Ricard Solé
@ricard_sole
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Scientist & skeptic. Dad. Pathologically curious. Complexity, synthetic transitions, liquid brains, Earth Terraformation. ICREA+SFI professor. Author. Humanist.
Barcelona, Krakozhia #1Octubre
Joined June 2011
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Farewell to mathematician John Conway. For us, complexity scientists, he will be remembered by the invention of the cellular automaton called the Game of Life, that inspired so many ideas about complexity, computation and life itself.
@sfiscience
@svalver
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Two types of brains have emerged in nature: solid (ours) and liquid (ant colonies, immune system). What can be computed by liquid brains? How can they learn? Are there universal rules? Here's our new paper on the statistical physics of liquid brains
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2K
How do we express Darwin's theory of Natural Selection in mathematical terms? One of the best and most elegant papers about this came from
@univienna
and
@sfiscience
external professor Peter Schuster
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Is evolution predictable? Would the biosphere look the same if we re-played the tape of evolution, as conjectured by SJ Gould? Here's an excellent paper on this challenging problem by Michael Lässig, Ville Mustonen and Aleksandra M. Walczak
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Is biological complexity predictable? Can genes explain development? No, due to the emergent nature of the genotype-phenotype map: higher-level properties are irreducible to lower-level ones. Here's my drawing with CH Waddington as a demon.
@manlius84
@sanewman1
@drmichaellevin
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"Every
#book
, every volume you see here, has a soul. The soul of the person who wrote it and of those who read it and lived and dreamed with it." Farewell to Carlos Ruiz Zafón, who wrote in "The Shadow of the Wind" about a Barcelona that still exists, but fights to survive.
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Why are not all whales dead from cancer? A simple calculation reveals that all other things equal, an animal 1000 times larger than us should be a thousand times more prone to develop cancer. This is not the case. Why? Maths suggests an answer
@cmaley
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What makes biology different from physics? Answer: computation. A great and not well known paper by John Hopfield
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How does complexity arise in evolution? How do innovations emerge? We must deal with networks and hierarchical patterns to answer this challenging question. Check the chapter by
@niles_eldredge
and I. Temkin in
@manlius84
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What is the origin of universality in complex systems? This 1979 paper by Ken Wilson in
@sciam
explains the Renormalization Group, one of the most powerful ideas in physics. Used to study everything from magnets and liquids to ecosystems and societies.
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Are complex systems predictable? Can we use (un)predictability to measure complexity? Here's a great review by A. Vulpiani and co-workers on how chaos, Lyapunov exponents, information theory and statistical physics get together to answer these questions
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How does complexity arise in (macro)evolution? Is it a continuous or a stepwise process? What about hierarchies? Check this new
@Trends_Ecol_Evo
review led by
@svalver
on the
@eldredge
and Gould's Theory of Punctuated Equilibrium across scales.
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What is complexity? What kind of approach is needed to define it? Here's a 1977 paper by Robert Rosen, one of the pioneers of System Science, discussing how information, error and scale are central to this problem,
@manlius84
@PedroM_Z
@_AlexArenas
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After many years of
@CSLab_UPF
teaching Bioengineering at
@UPFBarcelona
, today we started recording our lectures on Biological Design and Mathematical Biomodelling with a Complex Systems + Evolutionary perspective. Soon to be uploaded in a new Youtube channel.
@IBE_Barcelona
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Working on a chapter on Plant Cognition for my book "Liquid brains". Germination is one of the most exciting phenomena, which involves decision-making and dealing with future uncertainties. Overwhelmed by the diversity of seeds, biological time capsules that compute their worlds.
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1940, Jacques Monod Notebook: the curves show bacteria growth on one (left) and two sugars. He wrote about the second "I need to find the origin of this pain in the ass". A member of his PhD jury said the work was "uninteresting". But it ended in a revolution and a Nobel prize.
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Does technology evolve as biology? In many ways, it does. Is it continuous or occurs in bursts? By analyzing the evolution of programming languages with
@svalver
we found the answer. Research started at
@sfiscience
one of the best papers of
@CSLab_UPF
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Is chemistry reducible to physics? Is biology reducible to chemistry? Do we need QM to explain the brain? The answers are negative, due to emergent phenomena, but too often not well explained. Glad to work together with
@manlius84
on a paper on the origins of emergence.
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Does natural selection operate on non-reproducing, higher-level systems? Are ecosystems and societies the target of persistence-based selection? These are key questions to understand complexity. See this new paper
@sfiscience
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How similar are computational and biological systems? How can computer science get inspiration from biology? Here's a great
@EMBOpress
paper by
@umdcs
Saket Navlakha & Ziv Bar-Joseph on the convergence between biology and computer science:
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@michiokaku
Not true at all. This is the old reductionistic program thas has been shown to fail again and again. There is nothing that QM for example can say about why a given DNA sequence is relevant and DNA alone does not tell much about development, which does not explain cognition.
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What is the "right" level of detail required to model and understand a complex system? We know that, on different scales, details on lower levels are often unnecessary. Why? Gene networks are a perfect illustration. Check this comment by S. Bonhordlt
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What is complexity? A system is complex if it displays emergent properties that cannot be reduced to the properties of its parts. Study a single termite and you'll never understand how nests complexity emerges. Interactions are more important
@GTheraulaz
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Very excited to start writing my book for
@PrincetonUPress
on "Liquid brains". An exploration of cognitive systems beyond standard neural networks. Ants, Immune systems, swarms but also plants and beyond. All started at
@sfiscience
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At home, I have extensively used our kitchen wall as a whiteboard for drawing, explaining maths and science to my kids, and sometimes thinking my own stuff. As you can see, we have also been playing tribute to Stranger Things.
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Old picture, circa 1992, the first Complex Systems Lab, after a seminar on spatiotemporal chaos in ecosystems. From L2R, Jordi Delgado, Jordi Bascompte, me, Susanna Manrubia and Bartolo Luque. We had no money, and nobody believed the "Complexity" story. But it was a great time.
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The unpublished work by the late Alan Turing (1912-1954) is available at the Digital Archive site It includes many topics (how to play Go, eliptic functions...) and drawings and calculations related to his theory of morphogenesis. Go and dig around!
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It is unfortunate that the Nobel Prize has ignored the author of the groundbreaking discovery of CRISPR, Spanish scientist Francisco Mojica, who (with many difficulties) identified, understood and named it. One of the heroes of CRISPR
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@BernarGM
En Polònia reciben bofetadas todos los políticos, sin piedad. No hay que extrañarse que Pujol, Duran-Lleida o Rivera no lo puedan ver ni en pintura. Un ejercicio muy sano para todos y a menudo el mejor relato de como estan las cosas.
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How can we model the emergent complexity of microbial ecosystems? How to do the maths & predict their dynamics, from the gut & the soil to the biosphere? Here's a great
@NatureEcoEvo
review
@vdlorenzo_CNB
@BCNCollab
@ftmaestre
@VictorVmaull
@saramitri
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Are tumours like ecosystems? Cancer displays complex, heterogeneous populations that can be mathematically described as interacting species. Check our new paper with
@AguadeGuim
and
@ara_anderson
on generalized Lotka-Volterra models for cancer
@BCNCollab
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Will life be different on other planets? Can we build living systems that depart from what we know? In terms of the logic, maybe not. Check my last paper with several
@sfiscience
colleagues on the "Fundamental constraints on the logic of living systems"
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Can learning and cognition emerge without neurons? Here's a great review of how physical systems can implement neural-like complexity. Thanks to
@RichardWatson90
for pointing me to this conceptual framework.
@drmichaellevin
@UCLALuskin
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Lynn Margulis was born
#OTD
. In 1967 published (as Lynn Sagan) this groundbreaking paper in J. Theoretical Biology on Symbiosis. It had been rejected from many top journals (often based on prejudice) before it became a classic.
@JuliPereto
@IBE_Barcelona
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Why is connectivity so central to complex systems? Because it captures most of the systems-level universal properties of complexity. Here's a review paper by
@GeogDurham
Laura Turnbull and co. that explores this across systems and scales
@Ecohydrology
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While Roman engineers and architects were building cities, termites in Brazil were creating huge mounds that persisted until today and can be seen from space … A good reminder of the power and scale of collective intelligence.
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Great news today with the
@NobelPrize
to legendary Italian physicist Giorgio Parisi. His work had a major impact in biology, from molecular evolution to neural networks and the dynamics of complex adaptive systems. Very much deserved
@sfiscience
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Is there an arrow of time in the brain? Can Boltzmann and Shannon's ideas be used to understand it? Check this paper by
@icreacommunity
Gustavo Deco,
@ysanz6
Morten Kringelbach on how physics and information theory reveal how hierarchical cognition works
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14 years after Alan Turing's death, an unpublished manuscript emerged where he suggested the idea of a "disordered" computer that anticipated the rise of connectionism
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What separates non-living from living matter? When did natural selection start to shape biological complexity? One possibility comes from the physics of phase transitions. Check these papers by
@sfiscience
@Sara_Imari
and co
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Can Turing-like patterns be engineered? After years of hard work, trying many mathematical (thanks
@sfiscience
) and simulation models and experiments, we did it! Now our work is on the cover of
@ACSSynBio
Congratulations to all the team, specially to
@SDuranNebreda
@IBE_Barcelona
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Do ant colonies, biofilms or the immune system behave as neural nets? What is a brain? What is a liquid computer? Do plants support complex cognition? This and much more in our forthcoming issue on "Liquid Brains, Solid Brains" in Philosophical Transactions B
@sfiscience
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How did the human mind become so complex? We are singular in many ways. Why? Here's a
@sciam
paper about this, suggesting that two preconditions to mind's Big Bang were needed: imagining possible alternative futures + the drive to exchange thoughts.
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How do we approach the complexity of life as a nonequilibrium system? Using physics and, in particular, landscape and flux theory, many systems, from cells to ecology and cancer, can be adequately represented and modelled. Check this paper in Reviews of Modern Physics
@APSphysics
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Does the Red Queen reign in the Kingdom of Evolution? Many years after its formulation, Van Valen's hypothesis of evolution as an arms race is still inspiring scholars, from paleontology to game theory. Here's my multiscale picture for a paper on Van Valen's classic work
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Why is life complex? Can physics help understanding the origins and early avolution of life? Using statistical physics, it is possible to conjecture the phase transition from the pre- to the Darwinian world (LUCA & beyond)
@NigelGoldenfeld
@Sara_Imari
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50 years ago, Lynn Margulis (then Lynn Sagan) published her landmark paper on Symbiosis.
@JuliPereto
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What defines complexity? Answer: Emergent properties, i. e. when a system exhibits order at one scale that is irreducible to the properties of its parts. Here's a whole
@RSocPublishing
issue edited by
@manlius84
& Oriol Artime. A lot of great examples.
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What kinds of minds and brains are possible? Can we define a space for cognitions? My talk on "Possible and actual Minds: Mapping the Cognition Space" delivered at UCLA
https://2023symposium.ibp.ucla.edus
is available here
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Can a "theory of everything" explain complexity from atoms and molecules to societies? The answer is negative, and even within physics, emergent, irreducible phenomena exist. Check this paper by
@sfiscience
co-founder David Pines and RB Laughlin
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Can Turing patterns be engineered in synthetic biological populations? Yes: A recent paper by
@imperialcollege
Mark Isalan shows how to obtain regular and tunable Turing structures in growing colonies using
@synbio
:
@vdlorenzo_CNB
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Where does complexity live? In many cases, it seems to emerge close to critical points, as a result of a conflict between order and disorder. Here's my freshman course lecture on our
@CSLab_UPF
Youtube Channel on minimal models of complexity
@sfiscience
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Is biology predictable? This is a hard problem, relevant across scales, from conservation to the human microbiome. Check this
@NatureRevMicro
paper by
@AllisonLopatkin
& James Collins.
@BCNCollab
@vdlorenzo_CNB
@manlius84
@Daniel_R_Amor
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Are there general laws for the time evolution of ecological complexity, from microbiomes to forests? Is there a "least action" principle for community succession? In our new paper led by
@MIT
Serguei Saavedra and
@JieAliceDeng
, we propose such a principle
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Why do DNA, RNA and proteins interact the way they do? In other words, why the Central Dogma of molecular biology? Where does it come from? Using a multilevel selection model, Takeuchi and Kaneko found an answer (based on Symmetry Breaking). Check it out:
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Is evolution an algorithm? How can we mathematically define a fitness landscape? How to calculate the divergence time between species? We keep recording lectures for our "Principles of Biological Design"
@UPFBarcelona
course as part of a Youtube channel.
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What is the origin of hierarchy in complex systems? We addressed this challenging question with
@UniGraz
Bernat Corominas,
@jgonicor
&
@UMACiencias
Carlos Rodriguez caso. Take home message: a lot of hierarchy comes for free. Check our 2013
@pnas
paper:
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How can physics help us define the limits of cellular life? Tomorrow
@sfiscience
professor Chris Kempes will be talking about that at the Barcelona Collaboratorium
@BCNCollab
on "The physical limits of small life". his recent work:
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What is complexity? Complex Systems made of many interacting units display "emergence", i.e. global properties that cannot be reduced to the properties of the units. A new idea? WM Wheeler was one of the advocates of emergence, back in 1927
@sfiscience
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Are genes & cell regulation drivers of brain development? Not really: the complexity of brain folds (size, shape, placement, orientation) arise from an elementary mechanical instability modulated by fetal brain geometry. An amazing paper: .
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Simple nonlinear systems equations can display sensitivity to initial conditions. That's the origin of deterministic chaos. A demon with a vast knowledge of the past will not be able to predict the future beyond a given horizon. Here's my drawing (1st version) of the Chaos demon.
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Do plants develop cancer? Since trees live long and have many cells, shuld we expect to see "tumoral forests" as the on in the image (my drawing)? Spoiler: negative answers to both questions (with exceptions). Understanding why is a fascinating story
@ara_anderson
@AguadeGuim
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Back to Santa Fe
@sfiscience
, my intellectual home. I am working on my spot at the Cormac MacCarthy's Library. This time: liquid brains, universals in the logic of life and synthetic ecosystems. I look forward to some unexpected findings while working the night shift.
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Very sad news today. Farewell to Murray Gell-Mann, Nobel laureate, co-founder of the Santa Fe Institute and a true giant of physics. I will be always in debt to his kindness & support and never forget our many conversations at
@sfiscience
. It was a real honour.
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It's so sad news today. Farewell to Daniel Dennett, one of our most influential colleagues at
@sfiscience
. He was an extraordinary thinker, a phenomenal intellectual, and a brilliant writer. We will miss him enormously.
@danieldennett
@JuliPereto
@svalver
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Is there a unique law (natural selection) underlying the emergence of complexity? Are there alternatives? What can be said from physics? Here's -I believe-one piece of the answer from the great Manfred Eigen,
@JordiPinero
@manlius84
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In a debate with Richard Dawkins, cardinal George Pell made the usual (and rather arrogant) claim that only religious people can have a moral compass. Guess what: he was another child abuser, now found guilty. Just saying
#cardinalpell
@ThinkAtheist
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Soft-bodied marine animals have evolved all kinds of adaptations. Why do complex brains show up only in cephalopods? Why don't we see complex neural architectures in jellyfish? This is my drawing (the last version) of a brainy jellyfish. A missing piece in the cognitive biosphere
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What are the limits of biological computation? Can we engineer living computers (Beyond Turing) using synthetic biology? Check this cool paper by
@AngelGMoreno
in
@CACMmag
@martyn_amos
@vdlorenzo_CNB
@harfel3
@C4COMPUTATION
@drmichaellevin
@Gemma_DLC
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What is needed to achieve a true A.I.? Recently, researchers point to embodiment and social interactions. In this paper with
@brigan_raman
, we suggest that those are part of the necessary, perhaps inevitable evolutionary steps that shaped our brains.
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Is there a "language acquisition device" in our brains, as Chomsky suggested in 1960? Syntax networks in children support this idea. Here's our paper on phase transitions in language acquisition
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How do biological systems cope with their changing worlds? This is a deep problem within evolutionary biology. In this excellent paper by
@sfiscience
external faculty Lauren Ancel Meyers
@meyerslab
and James Bull, an elegant unifying picture is provided
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Is evolution predictable? Kauffman's Adjacent Possible theory suggests a negative answer. Here's my drawing (work in progress) of Kauffman's Demon: it observes the past but only can see how the future unfolds, unable to predict how combinations create novelty and innovation.
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Our first lectures with
@JordiPinero
of the Principles of Biological Design + Mathematical Biology freshman course at
@UPFBarcelona
are on Youtube channel: dynamical systems, evolution, complexity, neural nets, virus dynamics, gene nets ... and more.
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How close are living systems to optimal states? In our new paper in
@PhysRevResearch
with
@artemyte
and
@JordiPinero
we searched for universal bounds to this problem within the context of free energy harvesting, with special attention to molecular machines
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Do languages evolve in time in ways similar to microbes? Is there horizontal information transfer too? Pioneering work in this area was done by Tal Dagan
@kieluni
and co-workers using network science. See the paper here:
@RSocPublishing
@Gemma_DLC
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Liquid Brains, Solid Brains. Ants, termites, slime moulds, flatworms, chemical reactions, plants, neural networks, robot swarms: from theory to experiment, from design to evolution & complexity. Our Theme Issue in
@royalsociety
@RSocPublishing
@sfiscience
Out on Monday 22nd!
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What are the bounds to morphological complexity? Would plants on another planet look different from those here? Probably not due to fundamental evolutionary constraints. Check this
@sciam
paper by the great Karl Niklas
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I just got officially appointed as a member of the Editorial Board of Philosophical Transactions of the Royal Society Series B
@RSocPublishing
Glad to be part of the Journal that published so many groundbreaking works. My favourite: Turing's 1952 "Chemical Basis of Morphogenesis"
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Is evolution like a never-ending race, where species have to keep changing to avoid extinction? My paper on van Valen's Red Queen theory is out in
@BiolTheory
discussing its impact in our understanding of evolved complexity
@sfiscience
@IBE_Barcelona
6
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What is the nature of our (evolved) relationship with viruses? We are literally flooded by them. Welcome to the human virome, with harmful but also beneficial members. Great paper in
@sciam
"The Viruses Inside You"
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To understand the complexity of cells, circuits or nano-systems, we need to understand the deep connections between information and the second law of thermodynamics. Here's a great review of the problem(s)
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What is the proper scale to study virus dynamics? Multiple complexity levels and scales are involved, from cells to the biosphere, the immune system & pandemics. Here's our paper on phase transitions in virology with
@SantiagoFElena
and
@JosepSardanyes
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Octopuses evolved complex brains and intelligence that rivals those of vertebrates. Why are there no other brains in other invertebrates, such as jellyfish? What are the constraints? Here's my drawing (work in progress) of a brainy jellyfish (btw cubomedusae have camera eyes)
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What is the role of complexity, nonlinearity and phase transitions in conservation biology? What kind of lessons from maths can help preserve biodiversity? Here's my last paper in Biological Conservation.
@ftmaestre
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How can a complex organism emerge from simple, homogeneous cells? Symmetry breaking is the key and was first proposed (before Alan Turing) in 1940 by mathematician Nicolas Rashesvky. A largely overlooked paper by the father of theoretical biology
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How did the first protocells originate? Theoretical models suggest that the first genomes required cooperation, which can be challenged by parasites, but can become stable through encapsulation. New experimental work supports this. Check my piece in N&V
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Is cognition a universal feature of the living world? How can we define it? Is a nervous system needed? If so, why? If not, why not? Check the Theme Issue of
@RSocPublishing
led by
@drmichaellevin
and co. on Basal Cognition
3
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What is possible and what is not in complexity? How close are evolved versus designed systems? One way to explore these questions is using Information Theory to characterize network architecture. Check our paper with
@svalver
@IBE_Barcelona
@sfiscience
7
52
249
Is life an expected event? Are there many alternatives to life as we know it? When did information become a dominant component of early living systems? Glad to co-host with Chris Kempes a new Working Group at
@sfiscience
: "Origins of life: the possible and the actual" More soon.
3
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What are the challenges and intervention scenarios for biodiversity towards the 2050 horizon? "Ecological complexity and the biosphere: the next 30 years", our
paper in
@RSocPublishing
Phil Trans B with
@sfiscience
Simon Levin is freely available at
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Can ant colonies be described as a fluid neural network? What are the differences between these "liquid" brains and our "solid" brains? Our paper "Statistical Physics of Liquid Brains" with
@JordiPinero
is out in in arxiv:
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Last notes on the evolution of complexity and its universals in my 2022 notebook. What new adventures wait in 2023? So many plans but, as usual, looking forward to the unexpected.
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Complexity, maths, networks, brains, cells, genes, synbio and evolution: this week we keep recording lectures of our
@UPFBarcelona
course on "Principles of Biological Design" for our (forthcoming) YouTubeChannel with
@JordiPinero
@IBE_Barcelona
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Finishing our last video-recorded lectures for the Principles of Biological Design - Mathematical Systems Biology course at
@UPFBarcelona
Allometric scaling, complexity, and Aging. Soon to be available
@JordiPinero
. Nothing that blackboards to explain science.
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Why is symmetry relevant to our understanding of complexity? Because broken symmetries pervade emergence and are fundamental to our understanding of evolution. Check this paper by
@sfiscience
David Krakauer (&
@RSocPublishing
Theme Issue)
@drmichaellevin
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What is the role played by information theory in biology? Is evolution driven by information? As it happens with physics, information is becoming more central to our understand ecological complexity. A great review of ideas is here:
@bio_diverse
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Is there a universal logic for life here and elsewhere? I had the opportunity to talk about "The bounds of unbounded evolution" at the
@the_prbb
Pere Alberch memorial meeting. Thanks to the organizers
@AMartinezArias
@_JamesSharpe
@EMBLBarcelona
for the invitation.
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Would memories of learned events somehow survive in a body where the brain has been removed? Surprisingly, planarians (flatworms) do it, which challenges our cognition views. Check this paper in
@sciam
on
@drmichaellevin
's unique experiments.
@DoctorJosh
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Are cells like small liquid "brains"? Cells are capable of gathering and processing complex sets of signals and respond in adaptive ways. How close are they to standar neural networks? Here's the seminal 1995 paper by Dennis Bray on cells as computers
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