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Mystery at the heart of life

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By Biologic Institute’s Ann Gauger, at Christianity Today’s Behemoth, the secret life of cells:

Our bodies are made up of some 100 trillion cells. We tend to think of cells as static, because that’s how they were presented to us in textbooks. In fact, the cell is like the most antic, madcap, crowded (yet fantastically efficient) city you can picture. And at its heart lies a mystery—or I should say, several mysteries—involving three special kinds of molecules: DNA, RNA, and proteins.

These molecules are assembled into long chains called polymers, and are uniquely suited for the roles they play. More importantly, life absolutely depends upon them. We have to have DNA, RNA, and protein all present and active at the same time for a living organism to live.

How they work together so optimally and efficiently is not merely amazing, but also a great enigma, a mystery that lies at the heart of life itself. More. Paywall soon after. May be worth it.

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Comments
The search for real theories is more ambitious. It is important that we have concrete examples of biological systems that are operating near an optimum of information transmission or efficiency of representation, [...] [...] we don’t know is whether these are isolated instances, or examples of a general principle. [...] we believe that the coming years will see much more meaningful confrontations between theory and experiment, in a wide range of systems.
Information processing in living systems Gasper Tkacik and William Bialek DOI: 10.1146/annurev-conmatphys-031214-014803 arXiv:1412.8752 [q-bio.QM] arXiv:1412.8752v1 [q-bio.QM]
Complex complexity.Dionisio
February 8, 2017
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[...] connections between information and the phenomena of life have two very different flavors, one grounded in data and the other aiming for a theory in which the behaviors of real biological systems are derivable from some sort of optimization principle.
Information processing in living systems Gasper Tkacik and William Bialek DOI: 10.1146/annurev-conmatphys-031214-014803 arXiv:1412.8752 [q-bio.QM] arXiv:1412.8752v1 [q-bio.QM]
Complex complexity.Dionisio
February 8, 2017
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Cells and organisms sense, compute, and make decisions: to proliferate, to find food, to protect themselves against predators and unfavorable environmental changes, to act in unison with their neighbors within a collective, and—broadly speaking—to invest their limited resources to their maximal benefit.
Information processing in living systems Gasper Tkacik and William Bialek DOI: 10.1146/annurev-conmatphys-031214-014803 arXiv:1412.8752 [q-bio.QM] arXiv:1412.8752v1 [q-bio.QM]
cells make decisions? Wow! Complex complexity.Dionisio
February 8, 2017
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Life depends as much on the flow of information as on the flow of energy. Many of these analyses are motivated by the idea that biological systems may have evolved to optimize the gathering and representation of information.
Information processing in living systems Gasper Tkacik and William Bialek DOI: 10.1146/annurev-conmatphys-031214-014803 arXiv:1412.8752 [q-bio.QM] arXiv:1412.8752v1 [q-bio.QM]
may have evolved to optimize? huh? say what? evolved with a goal? evolution with purpose? Complex complexity.Dionisio
February 8, 2017
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During development the dierent identities of cells are determined by sequentially expressing particular subsets of genes in dierent parts of the embryo. Proper development relies on the correct spatial-temporal assignment of cell types. [...] the initial information about the position along the anterior-posterior (AP) axis is encoded in the exponentially decaying Bicoid gradient.
Precision of readout at the hunchback gene Jonathan Desponds, Huy Tran, Teresa Ferraro, Tanguy Lucas, Carmina Perez Romero, Aurelien Guillou, Cecile Fradin, Mathieu Coppey, Nathalie Dostatni, Aleksandra M Walczak doi: https://doi.org/10.1101/063784 PLOS Computational Biology doi: 10.1371/journal.pcbi.1005256
Complex complexity.Dionisio
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[...] the precision of the expression of the hunchback gene to measure its position along the anterior-posterior axis is low both at the boundary and in the anterior even at cycle 13, suggesting additional post-translational averaging mechanisms to provide the precision observed in fixed material.
Precision of readout at the hunchback gene Jonathan Desponds, Huy Tran, Teresa Ferraro, Tanguy Lucas, Carmina Perez Romero, Aurelien Guillou, Cecile Fradin, Mathieu Coppey, Nathalie Dostatni, Aleksandra M Walczak doi: https://doi.org/10.1101/063784 PLOS Computational Biology doi: 10.1371/journal.pcbi.1005256
Complex complexity.Dionisio
February 8, 2017
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It is commonly agreed that the most challenging problems in modern science and engineering involve the concurrent and nonlinear interaction of multiple phenomena, acting on a broad and disparate spectrum of scales in space and time. The multiscale and multi-level nature of these problems commands a paradigm shift in the way they need to be handled, both conceptually and in terms of the corresponding problem-solving computational tools.
Bridging the gaps at the physics–chemistry–biology interface P. V. Coveney,1 J. P. Boon,2 and S. Succi Philos Trans A Math Phys Eng Sci. 374(2080): 20160335. doi: 10.1098/rsta.2016.0335
Complex complexity.Dionisio
February 8, 2017
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Complex interactions between the host immune system and microbiota are of dynamic nature and hence, of fundamental importance when homeostasis is considered, as the host is exposed to trillions of indigenous microorganisms; bacteria, archaea, fungi, and viruses [...]
Pharmacometabolomics Informs Viromics toward Precision Medicine Angeliki Balasopoulou,1 George P. Patrinos,1,2 and Theodora Katsila Front Pharmacol. 7: 411. doi: 10.3389/fphar.2016.00411
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[...] through collection, analyses and sharing of standardized medically relevant data globally, evidence-based precision medicine will shift progressively from therapy to prevention, thus leading eventually to improved, clinician-to-patient communication, citizen-centered healthcare and sustained well-being.
Reconciling evidence-based medicine and precision medicine in the era of big data: challenges and opportunities. Beckmann JS, Lew D. Genome Med. ;8(1):134. DOI: 10.1186/s13073-016-0388-7
Dionisio
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We anticipate that our metabolomics community will have representation in large precision medicine initiatives to provide input with regard to sample acquisition/preservation, selection of optimal omics technologies, and key issues regarding data collection, interpretation, and dissemination. We strongly recommend the collection and biobanking of samples for precision medicine initiatives that will take into consideration needs for large-scale metabolic phenotyping studies.
Metabolomics enables precision medicine: "A White Paper, Community Perspective". Beger RD1, Dunn W2, Schmidt MA3, Gross SS4, Kirwan JA5, Cascante M6, Brennan L7, Wishart DS8, Oresic M9, Hankemeier T10, Broadhurst DI11, Lane AN12, Suhre K13, Kastenmüller G14, Sumner SJ15, Thiele I16, Fiehn O17, Kaddurah-Daouk R18; for “Precision Medicine and Pharmacometabolomics Task Group”-Metabolomics Society Initiative Metabolomics. 2016;12(10):149. Epub 2016 Sep 2. DOI: 10.1007/s11306-016-1094-6
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[...] the predictive power of genetic testing could be improved by taking a more comprehensive view of human genetics that encompasses our human and microbial genomes. Furthermore, unlike the human genome, the microbiome is rapidly altered by diet, pharmaceuticals, and other interventions, providing the potential to improve patient care by re-shaping our associated microbial communities.
Mirror, mirror on the wall: which microbiomes will help heal them all? Renuka R. Nayak and Peter J. Turnbaugh BMC Med. 14: 72. doi: 10.1186/s12916-016-0622-6
Complex complexity.Dionisio
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Intuitively, the explanatory power of models would increase as the number of molecular details increase. Failing to account for environmental and systemic constraints on lower-scale processes often result in a failure to understand the functionality of the system (Noble, 2012). The requirement of boundary conditions to represent such top-down influences may thus provide a concrete interpretation of top-down effects. Taken together, these aspects provide resistance to the view that macroscale properties are dispensable for explaining multi-scale biological systems.
Biology meets Physics: Reductionism and Multi-scale Modeling of Morphogenesis Sara Greena, Robert Batterman DOI: 10.1016/j.shpsc.2016.12.003 http://philsci-archive.pitt.edu/12711/
Complex complexity.Dionisio
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[...] although the composition of polypeptides is reducible to a sequence of amino acids, it has been argued that it is not possible to explain protein folding from physical laws and knowledge about amino acids alone (Love & Hütteman, 2011).
Biology meets Physics: Reductionism and Multi-scale Modeling of Morphogenesis Sara Greena, Robert Batterman DOI: 10.1016/j.shpsc.2016.12.003 http://philsci-archive.pitt.edu/12711/
Complex complexity.Dionisio
February 8, 2017
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The view that an ideal or fundamental physics would be sufficient to explain all macro-scale phenomena has been met with criticism from philosophers of biology. Scholars have stressed the irreducibility of biological features [...] [...] biological explanations are irreducible to physical laws and principles (e.g., Bechtel & Richardson, 1993; Bertalanffy, 1969; Burian et al., 1996; Dupré, 1993; Machamer et al., 2000; Mayr, 1988; 2004; Winther, 2009)
Biology meets Physics: Reductionism and Multi-scale Modeling of Morphogenesis Sara Greena, Robert Batterman DOI: 10.1016/j.shpsc.2016.12.003 http://philsci-archive.pitt.edu/12711/
Complex complexity.Dionisio
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An important reductionist assumption is that multi-scale systems can be described “bottom-up”, if only sufficient details about the states of the components are available. Historically, this assumption has been debated in philosophical discussions about whether biology is reducible to physics.
Biology meets Physics: Reductionism and Multi-scale Modeling of Morphogenesis Sara Greena, Robert Batterman DOI: 10.1016/j.shpsc.2016.12.003 http://philsci-archive.pitt.edu/12711/
Complex complexity.Dionisio
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A common reductionist assumption is that macro-scale behaviors can be described "bottom-up" if only sufficient details about lower-scale processes are available. The view that an "ideal" or "fundamental" physics would be sufficient to explain all macro-scale phenomena has been met with criticism from philosophers of biology. Specifically, scholars have pointed to the impossibility of deducing biological explanations from physical ones, and to the irreducible nature of distinctively biological processes such as gene regulation and evolution.
Biology meets Physics: Reductionism and Multi-scale Modeling of Morphogenesis Sara Greena, Robert Batterman DOI: 10.1016/j.shpsc.2016.12.003 http://philsci-archive.pitt.edu/12711/
Complex complexity.Dionisio
February 8, 2017
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Systems biology is a relatively new interdisciplinary approach that applies mathematical modeling and engineering approaches to the interpretation of biological datasets on regulatory interactions (e.g. gene regulation). An example is the pioneering work on motif-detection in transcriptional regulatory networks by Uri Alon’s group, at the Weizmann Institute of Science, Israel
Can biological complexity be reverse engineered? Green S Stud Hist Philos Biol Biomed Sci. 53:73-83. doi: 10.1016/j.shpsc.2015.03.008.
Professor Uri Alon's 2014 course is available online. Is it criticized here? Why? Complex complexity.Dionisio
February 8, 2017
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Request for clarification: Is this paper referenced @2760-2762 addressing a potential conflict between the approaches of traditional experimental biologists and systems biologists or neuroscience researchers? Are they raising an alarm in light of the growing number of references to design principles in biology? This paper mentions the word "design" or "designed" many times. Also are the papers referenced @2752-2754 and @2755-2759 respectively related to a criticism of certain systems biology concepts or approaches that may be considered biased by some traditional experimental biologists? Can somebody comment on this? Here's the paper: https://www.researchgate.net/profile/Sara_Green3/publication/275360137_Can_biological_complexity_be_reverse_engineered/links/557563eb08aeacff1ffcd01b/Can-biological-complexity-be-reverse-engineered.pdfDionisio
February 8, 2017
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[...] they criticize so-called reverse engineering approaches for investigating biological systems as if these were programmed and fully decomposable engineering systems, designed to conduct pre-designed functions
Can biological complexity be reverse engineered? Green S Stud Hist Philos Biol Biomed Sci. 53:73-83. doi: 10.1016/j.shpsc.2015.03.008.
apparently somebody is concerned about the idea of things being designed Complex complexity.Dionisio
February 7, 2017
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Reverse engineering methodologies are currently gaining terrain in biological fields such as systems biology and neuroscience. In response to these developments, experimental biologists have raised concerns regarding the associated quest for design principles that they take to imply an assumption of a rather static and modular design of organisms.
Can biological complexity be reverse engineered? Green S Stud Hist Philos Biol Biomed Sci. 53:73-83. doi: 10.1016/j.shpsc.2015.03.008.
Complex complexity.Dionisio
February 7, 2017
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Concerns with the use of engineering approaches in biology have recently been raised. I examine two related challenges to biological research that I call the synchronic and diachronic underdetermination problem. The former refers to challenges associated with the inference of design principles underlying system capacities when the synchronic relations between lower-level processes and higher-level systems capacities are degenerate (many-to-many). The diachronic underdetermination problem regards the problem of reverse engineering a system where the non-linear relations between system capacities and lower-level mechanisms are changing over time. Braun and Marom argue that recent insights to biological complexity leave the aim of reverse engineering hopeless - in principle as well as in practice. While I support their call for systemic approaches to capture the dynamic nature of living systems, I take issue with the conflation of reverse engineering with naïve reductionism. I clarify how the notion of design principles can be more broadly conceived and argue that reverse engineering is compatible with a dynamic view of organisms. It may even help to facilitate an integrated account that bridges the gap between mechanistic and systems approaches.
Can biological complexity be reverse engineered? Green S Stud Hist Philos Biol Biomed Sci. 53:73-83. doi: 10.1016/j.shpsc.2015.03.008.
Complex complexity.Dionisio
February 7, 2017
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Biological objects, i.e., organisms, are specific and hence they are not interchangeable. [...] biological objects are the result of a history that represents a cascade of changes of their regularities, they exhibit variability and show contextuality; unlike inert objects they are agents. [...] the zygote is both a cell and an organism, and with each cell division, these two levels of individuation become more obvious.
Toward a theory of organisms: Three founding principles in search of a useful integration Ana M. Soto, Giuseppe Longo, Paul-Antoine Miquel, Maël Montevil, Matteo Mossio, Nicole Perret, Arnaud Pocheville, Carlos Sonnenschein http://dx.doi.org/10.1016/j.pbiomolbio.2016.07.006 Progress in Biophysics and Molecular Biology Volume 122, Issue 1, Pages 77–82 From the Century of the Genome to the Century of the Organism: New Theoretical Approaches Edited By Ana M Soto, Giuseppe Longo and Denis Noble
Complex complexity.Dionisio
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[...] organismal biology still lacks a widely accepted global theory. [...] biological systems are characterized by the simultaneous co-existence of opposites as exemplified by change and stability, the incomplete separation between internal and external (topology), and before and after (time) the notions of extended present, memory and anticipation [...] [...] the system is historical and in relentless change from fertilization to death, being built and remodeled throughout life.
Toward a theory of organisms: Three founding principles in search of a useful integration Ana M. Soto, Giuseppe Longo, Paul-Antoine Miquel, Maël Montevil, Matteo Mossio, Nicole Perret, Arnaud Pocheville, Carlos Sonnenschein http://dx.doi.org/10.1016/j.pbiomolbio.2016.07.006 Progress in Biophysics and Molecular Biology Volume 122, Issue 1, Pages 77–82 From the Century of the Genome to the Century of the Organism: New Theoretical Approaches Edited By Ana M Soto, Giuseppe Longo and Denis Noble
Complex complexity.Dionisio
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[...] three principles are proposed to postulate a theory of organisms, namely: 1) the default state of proliferation with variation and motility, which is rooted in the cell theory, 2) the principle of organization, and 3) the principle of variation which applies to morphogenesis and inheritance.
Toward a theory of organisms: Three founding principles in search of a useful integration Ana M. Soto, Giuseppe Longo, Paul-Antoine Miquel, Maël Montevil, Matteo Mossio, Nicole Perret, Arnaud Pocheville, Carlos Sonnenschein http://dx.doi.org/10.1016/j.pbiomolbio.2016.07.006 Progress in Biophysics and Molecular Biology Volume 122, Issue 1, Pages 77–82 From the Century of the Genome to the Century of the Organism: New Theoretical Approaches Edited By Ana M Soto, Giuseppe Longo and Denis Noble
Complex complexity.Dionisio
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The first decade of the new millennium was dubbed as the beginning of “the post-genomic era.” Its arrival was greeted by the biological sciences establishment and the pharmaceutical industry with the exceedingly optimistic view that new technology and the usual reductionist approaches that characterized the last half of the 20th century [...] [...] the limitations posed by the hegemonic, reductionist, dominant world view which is metaphor rich and theory poor.
Toward a theory of organisms: Three founding principles in search of a useful integration Ana M. Soto, Giuseppe Longo, Paul-Antoine Miquel, Maël Montevil, Matteo Mossio, Nicole Perret, Arnaud Pocheville, Carlos Sonnenschein http://dx.doi.org/10.1016/j.pbiomolbio.2016.07.006 Progress in Biophysics and Molecular Biology Volume 122, Issue 1, Pages 77–82 From the Century of the Genome to the Century of the Organism: New Theoretical Approaches Edited By Ana M Soto, Giuseppe Longo and Denis Noble
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Organisms, be they uni- or multi-cellular, are agents capable of creating their own norms; they are continuously harmonizing their ability to create novelty and stability, that is, they combine plasticity with robustness. [...] principles for a theory of organisms [...] [1] the default state of proliferation with variation and motility, [2] the principle of variation and [3] the principle of organization. These principles profoundly change both biological observables and their determination with respect to the theoretical framework of physical theories. This radical change opens up the possibility of anchoring mathematical modeling in biologically proper principles
Toward a theory of organisms: Three founding principles in search of a useful integration Ana M. Soto, Giuseppe Longo, Paul-Antoine Miquel, Maël Montevil, Matteo Mossio, Nicole Perret, Arnaud Pocheville, Carlos Sonnenschein http://dx.doi.org/10.1016/j.pbiomolbio.2016.07.006 Progress in Biophysics and Molecular Biology Volume 122, Issue 1, Pages 77–82 From the Century of the Genome to the Century of the Organism: New Theoretical Approaches Edited By Ana M Soto, Giuseppe Longo and Denis Noble
Complex complexity.Dionisio
February 7, 2017
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Often times, modelers entering biological research treat biological objects as if they were either physical objects or computer programs. [...] the metaphorical use of information pushes the experimenter to seek causality in terms of discrete structures, namely molecules, in particular DNA. In this initial modeling effort, applying the two principles (default state and constraints leading to closure) were sufficient to show the formation of ducts and acini. Cells generated forces that were transmitted to neighboring cells and collagen fibers, which in turn created constraints to movement and proliferation.
Modeling mammary organogenesis from biological first principles: Cells and their physical constraints Maël Montévil, Lucia Speroni, Carlos Sonnenschein, Ana M. Soto DOI: http://dx.doi.org/10.1016/j.pbiomolbio.2016.08.004 Progress in Biophysics and Molecular Biology Volume 122, Issue 1, Pages 58–69 From the Century of the Genome to the Century of the Organism: New Theoretical Approaches Edited By Ana M Soto, Giuseppe Longo and Denis Noble
Complex complexity.Dionisio
February 7, 2017
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Scientific theories provide organizing principles and construct objectivity by framing observations and experiments (Longo & Soto, this issue). On the one hand, theories construct the proper observables and on the other they provide the framework for studying them. [...] a theory does not need to be “right” to guide the praxis of good experiments. Even a wrong theory can be useful if, when proven incorrect it is modified or even dismissed. [...] the application of the principles we propose to use for the construction of a theory of organisms results in a better understanding of morphogenesis (the generation of biological form) than the common practice of using metaphors derived from the mathematical theory of information as theoretical background [...]
Modeling mammary organogenesis from biological first principles: Cells and their physical constraints Maël Montévil, Lucia Speroni, Carlos Sonnenschein, Ana M. Soto DOI: http://dx.doi.org/10.1016/j.pbiomolbio.2016.08.004 Progress in Biophysics and Molecular Biology Volume 122, Issue 1, Pages 58–69 From the Century of the Genome to the Century of the Organism: New Theoretical Approaches Edited By Ana M Soto, Giuseppe Longo and Denis Noble
Complex complexity.Dionisio
February 7, 2017
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In multicellular organisms, relations among parts and between parts and the whole are contextual and interdependent. These organisms and their cells are ontogenetically linked: an organism starts as a cell that divides producing non-identical cells, which organize in tri-dimensional patterns. These association patterns and cells types change as tissues and organs are formed. Implementing the mathematical model shows that constraints to the default state are sufficient to explain ductal and acinar formation, and points to a target of future research, namely, to inhibitors of cell proliferation and motility generated by the epithelial cells.
Modeling mammary organogenesis from biological first principles: Cells and their physical constraints Maël Montévil, Lucia Speroni, Carlos Sonnenschein, Ana M. Soto DOI: http://dx.doi.org/10.1016/j.pbiomolbio.2016.08.004 Progress in Biophysics and Molecular Biology Volume 122, Issue 1, Pages 58–69 From the Century of the Genome to the Century of the Organism: New Theoretical Approaches Edited By Ana M Soto, Giuseppe Longo and Denis Noble
Complex complexity.Dionisio
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[...] limiting the contractile forces of the cell cortex is an integral part of epithelial cell adhesion to blood capillaries. [...] the altered biomechanical properties of the endocrine tissue prompted the observed vascular phenotype [...] [...] the biomechanical stiffness of several tissues inversely correlates with their microvascular densities [...] By stepping away from a pure endothelial-centric perspective, future studies might leverage the biomechanical properties of growing or hypertrophic tissues to inhibit or promote vascularization.
The biomechanical properties of an epithelial tissue determine the location of its vasculature Martin Kragl, Rajib Schubert, Haiko Karsjens, Silke Otter, Barbara Bartosinska, Kay Jeruschke, Jürgen Weiss, Chunguang Chen, David Alsteens, Oliver Kuss, Stephan Speier, Daniel Eberhard, Daniel J. Müller and Eckhard Lammert Nat Commun. 7: 13560. doi: 10.1038/ncomms13560
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