is the Genetic Paradigm of Cancer Complete?
” Radiology 284: 1–3.
33.
GilbertW.1992. “A Vision of the Grail. ” In The Code of Codes: Scientific and Social Issues in the Human Genome Project , edited by KevlesDaniel J., and LeroyE., 83–97. Cambridge: Harvard U.P.
34.
GilbertS. F., and SarkarS.. 2000. “Embracing Complexity: Organicism for the 21st Century. ” Developmental Dynamics 219 (1): 1–9.
35.
GiulianiA.2010. “Collective Motions and Specific Effectors: A Statistical Mechanics Perspective on Biological Regulation. ” BMC Genomics 11 (suppl 1): S2.
GouldS. J.2002. The Structure of Evolutionary Theory . Cambridge, MA: Harvard University Press.
38.
GouyonP. H., HenryJ. P., and ArnoudJ.. 2002. Gene Avatars, the Neo-Darwinian Theory of Evolution . New York: Kluwer.
39.
HamiltonW. R.1833. On a General Method in Dynamics . Dublin: Trinity College.
40.
HeardE.2016. Epigénétique et mémoire cellulaire. Léçons inaugurales au Collège de France . Paris: Fayard.
41.
JacobF.1973. The Logic of Life . New York: Pantheon Books.
42.
JacobF.1974. “Le modèle linguistique en biologie. ” Critique XXX: 197–205.
43.
JacobF., and MonodJ.. 1961. “Genetic Regulatory Mechanisms in the Synthesis of Proteins. ” Journal of Molecular Biology 3: 318–356.
44.
KauffmanS.1969. “Metabolic Stability and Epigenesis in Randomly Constructed Genetic Nets. ” Journal of Theoretical Biology 22 (3): 437–467.
45.
KauffmanS.2000. Investigations . Oxford: Oxford University Press.
46.
KellerE. F.2000. “Decoding the Genetic Program: Or, Some Circular Logic in the Logic of Circularity. ” In The Concept of the Gene in Development and Evolution. Historical and Epistemological Perspectives , edited by BeurtonPeter, FalkRaphael, and RheinbergerHans-Jörg, 159–177. Cambridge: Cambridge University Press.
47.
KellerE. F.2001. The Century of the Gene . Cambridge, MA: Harvard University Press.
48.
KellerE. F.2003. A Feeling for the Organism. Life and Work of Barbara McClintock . New York: Freeman.
49.
KellerE. F.2015. “Cognitive Functions of Metaphor in the Natural Sciences. ” Philosophical Enquiries 3 (1): 113–132.
50.
KivietD. J., NgheP., WalkerN., BoulineauS., SunderlikovaV., and TansS. J.. 2014. “Stochasticity of Metabolism and Growth at the Single-cell Level. ” Nature 514: 376.
51.
Kosman-SchwarbackY.2010. The Noether Theorems: Invariance and Conservation Laws in the Twentieth Century . Berlin: Springer-Verlag.
52.
KupiecJ. J.1983. “A Probabilistic Theory for Cell Differentiation, Embryonic Mortality and DNA C-Value Paradox. ” Speculations in Science and Technology 6: 471–478.
53.
KupiecJ. J.1997. “A Darwinian Theory for the Origin of Cellular Differentiation. ” Molecular and General Genetics MGG 255: 201–208.
54.
LongoG.1988. “The Lambda-Calculus: Connections to Higher Type Recursion Theory, Proof-Theory, Category Theory. Conference on ‘Church's Thesis after 50 Years’. ” Annals of Pure and Applied Logic 40: 93–133.
55.
LongoG.2018a. “How Future Depends on Past Histories and Rare Events in Systems of Life. ” Foundations of Science
(23): 443–474.
56.
LongoG.2018b. “Information and Causality: Mathematical Reflections on Cancer Biology. ” Organisms Journal of Biological Sciences 2 (1): 83–104.
57.
LongoG.2019. “Interfaces of Incompleteness. ” In Systemics of Incompleteness and Quasi-systems , edited by MinatiG., AbramM., and PessaE., 3–55. New York, NY: Springer. (preliminary version: “Incompletezza” per La Matematica, vol. 4, Einaudi).
58.
LongoG.2020. “Information at the Threshold of Interpretation, Science as Human Construction of Sense. ” In A Critical Reflection on Automated Science – Will Science Remain Human? , edited by BertolasoM. and SterpettiF., 67–99. Dordrecht: Springer.
59.
LongoG. in press. “Confusing Biological Twins and Atomic Clocks. Today's Ecological Relevance of Bergson-Einstein Debate on time.” “What Is Time? Einstein and Bergson 100 Years Later”, April 4–6, 2019 (proceedings in preparation, Campo, Ronchi eds).
60.
LongoG., and LongoS.. 2020. “Infinity of God and Space of Men in Painting, Conditions of Possibility for the Scientific Revolution. ” In Mathematics in the Visual Arts , edited by SchepsR. and MaurelM.-C.. London: ISTE-WILEY Ltd. doi: 10.21494/ISTE.OP.2020.0486.
61.
LongoG., MiquelP. A., SonnenscheinC., and SotoA.. 2012. “Is Information a Proper Observable for Biological Organization?
” Progress in Biophysics and Molecular Biology 109 (3): 108–114.
62.
LongoG., PalamidessiC., and PaulT.. 2010. “Some Bridging Results and Challenges in Classical, Quantum and Computational Randomness. ” In Randomness through Computation , edited by ZenilH., 73–92. Singapore: World Scientific.
63.
LongoG., and SotoA. M.. 2016. “Why Do We Need Theories?
” Progress in Biophysics and Molecular Biology 122: 4–10.
64.
MarinucciA.2011. Tra ordine e caos. Metodi e linguaggi tra fisica, matematica e filosofia . Roma: Aracne.
65.
Maynard-SmithJ.1999. “The Idea of Information in Biology. ” The Quarterly Review of Biology 74: 495–400.
66.
MayrE.1961. “Cause and Effect in Biology: Kinds of Causes, Predictability, and Teleology Are Viewed by a Practicing Biologist. ” Science 134: 1501–1506.
67.
MonodJ.1971. Chance and Necessity: An Essay on the Natural Philosophy of Modern Biology . New York: Alfred A. Knopf.
68.
MontévilM., and MossioM.. 2015. “Closure of Constraints in Biological Organisation. ” Journal of Theoretical Biology 372: 179–191.
69.
MontévilM., MossioM., PochevilleA., and LongoG.. 2016. “Theoretical Principles for Biology: Variation. ” Progress in Biophysics and Molecular Biology 122 (1): 36–50.
70.
MorenoA., and MossioM.. 2015. Biological Autonomy. A Philosophical and Theoretical Enquiry . Dordrecht: Springer.
71.
MossioM., and BichL.. 2017. “What Makes Biological Organisation Teleological?
” Synthese 194: 1089–1114.
72.
MossioM., MontévilM., and LongoG.. 2016. “Theoretical Principles for Biology: Organisation. ” Progress in Biophysics and Molecular Biology 122 (1): 24–35.
73.
Mugur-SchachterM., and LongoG., eds. 2014. Developments of the Concepts of Randomness, Statistic, and Probability, Special Issue of Mathematical Structures in Computer Science . Cambridge: Cambridge University Press. vol. 24, n. 3.
74.
NicholsonD. J.2014. “The Machine Conception of the Organism in Development and Evolution: A. Critical Analysis. ” Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 48: 162–174.
75.
NobleD.1979. The Initiation of the Heartbeat . Oxford: Oxford University Press.
76.
NobleD.2012. “A Theory of Biological Relativity: No Privileged Level of Causation. ” Interface Focus 2 (1): 55–64.
PavesiAngelo, VianelliAlberto, ChiricoNicola, BaoYiming, BlinkovaOlga, BelshawRobert, FirthAndrew, KarlinDavid, and JanEric. 2018. “Overlapping Genes and the Proteins They Encode Differ Significantly in Their Sequence Composition from Non-overlapping Genes. ” PLoS ONE 13 (10): e0202513. doi: 10.1371/journal.pone.0202513.
79.
PeluffoA.2015. “The ‘Genetic Program’: Behind the Genesis of an Influential Metaphor. ” Genetics 200: 685–696.
80.
PerretN., and LongoG.. 2016. “Reductionist Perspectives and the Notion of Information. ” Progress in Biophysics and Molecular Biology 122: 11.
81.
PlominR.2018. BLUEPRINT. How DNA Makes Us Who We Are . London: Penguin.
82.
PoincaréH.1892. Les Méthodes Nouvelles de la Mécanique Celeste . Paris: Gauthier-Villars.
83.
PouilleP. A., AhmadiP., BrunetA. C., and FargeE.. 2009. “Mechanical Signals Trigger Myosin II Redistribution and Mesoderm Invagination in Drosophila Embryos. ” Science Signaling 2: ra16.
84.
PouilleP. A., and FargeE.. 2008. “Hydrodynamic Simulation of Multicellular Embryo Invagination. ” Physical Biology 5: 015005.
RosenR.1991. Life Itself. A Comprehensive Enquiry Into the Nature, Origin and Fabrication of Life . New York: Columbia University Press.
89.
RosenbergA.2007. “Reductionism (and Antireductionism) in Biology. ” In The Cambridge Companion to the Philosophy of Biology , edited by HullD. and RuseM., 120–138. Cambridge: Cambridge University Press.
90.
SchmittA. O., and HerzelH.. 1997. “Estimating the Entropy of DNA Sequences. ” Journal of Theoretical Biology 188: 369–377.
91.
SchrödingerE.1944. What Is Life? The Physical Aspect of the Living Cell . Cambridge: Cambridge University Press.
92.
SelzamS., KrapohlE., von StummS., O'ReillyP. F., RimfeldK., KovasY., DaleP. S., LeeJ. J., and PlominR.. 2016. “Predicting Educational Achievement from DNA. ” Molecular Psychiatry 22: 267. 19 July
online https://www.nature.com/articles/mp2016107.
93.
SimpsonM. L., CoxC. D., AllenM. S., McCollumJ. M., DarR. D., KarigD. K., and CookeJ. F.. 2009. “Noise in Biological Circuits. ” WIREs Nanomedicine and Nanotechnology 1: 214–225.
94.
SonnenscheinC., and SotoA. M.. 2016. “Carcinogenesis Explained within the Context of a Theory of Organisms. ” Progress in Biophysics and Molecular Biology 122 (1): 70–76.
95.
SkotheimR. I., and NeesM.. 2007. “Alternative Splicing in Cancer: Noise, Functional, or Systematic?
” The International Journal of Biochemistry and Cell Biology 39 (7–8): 1432–1449.
96.
TuringA.1950. “Computing Machinery and Intelligence. ” Mind; A Quarterly Review of Psychology and Philosophy LIX: 433–460.
97.
van FrassenB. C.1970. An Introduction to the Philosophy of Space and Time . New York: Random House.
98.
YoungJ., NilsenRoger, WaymireKatrina G., MacGregorGrant R., and InselThomas R.. 1999. “Increased Affiliative Response to Vasopressin in Mice Expressing the V1a Receptor from a Monogamous Vole. ” Nature 400: 766–768.
99.
WalshD.2015. Organisms, Agency, and Evolution . Cambridge: Cambridge University Press.
100.
WeinbergR.2014. “Coming Full Circle – From Endless Complexity to Simplicity and Back Again. ” Cell 157: 267–271.
101.
West-EberhardM.-J.2003. Developmental Plasticity and Evolution . New York: Oxford University Press.
102.
WeylH.1949. Philosophy of Mathematics and of Natural Sciences . Princeton: Princeton University Press.
103.
WienerR.1948. Cybernetics: Or Control and Communication in the Animal and the Machine . Cambridge, MA: MIT Press.
104.
WolfeC.2010. “Do Organisms Have an Ontological Status?
” History and Philosophy of the Life Sciences 32 (2–3): 195–232.
