I. A. Hatton, K. S. Mccann, and J. M. Fryxell, e predatorprey power law: biomass scaling across terrestrial and aquatic biomes, Science, vol.349, issue.6252, 2015.

S. Kéfi, V. Miele, E. Wieters, S. Navarrete, and E. Berlow, How structured is the entangled bank? e surprisingly simple organization of multiplex ecological networks leads to increased persistence and resilience, PLoS Biology, vol.14, issue.8, 2016.

R. M. May, Stability and Complexity of Model Ecosystems, 1974.

E. Ébault and C. Fontaine, Stability of ecological communities and the architecture of mutualistic and trophic networks, Science, vol.329, issue.5993, pp.853-856, 2010.

R. C. Dewar, C. H. Lineweaver, R. K. Niven, and K. Regenauer-lieb, Beyond the second law, Entropy Production and Non-Equilibrium Systems, 2011.

B. C. Patten, Network integration of ecological extremal principles: exergy, emergy, power, ascendency, and indirect effects, Ecological Modelling, vol.79, issue.1-3, pp.75-84, 1995.

E. Ostrom, A general framework for analyzing sustainability of social-ecological systems, Science, vol.325, issue.5939, pp.419-422, 2009.

I. Steffan-dewenter, M. Kessler, and J. Barkmann, Tradeoffs between income, biodiversity, and ecosystem functioning during tropical rainforest conversion and agroforestry intensification, Proceedings of the National Academy of Sciences, vol.104, issue.12, pp.4973-4978, 2007.

C. Gaucherel, Ecosystem complexity through the lens of logical depth: capturing ecosystem individuality, Biological eory, vol.9, issue.4, pp.440-451, 2014.
URL : https://hal.archives-ouvertes.fr/hal-02632869

S. P. Frontier, D. A. Lepêtre, D. Davoult, and C. Luczak, Ecosystèmes. Structure, Fonctionnement, Evolution, 2008.

C. Gaucherel, Physical concepts and ecosystem ecology: a revival?, Journal of Ecosystem and Ecography, vol.8, 2018.
URL : https://hal.archives-ouvertes.fr/hal-02166073

R. E. Ricklefs and G. L. Miller, Ecology, 2000.

R. H. Mac-arthur and E. O. Wilson, e eory of Insular Zoogeography, 1963.

C. S. Holling, Resilience and stability of ecological systems, Annual Review of Ecology and Systematics, vol.4, issue.1, pp.1-23, 1973.

M. Scheffer, Critical Transitions in Nature and Society, 2009.

M. Scheffer, S. Carpenter, J. A. Foley, C. Folke, and B. Walker, Catastrophic shifts in ecosystems, Nature, vol.413, issue.6856, pp.591-596, 2001.
URL : https://hal.archives-ouvertes.fr/hal-02195560

B. Walker, C. S. Holling, S. R. Carpenter, and A. Kinzig, Resilience, adaptability and transformability in social-ecological systems, Ecology and Society, vol.9, issue.2, 2004.

C. Gaucherel, H. Éro, A. Puiseux, and V. Bonhomme, Understand ecosystem regime shifts by modelling ecosystem development using boolean networks, Ecological Complexity, vol.31, pp.104-114, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01556324

R. V. Solé and J. Bascompte, Self-Organization in Complex Ecosystems, 2006.

M. Hirota, M. Holmgren, E. H. Van-nes, and M. Scheffer, Global resilience of tropical forest and savanna to critical transitions, Science, vol.334, issue.6053, pp.232-235, 2011.

B. W. Brook, E. C. Ellis, M. P. Perring, A. W. Mackay, and L. Blomqvist, Does the terrestrial biosphere have planetary tipping points?, Trends in Ecology & Evolution, vol.28, issue.7, pp.396-401, 2013.

C. Gaucherel and V. Moron, Potential stabilizing points to mitigate tipping point interactions in earth's climate, International Journal of Climatology, vol.37, issue.1, pp.399-408, 2016.

E. H. Van-nes, M. Hirota, M. Holmgren, and M. Scheffer, Tipping points in tropical tree cover: linking theory to data, Global Change Biology, vol.20, issue.3, pp.1016-1021, 2014.

R. Badii and A. Politi, Hierarchical Structures and Scaling in Physics, 1997.

R. Om, Structural Stability and Morphogenesis, 1975.

F. Accatino, C. De-michele, R. Vezzoli, D. Donzelli, and R. J. Scholes, Tree-grass co-existence in savanna: interactions of rain and fire, Journal of eoretical Biology, vol.267, issue.2, pp.235-242, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00629962

M. Scheffer, S. H. Hosper, M. Meijer, B. Moss, and E. Jeppesen, Alternative equilibria in shallow lakes, Trends in Ecology & Evolution, vol.8, issue.8, pp.275-279, 1993.

A. C. Staver, S. Archibald, and S. Levin, Tree cover in sub-Saharan Africa: rainfall and fire constrain forest and savanna as alternative stable states, Ecology, vol.92, issue.5, pp.1063-1072, 2011.

E. H. Van-nes and M. Scheffer, Slow recovery from perturbations as a generic indicator of a nearby catastrophic shift, American Naturalist, vol.169, issue.6, pp.738-747, 2007.

C. Gaucherel and F. Pommereau, Using discrete systems to exhaustively characterize the dynamics of an integrated ecosystem, Methods in Ecology and Evolution, vol.10, issue.9, pp.1-13, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02265554

F. Pommereau, Algebras of Coloured Petri Nets, 2010.
URL : https://hal.archives-ouvertes.fr/tel-02309973

C. Hély, H. H. Shuggart, B. Swap, and C. Gaucherel, e drape concept to understand ecosystem dynamics and its tipping points, 2020.

H. Ehrig, M. Pfender, and H. J. Schneider, Graph-grammars: an algebraic approach, Proceedings of the 14th Annual Symposium on Switching and Automata eory, pp.167-180, 1973.

J. Giavitto and O. Michel, Modeling the topological organization of cellular processes, Biosystems, vol.70, issue.2, pp.149-163, 2003.

W. Reisig, Understanding Petri Nets, 2013.

J. S. Turner, e Extended Organism: e Physiology of Animal-Built Structures, 2009.

M. Cosme, C. Hély, and F. Pommereau, East-African rangeland dynamics: from a knowledge-based model to the possible futures of an integrated social-ecological system

C. Gaucherel, C. Carpentier, I. R. Geijzendorffer, C. Noûs, and P. F. , Long term development of a realistic and integrated ecosystem, 2020.

H. G. Fowler, V. Pereira-da-silva, L. C. Forti, and N. B. Saes, Population dynamics of leaf cutting ants: a brief review, Fire Ants and Leaf-Cutting Ants, pp.123-145, 1986.

M. A. Blätke, M. Heiner, and W. Marwan, Tutorial, Petri Nets in Systems Biology, 2011.

J. Giavitto, H. Klaudel, and F. Pommereau, Integrated regulatory networks (IRNs): spatially organized biochemical modules, eoretical Computer Science, vol.431, pp.219-234, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00769275

J. M. Dambacher, H. K. Luh, H. W. Li, and P. A. Rossignol, Qualitative stability and ambiguity in model ecosystems, American Naturalist, vol.161, issue.6, pp.876-888, 2003.

B. T. Bestelmeyer, A. Ash, and J. R. Brown, State and transition models: theory, applications, and challenges, pp.303-345, 2017.

M. Scheffer, S. R. Carpenter, V. Dakos, and E. H. Van-nes, Generic indicators of ecological resilience: inferring the chance of a critical transition, Evolution, and Systematics, vol.46, issue.1, pp.145-167, 2015.
URL : https://hal.archives-ouvertes.fr/hal-02195020

B. Berthomieu, P. Ribet, and F. Vernadat, e tool TINA-construction of abstract state spaces for petri nets and time petri nets, International Journal of Production Research, vol.42, 2004.

V. N. Livina, F. Kwasniok, and T. M. Lenton, Potential analysis reveals changing number of climate states during the last 60 kyr, Climate of the Past, vol.6, issue.1, pp.77-82, 2010.

T. M. Lenton, V. N. Livina, V. Dakos, and M. Scheffer, Climate bifurcation during the last deglaciation?, Climate of the Past, vol.8, issue.4, pp.1127-1139, 2012.
URL : https://hal.archives-ouvertes.fr/hal-02195158

S. H. Strogatz, Nonlinear Dynamics and Chaos: With Applications to Physics, 2001.

J. Lovelock, Ages of Gaia: A Biography of Our Living Earth, 2000.

O. Lejeune, M. Tlidi, and P. Couteron, Localized vegetation patches: a self-organized response to resource scarcity, Physical Review E, vol.66, issue.1, 2002.

C. H. Waddington, e epigenotype, Endeavour, vol.1, pp.18-20, 1942.

S. Gavrilets, Highimensional fitness landscapes and speciation, Evolution-e Extended Synthesis, pp.45-79, 2010.

H. Ledford, Language: disputed definitions, Nature, vol.455, issue.7216, pp.1023-1028, 2008.

V. V. Ogryzko, Erwin schroedinger, francis crick and epigenetic stability, Biology Direct, vol.3, issue.1, p.15, 2008.

J. Vollmer, Chaos, spatial extension, transport, and non-equilibrium thermodynamics, Physics Reports, vol.372, issue.2, pp.131-267, 2002.

C. Gaucherel, P. H. Gouyon, and J. L. Dessalles, Information, the Hidden Side of Life, ISTE, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02273778

E. P. Odum, Energy flow in ecosystems: a historical review, American Zoologist, vol.8, issue.1, pp.11-18, 1968.

F. Bouchard, How ecosystem evolution strengthens the case for functional pluralism, Functions: Selection and Mechanisms, pp.83-95, 2013.

S. J. Gould, Wonderful Life: e Burgess Shale and the Nature of History, 1989.

C. Hély, P. Braconnot, J. Watrin, and W. Zheng, Climate and vegetation: simulating the African humid period, Comptes Rendus Geoscience, vol.341, issue.8-9, pp.671-688, 2009.

K. Sterelny, Contingency and history, Philosophy of Science, vol.83, pp.1-18, 2015.

J. Ratnam, W. J. Bond, and R. J. Fensham, When is a "forest" a savanna, and why does it matter?, Global Ecology and Biogeography, vol.20, issue.5, pp.653-660, 2011.

Y. Bergeron and A. Leduc, Relationships between change in fire frequency and mortality due to spruce budworm outbreak in the southeastern Canadian boreal forest, Journal of Vegetation Science, vol.9, pp.493-500, 1998.

B. J. Stocks, M. A. Fosberg, and T. J. Lynham, Climate change and forest fire potential in Russian and Canadian boreal forests, Climatic Change, vol.38, issue.1, pp.1-13, 1998.

A. G. Tansley, e use and abuse of vegetational concepts and terms, Ecology, vol.16, issue.3, pp.284-307, 1935.

N. Chomsky, Studies on Semantics in Generative Grammar, 1972.

C. Gaucherel, F. Boudon, T. Houet, M. Castets, and C. Godin, Understanding patchy landscape dynamics: towards a landscape language, PLoS One, vol.7, issue.9, 2012.
URL : https://hal.archives-ouvertes.fr/halshs-00750971

C. Godin, Representing and encoding plant architecture: a review, Annals of Forest Science, vol.57, issue.5, pp.413-438, 2000.
URL : https://hal.archives-ouvertes.fr/hal-00827475

C. L. Crumley, Historical ecology: a multidimensionalecological orientation, Historical Ecology: Cultural Knowledge and Changing Landscapes, C. L. Crumley, pp.1-16, 1994.

C. Hély, L. Bremond, S. Alleaume, B. Smith, M. T. Sykes et al., Sensitivity of African biomes to changes in the precipitation regime, Global Ecology and Biogeography, vol.15, issue.3, pp.258-270, 2006.

M. J. Wade, J. Harmand, and B. Benyahia, Perspectives in mathematical modelling for microbial ecology, Ecological Modelling, vol.321, pp.64-74, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01227423

C. Gaucherel, e Languages of Nature. When Nature Writes to Itself, Lulu editions, 2019.