Entangled Life and Code: A Computational Design Taxonomy for Synergistic Bio-Digital Systems

TL;DR

The paper introduces a computational design taxonomy to bridge biology and computing for synergistic bio-digital systems. It defines eight functional layers (Input, Transduction, Evaluation/Comparison, Routing/Selection, Memory/State, Adaptation, Output, Power) and maps biological and digital roles across 70 analyzed systems, supported by an open-source database and interactive visualization. The authors demonstrate that current designs mostly repurpose organisms as transducers and digital components as simple inputs/outputs, revealing substantial underexploited potential in areas like biological memory with digital routing and multi-modal, multi-species collaborations. Ultimately, the work argues for regenerative ecologies and human-centered computation enabled by a shared design language, while acknowledging methodological and ethical challenges and outlining rich directions for future development and community collaboration.

Abstract

Bio-digital systems that merge microbial life with technology promise new modes of computation, combining biological adaptability with digital precision. Yet realizing this potential symbiotically -- where biological and digital agents co-adapt and co-process -- remains elusive, largely due to the absence of a shared vocabulary bridging biology and computing. Consequently, microbes are often constrained to uni-directional roles, functioning as sensors or actuators rather than as active, computational partners in bio-digital systems. In response, we propose a taxonomy and pathways that articulate and expand the roles of biological and digital entities for synergetic bio-digital computation. Using this taxonomy, we analysed 70 systems across HCI, design, and engineering, identifying how biological mechanisms can be mapped onto computational abstractions. We argue that such mappings enable computationally actionable directions that foster richer and reciprocal relationships in bio-digital systems, supporting regenerative ecologies across time and scale while inspiring new paradigms for computation in HCI.

Figures (10)

• Figure 1: Images of the microorganism-based bio-digital systems selected for analysis (listed in Appendix \ref{['app:included']}) 1 swamp_tardigotchi_2012 2 lam_pac-euglena_2020 3 esparza_bio-electrolisis_2022 4 chen_nukabot_2021 5 whiting_slime_2014 6 zhou_cyano-chromic_2023 7 lu_integrating_2022 8 zajdel_towards_2017 9 lee_trap_2015 10 vu_addressing_2024 11 riggs_mold_2025 12 grebenstein_biological_2018 13 adamatzky_physarum-based_2016 14 inozemtseva_archaean_2022 15 kudla_crucible_2008 16 interspecifics_gfp_2015 17 tabor_programming_2007 18 armstrong_active_2020 19 riedel-kruse_design_2010 20 barati_living_2021 21 bilir_biodegradable_2024 22 lee_microaquarium_2020 23 miranda_composing_2018 24 munnik_microscopic_2011 25 team_biota_2017 26 mishra_sensorimotor_2024 27 henriques_caravel_2016 28 ieropoulos_ecobot-ii_2005 29 dobbs_bioartbot_2019 30 sedbon_cmd_2019 31 song_precisely_2023 32 liu_microbial_2022 33 pinelis_micro_2006 34 steiner_bixels_2017 35 ecologicstudio_urban_2015 36 hamidi_rafigh_2014 37 adamatzky_reactive_2021 38 bell_bio-digital_2024 39 c-lab_stress-o-stat_2011 40 douenias_living_2020 41 philips_design_microbial_2011 42 diblasi_beauty_2023 43 sedbon_cryptographic_2022 44 castellanos_microbial_2017 45 breed_algae_2024 46 guo_slimo_2025 47 andre_preliminary_2007 48 rossi_let_2017 49 c-lab_living_2013 50 kim_new_2018 51 riedel-kruse_design_2010 52 lee_euglpollock_2022 53 isitan_where_2016 54 roberts_mining_2022 55 puello_living_2017 56 gerber_biographr_2016 57 nova_innova_pond_2020 58 interspecifics_micro-rhythms_2016 59 rossi_long_2017 60 cheok_empathetic_2008 61 henriques_symbiotic_2014 62 sedbon_c_2022 63 akolpoglu_navigating_2025 64 henriques_bacterbrain_2019 65 postl_mold_2024 66 igem_paris_bettencourt_bacterial_2022 67 lee_tangible_2015 68 ikeya_designing_2023 69 wijesinghe_light-deformable_2024 70 esparza_biosonot_2017
• Figure 2: Interactions in the Pac-Euglena system lam_pac-euglena_2020. From left to right: A user presses a key; LED light is turned ON (digital $\rightarrow$ organism role: input (activate)); the Euglena cell moves away from the light (organism $\rightarrow$ digital role: transduction); the movement is captured through computer vision (digital $\rightarrow$ organism role: evaluation/comparison) and displayed back on a computer (digital $\rightarrow$ organism role: output (connect to humans)).
• Figure 3: Our online interactive visualization platform.
• Figure 4: An example exploration using our visualization platform of the intersection between "electrical" observable outputs and $\leq$1 second reaction speeds. The red dashed line around the $\leq$1 second "Speed" node indicates that we had previously clicked on that node, highlighting connections in blue. Subsequent hovering over nodes and links, such as the "electrical" observable output here, highlights intersections in green.
• Figure 5: System Detail View for bio-digital systems in which the biological organism plays a "power" role for the system.