Ricard Sole

Ricard Sole
University Pompeu Fabra | UPF · Faculty of Health and Life Sciences

Phd Physics

About

415
Publications
89,222
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
20,825
Citations
Citations since 2017
50 Research Items
6298 Citations
201720182019202020212022202302004006008001,000
201720182019202020212022202302004006008001,000
201720182019202020212022202302004006008001,000
201720182019202020212022202302004006008001,000
Additional affiliations
January 2001 - present
Institute of Evolutionary Biology
Position
  • ICREA Research Professor
January 1997 - present
Santa Fe Institute
Position
  • External professor

Publications

Publications (415)
Article
Full-text available
It has been recently suggested that engineered microbial strains could be used to protect ecosystems from undesirable tipping points and biodiversity loss. A major concern in this context is the potential unintended consequences, which are usually addressed in terms of designed genetic constructs aimed at controlling overproliferation. Here we pres...
Poster
Full-text available
Current ecosystems are suffering from the Anthropogenic threats that are risking our own existence. The effects of human societies are pushing the biomes to cross their own limits, even reaching their tipping points. For instance, the rise of global temperature is increasing the aridity in already arid, and thus promoting changes in for instance th...
Article
Full-text available
Cognitive networks have evolved to cope with uncertain environments in order to make reliable decisions. Such decision making circuits need to respond to the external world in efficient and flexible ways, and one potentially general mechanism of achieving this is grounded in critical states. Mounting evidence has shown that brains operate close to...
Preprint
Cognitive networks have evolved to cope with uncertain environments in order to make reliable decisions. Such decision making circuits need to respond to the external world in efficient and flexible ways, and one potentially general mechanism of achieving this is grounded in critical states. Mounting evidence has shown that brains operate close to...
Article
Full-text available
Complex dynamical fluctuations, from intracellular noise, brain dynamics or computer traffic display bursting dynamics consistent with a critical state between order and disorder. Living close to the critical point has adaptive advantages and it has been conjectured that evolution could select these critical states. Is this the case of living cells...
Preprint
With ongoing climate change, the probability of crossing environmental thresholds promoting abrupt changes in ecosystem structure and functioning is higher than ever. In drylands (sites where it rains less than 60% of what is evaporated), recent research has shown how the crossing of three particular aridity thresholds (defining three consecutive p...
Article
Full-text available
Multicellular entities are characterized by intricate spatial patterns, intimately related to the functions they perform. These patterns are often created from isotropic embryonic structures, without external information cues guiding the symmetry breaking process. Mature biological structures also display characteristic scales with repeating distri...
Preprint
Full-text available
Complex dynamical fluctuations, from molecular noise within cells, collective intelligence, brain dynamics or computer traffic have been shown to display noisy behaviour consistent with a critical state between order and disorder. Living close to the critical point can have a number of adaptive advantages and it has been conjectured that evolution...
Preprint
Full-text available
Complex dynamical fluctuations, from molecular noise within cells, collective intelligence, brain dynamics or computer traffic have been shown to display noisy behaviour consistent with a critical state between order and disorder. Living close to the critical point can have a number of adaptive advantages and it has been conjectured that evolution...
Preprint
Viruses have established symbiotic relationships with almost every other living organism on Earth and at all levels of biological organisation, from other viruses up to entire ecosystems. In most cases, peacefully coexisting with their hosts, but in most relevant cases, parasitising them and inducing diseases. Viruses are playing an essential role...
Article
Metazoans gather information from their environments and respond in predictable ways. These computational tasks are achieved with neural networks of varying complexity. Their performance must be reliable over an individual’s lifetime while dealing with the shorter lifespan of cells and connection failure—thus rendering ageing a relevant feature. Ho...
Preprint
Full-text available
Multicellular entities are characterized by exquisite spatial patterns, intimately related to the functions they perform. Oftentimes these patterns emerge as periodic structures with a well-defined characteristic scale. A candidate mechanism to explain their origins was early introduced by Alan Turing through the interaction and diffusion of two so...
Preprint
Viruses have established symbiotic relationships with almost every other living organism on Earth and at all levels of biological organization, from other viruses up to entire ecosystems. In most cases, peacefully coexisting with their hosts, but in most relevant cases, parasitizing them and inducing diseases. Viruses are playing an essential role...
Article
Full-text available
What is the potential for synthetic biology as a way of engineering, on a large scale, complex ecosystems? Can it be used to change endangered ecological communities and rescue them to prevent their collapse? What are the best strategies for such ecological engineering paths to succeed? Is it possible to create stable, diverse synthetic ecosystems...
Article
Full-text available
What are relevant levels of description when investigating human language? How are these levels connected to each other? Does one description yield smoothly into the next one such that different models lie naturally along a hierarchy containing each other? Or, instead, are there sharp transitions between one description and the next, such that to g...
Preprint
What are relevant levels of description when investigating human language? How are these levels connected to each other? Does one description yield smoothly into the next one such that different models lie naturally along a hierarchy containing each other? Or, instead, are there sharp transitions between one description and the next, such that to g...
Preprint
Full-text available
What is the potential for synthetic biology as a way of engineering, on a large scale, complex ecosystems? Can it be used to change endangered ecological communities and rescue them to prevent their collapse? What are the best strategies for such ecological engineering paths to succeed? Is it possible to create stable, diverse synthetic ecosystems...
Preprint
Semiarid ecosystems are threatened by global warming due to longer dehydration times and increasing soil degradation. Mounting evidences indicate that, given the current trends, drylands are likely to expand and possibly experience catastrophic shifts from vegetated to desert states. Here we explore a recent suggestion based on the concept of ecosy...
Preprint
Ecological systems are complex dynamical systems. Modelling efforts on ecosystems' dynamical stability have revealed that population dynamics, being highly nonlinear, can be governed by complex fluctuations. Indeed, experimental and field research has provided mounting evidence of chaos in species' abundances, especially for discrete-time systems....
Article
Habitat loss is known to pervade extinction thresholds in metapopulations. Such thresholds result from a loss of stability that can eventually lead to collapse. Several models have been developed to understand the nature of these transitions and how they are affected by the locality of interactions, fluctuations or external drivers. Most models con...
Preprint
A common trait of complex systems is that they can be represented by means of a network of interacting parts. It is, in fact, the network organisation (more than the parts) what largely conditions most higher-level properties, which are not reducible to the properties of the individual parts. Can the topological organisation of these webs provide s...
Poster
Full-text available
Climate change is pushing ecosystems towards extreme conditions and possibly towards tipping points. In drylands, this means to shift from vegetated to desert landscapes. In this poster, we present two approaches to stop the advances of the deserts across the nowadays vegetated semiarid ecosystems. First, replanting vegetation from time to time. Se...
Poster
Full-text available
Semiarid ecosystems are intrinsically bistable. They are systems that can be vegetated or desert under the same climatic conditions. Nowadays, in the global warming conditions, they are pushed towards the tipping points. From dynamical systems, it is known that there is the so-called ghost phenomenon just after the tipping point. In this poster, we...
Article
Full-text available
The emergence of syntax during childhood is a remarkable example of how complex correlations unfold in nonlinear ways through development. In particular, rapid transitions seem to occur as children reach the age of two, which seems to separate a two-word, tree-like network of syntactic relations among words from the scale-free graphs associated wit...
Preprint
Liquid neural networks (or ''liquid brains'') are a widespread class of cognitive living networks characterised by a common feature: the agents (ants or immune cells, for example) move in space. Thus, no fixed, long-term agent-agent connections are maintained, in contrast with standard neural systems. How is this class of systems capable of display...
Article
Full-text available
Language can be described as a network of interacting objects with different qualitative properties and complexity. These networks include semantic, syntactic, or phonological levels and have been found to provide a new picture of language complexity and its evolution. A general approach considers language from an information theory perspective tha...
Article
Semiarid ecosystems (including arid, semiarid and dry-subhumid ecosystems) span more than 40% of extant habitats and contain a similar percentage of the human population. Theoretical models and palaeoclimatic data predict a grim future, with rapid shifts towards a desert state, with accelerated diversity losses and ecological collapses. These shift...
Article
Full-text available
Multicellularity is a crucial innovation that has taken place independently at least 25 times in the evolution of life on our planet. Uncovering the evolutionary rules associated to the emergence of this transition has been partially achieved thanks to a combination of comparative cell biology,phylogenetic, paleobiology and genomic studies of primi...
Article
Full-text available
Life evolved on our planet by means of a combination of Darwinian selection and innovations leading to higher levels of complexity. The emergence and selection of replicating entities is a central problem in prebiotic evolution. Theoretical models have shown how populations of different types of replicating entities exclude or coexist with other cl...
Article
Full-text available
A major force contributing to the emergence of novelty in nature is the presence of cooperative interactions, where two or more components of a system act in synergy, sometimes leading to higher-order, emergent phenomena. Within molecular evolution, the so called hypercycle defines the simplest model of an autocatalytic cycle, providing major theor...
Data
Malthusian and hypercycle growth rates for the synthetic strains. a) Time series for the fluorescence of the I - strain, when cultured in M63 medium supplemented with 100 μM of both iso and leu. Coloured dots stand for the average values across 9 replicates (three technical replicates from each of three biological replicates), shaded area indicates...
Data
Agent-based simulations capture the spatial dynamics of hypercycle range expansions. a) Agent-based simulations show analogous scenarios to those observed in Fig 3a. Values on the vertical and horizontal axis indicate the parameter values for the initial extracellular concentration of amino acids (I0 and L0, respectively, see S1 Table). b) Patch wi...
Data
Fraction of P strain in range expansions. a) In silico, fraction of territory colonized by P cells in three-species population range expansions (curves show average values over 5 simulations). Three different scenarios are shown: no ampicillin (Ampi0 = 0.0, see S1 Table), moderate ampicillin concentration (Ampi0 = 2.0), and high ampicillin concentr...
Data
Mutant sectors occasionally arised during experiments. Such mutant sectors were infrequent (less than one mutant sector per colony on average) and were not taken into account for the analysis in the Main text. a) The arrow indicates a mutant sector that reached a significantly wider length than the average length for a L- sector in the colony (obli...
Data
Relevant parameters in the agent-based model. The table shows the main parameters of the agent-based model, as well as the main processes they affect. Unless stated otherwise in the text, the parameter values used in simulations correspond to those in the source code (S2 Text). (PDF)
Data
Growth rates in well-mixed conditions. Approximations for low-density population dynamics used to infer Malthusian and hyperbolic growth rates from experimental data in well-mixed conditions. (PDF)
Data
Spatial structure close to the edge of the population front after four days of incubation. Different concentrations of supplemented iso and leu lead to different spatial dynamics at the edge of the front (e.g., [iso] = 0 and leu = 10−4M leads the L- strain to govern the front). White rectangles indicate the obligate mutualism, facultative mutualism...
Data
Cell concentration scales linearly to fluorescence for the three species. a) Cell concentration in liquid cultures of the I - strain according to their fluorescence. The value of a indicates the slope (in ml−1) obtained by linear regression of the data points. b) In agreement with cell concentration, optical density also scales linearly to fluoresc...
Data
Front speed for one-species hypercycles. Derivation of the theoretical front speed for one-species hypercycles. (PDF)
Data
Cell shape influences mesoscopic boundary domains. a) Fractal dimension for the boundaries between I - and L- patches in the obligate mutualism scenario. Bars indicate average values, while vertical lines indicate standard deviation from three different simulations. b) A snapshot showing the patches of the I - strain (in white), when de division si...
Data
Front shape from reaction-diffusion model for hypercycles. Population density profiles during range expansion of hypercycle strains for different Malthusian growth rates (which models the effect of supplemented amino acids in the medium). The top panel shows the obligate (μi = 0) hypercycle case: the coupled populations propagate as two travelling...
Data
Agent based simulations source code. Source code used to run our simulations in the gro package [63]. (PDF)
Article
Full-text available
We briefly review how microbial biotechnology can contribute to improve activities aiming to restore degraded drylands and to combat their desertification, which are an integral part of the Sustainable Development Goal 15 of the 2030 Agenda. Microbial biotechnology offers notable promise to improve restoration actions based on the use of biocrust-f...
Article
Full-text available
The dynamics of heterogeneous tumor cell populations competing with healthy cells is an important topic in cancer research with deep implications in biomedicine. Multitude of theoretical and computational models have addressed this issue, especially focusing on the nature of the transitions governing tumor clearance as some relevant model parameter...
Preprint
Full-text available
Although the presence of vast amounts of plastic in the open ocean has generated great concern due to its potential ecological consequences, recent studies reveal that its measured abundance is much smaller than expected. Regional and global studies indicate that the difference between expected and actual estimates is enormous, suggesting that a la...
Article
Full-text available
Early theoretical work revealed that the simplest class of autocatalytic cycles, known as hypercycles, provide an elegant framework for understanding the evolution of mutualism. Furthermore, hypercycles are highly susceptible to parasites, spatial structure constituting a key protection against them. However, there is an insufficient experimental v...
Article
Full-text available
Mutualistic networks have been shown to involve complex patterns of interactions among animal and plant species. The architecture of these webs seems to pervade some of their robust and fragile behaviour. Recent work indicates that there is a strong correlation between the patterning of animal-plant interactions and their phylogenetic organisation....
Article
Full-text available
Changing environments pose a challenge to living organisms. Cells need to gather and process incoming information, adapting to changes in predictable ways. This requires in particular the presence of memory, which allows to store different internal states. Biological memory can be stored by switches that retain information of past and present event...
Article
Full-text available
The rise of multicellularity in the early evolution of life represents a major challenge for evolutionary biology. Guidance for finding answers has emerged from disparate fields, from phylogenetics to modelling and synthetic biology, but little is known about the potential origins of multicellular aggregates before genetic programs took full contro...
Article
Full-text available
Efforts in evolutionary developmental biology have shed light on how organs are developed and why evolution has selected some structures instead of others. These advances in the understanding of organogenesis along with the most recent techniques of organotypic cultures, tissue bioprinting and synthetic biology provide the tools to hack the physica...
Article
Full-text available
A major force shaping form and patterns in biology is based in the presence of amplification mechanisms able to generate ordered, large-scale spatial structures out of local interactions and random initial conditions. Turing patterns are one of the best known candidates for such ordering dynamics, and their existence has been proved in both chemica...
Preprint
Full-text available
Background: The dynamics of heterogeneous tumor cell populations competing with healthy cells is an important topic in cancer research with deep implications in biomedicine. Multitude of theoretical and computational models have addressed this issue, especially focusing on the nature of the transitions governing tumor clearance as some relevant mod...
Article
Full-text available
Engineered synthetic biological devices have been designed to perform a variety of functions from sensing molecules and bioremediation to energy production and biomedicine. Notwithstanding, a major limitation of in vivo circuit implementation is the constraint associated to the use of standard methodologies for circuit design. Thus, future success...
Data
Fitting parameters and correlation coefficient r. (DOCX)
Data
Representative FACS analysis using quantitative single cell output. Fluorescence from Output Layer and Buffer Layer cells was assessed by flow cytometry. A total of 10.000 cells were analyzed. (A) Representative FACS plot of a wild type W303 cells. (B) Panel shows mCherry intensity (Y axis) versus autofluorescence (X axis) and allows selecting the...
Data
Theoretical implementation in single cell of a MUX4to1 multiplexer circuit according to standard methodology for circuit design. This circuit requires 10 different promoters, 6 regulated by the external inputs A, B, C, D, E, and F, and 4 for internal connections. Additionally, 8 different wires are necessary (dashed lines), implemented by 8 differe...
Data
Example of computational output detection and data quantification. (A) The quantification of one majority rule experiment is showed as an illustrative example of all circuits’ quantification and data treatment. For every chamber, and for each combination of inputs, fluorescence intensity of the subsets of OL cells was measured versus autofluorescen...
Data
Yeast strains used in this study. (DOCX)
Data
Graphic representation of the architecture of the Input, Output and Buffer Layers cells. (A) Identity cells (ID; top) express the S. cerevisiae alpha factor pheromone under the control of an input-inducible promoter. NOT cells (NOT; bottom) constitutively express this pheromone under the control of a modified TEF1 promoter (TEF1-OplacI). In the pre...
Data
Transfer Function analyses of the Input Layer cell library. Input Layer cells were mixed with the Output Layer GFP cells (OL1) and treated with different inputs concentrations. Samples were incubated for 4h at 30°C and analyzed by FACS. Data are expressed as the percentage of GFP positive cells and represent the mean and standard deviation of three...
Data
Growth curve of the Output Layer and Buffer Layer cells. (A) Output Layer cells OL1 (upper left), OL2 (upper right) and OL3 (lower left) growth curve was measured as in S8 Fig. (B) Buffer Layer cells growth curve was measured as in S8 Fig. (TIF)
Data
Examples of 2-inputs logic gates implemented with the library of cells. (A) AND gate. (B) NOR gate. C) N-IMPLIES gate. Schematic representation of the cells used in the circuits (left). Truth table (middle). Percentage of OL1 GFP-positive cells (right). Cells were mixed proportionally and treated with different combinations of inputs. After computi...
Data
Logic representation of the circuits implemented according to the standard methodology or the novel approach based on ILF. Despite the logic representation of circuits based on ILF involves NOT and OR logic gates, only NOT gates are genetically implemented. OR logic is implicitly implemented by spatial segregation of the consortia. In each consorti...
Data
Supporting information including: Design of minimal logic circuits based on inverted logic formulation (ILF), transfer function fitting, fluorescence data analysis, full description of each cell used in the biological circuits and Engineered Input Layer cells that respond to hormones. (DOCX)
Data
Plasmids strains used in this study. (DOCX)
Data
Relationship between the number of implementable functions and the number of cells and modules required. (A, B, C) Dependence of the number of possible implementable functions with respect to the number of different cells required. Data for functions with 2, 3 and 4 inputs are shown. (D, E, F) Dependence of the number of possible implementable func...
Data
Schematic representation and basic genetic information of the Input Layer cells. Cells in the library respond to six different inputs (DOX; doxycycline, PRO; progesterone, ALD; aldosterone, αCa; C. albicans alpha factor, EST; 17-β-estradiol, DEX; dexamethasone) with two different logics. In the presence of the input, Identity cells (ID, left) expre...
Data
Schematic representation and basic genetic information of the Output Layer and Buffer Layer cells. (A) The Output Layer cells sense S. cerevisiae alpha factor and shut down the expression of a fluorescent protein (GFP, mCherry) or the production of C. albicans alpha factor. All cells are W303 derivatives. (B) The Buffer Layer cell sense C. albicans...
Data
Transfer Function analyses of the Output Layer and Buffer Layer cells. (A) Output Layer cells OL1 (upper left) and OL2 (upper right) were incubated with different concentrations of S. cerevisiae alpha-factor and analyzed as in S6 Fig. Output Layer cells OL3 (lower left) were incubated with Buffer Layer cells in the presence of different concentrati...
Data
Growth curve of the Input Layer cells library. Exponential cultures of Input Layer cells were diluted to OD660 nm ≈ 0.02 and their growth curve was measured using Synergy H1 BioTeK for 24 h. Data represent the mean and standard deviation of three independent experiments. (TIF)
Data
GFP data analysis. (A) Transfer function data of the OL1 cells expressed as GFP a.u. Values ranges from maximum of 1600 to a minimum of 450 GFP a.u and the curve presents a step like shape. Experimental transfer function data were fitted to a Hill equation as described in S1 Text. (B) Normalized GFP (a.u.) transfer function of OL1 cells (round circ...
Data
Design and in vivo implementation of a 3-input majority rule. (A) Schematic representation and spatial distribution of the cells used in the majority rule circuit. The circuit is the same as in Fig 3 except here we used IL7 cells, which respond to DOX (right), instead of the previously used IL12 cells, which respond to DEX (left). (B) Truth table (...
Article
Full-text available
It has been suggested that innovations occur mainly by combination: the more inventions accumulate, the higher the probability that new inventions are obtained from previous designs. Additionally, it has been conjectured that the combinatorial nature of innovations naturally leads to a singularity: at some finite time, the number of innovations sho...