Biology subjects

Walker, S. I.

Publications and source records attributed to Walker, S. I..

8 recordsLinked to original sources

bioRxiv2024

Revealing non-trivial information structures in aneural biological tissues via functional connectivity

A central challenge in the progression of a variety of open questions in biology, such as morphogenesis, wound healing, and development, is learning from empirical data how information is integrated to support tissue-level function and behavior. Information-theoretic approaches provide a quantitative framework for extracting patterns from data, but so far have been predominantly applied to neuronal systems at the tissue-level. Here, we demonstrate how time series of Ca2+ dynamics can be used to identify the structure and information dynamics of other biological tissues. To this end, we expressed the calcium reporter GCaMP6s in an organoid system of explanted amphibian epidermis derived from the African clawed frog Xenopus laevis, and imaged calcium activity pre- and post- a puncture injury, for six replicate organoids. We constructed functional connectivity networks by computing mutual information between cells from time series derived using medical imaging techniques to track intracellular Ca2+. We analyzed network properties including degree distribution, spatial embedding, and modular structure. We find organoid networks exhibit more connectivity than null models, with high degree hubs and mesoscale community structure with spatial clustering. Utilizing functional connectivity networks, we show the tissue retains non-random features after injury, displays long range correlations and structure, and non-trivial clustering that is not necessarily spatially dependent. Our results suggest increased integration after injury, possible cellular coordination in response to injury, and some type of generative structure of the anatomy. While we study Ca2+ in Xenopus epidermal cells, our computational approach and analyses highlight how methods developed to analyze functional connectivity in neuronal tissues can be generalized to any tissue and fluorescent signal type. Our framework therefore provides a bridge between neuroscience and more basal modes of information processing. Author summaryA central challenge in understanding several diverse processes in biology, including morphogenesis, wound healing, and development, is learning from empirical data how information is integrated to support tissue-level function and behavior. Significant progress in understanding information integration has occurred in neuroscience via the use of observable live calcium reporters throughout neural tissues. However, these same techniques have seen limited use in the non-neural tissues of multicellular organisms despite similarities in tissue communication. Here we utilize methods designed for neural tissues and modify them to work on any tissue type, demonstrating how non-neural tissues also contain non-random and potentially meaningful structures to be gleaned from information theoretic approaches. In the case of epidermal tissue derived from developing amphibians, we find non-trivial informational structure over greater spatial and temporal scales than those found in neural tissue. This hints at how more exploration into information structures within these tissue types could provide a deeper understanding into information processing within living systems beyond the nervous system.

systems biology↗

bioRxiv2023

Observations of Elemental Composition of Enceladus Consistent with Generalized Models of Theoretical Ecosystems

Recent analysis of data from the Cassini Cosmic Dust Analyzer confirm geochemical modeling work that shows that the ocean of Enceladus contains considerable quantities of inorganic phosphorus as well as ammonium [55]. Technological advancement in flight instrumentation will continue to yield increasingly detailed data about the relative elemental and molecular composition of life detection candidates. Apart from speculating about threshold concentrations of bioactive compounds to support ecosystems, metabolic and ecological theory can provide a powerful interpretative lens to assess whether extraterrestrial environments are compatible with living ecosystems. Using multiple levels of ecological analysis, spanning from assuming strictly Earth-like organismal physiology to more agnostic understandings of putative biochemistries, we compare the proposed N:P stoichiometries of the Enceledus ocean to possible ecologies. We use chemostat models to predict potentially supportable biomass concentrations under different energy and matter flux regimes, macromolecular allometric theory to compare hypothetical biomass N:P ratios to possible environmental N:P supply ratios, and finally take a data-driven biogeochemical approach to predict possible biomass N:P ratios from the observed dissolved ratios. All three of our modeling approaches suggest marginal compatibility of an ecosystem with the ranges of dissolved N and P concentrations in the Enceledean ocean. Based on our analysis, we suggest two main priorities for further research into terrestrial analogs to improve our ability to interpret geochemical ratios as a life detection instrument.

microbiology↗

bioRxiv2021

The information signature of diverging lineages

Divergence and speciation are the generators of biodiversity on Earth. Yet, we still seek to understand why species are unevenly distributed across taxa and geographic settings. This is partly because we lack a way to directly compare aspects of population divergence across unrelated species and an integrative quantitative framework for how geographical setting relates to genetic divergence. Here we postulate that, based on communications theory, there is a communications channel between Earths surface and the structuring of genomic information among populations. Each species is a separate receiver of this message. Organism traits determine the clarity of that channel. Calculating the partial information decomposition (PID) of genetic metrics under different evolutionary scenarios can measure the signature of this communication. We show in silico how the informational decomposition of 97,200 genetic lattices varies as lineages diverge. The decomposed nodes of Tajimas D, {theta}W, and {pi} show strong context-dependent information signatures, while FST was least informative. Specific decompositions detected whether lineages divergence with or without gene flow better than current SFS-based tools. The study of information in an evolutionary genomic and landscape context suggests it may be a helpful framework and for understanding the diversity of life across Earth and their coevolution.

evolutionary biology↗

bioRxiv2021

Naïve individuals promote collective exploration in homing pigeons

Group-living animals that rely on stable foraging or migratory routes can develop behavioural traditions to pass route information down to inexperienced individuals. Striking a balance between exploitation of social information and exploration for better alternatives is essential to prevent the spread of maladaptive traditions. We investigated this balance during cumulative route development in the homing pigeon Columba livia. We quantified information transfer within pairs of birds in a transmission-chain experiment and determined how birds with different levels of experience contributed to the exploration- exploitation trade-off. Newly introduced naive individuals were initially more likely to initiate exploration than experienced birds, but the pair soon settled into a pattern of alternating leadership with both birds contributing equally. Experimental pairs showed an oscillating pattern of exploration over generations that might facilitate the discovery of more efficient routes. Our results introduce a new perspective on the roles of leadership and information pooling in the context of collective learning.

animal behavior and cognition↗

bioRxiv2021

On the Non-uniqueness Problem in Integrated Information Theory

Integrated Information Theory is currently the leading mathematical theory of consciousness. The core of the theory relies on the calculation of a scalar mathematical measure of consciousness, {Phi}, which is deduced from the phenomenological axioms of the theory. Here, we show that despite its widespread use, {Phi} is not a well-defined mathematical concept in the sense that the value it specifies is neither unique nor specific. This problem, occasionally referred to as "undetermined qualia", is the result of degeneracies in the optimization routine used to calculate {Phi}, which leads to ambiguities in determining the consciousness of systems under study. As demonstration, we first apply the mathematical definition of {Phi} to a simple AND+OR logic gate system and show 83 non-unique {Phi} values result, spanning a substantial portion of the range of possibilities. We then introduce a Python package called PyPhi-Spectrum which, unlike currently available packages, delivers the entire spectrum of possible {Phi} values for a given system. We apply this to a variety of examples of recently published calculations of {Phi} and show how virtually all {Phi} values from the sampled literature are chosen arbitrarily from a set of non-unique possibilities, the full range of which often includes both conscious and unconscious predictions. Lastly, we review proposed solutions to this degeneracy problem, and find none to provide a satisfactory solution, either because they fail to specify a unique {Phi} value or yield {Phi} = 0 for systems that are clearly integrated. We conclude with a discussion of requirements moving forward for scientifically valid theories of consciousness that avoid these degeneracy issues.

neuroscience↗

bioRxiv2019

Division of labor promotes the spread of information in colony emigrations by the ant Temnothorax rugatulus

The fitness of group-living animals often depends on how well members share information needed for collective decision-making. Theoretical studies have shown that collective choices can emerge in a homogeneous group of individuals following identical rules, but real animals show much evidence for heterogeneity in the degree and nature of their contribution to group decisions. In social insects, for example, the transmission and processing of information is influenced by a well-organized division of labour. Studies that accurately quantify how this behavioural heterogeneity affects the spread of information among group members are still lacking. In this paper, we look at nest choices during colony emigrations of the ant Temnothorax rugatulus and quantify the degree of behavioural heterogeneity of workers. Using methods from both machine learning and network analysis, we identify and characterize four behavioural castes of workers - primary, secondary, passive, and wandering - covering distinct roles in the spread of information during each emigration. This detailed characterization of the contribution of each worker can improve models of collective decision-making in this species and promises a deeper understanding of behavioural variation at the colony level.

animal behavior and cognition↗

bioRxiv2019

Ants acknowledge information to control its rate of transfer

Behavioral correlations stretching over time are an essential but often neglected aspect of interactions among animals. These correlations pose a challenge to current behavioral-analysis methods that lack effective means to analyze complex series of interactions. Here we show that non-invasive information-theoretic tools can be used to reveal communication protocols that guide complex social interactions by measuring simultaneous flows of different types of information between subjects. We demonstrate this approach by showing that the tandem-running behavior of the ant Temnothorax rugatulus and that of the termites Coptotermes formosanus and Reticulitermes speratus are governed by different communication protocols. Our discovery reconciles the diverse ultimate causes of tandem running across these two taxa with their apparently similar signaling mechanisms. We show that bidirectional flow of information is present only in ants and is consistent with the use of acknowledgement signals to regulate the flow of directional information.

animal behavior and cognition↗

bioRxiv2019

Assessing the viability of biochemical networks across planets

The concept of the origin of life implies that initially, life emerged from a non-living medium. If this medium was Earths geochemistry, then that would make life, by definition, a geochemical process. The extent to which life on Earth today could subsist outside of the geochemistry from which it is embedded is poorly quantified. By leveraging large biochemical datasets in conjunction with planetary observations and computational tools, this research provides a methodological foundation for the quantitative assessment of our biologys viability in the context of other geospheres. Investigating a case study of alkaline prokaryotes in the context of Enceladus, we find that the chemical compounds observed on Enceladus thus far would be insufficient to allow even these extremophiles to produce the compounds necessary to sustain a viable metabolism. The environmental precursors required by these organisms provides a map for the compounds which should be prioritized for detection in future planetary exploration missions. The results of this framework have further consequences in the context of planetary protection, and hint that forward contamination may prove infeasible without meticulous intent.

systems biology↗