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Compositional Proofreading through Critical Self-Tuning

Omer Karin

Phys. Rev. Lett. 137, 188401 – Published 28 October, 2026

DOI: https://doi.org/10.1103/gz26-8ryj

Abstract

High-dimensional multicomponent systems, including immune and epigenetic repertoires, must selectively retain rare, beneficial components while purging a large influx of suboptimal variants. I demonstrate that critical tuning of component control parameters through competition naturally implements proofreading in these systems. Competition for shared inputs pins the system to the marginal stability threshold of the most persistent species. This grants that species an extended lifetime and concentrates a macroscopic fraction of the population in that species, while forcing less-stable variants into rapid drift-driven turnover. When the aggregate drive exceeds a critical influx, pinning fails and all components enter a rapid-turnover regime. Applying this framework to biological memory, I identify the hallmarks of this effect in plasma cell accumulation dynamics and propose that altered pinning dynamics may represent failure points across biological domains, including cancer, immunodeficiencies, and the aberrant activation of harmful genomic elements during aging.

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References (91)

  1. J. J. Hopfield, Kinetic proofreading: A new mechanism for reducing errors in biosynthetic processes requiring high specificity, Proc. Natl. Acad. Sci. U.S.A. 71, 4135 (1974).
  2. J. Ninio, Kinetic amplification of enzyme discrimination, Biochimie 57, 587 (1975).
  3. T. W. McKeithan, Kinetic proofreading in T-cell receptor signal transduction, Proc. Natl. Acad. Sci. U.S.A. 92, 5042 (1995).
  4. A. Murugan, D. A. Huse, and S. Leibler, Discriminatory proofreading regimes in nonequilibrium systems, Phys. Rev. X 4, 021016 (2014).
  5. R. Ravasio, K. Husain, C. G. Evans, R. Phillips, M. Ribezzi, J. W. Szostak, and A. Murugan, A minimal scenario for the origin of non-equilibrium order, arXiv:2405.10911.
  6. S. Tonegawa, Somatic generation of antibody diversity, Nature (London) 302, 575 (1983).
  7. A. Radbruch, G. Muehlinghaus, E. O. Luger, A. Inamine, K. G. Smith, T. Dörner, and F. Hiepe, Competence and competition: The challenge of becoming a long-lived plasma cell, Nat. Rev. Immunol. 6, 741 (2006).
  8. G. Altan-Bonnet, T. Mora, and A. M. Walczak, Quantitative immunology for physicists, Phys. Rep. 849, 1 (2020).
  9. B. D. Simons and O. Karin, Tuning of plasma cell lifespan by competition explains the longevity and heterogeneity of antibody persistence, Immunity 57, 600 (2024).
  10. T. Beltran, V. Shahrezaei, V. Katju, and P. Sarkies, Epimutations driven by small RNAs arise frequently but most have limited duration in Caenorhabditis elegans, Nat. Ecol. Evol. 4, 1539 (2020).
  11. O. Karin, E. A. Miska, and B. D. Simons, Epigenetic inheritance of gene silencing is maintained by a self-tuning mechanism based on resource competition, Cell Syst. 14, 24 (2023).
  12. D. Purves and J. W. Lichtman, Elimination of synapses in the developing nervous system, Science 210, 153 (1980).
  13. C. S. Goodman and C. J. Shatz, Developmental mechanisms that generate precise patterns of neuronal connectivity, Cell 72, 77 (1993).
  14. K. Bentley, G. Mariggi, H. Gerhardt, and P. A. Bates, Tipping the balance: Robustness of tip cell selection, migration and fusion in angiogenesis, PLoS Comput. Biol. 5, e1000549 (2009).
  15. S. M. van Neerven and L. Vermeulen, Cell competition in development, homeostasis and cancer, Nat. Rev. Mol. Cell Biol. 24, 221 (2023).
  16. B. D. Simons and O. Karin, Cell cycle criticality as a mechanism for robust cell population control, Mol. Syst. Biol. 22, 241 (2025).
  17. J. Gerhart and M. Kirschner, The theory of facilitated variation, Proc. Natl. Acad. Sci. U.S.A. 104, 8582 (2007).
  18. E. Bagci, Y. Vodovotz, T. Billiar, G. Ermentrout, and I. Bahar, Bistability in apoptosis: Roles of Bax, Bcl-2, and mitochondrial permeability transition pores, Biophys. J. 90, 1546 (2006).
  19. J. G. Albeck, J. M. Burke, S. L. Spencer, D. A. Lauffenburger, and P. K. Sorger, Modeling a snap-action, variable-delay switch controlling extrinsic cell death, PLoS Biol. 6, e299 (2008).
  20. G. Yao, C. Tan, M. West, J. R. Nevins, and L. You, Origin of bistability underlying mammalian cell cycle entry, Mol. Syst. Biol. 7, 485 (2011).
  21. A. Briffa, G. Menon, A. Movilla Miangolarra, and M. Howard, Dissecting mechanisms of epigenetic memory through computational modeling, Annu. Rev. Plant Biol. 75, 265 (2024).
  22. A. Stanoev, A. P. Nandan, and A. Koseska, Organization at criticality enables processing of time-varying signals by receptor networks, Mol. Syst. Biol. 16, e8870 (2020).
  23. D. Koch, A. Nandan, G. Ramesan, and A. Koseska, Biological computations: Limitations of attractor-based formalisms and the need for transients, Biochem. Biophys. Res. Commun. 720, 150069 (2024).
  24. T. Mora and W. Bialek, Are biological systems poised at criticality?, J. Stat. Phys. 144, 268 (2011).
  25. T. Agranov, N. Wiegenfeld, O. Karin, and B. D. Simons, Self-organized hyperuniformity in a minimal model of population dynamics, Phys. Rev. Lett. 137, 117401 (2026).
  26. D. S. Fisher, Collective transport in random media: From superconductors to earthquakes, Phys. Rep. 301, 113 (1998).
  27. C. Reichhardt and C. J. Olson Reichhardt, Depinning and nonequilibrium dynamic phases of particle assemblies driven over random and ordered substrates: A review, Rep. Prog. Phys. 80, 026501 (2017).
  28. See Supplemental Material at http://link.aps.org/supplemental/10.1103/gz26-8ryj for derivations, simulation details, and further discussion, which includes Refs. [29–44].
  29. P. Boxler, A stochastic version of center manifold theory, Probab. Theory Relat. Fields 83, 509 (1989).
  30. S. H. Strogatz, Nonlinear Dynamics and Chaos: With Applications to Physics, Biology, Chemistry, and Engineering (Chapman and Hall/CRC, London, 2024).
  31. D. Hathcock and J. P. Sethna, Reaction rates and the noisy saddle-node bifurcation: Renormalization group for barrier crossing, Phys. Rev. Res. 3, 013156 (2021).
  32. M. Fucho-Rius, S. Maretvadakethope, À. Haro, T. Alarcón, J. Sardanyés, and R. Pérez-Carrasco, Local nearby bifurcations lead to synergies in critical slowing down: The case of mushroom bifurcations, Phys. Rev. E 111, 024213 (2025).
  33. A. Vespignani and S. Zapperi, How self-organized criticality works: A unified mean-field picture, Phys. Rev. E 57, 6345 (1998).
  34. J. A. Bonachela and M. A. Muñoz, Self-organization without conservation: true or just apparent scale-invariance?, J. Stat. Mech. (2009) P09009.
  35. S. Di Santo, R. Burioni, A. Vezzani, and M. A. Muñoz, Self-organized bistability associated with first-order phase transitions, Phys. Rev. Lett. 116, 240601 (2016).
  36. V. Buendía, S. Di Santo, J. A. Bonachela, and M. A. Muñoz, Feedback mechanisms for self-organization to the edge of a phase transition, Front. Phys. 8, 333 (2020).
  37. S. Camalet, T. Duke, F. Jülicher, and J. Prost, Auditory sensitivity provided by self-tuned critical oscillations of hair cells, Proc. Natl. Acad. Sci. U.S.A. 97, 3183 (2000).
  38. G. Bianconi and M. Marsili, Clogging and self-organized criticality in complex networks, Phys. Rev. E 70, 035105(R) (2004).
  39. M. Liu and K. E. Bassler, Emergent criticality from coevolution in random Boolean networks, Phys. Rev. E 74, 041910 (2006).
  40. S. N. Dorogovtsev, A. V. Goltsev, and J. F. F. Mendes, Critical phenomena in complex networks, Rev. Mod. Phys. 80, 1275 (2008).
  41. I. R. Graf and B. B. Machta, A bifurcation integrates information from many noisy ion channels and allows for Millikelvin thermal sensitivity in the snake pit organ, Proc. Natl. Acad. Sci. U. S. A. 121, e2308215121 (2024).
  42. G. F. Gause, The Struggle for Existence: A Classic of Mathematical Biology and Ecology (Courier Dover Publications, New York, 2019).
  43. R. A. Armstrong and R. McGehee, Competitive exclusion, Am. Nat. 115, 151 (1980).
  44. D. Tilman, Resource Competition and Community Structure (Princeton University Press, Princeton, NJ, 1982), Vol. 17.
  45. E. Fontich and J. Sardanyés, General scaling law in the saddle–node bifurcation: A complex phase space study, J. Phys. A 41, 015102 (2008).
  46. C. Kuehn, Scaling of saddle-node bifurcations: Degeneracies and rapid quantitative changes, J. Phys. A 42, 045101 (2009).
  47. J. Knebel, M. F. Weber, T. Krüger, and E. Frey, Evolutionary games of condensates in coupled birth–death processes, Nat. Commun. 6, 6977 (2015).
  48. N. P. Proukakis, A century of Bose-Einstein condensation, Commun. Phys. 8, 264 (2025).
  49. I. J. Amanna and M. K. Slifka, Mechanisms that determine plasma cell lifespan and the duration of humoral immunity, Immunological Reviews 236, 125 (2010).
  50. M. K. Slifka and I. J. Amanna, Role of multivalency and antigenic threshold in generating protective antibody responses, Front. Immunol. 10, 956 (2019).
  51. J. Mulder, J. Scrofani, K. Chheng, K. O’Donnell, D. M. Tarlinton, M. J. Robinson, and Z. Ding, Examining the conditions associated with establishing plasma cell persistence, J. Immunol. 214, 2112 (2025).
  52. S. F. Brynjolfsson, L. Persson Berg, T. Olsen Ekerhult, I. Rimkute, M.-J. Wick, I.-L. Mårtensson, and O. Grimsholm, Long-lived plasma cells in mice and men, Front. Immunol. 9, 2673 (2018).
  53. Z. Jing, P. Galbo, L. Ovando, M. Demouth, S. Welte, R. Park, K. Chandran, Y. Wu, T. MacCarthy, D. Zheng et al., Fine-tuning spatial-temporal dynamics and surface receptor expression support plasma cell-intrinsic longevity, eLife 12, RP89712 (2024).
  54. Z. Benet, Z. Jing, and D. R. Fooksman, Plasma cell dynamics in the bone marrow niche, Cell Rep. 34, 108733 (2021).
  55. M. Eslami, S. Schuepbach-Mallepell, D. Diana, L. Willen, C. Kowalczyk-Quintas, C. Desponds, B. Peter, M. Vigolo, F. Renevey, O. Donzé et al., Unique and redundant roles of mouse BCMA, TACI, BAFF, APRIL, and IL-6 in supporting antibody-producing cells in different tissues, Proc. Natl. Acad. Sci. U.S.A. 121, e2404309121 (2024).
  56. R. Park, Z. Benet, Z. Jing, J. Enright, and D. R. Fooksman, CD138 and APRIL regulate plasma cell survival, competition, and retention in the bone marrow niche, Cell Rep. 44, 116123 (2025).
  57. R. D. de Vries, S. McQuaid, G. van Amerongen, S. Yüksel, R. J. Verburgh, A. D. Osterhaus, W. P. Duprex, and R. L. de Swart, Measles immune suppression: Lessons from the macaque model, PLoS Pathogens 8, e1002885 (2012).
  58. M. J. Mina, C. J. E. Metcalf, R. L. De Swart, A. Osterhaus, and B. T. Grenfell, Long-term measles-induced immunomodulation increases overall childhood infectious disease mortality, Science 348, 694 (2015).
  59. R. H. Webster, A. R. Dvorscek, Z. Ding, D. M. Tarlinton, and M. J. Robinson, Radiation resistance is a property of long-lived plasma cells but not their precursors, Immunother. Adv. 6, ltag016 (2026).
  60. A. Q. Xu, R. R. Barbosa, and D. P. Calado, Genetic timestamping of plasma cells in vivo reveals tissue-specific homeostatic population turnover, eLife 9, e59850 (2020).
  61. X. Liu, J. Yao, Y. Zhao, J. Wang, and H. Qi, Heterogeneous plasma cells and long-lived subsets in response to immunization, autoantigen and microbiota, Nat. Immunol. 23, 1564 (2022).
  62. T. Koike, K. Fujii, K. Kometani, N. S. Butler, K. Funakoshi, S. Yari, J. Kikuta, M. Ishii, T. Kurosaki, and W. Ise, Progressive differentiation toward the long-lived plasma cell compartment in the bone marrow, J. Exp. Med. 220, e20221717 (2022).
  63. M. J. Robinson, Z. Ding, M. R. Dowling, D. L. Hill, R. H. Webster, C. McKenzie, C. Pitt, K. O’Donnell, J. Mulder, E. Brodie et al., Intrinsically determined turnover underlies broad heterogeneity in plasma-cell lifespan, Immunity 56, 1596 (2023).
  64. M. J. Mina, T. Kula, Y. Leng, M. Li, R. D. De Vries, M. Knip, H. Siljander, M. Rewers, D. F. Choy, M. S. Wilson et al., Measles virus infection diminishes preexisting antibodies that offer protection from other pathogens, Science 366, 599 (2019).
  65. A. V. Gulino, D. Moratto, S. Sozzani, P. Cavadini, K. Otero, L. Tassone, L. Imberti, S. Pirovano, L. D. Notarangelo, R. Soresina et al., Altered leukocyte response to CXCL12 in patients with warts hypogammaglobulinemia, infections, myelokathexis (WHIM) syndrome, Blood 104, 444 (2004).
  66. P. J. Mc Guire, C. Cunningham-Rundles, H. Ochs, and G. A. Diaz, Oligoclonality, impaired class switch and B-cell memory responses in WHIM syndrome, Clin. Immunol. 135, 412 (2010).
  67. V. Biajoux, J. Natt, C. Freitas, N. Alouche, A. Sacquin, P. Hemon, F. Gaudin, N. Fazilleau, M. Espeli, and K. Balabanian, Efficient plasma cell differentiation and trafficking require Cxcr4 desensitization, Cell Rep. 17, 193 (2016).
  68. J. Moreaux, E. Legouffe, E. Jourdan, P. Quittet, T. Rème, C. Lugagne, P. Moine, J.-F. Rossi, B. Klein, and K. Tarte, BAFF and APRIL protect myeloma cells from apoptosis induced by interleukin 6 deprivation and dexamethasone, Blood 103, 3148 (2004).
  69. Y.-T. Tai, C. Acharya, G. An, M. Moschetta, M. Y. Zhong, X. Feng, M. Cea, A. Cagnetta, K. Wen, H. van Eenennaam et al., APRIL and BCMA promote human multiple myeloma growth and immunosuppression in the bone marrow microenvironment, Blood 127, 3225 (2016).
  70. M. Chahin, Z. Branham, A. Fox, C. Leurinda, and A. R. Keruakous, Clinical considerations for immunoparesis in multiple myeloma, Cancers 14, 2278 (2022).
  71. B. Paiva, M. Pérez-Andrés, M. Vidriales, J. Almeida, N. de Las Heras, M. Mateos, L. López-Corral, N. Gutiérrez, J. Blanco, A. Oriol et al., Competition between clonal plasma cells and normal cells for potentially overlapping bone marrow niches is associated with a progressively altered cellular distribution in MGUS vs myeloma, Leukemia 25, 697 (2011).
  72. K. Banerjee, A. B. Kolomeisky, and O. A. Igoshin, Elucidating interplay of speed and accuracy in biological error correction, Proc. Natl. Acad. Sci. U.S.A. 114, 5183 (2017).
  73. Y. Savir and T. Tlusty, Conformational proofreading: The impact of conformational changes on the specificity of molecular recognition, PLoS One 2, e468 (2007).
  74. P. Bak, C. Tang, and K. Wiesenfeld, Self-organized criticality: An explanation of the 1/f noise, Phys. Rev. Lett. 59, 381 (1987).
  75. H. J. Jensen, Self-Organized Criticality: Emergent Complex Behavior in Physical and Biological Systems, Vol. 10 (Cambridge University Press, Cambridge, England, 1998).
  76. N. W. Watkins, G. Pruessner, S. C. Chapman, N. B. Crosby, and H. J. Jensen, 25 years of self-organized criticality: Concepts and controversies, Space Sci. Rev. 198, 3 (2016).
  77. M. A. Muñoz, Colloquium: Criticality and dynamical scaling in living systems, Rev. Mod. Phys. 90, 031001 (2018).
  78. Z. Lippman, A.-V. Gendrel, M. Black, M. W. Vaughn, N. Dedhia, W. Richard McCombie, K. Lavine, V. Mittal, B. May, K. D. Kasschau et al., Role of transposable elements in heterochromatin and epigenetic control, Nature (London) 430, 471 (2004).
  79. P. Oberdoerffer, S. Michan, M. McVay, R. Mostoslavsky, J. Vann, S.-K. Park, A. Hartlerode, J. Stegmuller, A. Hafner, P. Loerch et al., SIRT1 redistribution on chromatin promotes genomic stability but alters gene expression during aging, Cell 135, 907 (2008).
  80. R. C. Allshire and H. D. Madhani, Ten principles of heterochromatin formation and function, Nat. Rev. Mol. Cell Biol. 19, 229 (2018).
  81. J. S. Smith, C. B. Brachmann, L. Pillus, and J. D. Boeke, Distribution of a limited Sir2 protein pool regulates the strength of yeast rDNA silencing and is modulated by Sir4p, Genetics 149, 1205 (1998).
  82. D. S. Saxton and J. Rine, Distinct silencer states generate epigenetic states of heterochromatin, Mol. Cell 82, 3566 (2022).
  83. Y. V. Makeyeva, M. Shirayama, and C. C. Mello, Cues from mRNA splicing prevent default Argonaute silencing in C. elegans, Dev. Cell 56, 2636 (2021).
  84. M. Seczynska, S. Bloor, S. M. Cuesta, and P. J. Lehner, Genome surveillance by HUSH-mediated silencing of intronless mobile elements, Nature (London) 601, 440 (2022).
  85. P. J. Lehner, Silencing by the HUSH epigenetic transcriptional repressor complex, Annu. Rev. Biochem. 94, 361 (2025).
  86. J. G. Wood, B. C. Jones, N. Jiang, C. Chang, S. Hosier, P. Wickremesinghe, M. Garcia, D. A. Hartnett, L. Burhenn, N. Neretti et al., Chromatin-modifying genetic interventions suppress age-associated transposable element activation and extend life span in Drosophila, Proc. Natl. Acad. Sci. U.S.A. 113, 11277 (2016).
  87. V. Gorbunova, A. Seluanov, P. Mita, W. McKerrow, D. Fenyö, J. D. Boeke, S. B. Linker, F. H. Gage, J. A. Kreiling, A. P. Petrashen et al., The role of retrotransposable elements in ageing and age-associated diseases, Nature (London) 596, 43 (2021).
  88. M. Van Meter, M. Kashyap, S. Rezazadeh, A. J. Geneva, T. D. Morello, A. Seluanov, and V. Gorbunova, SIRT6 represses LINE1 retrotransposons by ribosylating KAP1 but this repression fails with stress and age, Nat. Commun. 5, 5011 (2014).
  89. A. Korotkov, A. Seluanov, and V. Gorbunova, Sirtuin 6: Linking longevity with genome and epigenome stability, Trends Cell Biol. 31, 994 (2021).
  90. Y. Li, M. Jin, R. O’Laughlin, P. Bittihn, L. S. Tsimring, L. Pillus, J. Hasty, and N. Hao, Multigenerational silencing dynamics control cell aging, Proc. Natl. Acad. Sci. U.S.A. 114, 11253 (2017).
  91. https://github.com/karin-lab/compositional.

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