Hyobin Kim, Amit Kumar, Cecilia Lövkvist, António M Palma, Patrick Martin, Junil Kim, Praveen Bhoopathi, Jose Trevino, Paul Fisher. Esha Madan, Rajan Gogna, Kyoung Jae Won
Molecular Systems Biology (2023)19:e11670

Cells have evolved their communication methods to sense their microenvironments and send biological signals. In addition to communication using ligands and receptors, cells use diverse channels including gap junctions to communicate with their immediate neighbors. Current approaches, however, cannot effectively capture the influence of various microenvironments. Here, we propose a novel approach to investigate cell neighbor-dependent gene expression (CellNeighborEX) in spatial transcriptomics (ST) data. To categorize cells based on their microenvironment, CellNeighborEX uses direct cell location or the mixture of transcriptome from multiple cells depending on ST technologies. For each cell type, CellNeighborEX identifies diverse gene sets associated with partnering cell types, providing further insight. We found that cells express different genes depending on their neighboring cell types in various tissues including mouse embryos, brain, and liver cancer. Those genes are associated with critical biological processes such as development or metastases. We further validated that gene expression is induced by neighboring partners via spatial visualization. The neighbor-dependent gene expression suggests new potential genes involved in cell–cell interactions beyond what ligand-receptor co-expression can discover.

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“To be a part of the universe that gets to spin for a time, and to create a unique pocket of meaning: That is indeed something to be grateful for…”

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Jaime Gómez-Márquez

The Science of Nature  110, Article number: 53 (2023)

What is life? Multiple definitions have been proposed to answer this question, but unfortunately, none of them has reached the consensus of the scientific community. Here, the strategy used to define what life is was based on first establishing which characteristics are common to all living systems (organic nature, entropy-producing system, self-organizing, reworkable pre-program, capacity to interact and adapt, reproduction and evolution) and from them constructing the definition taking into account that reproduction and evolution are not essential for life. On this basis, life is defined as an interactive process occurring in entropy-producing, adaptive, and informative (organic) systems. An unforeseen consequence of the inseparable duality between the system (living being) and the process (life) is the interchangeability of the elements of the definition to obtain other equally valid alternatives. In addition, in the light of this definition, cases of temporarily lifeless living systems (viruses, dormant seeds, and ultracold cells) are analyzed, as well as the status of artificial life entities and the hypothetical nature of extraterrestrial life. All living systems are perishable because the passage of time leads to increasing entropy. Life must create order by continuously producing disorder and exporting it to the environment and so we move and stay in the phase transition between order and chaos, far from equilibrium, thanks to the input of energy from the outside. However, the passage of time eventually leads us to an end in which life disappears and entropy increases.

Read the full article at: link.springer.com

Ana Teixeira de Melo Leo Simon Dominic Caves Charbel N. El-Hani Letícia Renault Carlos Gershenson Jorge Soto-Andrade Raquel Ribeiro Tina Röck Stefan Pernar Isabel Britez Lee Fredric Mondshein Jonny Morell

The study of complex systems has led to deep transformations in our modes of thinking, challenging our conceptions of reality and, with them, our roles and possibilities for action as agents in a complex world. A variety of modes of thinking co-exist within the fuzzy boundaries of the domain of complexity studies. Different modes of thinking complexity and of thinking ‘in’ complexity (enacting its principles) can be distinguished in the literature, even though they are not always explicitly identified. Despite the seminal calls of Edgar Morin for the development of more generalised modes of complex thinking, this is still an underdeveloped area of research and practice under the scope of Complexity Studies.

This paper aims to make a contribution to the understanding of complexity and complex systems by offering a discussion around the complexity of the modes of thinking complexity. We report both the process and the outcomes of an interdisciplinary workshop aimed at identifying key theoretical, empirical, methodological and pragmatic challenges and questions pertaining to how we think, build, coordinate and practise different modes of thinking complexity and of thinking in complexity (thinking complexly). The workshop adopted a collaborative and dialogical approach organised by a methodology grounded in a theoretical framework for the practice of complex thinking. The methodology was designed to support complex relational dialogues and facilitate emergence (e.g. of new ideas; approaches; levels of understanding; solutions) in the collective discussion. We conducted a mixed-method evaluation of both the process and contents of the discussion using a combination of inductive qualitative thematic analysis and network analysis. The results point towards new areas for interdisciplinary research and practice, signposting domains that have been under explored within the realm of complexity studies and complexity sciences.

Read the full article at: osf.io