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class="ds-work-card--work-metadata"><div class="ds-work-card--work-metadata__stat"><span class="material-symbols-outlined" style="font-size: 20px" translate="no">visibility</span><p class="ds2-5-body-sm" id="work-metadata-view-count">…</p></div><div class="ds-work-card--work-metadata__stat"><span class="material-symbols-outlined" style="font-size: 20px" translate="no">description</span><p class="ds2-5-body-sm">22 pages</p></div><div class="ds-work-card--work-metadata__stat"><span class="material-symbols-outlined" style="font-size: 20px" translate="no">link</span><p class="ds2-5-body-sm">1 file</p></div></div><script>(async () => { const workId = 9893899; const worksViewsPath = "/v0/works/views?subdomain_param=api&work_ids%5B%5D=9893899"; const getWorkViews = async (workId) => { const response = await fetch(worksViewsPath); if (!response.ok) { throw new Error('Failed to load work views'); } const data = await response.json(); return data.views[workId]; }; // Get the view count for the work - we send this immediately rather than waiting for // the DOM to load, so it can be available as soon as possible (but without holding up // the backend or other resource requests, because it's a bit expensive and not critical). const viewCount = await getWorkViews(workId); const updateViewCount = (viewCount) => { try { const viewCountNumber = parseInt(viewCount, 10); if (viewCountNumber === 0) { // Remove the whole views element if there are zero views. document.getElementById('work-metadata-view-count')?.parentNode?.remove(); return; } const commaizedViewCount = viewCountNumber.toLocaleString(); const viewCountBody = document.getElementById('work-metadata-view-count'); if (!viewCountBody) { throw new Error('Failed to find work views element'); } viewCountBody.textContent = `${commaizedViewCount} views`; } catch (error) { // Remove the whole views element if there was some issue parsing. document.getElementById('work-metadata-view-count')?.parentNode?.remove(); throw new Error(`Failed to parse view count: ${viewCount}`, error); } }; // If the DOM is still loading, wait for it to be ready before updating the view count. if (document.readyState === "loading") { document.addEventListener('DOMContentLoaded', () => { updateViewCount(viewCount); }); // Otherwise, just update it immediately. } else { updateViewCount(viewCount); } })();</script></div><p class="ds-work-card--work-abstract ds-work-card--detail ds2-5-body-md">We present here the recent developments in the studies of self-organization in abiotic, biotic (bacterial) colonies and man-made (programmable chips) systems, aimed at seeking to unravel the general principles of biotic self-organization.</p><div class="ds-work-card--button-container"><button class="ds2-5-button js-swp-download-button" 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data-moment_callback="onGoogleOneTapEvent" id="g_id_onload"></div><div class="ds-top-related-works--grid-container"><div class="ds-related-content--container ds-top-related-works--container"><h2 class="ds-related-content--heading">Related papers</h2><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="0" data-entity-id="12230542" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/12230542/Self_engineering_capabilities_of_bacteria">Self-engineering capabilities of bacteria</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="30730391" href="https://independent.academia.edu/EshelBenJacob">Eshel Ben-Jacob</a></div><p class="ds-related-work--metadata ds2-5-body-xs">2006</p><p class="ds-related-work--abstract ds2-5-body-sm">Under natural growth conditions, bacteria can utilize intricate communication capabilities (e.g. quorum-sensing, chemotactic signalling and plasmid exchange) to cooperatively form (self-organize) complex colonies with elevated adaptability-the colonial pattern is collectively engineered according to the encountered environmental conditions. Bacteria do not genetically store all the information required for creating all possible patterns. Instead, additional information is cooperatively generated as required for the colonial selforganization to proceed.</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Self-engineering capabilities of bacteria","attachmentId":46292539,"attachmentType":"pdf","work_url":"https://www.academia.edu/12230542/Self_engineering_capabilities_of_bacteria","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/12230542/Self_engineering_capabilities_of_bacteria"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="1" data-entity-id="12230638" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/12230638/Bacterial_self_organization_co_enhancement_of_complexification_and_adaptability_in_a_dynamic_environment">Bacterial selforganization: coenhancement of complexification and adaptability in a dynamic environment</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="30730391" href="https://independent.academia.edu/EshelBenJacob">Eshel Ben-Jacob</a></div><p class="ds-related-work--metadata ds2-5-body-xs">… Transactions of the Royal Society of …, 2003</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Bacterial selforganization: coenhancement of complexification and adaptability in a dynamic environment","attachmentId":46292465,"attachmentType":"pdf","work_url":"https://www.academia.edu/12230638/Bacterial_self_organization_co_enhancement_of_complexification_and_adaptability_in_a_dynamic_environment","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/12230638/Bacterial_self_organization_co_enhancement_of_complexification_and_adaptability_in_a_dynamic_environment"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="2" data-entity-id="8277873" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/8277873/Adaptive_self_organization_during_growth_of_bacterial_colonies">Adaptive self-organization during growth of bacterial colonies</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="38867264" href="https://telaviv.academia.edu/HaimShmueli">Haim Shmueli</a><span>, </span><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="16417341" href="https://independent.academia.edu/OferShochet">Ofer Shochet</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Physica A-statistical Mechanics and Its Applications, 1992</p><p class="ds-related-work--abstract ds2-5-body-sm">We present a study of interfacial pattern formation during diffusion-limited growth of Bacillus subtilis. It is demonstrated that bacterial colonies can develop patterns similar to morphologies observed during diffusion-limited growth in nonqiving (azoic) systems such as solidification and electro-chemical deposition. The various growth morphologies, that is the global structure of the colony, are observed as we vary the growth conditions. These include fractal growth, dense-branching growth, compact growth, dendritic growth and chiral growth. The results demonstrate the action of a singular interplay between the micro-level (individual bacterium) and macro-level (the colony) in selecting the observed morphologies as is understood for non-living systems. Furthermore, the observed morphologies can be organized within a morphology diagram indicating the existence of a morphology selection principle similar to the one proposed for azoic systems. We propose a phase-field-like model (the phase being the bacterial concentration and the field being the nutrient concentration) to describe the growth. The bacteria-bacteria interaction is manifested as a phase dependent diffusion constant. Growth of a bacterial colony presents an inherent additional level of complexity compared to azoic systems, since the building blocks themselves are living systems. Thus, our studies also focus on the transition between morphologies. We have observed extended morphology transitions due to phenotypic changes of the bacteria, as well as bursts of new morphologies resulting from genotypic changes. In addition, we have observed extended and heritable transitions (mainly between dense branching growth and chiral growth) as well as phenotypic transitions that turn genotypic over time. We discuss the implications of our results in the context of the evolving picture of genome cybernetics. Diffusion limited growth of bacterial colonies combined with new understanding of pattern formation in azoic systems provide new tools for the study of adaptive self-organization and mutation in the presence of selective pressures. We include brief reviews of both the recent developments in the study of interfacial pattern formation in non-living systems and the current trends in the view of mutation dynamics. Growth of a bacterial colony presents an inherent additional level of</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Adaptive self-organization during growth of bacterial colonies","attachmentId":48157454,"attachmentType":"pdf","work_url":"https://www.academia.edu/8277873/Adaptive_self_organization_during_growth_of_bacterial_colonies","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/8277873/Adaptive_self_organization_during_growth_of_bacterial_colonies"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="3" data-entity-id="1041977" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/1041977/Communication_based_regulated_freedom_of_response_in_bacterial_colonies">Communication-based regulated freedom of response in bacterial colonies</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="878409" href="https://independent.academia.edu/VladislavVolman">Una Qiu</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Physica A: Statistical …, 2003</p><p class="ds-related-work--abstract ds2-5-body-sm">Bacteria have developed intricate communication capabilities on all levels-the genome, the individual bacteria, the colony, and multi-colonial eco-systems of di erent bacterial species. All manner of biochemical messages are utilized for communication, including simple and complex abiotic molecules, peptides, proteins and even genetic sequences. These communication capabilities are required for bacterial cooperative self-organization into multicellular hierarchically structured colonies with complex spatio-temporal patterning. A colonial higher complexity is required for better colonial adaptability in a dynamic environment. The communication-based cooperative self-organization goes hand in hand with changes in cell structure and behavior. We identify two classes of such changes: (1) automatic and predetermined changes, which are triggered by inducive messages. (2) Regulated "decision-making" changes, which represent cellular regulated freedom of response to informative (semantic) messages. Each bacterium has internal degrees of freedom and informatics capabilities (storage, processing and interpretation of information). These features are required for the freedom of response in self-alteration (self-plasticity). Additionally, the cell can send messages to alter other bacteria in a self-regulated manner. To convert the above seemingly blurred notions into testable concepts we present the ÿrst steps towards quantiÿcation of colonial features associated with "regulated freedom". For this we extract a binary representation of the observed patterns to show the existence of LÃ evy distributions with parameters that range from near the Cauchy limit to the Gaussian limit. The assumption about bacterial "regulated freedom" or "decision-making" appears in contradict the fundamental principle of time causality. We propose, that this apparent di culty might be resolved by applying the recent understandings of biotic and abiotic self-organization, to the dynamics of the cells' internal biochemical gel.</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Communication-based regulated freedom of response in bacterial colonies","attachmentId":6365565,"attachmentType":"pdf","work_url":"https://www.academia.edu/1041977/Communication_based_regulated_freedom_of_response_in_bacterial_colonies","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/1041977/Communication_based_regulated_freedom_of_response_in_bacterial_colonies"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="4" data-entity-id="111772064" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/111772064/Programming_the_group_behaviors_of_bacterial_communities_with_synthetic_cellular_communication">Programming the group behaviors of bacterial communities with synthetic cellular communication</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="203807186" href="https://independent.academia.edu/Venhar%C3%87EL%C4%B0K">Venhar ÇELİK</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Bioresources and Bioprocessing, 2014</p><p class="ds-related-work--abstract ds2-5-body-sm">Synthetic biology is a newly emerged research discipline that focuses on the engineering of novel cellular behaviors and functionalities through the creation of artificial gene circuits. One important class of synthetic circuits currently under active development concerns the programming of bacterial cellular communication and collective population-scale behaviors. Because of the ubiquity of cell-cell interactions within bacterial communities, having an ability of engineering these circuits is vital to programming robust cellular behaviors. Here, we highlight recent advances in communication-based synthetic gene circuits by first discussing natural communication systems and then surveying various functional engineered circuits, including those for population density control, temporal synchronization, spatial organization, and ecosystem formation. We conclude by summarizing recent advances, outlining existing challenges, and discussing potential applications and future opportunities.</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Programming the group behaviors of bacterial communities with synthetic cellular communication","attachmentId":109209093,"attachmentType":"pdf","work_url":"https://www.academia.edu/111772064/Programming_the_group_behaviors_of_bacterial_communities_with_synthetic_cellular_communication","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/111772064/Programming_the_group_behaviors_of_bacterial_communities_with_synthetic_cellular_communication"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="5" data-entity-id="7767988" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/7767988/Bacterial_colony_Information_processing_and_computational_behavior">Bacterial colony: Information processing and computational behavior</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="14278911" href="https://mackenzie-br.academia.edu/NizamOmar">Nizam Omar</a></div><p class="ds-related-work--metadata ds2-5-body-xs">2011</p><p class="ds-related-work--abstract ds2-5-body-sm">A bacterium presents rudimentary, though powerful, cognitive functions, such as sensing the environment, processing information and contextual interpretation. When part of a colony, bacteria show collective memory, distributed information storage and processing, collective decision making abilities, cooperation and competition, various communication methods and learning at different levels. These features and capabilities allow us to view bacteria colonies as complex adaptive systems, from which much inspiration can be taken to the design of bioinspired tools and algorithms for problem solving and the modeling of biological phenomena. Despite some effort has been taken in this direction, emphasizing applications in optimization, the present paper brings a discussion of bacteria as useful information processing systems under an intelligent agent framework. The main benefits of this discussion, thus, are the presentation of an intelligent agent-based perspective of bacteria, the stress of the main communication skills and mechanisms of bacteria, and a structured discussion of their main information processing and learning. Our hope is that this paper paves the conceptual ground for the design of novel bacteria inspired algorithms with applications over several areas, from the mining of large databases, to the design of sophisticated decision-making mechanisms for collective robotics.</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Bacterial colony: Information processing and computational behavior","attachmentId":48347554,"attachmentType":"pdf","work_url":"https://www.academia.edu/7767988/Bacterial_colony_Information_processing_and_computational_behavior","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/7767988/Bacterial_colony_Information_processing_and_computational_behavior"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="6" data-entity-id="85123112" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/85123112/Toward_Engineering_Biosystems_With_Emergent_Collective_Functions">Toward Engineering Biosystems With Emergent Collective Functions</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="217796623" href="https://independent.academia.edu/VittorioBartoli1">Vittorio Bartoli</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Frontiers in Bioengineering and Biotechnology, 2020</p><p class="ds-related-work--abstract ds2-5-body-sm">Many complex behaviors in biological systems emerge from large populations of interacting molecules or cells, generating functions that go beyond the capabilities of the individual parts. Such collective phenomena are of great interest to bioengineers due to their robustness and scalability. However, engineering emergent collective functions is difficult because they arise as a consequence of complex multi-level feedback, which often spans many length-scales. Here, we present a perspective on how some of these challenges could be overcome by using multi-agent modeling as a design framework within synthetic biology. Using case studies covering the construction of synthetic ecologies to biological computation and synthetic cellularity, we show how multi-agent modeling can capture the core features of complex multi-scale systems and provide novel insights into the underlying mechanisms which guide emergent functionalities across scales. The ability to unravel design rules underpinning these behaviors offers a means to take synthetic biology beyond single molecules or cells and toward the creation of systems with functions that can only emerge from collectives at multiple scales.</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Toward Engineering Biosystems With Emergent Collective Functions","attachmentId":89920488,"attachmentType":"pdf","work_url":"https://www.academia.edu/85123112/Toward_Engineering_Biosystems_With_Emergent_Collective_Functions","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/85123112/Toward_Engineering_Biosystems_With_Emergent_Collective_Functions"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="7" data-entity-id="73043512" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/73043512/Towards_Engineering_Biosystems_with_Emergent_Collective_Functions">Towards Engineering Biosystems with Emergent Collective Functions</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="8111814" href="https://bham.academia.edu/JanUlrichKreft">Jan-Ulrich Kreft</a></div><p class="ds-related-work--abstract ds2-5-body-sm">Many complex behaviours in biological systems emerge from large populations of interacting molecules or cells, generating functions that go beyond the capabilities of the individual parts. Such collective phenomena are of great interest to bioengineers due to their robustness and scalability. However, engineering emergent collective functions is difficult because they arise as a consequence of complex multi-level feedback, which often spans multiple length-scales. Here, we present a perspective on how some of these challenges could be overcome by using multi-agent modelling as a design framework within synthetic biology. Using case studies covering the construction of synthetic ecologies to biological computation and synthetic cellularity, we show how multi-agent modelling can capture the core features of complex multi-scale systems and provide novel insights into the underlying mechanisms which guide emergent functionalities across scales. The ability to unravel design rules underp...</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Towards Engineering Biosystems with Emergent Collective Functions","attachmentId":81722495,"attachmentType":"pdf","work_url":"https://www.academia.edu/73043512/Towards_Engineering_Biosystems_with_Emergent_Collective_Functions","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/73043512/Towards_Engineering_Biosystems_with_Emergent_Collective_Functions"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="8" data-entity-id="18387588" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/18387588/Bacterial_computing_a_form_of_natural_computing_and_its_applications">Bacterial computing: a form of natural computing and its applications</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="4748377" href="https://independent.academia.edu/RafaelLahozBeltra">Rafael Lahoz-Beltra</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Frontiers in microbiology, 2014</p><p class="ds-related-work--abstract ds2-5-body-sm">The capability to establish adaptive relationships with the environment is an essential characteristic of living cells. Both bacterial computing and bacterial intelligence are two general traits manifested along adaptive behaviors that respond to surrounding environmental conditions. These two traits have generated a variety of theoretical and applied approaches. Since the different systems of bacterial signaling and the different ways of genetic change are better known and more carefully explored, the whole adaptive possibilities of bacteria may be studied under new angles. For instance, there appear instances of molecular &quot;learning&quot; along the mechanisms of evolution. More in concrete, and looking specifically at the time dimension, the bacterial mechanisms of learning and evolution appear as two different and related mechanisms for adaptation to the environment; in somatic time the former and in evolutionary time the latter. In the present chapter it will be reviewed the...</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Bacterial computing: a form of natural computing and its applications","attachmentId":42212653,"attachmentType":"pdf","work_url":"https://www.academia.edu/18387588/Bacterial_computing_a_form_of_natural_computing_and_its_applications","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/18387588/Bacterial_computing_a_form_of_natural_computing_and_its_applications"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="9" data-entity-id="50278173" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/50278173/Exploiting_Self_organization_in_Bioengineered_Systems_A_Computational_Approach">Exploiting Self-organization in Bioengineered Systems: A Computational Approach</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="47905598" href="https://independent.academia.edu/GregoryPodgorski">Gregory Podgorski</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Frontiers in Bioengineering and Biotechnology</p><p class="ds-related-work--abstract ds2-5-body-sm">The productivity of bioengineered cell factories is limited by inefficiencies in nutrient delivery and waste and product removal. Current solution approaches explore changes in the physical configurations of the bioreactors. This work investigates the possibilities of exploiting self-organizing vascular networks to support producer cells within the factory. A computational model simulates de novo vascular development of endothelial-like cells and the resultant network functioning to deliver nutrients and extract product and waste from the cell culture. Microbial factories with vascular networks are evaluated for their scalability, robustness, and productivity compared to the cell factories without a vascular network. Initial studies demonstrate that at least an order of magnitude increase in production is possible, the system can be scaled up, and the self-organization of an efficient vascular network is robust. The work suggests that bioengineered multicellularity may offer efficiency improvements difficult to achieve with physical engineering approaches.</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Exploiting Self-organization in Bioengineered Systems: A Computational Approach","attachmentId":68323700,"attachmentType":"pdf","work_url":"https://www.academia.edu/50278173/Exploiting_Self_organization_in_Bioengineered_Systems_A_Computational_Approach","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/50278173/Exploiting_Self_organization_in_Bioengineered_Systems_A_Computational_Approach"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div></div></div><div class="ds-sticky-ctas--wrapper js-loswp-sticky-ctas hidden"><div class="ds-sticky-ctas--grid-container"><div class="ds-sticky-ctas--container"><button class="ds2-5-button js-swp-download-button" data-signup-modal="{"location":"continue-reading-button--sticky-ctas","attachmentId":36051985,"attachmentType":"pdf","workUrl":null}">See full PDF</button><button class="ds2-5-button ds2-5-button--secondary js-swp-download-button" data-signup-modal="{"location":"download-pdf-button--sticky-ctas","attachmentId":36051985,"attachmentType":"pdf","workUrl":null}"><span class="material-symbols-outlined" style="font-size: 20px" translate="no">download</span>Download PDF</button></div></div></div><div class="ds-below-fold--grid-container"><div class="ds-work--container js-loswp-embedded-document"><div class="attachment_preview" data-attachment="Attachment_36051985" style="display: none"><div class="js-scribd-document-container"><div class="scribd--document-loading js-scribd-document-loader" style="display: block;"><img alt="Loading..." src="//a.academia-assets.com/images/loaders/paper-load.gif" /><p>Loading Preview</p></div></div><div style="text-align: center;"><div class="scribd--no-preview-alert js-preview-unavailable"><p>Sorry, preview is currently unavailable. You can download the paper by clicking the button above.</p></div></div></div></div><div class="ds-sidebar--container js-work-sidebar"><div class="ds-related-content--container"><h2 class="ds-related-content--heading">Related papers</h2><div class="ds-related-work--container js-related-work-sidebar-card" data-collection-position="0" data-entity-id="68962147" data-sort-order="default"><a class="ds-related-work--title js-related-work-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/68962147/Self_organization_of_Symbiotic_Multicellular_Structures">Self-organization of Symbiotic Multicellular Structures</a><div class="ds-related-work--metadata"><a class="js-related-work-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="70375534" href="https://independent.academia.edu/YvesDuthen">Yves Duthen</a></div><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Self-organization of Symbiotic Multicellular Structures","attachmentId":79245570,"attachmentType":"pdf","work_url":"https://www.academia.edu/68962147/Self_organization_of_Symbiotic_Multicellular_Structures","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-related-work-grid-card-view-pdf" href="https://www.academia.edu/68962147/Self_organization_of_Symbiotic_Multicellular_Structures"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-related-work-sidebar-card" data-collection-position="1" data-entity-id="7131081" data-sort-order="default"><a class="ds-related-work--title js-related-work-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/7131081/Bio_inspired_self_organizing_cellular_systems">Bio-inspired self-organizing cellular systems</a><div class="ds-related-work--metadata"><a class="js-related-work-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="12289713" href="https://hes-so.academia.edu/FabienVannel">Fabien Vannel</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Biosystems, 2008</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Bio-inspired self-organizing cellular systems","attachmentId":48589215,"attachmentType":"pdf","work_url":"https://www.academia.edu/7131081/Bio_inspired_self_organizing_cellular_systems","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-related-work-grid-card-view-pdf" href="https://www.academia.edu/7131081/Bio_inspired_self_organizing_cellular_systems"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-related-work-sidebar-card" data-collection-position="2" data-entity-id="73326531" data-sort-order="default"><a class="ds-related-work--title js-related-work-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/73326531/Digital_organ_cooperation_toward_the_assembly_of_a_self_feeding_organism">Digital organ cooperation: toward the assembly of a self-feeding organism</a><div class="ds-related-work--metadata"><a class="js-related-work-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="70375534" href="https://independent.academia.edu/YvesDuthen">Yves Duthen</a></div><p class="ds-related-work--metadata ds2-5-body-xs">… in Artificial Life. 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translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-related-work-sidebar-card" data-collection-position="3" data-entity-id="12230526" data-sort-order="default"><a class="ds-related-work--title js-related-work-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/12230526/Cooperative_Strategies_and_Genome_Cybernetics_in_Formation_of_Complex_Bacterial_Patterns">Cooperative Strategies and Genome Cybernetics in Formation of Complex Bacterial Patterns</a><div class="ds-related-work--metadata"><a class="js-related-work-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="30730391" href="https://independent.academia.edu/EshelBenJacob">Eshel Ben-Jacob</a></div><p class="ds-related-work--metadata ds2-5-body-xs">1994</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" 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js-related-work-sidebar-card" data-collection-position="4" data-entity-id="85519897" data-sort-order="default"><a class="ds-related-work--title js-related-work-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/85519897/Engineered_communications_for_microbial_robotics">Engineered communications for microbial robotics</a><div class="ds-related-work--metadata"><a class="js-related-work-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="103895521" href="https://independent.academia.edu/LitonRoy3">Liton Roy</a></div><p class="ds-related-work--metadata ds2-5-body-xs">DNA Computing, 2001</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Engineered communications for microbial 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href="https://www.academia.edu/73987026/Bacterial_computing_with_engineered_populations">Bacterial computing with engineered populations</a><div class="ds-related-work--metadata"><a class="js-related-work-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="67839087" href="https://independent.academia.edu/AlfonsoJaramillo5">Alfonso Jaramillo</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Philosophical transactions. Series A, Mathematical, physical, and engineering sciences, 2015</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Bacterial computing with engineered populations","attachmentId":82305012,"attachmentType":"pdf","work_url":"https://www.academia.edu/73987026/Bacterial_computing_with_engineered_populations","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-related-work-grid-card-view-pdf" href="https://www.academia.edu/73987026/Bacterial_computing_with_engineered_populations"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div 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