复杂文摘翻译第三期－(摘自Complex Digest 2016.4月文章)
复杂文摘翻译第三期－(摘自Complex Digest 2016.4月文章)
From onlinelibrary.wiley.com April 1, 12:39 AM
By Aldo Mascareño, Eric Goles, and Gonzalo A. Ruz
(Translated by -王与剑-生物物理学-呼和浩特)
The article argues that crises are a distinctive feature of complex social systems. A quest for connectivity of communication leads to increase systems' own robustness by constantly producing further connections. When some of these connections have been successful in recent operations, the system tends to reproduce the emergent pattern, thereby engaging in a non-reflexive, repetitive escalation of more of the same communication. This compulsive growth of systemic communication in crisis processes, or logic of excess, resembles the dynamic of self-organized criticality. Accordingly, we first construct the conceptual foundations of our approach. Second, we present three core assumptions related to the generative mechanism of social crises, their temporal transitions (incubation, contagion, restructuring), and the suitable modeling techniques to represent them. Third, we illustrate the conceptual approach with a percolation model of the crisis in Chilean education system.
Does Stress Speed Up Evolution?
From nautil.us April 1, 5:36 PM
By Andreas von Bubnoff
(Translated by -)
Organisms under stress have a higher mutation rate, even though they are not dividing.
遗传环路设计自动化 (Genetic circuit design automation)
From Science 01 Apr 2016:Vol. 352, Issue 6281 April 1, 9:45 PM
By Alec A. K. Nielsen, et al.
(Translated by - 刘清晴)
Computation can be performed in living cells by DNA-encoded circuits that process sensory information and control biological functions. Their construction is time-intensive, requiring manual part assembly and balancing of regulator expression. We describe a design environment, Cello, in which a user writes Verilog code that is automatically transformed into a DNA sequence. Algorithms build a circuit diagram, assign and connect gates, and simulate performance. Reliable circuit design requires the insulation of gates from genetic context, so that they function identically when used in different circuits. We used Cello to design 60 circuits for Escherichia coli (880,000 base pairs of DNA), for which each DNA sequence was built as predicted by the software with no additional tuning. Of these, 45 circuits performed correctly in every output state (up to 10 regulators and 55 parts), and across all circuits 92% of the output states functioned as predicted. Design automation simplifies the incorporation of genetic circuits into biotechnology projects that require decision-making, control, sensing, or spatial organization.
一个生物体能否大如星系？Can a Living Creature Be as Big as a Galaxy?
From nautil.us April 1, 7:38 PM
By Gregory Laughlin
(Translated by -陈开壮, Edited by Jake)
Why life is constrained to be about the sizes we see on Earth.
The size of things in our universe runs all the way from the tiny 10^-19 meter scale that characterizes quark interactions, to the cosmic horizon 10^26 meters away. In these 45 possible orders of magnitude, life, as far as we know it, is confined to a relatively tiny bracket of just over nine orders of magnitude, roughly in the middle of the universal range: Bacteria and viruses can measure less than a micron, or 10^-6 meters, and the height of the largest trees reaches roughly 100 meters. The honey fungus that lives under the Blue Mountains in Oregon, and is arguably a single living organism, is about 4 kilometers across.When it comes to known sentient life, the range in scale is even smaller, at about three orders of magnitude.
信息驱动协调现象的动力学：基于转移熵的分析 The dynamics of information-driven coordination phenomena: A transfer entropy analysis
From Science Advances 01 Apr 2016:Vol. 2, no. 4, e1501158 April 2, 8:09 PM
By Javier Borge-Holthoefer, Nicola Perra, Bruno Gonçalves, Sandra González-Bailón, Alex Arenas, Yamir Moreno, and Alessandro Vespignani
(Translated by 蔡嘉文，Edited by Jake)
Data from social media provide unprecedented opportunities to investigate the processes that govern the dynamics of collective social phenomena. We consider an information theoretical approach to define and measure the temporal and structural signatures typical of collective social events as they arise and gain prominence. We use the symbolic transfer entropy analysis of microblogging time series to extract directed networks of influence among geolocalized subunits in social systems. This methodology captures the emergence of system-level dynamics close to the onset of socially relevant collective phenomena. The framework is validated against a detailed empirical analysis of five case studies. In particular, we identify a change in the characteristic time scale of the information transfer that flags the onset of information-driven collective phenomena. Furthermore, our approach identifies an order-disorder transition in the directed network of influence between social subunits. In the absence of clear exogenous driving, social collective phenomena can be represented as endogenously driven structural transitions of the information transfer network. This study provides results that can help define models and predictive algorithms for the analysis of societal events based on open source data.
FromEPJ Data Science 2016 5:14 April 3, 3:00 PM
By Evangelos Pournaras, Jovan Nikolic, Pablo Velásquez, Marcello Trovati, Nik Bessis and Dirk Helbing
(Translated by -阎赫, Edited by Jake )
Participation in social sensing applications is challenged by privacy threats. Large-scale access to citizens’ data allow surveillance and discriminatory actions that may result in segregation phenomena in society. On the contrary are the benefits of accurate computing analytics required for more informed decision-making, more effective policies and regulation of techno-socio-economic systems supported by ‘Internet-of Things’ technologies. In contrast to earlier work that either focuses on privacy protection or Big Data analytics, this paper proposes a self-regulatory information sharing system that bridges this gap. This is achieved by modeling information sharing as a supply-demand system run by computational markets. On the supply side lie the citizens that make incentivized but self-determined decisions about the level of information they share. On the demand side stand data aggregators that provide rewards to citizens to receive the required data for accurate analytics. The system is empirically evaluated with two real-world datasets from two application domains: (i) Smart Grids and (ii) mobile phone sensing. Experimental results quantify trade-offs between privacy-preservation, accuracy of analytics and costs from the provided rewards under different experimental settings. Findings show a higher privacy-preservation that depends on the number of participating citizens and the type of data summarized. Moreover, analytics with summarization data tolerate high local errors without a significant influence on the global accuracy. In other words, local errors cancel out. Rewards can be optimized to be fair so that citizens with more significant sharing of information receive higher rewards. All these findings motivate a new paradigm of truly decentralized and ethical data analytics.
一种度量系统复杂性的通用框架（A general framework for measuring system complexity）
From onlinelibrary.wiley.com April 3, 12:47 AM
By Mahmoud Efatmaneshnik and Michael J. Ryan
(Translated by - 龚力，edited by 傅渥成)
In this work, we are motivated by the observation that previous considerations of appropriate complexity measures have not directly addressed the fundamental issue that the complexity of any particular matter or thing has a significant subjective component in which the degree of complexity depends on available frames of reference. Any attempt to remove subjectivity from a suitable measure therefore fails to address a very significant aspect of complexity. Conversely, there has been justifiable apprehension toward purely subjective complexity measures, simply because they are not verifiable if the frame of reference being applied is in itself both complex and subjective. We address this issue by introducing the concept of subjective simplicity—although a justifiable and verifiable value of subjective complexity may be difficult to assign directly, it is possible to identify in a given context what is “simple” and, from that reference, determine subjective complexity as distance from simple. We then propose a generalized complexity measure that is applicable to any domain, and provide some examples of how the framework can be applied to engineered systems.
Remark by fuwocheng: (1) frames of reference 参考系
From cacm.acm.org April 4, 5:40 PM
By Manuel Cebrian, Iyad Rahwan, Alex "Sandy" Pentland
(Translated by - 秦堉朗-ATC-ABM-Canton，edited by 傅渥成)
The golden age of social media coincides with a worldwide leadership crisis, manifested by our seeming inability to address any major global issue in recent years.32 These days, no one—be they a charismatic leader or a nameless crowd—seems to be able to make issues popular for long enough to mobilize society into action. As a result of this leadership vacuum, social progress of all sorts seems to have become stymied and frozen. How can this happen precisely in a time when social media, praised as the ultimate tool to raise collective awareness and mobilize society, has reached maturity and widespread use? Here, we argue the coexistence of social media technologies with 'The End of Power'18 is anything but a coincidence, presenting the first techno-social paradox of the 21st century.
In recent years, we have witnessed social media playing a major role in social mobilization events of historic proportions, such as the Arab Spring, the Occupy Wall Street movement, Ukraine's Euromaidan, and the chaos generated by the England Riots and Boston Marathon bombing manhunt. There has been substantial emphasis on the role of digital social media platforms, particularly Facebook and Twitter, as the facilitators of these mobilizations. Data availability has made it possible, for the first time, to observe the evolution of these events in detail.10,11,13,33 Analysis of these events makes it clear that political activists find it difficult to use social media to create mass mobilization; and even when they succeed it is difficult to sustain the focus of the protest until it is able to mobilize politicians, institutions, and society at large. As a result, most of these events burst upon the scene, occupy our attention for a few days, and then fade into oblivion with nothing substantial having been accomplished. Given all we have learned about social mobilization, why isn't social media a more reliable channel for constructive social change?
Remark by fuwocheng: 翻译得非常好。 一些语法的细节问题，如句子 "and the chaos generated by the England Riots and Boston Marathon bombing manhunt"，注意到这里出现了两个 and，因此应该理解为「由于英国骚乱和波士顿马拉松爆炸嫌犯追捕所带来的混乱」。
多层随机分块模型揭示复杂网络的多层结构（Multilayer Stochastic Block Models Reveal the Multilayer Structure of Complex Networks）
From Phys. Rev. X 6, 011036 – Published 31 March 2016 April 5, 5:46 PM
By Toni Vallès-Català, Francesco A. Massucci, Roger Guimerà, and Marta Sales-Pardo
(Translated by -dan，edited by 傅渥成)
In complex systems, the network of interactions we observe between systems components is the aggregate of the interactions that occur through different mechanisms or layers. Recent studies reveal that the existence of multiple interaction layers can have a dramatic impact in the dynamical processes occurring on these systems. However, these studies assume that the interactions between systems components in each one of the layers are known, while typically for real-world systems we do not have that information. Here, we address the issue of uncovering the different interaction layers from aggregate data by introducing multilayer stochastic block models (SBMs), a generalization of single-layer SBMs that considers different mechanisms of layer aggregation. First, we find the complete probabilistic solution to the problem of finding the optimal multilayer SBM for a given aggregate-observed network. Because this solution is computationally intractable, we propose an approximation that enables us to verify that multilayer SBMs are more predictive of network structure in real-world complex systems.
实时情境中社会习俗的形成(The Formation of Social Conventions in Real-Time Environments)
From PLoS ONE 11(3): e0151670. April 6, 12:25 AM
By Hawkins RXD, Goldstone RL，Hawkins RXD
(Translated by 阿勺)
Why are some behaviors governed by strong social conventions while others are not? We experimentally investigate two factors contributing to the formation of conventions in a game of impure coordination: the continuity of interaction within each round of play (simultaneous vs. real-time) and the stakes of the interaction (high vs. low differences between payoffs). To maximize efficiency and fairness in this game, players must coordinate on one of two equally advantageous equilibria. In agreement with other studies manipulating continuity of interaction, we find that players who were allowed to interact continuously within rounds achieved outcomes with greater efficiency and fairness than players who were forced to make simultaneous decisions. However, the stability of equilibria in the real-time condition varied systematically and dramatically with stakes: players converged on more stable patterns of behavior when stakes are high. To account for this result, we present a novel analysis of the dynamics of continuous interaction and signaling within rounds. We discuss this previously unconsidered interaction between within-trial and across-trial dynamics as a form of social canalization. When stakes are low in a real-time environment, players can satisfactorily coordinate ‘on the fly’, but when stakes are high there is increased pressure to establish and adhere to shared expectations that persist across rounds.
Remark by 傅渥成： 要注意翻译的时候一些最最关键的词不能漏掉，这篇文章的一个关键就是「实验」，experimentally，只看到 investigate，把这句话翻译成调研，就把意思完全弄错了。还有一些低级错误，如 game 是「博弈」， signaling within rounds，round就是博弈中的「轮」。
理解群体动力学与团队的成功（Understanding the group dynamics and success of teams）
From Royal Society Open Science April 7, 6:57 PM
By Michael Klug, James P. Bagrow
(Translated by -猪哥, edited by 傅渥成)
Complex problems often require coordinated group effort and can consume significant resources, yet our understanding of how teams form and succeed has been limited by a lack of large-scale, quantitative data. We analyse activity traces and success levels for approximately 150, 000 self-organized, online team projects. While larger teams tend to be more successful, workload is highly focused across the team, with only a few members performing most work. We find that highly successful teams are significantly more focused than average teams of the same size, that their members have worked on more diverse sets of projects, and the members of highly successful teams are more likely to be core members or ‘leads’ of other teams. The relations between team success and size, focus and especially team experience cannot be explained by confounding factors such as team age, external contributions from non-team members, nor by group mechanisms such as social loafing. Taken together, these features point to organizational principles that may maximize the success of collaborative endeavours.'
Remark by 傅渥成：翻译得非常好。
对企业所有权的透明度和黑金而言，巴拿马文件意味着什么？（What the Panama Papers Mean for Transparency and ‘Dark Money’）
From knowledge.wharton.upenn.edu April 8, 7:46 PM
By Aldo Mascareño, Eric Goles andGonzalo A. Ruz
(Translated by -jeffersonchou)
Last Sunday, the International Consortium of Investigative Journalists (ICIJ) published a massive leak of some 11.5 million documents covering nearly 40 years, from 1977 through 2015, that showed how world leaders, politicians and businesses hide and launder their money, evade taxes and finance arms and drug deals. The source of the leak is a little-known but powerful law firm in Panama called Mossack Fonseca, which is one of the top creators of shell companies and corporate structures that can be used to hide ownership of assets. The leaked data provide a day-to-day, decade-by-decade look at how dark money flows through the global financial system, breeding crime and stripping national treasuries of tax revenues.
The ICIJ published these documents after a year long investigation along with German newspaper Süddeutsche Zeitung and more than 100 other news organizations. The leaks which is just one part and the beginning of a wider scandal, reveal the offshore holdings of 140 politicians and public officials around the world, including a dozen current and former world leaders. The ICIJ has said it would release the full list of companies and people linked to it in early May.
The Panama Papers, as the leaked documents are called, exposes just one firm in a larger industry. The trouble is it is legal to set these anonymous companies up in various jurisdictions around the world. The Panama Papers offer a rare opportunity to regulators in the U.K., the U.S. and other countries to bring about greater transparency in the ownership of the firms，to tighten their regulations to prevent abuse by the companies they incorporate.
A positive outcome of the Panama Papers scandal is that it brings this into the public realm, making it possible for citizens to see the effects of these companies, to see policies that are enforced in their countries that enable these types of activities to happen and to engage with their governments to take action to fix it. The ICIJ has make it easy for prosecution, and governments need to start following their lead.
上周日，国际记者调查联盟（ICIJ）公布公布了约1150万份文件，这些大规模泄漏的文件，揭露了从1977年到2015年的40年间，世界各国领导人、政治家和商人，是如何隐瞒收入、洗钱、逃税和资助军火和毒品交易的。泄漏的文件来源于巴拿马一个鲜为人知但很有影响力的律师事务所——莫萨克·丰塞卡律师事务所 (Mossack Fonseca)，它是一家通过创造空壳公司，设计企业架构，帮助客户隐瞒资产所有权的顶尖服务供应商。这些泄露的数据提供了一个逐天、逐年的视角，来观察黑暗金钱是如何流入全球金融体系，滋生犯罪和偷逃国库收入的。
edited by 傅渥成
持续减少跨性别歧视：一场关于逐户拉票的田野实验（Durably reducing transphobia: A field experiment on door-to-door canvassing ）
Science 08 Apr 2016: Vol. 352, Issue 6282, pp. 220-224 April 8, 10:10 PM
BY David Broockman, Joshua Kalla
(Translated by -北宁)
Existing research depicts intergroup prejudices as deeply ingrained, requiring intense intervention to lastingly reduce. Here, we show that a single approximately 10-minute conversation encouraging actively taking the perspective of others can markedly reduce prejudice for at least 3 months. We illustrate this potential with a door-to-door canvassing intervention in South Florida targeting antitransgender prejudice. Despite declines in homophobia, transphobia remains pervasive. For the intervention, 56 canvassers went door to door encouraging active perspective-taking with 501 voters at voters’ doorsteps. A randomized trial found that these conversations substantially reduced transphobia, with decreases greater than Americans’ average decrease in homophobia from 1998 to 2012. These effects persisted for 3 months, and both transgender and nontransgender canvassers were effective. The intervention also increased support for a nondiscrimination law, even after exposing voters to counterarguments.
edited by 傅渥成
为什么自然钟情于正六边形？ （Why Nature Prefers Hexagons）
Nautilus April 9, 8:04 PM
BY PHILIP BALL
(Translated by -刘清晴、陈开壮、李宇峰)
How do bees do it? The honeycombs in which they store their amber nectar are marvels of precision engineering, an array of prism-shaped cells with a perfectly hexagonal cross-section. The wax walls are made with a very precise thickness, the cells are gently tilted from the horizontal to prevent the viscous honey from running out, and the entire comb is aligned with the Earth’s magnetic field. Yet this structure is made without any blueprint or foresight, by many bees working simultaneously and somehow coordinating their efforts to avoid mismatched cells.
The ancient Greek philosopher Pappus of Alexandria thought that the bees must be endowed with “a certain geometrical forethought.” And who could have given them this wisdom, but God? According to William Kirby in 1852, bees are “Heaven-instructed mathematicians.” Charles Darwin wasn’t so sure, and he conducted experiments to establish whether bees are able to build perfect honeycombs using nothing but evolved and inherited instincts, as his theory of evolution would imply.
Why hexagons, though? It’s a simple matter of geometry. If you want to pack together cells that are identical in shape and size so that they fill all of a flat plane, only three regular shapes (with all sides and angles identical) will work: equilateral triangles, squares, and hexagons. Of these, hexagonal cells require the least total length of wall, compared with triangles or squares of the same area. So it makes sense that bees would choose hexagons, since making wax costs them energy, and they will want to use up as little as possible—just as builders might want to save on the cost of bricks. This was understood in the 18th century, and Darwin declared that the hexagonal honeycomb is “absolutely perfect in economizing labor and wax.”
Darwin thought that natural selection had endowed bees with instincts for making these wax chambers, which had the advantage of requiring less energy and time than those with other shapes. But even though bees do seem to possess specialized abilities to measure angles and wall thickness, not everyone agrees about how much they have to rely on them. That’s because making hexagonal arrays of cells is something that nature does anyway.
If you blow a layer of bubbles on the surface of water—a so-called “bubble raft”—the bubbles become hexagonal, or almost so. You’ll never find a raft of square bubbles: If four bubble walls come together, they instantly rearrange into three-wall junctions with more or less equal angles of 120 degrees between them, like the center of the Mercedes-Benz symbol.
Evidently there are no agents shaping these rafts as bees do with their combs. All that’s guiding the pattern are the laws of physics. Those laws evidently have definite preferences, such as the bias toward three-way junctions of bubble walls. The same is true of more complicated foams. If you pile up bubbles in three dimensions by blowing through a straw into a bowl of soapy water you’ll see that when bubble walls meet at a vertex, it’s always a four-way union with angles between the intersecting films roughly equal to about 109 degrees—an angle related to the four-faceted geometric tetrahedron.
What determines these rules of soap-film junctions and bubble shapes? Nature is even more concerned about economy than the bees are. Bubbles and soap films are made of water (with a skin of soap molecules) and surface tension pulls at the liquid surface to give it as small an area as possible. That’s why raindrops are spherical (more or less) as they fall: A sphere has less surface area than any other shape with the same volume. On a waxy leaf, droplets of water retract into little beads for the same reason.
This surface tension explains the patterns of bubble rafts and foams. The foam will seek to find the structure that has the lowest total surface tension, which means the least area of soap-film wall. But the configuration of bubble walls also has to be mechanically stable: The tugs in different directions at a junction have to balance perfectly, just as the forces must be balanced in the walls of a cathedral if the building is going to stand up. The three-way junction in a bubble raft, and the four-way junctions in foam, are the configurations that achieve this balance.
这种表面张力解释了气泡筏(bubble rafts)和泡沫的模式。泡沫会努力实现拥有最小表面张力的结构，这意味着肥皂泡薄膜墙面积最小。然而气泡墙(bubble wall)的架构也必须在力学上是稳定的：各个方向的拉力在结合部位必须完美地平衡，正如一所大教堂墙面的全部受力必须保持平衡一样，如果该建筑要矗立起来。气泡筏(bubble rafts)中的三向连接(three-way junction)以及泡沫中的四向连接(four-way junctions)就是实现这种平衡的架构。
But those who think (as some do) that the honeycomb is just a solidified bubble raft of soft wax might have trouble explaining how the same hexagonal array of cells is found in the nests of paper wasps, who build not with wax but with chewed-up wads of fibrous wood and plant stem, from which they make a kind of paper. Not only can surface tension have little effect here, but it also seems clear that different types of wasp have different inherited instincts for their architectural designs, which can vary significantly from one species to another.
Although the geometry of soap-film junctions is dictated by this interplay of mechanical forces, it doesn’t tell us what the shape of the foam will be. A typical foam contains polyhedral cells of many different shapes and sizes. Look closely and you’ll see that their edges are rarely perfectly straight; they’re a little curved. That’s because the pressure of the gas inside a cell or bubble gets bigger as the bubble gets smaller, so the wall of a small bubble next to a larger one will bulge outward slightly. What’s more, some facets have five sides, some six, and some just four or even three. With a little bending of the walls, all of these shapes can acquire four-way junctions close to the “tetrahedral” arrangement needed for mechanical stability. So there’s a fair bit of flexibility (literally) in the shapes of the cells. Foams, while subject to geometrical rules, are rather disorderly.
尽管肥皂泡薄膜连接的几何图形是用物理上力的相互作用表述的，但它没有告诉我们泡沫的形状将会是什么。典型的泡沫包括了许多不同形状和尺寸的多面体单元。近距离观察你就会发现它们的边缘很少是完全直的，它们有一点弯曲。那是因为细胞和气泡中气体的压力在气泡变小时变得更大了，因此靠近较大气泡的小气泡墙朝外轻微凸起。此外，有些面有五边、有的六边，甚至有的只有四边或者三边。只要气泡墙(bubble wall)发生小小的变形，所有这些形状就可以变成接近力学稳定性所需“四面体”结构的四向连接(four-way junctions)。所以，在这样的单元形状中，这真的有点柔性（这种柔性的确对应于物理学上的柔性）。泡沫，在遵循几何规则时，是相当不规则的。
Suppose that you could make a “perfect” foam in which all the bubbles are the same size. What then is the ideal cell shape that makes the total bubble wall area as small as possible while satisfying the demands for the angles at the junctions? That has been debated for many years, and for a long time it was thought that the ideal cell shape was a 14-sided polyhedron with square and hexagonal faces. But in 1993 a slightly more economical—although less orderly—structure was discovered, consisting of a repeating group of eight different cell shapes. This more complex pattern was used as the inspiration for the foam-like design of the swimming stadium of the 2008 Olympic Games in Beijing.
设想你能做一个“理想”泡沫，泡沫中所有的气泡都具有相同的尺寸，那么在连接处满足所有角度要求使总的气泡墙(bubble wall)面积尽可能小的理想单元形状是什么？这个问题已经争论了很多年了，而且在相当长一段时间内被认为理想的单元形状是一个同时具有矩形面和六边形面的14边多面体。可在1993年，一种稍微更加经济的——尽管不是很有序——结构被发现了，该结构由包含八种不同单元形状的重复团(repeating group)构成，这种更复杂的模式被用作2008年北京奥运会游泳场馆气泡状设计的灵感。
The rules of cell shapes in foams also control some of the patterns seen in living cells. Not only does a fly’s compound eye show the same hexagonal packing of facets as a bubble raft, but the light-sensitive cells within each of the individual lenses are also clustered in groups of four that look just like soap bubbles. In mutant flies with more than four of these cells per cluster, the arrangements are also more or less identical to those that bubbles would adopt.
Because of surface tension, a soap film stretching across a loop of wire is pulled flat like the springy membrane of a trampoline. If the wire frame is bent, the film also bends with an elegant contour that automatically tells you the most economical way, in terms of material, to cover over the space enclosed by the frame. That can show an architect how to make a roof for a complicated structure using the least amount of material. However, it’s as much because of the beauty and elegance of these so-called “minimal surfaces,” as because of their economy that architects such as Frei Otto have used them in their buildings.
由于表面张力，线圈中间的肥皂泡薄膜会像蹦床那有弹性的床面一样被拉成平面。如果将线圈弯曲，那么肥皂泡薄膜会随之弯成一个优雅的轮廓，自动告诉你最经济的做法。用材料学术语来说，就是遮没（cover over）被线圈所包围的空间。这可以让建筑师知道该如何使用最少的材料给一个结构复杂的建筑造一个屋顶。无论如何，由于这些被称为“最小曲面（minimal surfaces）”的美丽优雅，以及它们的经济性，弗雷·奥托（Frei Otto）等建筑师已经将它们应用在了自己的建筑中。
These surfaces minimize not only their surface area, but also their total curvature. The tighter the bend, the greater the curvature. Curvature can be positive (bulges) or negative (dips, depressions, and saddles). A curved surface can therefore have zero mean curvature so long as the positives and negatives cancel each other out.
So a sheet can be full of curvature and yet have very little or even no mean curvature. Such a minimally curved surface can divide up space into an orderly labyrinth of passageways and channels—a network. These are called periodic minimal surfaces. (Periodic just means a structure that repeats identically again and again, or in other words, a regular pattern.) When such patterns were discovered in the 19th century, they seemed to be just a mathematical curiosity. But now we know that nature makes use of them.
The cells of many different types of organisms, from plants to lampreys to rats, contain membranes with microscopic structures like this. No one knows what they are for, but they are so widespread that it’s fair to assume they have some sort of useful role. Perhaps they isolate one biochemical process from another, avoiding crosstalk and interference. Or maybe they are just an efficient way of creating lots of “work surface,” since many biochemical processes take place at the surface of membranes, where enzymes and other active molecules may be embedded. Whatever its function, you don’t need complicated genetic instructions to create such a labyrinth: The laws of physics will do it for you.
Some butterflies, such as the European green hairstreak and the emerald-patched cattleheart, have wing scales containing an orderly labyrinth of the tough material called chitin, shaped like a particular periodic minimal surface called the gyroid. Interference between light waves bouncing regular arrays of ridges and other structures on the wing-scale surface causes some wavelengths—that is, some colors—to disappear while others reinforce each other. So here the patterns offer a means of producing animal color.
一些蝴蝶，比如Europe green hairstreak和emerald-patched cattleheart，它们翅膀鳞片中含有由一种叫做几丁质的坚韧物质整齐排列而成的迷宫状结构，类似于一种被称作螺旋二十四面体的周期性最小曲面。光照射到翅膀鳞片表面这些有序的结构和其他结构上，发生反射并产生干涉，使某些波长的光——也就是颜色——消失，同时另一些波长的光增强。于是，这些微观结构有了一个作用，就是使蝴蝶翅膀呈现出五彩斑斓的色彩。
The skeleton of the sea urchin Cidaris rugosa is a porous mesh with the shape of another kind of periodic minimal surface. It’s actually an exoskeleton, sitting outside the organism’s soft tissue, a protective shell that sprouts dangerous-looking spines made from the same mineral as chalk and marble. The open lattice structure means that the material is strong without being too heavy, rather like the metal foams used for building aircraft.
To make orderly networks from hard, stiff mineral, these organisms apparently make a mold from soft, flexible membranes and then crystallize the hard material inside one of the interpenetrating networks. Other creatures may cast orderly mineral foams this way for more sophisticated purposes. Because of the way that light bounces off the elements of the patterned structure, such trellises can act rather like mirrors to confine and guide light. A honeycomb arrangement of hollow microscopic channels within the chitin spines of a peculiar marine worm known as the sea mouse turns these hair-like structures into natural optical fibers that can channel light, making the creature change from red to bluish green depending on the direction of the illumination. This color change might serve to deter predators.
This principle of using soft tissues and membranes as molds for forming patterned mineral exoskeletons is widely used in the sea. Some sponges have exoskeletons made of bars of mineral linked like climbing frames, which look remarkably similar to the patterns formed by the edges and junctions of soap films in foam—no coincidence, if surface tension dictates the architecture.
Such processes, known as biomineralization, generate spectacular results in marine organisms called radiolarians and diatoms. Some of these have delicately patterned exoskeletons made from a mesh of mineral hexagons and pentagons: You might call them the honeycombs of the sea. When the German biologist (and talented artist) Ernst Haeckel first saw their shapes in a microscope in the late 19th century, he made them the star attraction of a portfolio of drawings called Art Forms in Nature, which were very influential among artists of the early 20th century and still inspire admiration today. To Haeckel, they seemed to offer evidence of a fundamental creativity and artistry in the natural world—a preference for order and pattern built into the very laws of nature. Even if we don’t subscribe to that notion now, there’s something in Haeckel’s conviction that patterns are an irrepressible impulse of the natural world—one that we have every right to find beautiful.
这种被称为生物矿物化的过程在放射虫和矽藻这些海洋生物中产生了惊人的效果。它们中的某些种类具有精致的网格状矿物质外骨骼，由六边形和五边形组成：你或许可以称之为海洋中的蜂巢。19世纪末，当德国生物学家（同时也是一个有才华的艺术家）Ernst Haeckel第一次用显微镜看到它们的形态的时候，他将它们画下来并集结成册，名为《自然界的艺术形式（art forms in nature）》，使它们有了明星般的吸引力。这本画集在20世纪初的艺术家中很有影响力，直到今天仍然广受赞誉。对于Haeckel来说，它们似乎为自然界以创造性和艺术性为本的观点提供了证据——对于秩序和模式的偏好是内置在基本自然法则中的。虽然我们现在并不赞同这个观点，但是正如Haeckel所确信的那样，模式的形成是自然界抑制不住的冲动，我们完全有权利去探寻美。
edited by 傅渥成
为什么国家卫生研究院（NIH）应该用抽签替换同行评审(Why the National Institutes of Health Should Replace Peer Review With a Lottery)
PSMAG April 11, 3:39 PM
BY Michael White
(Translated by - 李昉)
A major advantage of using a funding lottery would be that, by reducing its reliance on peer-review rankings, the NIH would have more room to address the urgent problem of bias. A suitably designed lottery system could help eliminate the small but persistent gender gap, and the larger racial gap in the funding it awards, by giving NIH officers more leeway to include a representative set of proposals. And importantly, a lottery would be an honest acknowledgement of what most scientists already sense: that, despite its reputation for basing decisions on merit, peer review is a much more random process than we would like to admit.
用抽签决定基金的主要好处是减少对同行评审排名的依赖，国家卫生研究院(NIH)将有更多的空间来解决这个紧急问题。适当设计的抽签系统可以帮助消除微小但持续的性别差距，以及获取基金方面巨大的种族差异，并给予 NIH 工作人员在选择具有代表性的研究计划时更多的回旋余地。重要的是，对于抽签，大多数科学家已经坦然承认，尽管根据价值作出决策取得很多成绩，但同行评审是一个比我们理解的更具随机性的过程。
edited by 傅渥成
混合型社会：设计自组织系统集群行为的挑战及前景 Hybrid Societies: Challenges and Perspectives in the Design of Collective Behavior in Self-organizing Systems
Robotics and AI, April 11, 5:44 PM
BY Heiko Hamann, Yara Khaluf, Jean Botev, Mohammad Divband Soorati, Eliseo Ferrante, Oliver Kosak, Jean-Marc Montanier, Sanaz Mostaghim, Richard Redpath, Jonathan Timmis, Frank Veenstra, Mostafa Wahby, Aleš Zamuda
(Translated by -xiaomuqiu)
Hybrid societies are self-organizing, collective systems, which are composed of different components, for example, natural and artificial parts (bio-hybrid) or human beings interacting with and through technical systems (socio-technical). Many different disciplines investigate methods and systems closely related to the design of hybrid societies. A stronger collaboration between these disciplines could allow for re-use of methods and create significant synergies.We identify three main areas of challenges in the design of self-organizing hybrid societies. First, we identify the formalization challenge.There is an urgent need for a generic model that allows a description and comparison of collective hybrid societies. Second, we identify the system design challenge. Starting from the formal specification of the system, we need to develop an integrated design process. Third, we identify the challenge of interdisciplinarity. Current research on self-organizing hybrid societies stretches over many different fields and hence requires the re-use and synthesis of methods at intersections between disciplines. We then conclude by presenting our perspective for future approaches with high potential in this area.
edited by 傅渥成
通过稀疏识别从数据中发掘非线性动力系统的控制方程(Discovering governing equations from data by sparse identification of nonlinear dynamical systems)
PNAS April 13, 3:45 PM
BY Steven L. Brunton, Joshua L. Proctor, and J. Nathan Kutz
(Translated by - Darthy)
Extracting governing equations from data is a central challenge in many diverse areas of science and engineering. Data are abundant whereas models often remain elusive, as in climate science, neuroscience, ecology, finance, and epidemiology, to name only a few examples. In this work, we combine sparsity-promoting techniques and machine learning with nonlinear dynamical systems to discover governing equations from noisy measurement data. The only assumption about the structure of the model is that there are only a few important terms that govern the dynamics, so that the equations are sparse in the space of possible functions; this assumption holds for many physical systems in an appropriate basis. In particular, we use sparse regression to determine the fewest terms in the dynamic governing equations required to accurately represent the data. This results in parsimonious models that balance accuracy with model complexity to avoid overfitting. We demonstrate the algorithm on a wide range of problems, from simple canonical systems, including linear and nonlinear oscillators and the chaotic Lorenz system, to the fluid vortex shedding behind an obstacle. The fluid example illustrates the ability of this method to discover the underlying dynamics of a system that took experts in the community nearly 30 years to resolve. We also show that this method generalizes to parameterized systems and systems that are time-varying or have external forcing.
(Edited by 唐璐)
PNAS April 13, 9:14 PM
BY Frank Groenewoud, Joachim Gerhard Frommena, Dario Josi, Hirokazu Tanaka, Arne Jungwirth, and Michael Taborsky
(Translated by -秦堉朗-ATC-ABM-Canton)
It is widely accepted that high predation risk may select for group living, but predation is not regarded as a primary driver of social complexity. This view neglects the important effect of predation on dispersal and offspring survival, which may require cooperation among group members. The significance of predation for the evolution of social complexity can be well illustrated by behavioral and morphological adaptations of highly social animals showing division of labor, such as eusocial insects and cooperatively breeding fishes. By examining the diversity of social organization in a cooperative cichlid in relation to ecological variation, we show that predation risk has the greatest explanatory power of social complexity. This stresses the significance of predation for social evolution.
Predation risk is a major ecological factor selecting for group living. It is largely ignored, however, as an evolutionary driver of social complexity and cooperative breeding, which is attributed mainly to a combination of habitat saturation and enhanced relatedness levels. Social cichlids neither suffer from habitat saturation, nor are their groups composed primarily of relatives. This demands alternative ecological explanations for the evolution of advanced social organization. To address this question, we compared the ecology of eight populations of Neolamprologus pulcher, a cichlid fish arguably representing the pinnacle of social evolution in poikilothermic vertebrates. Results show that variation in social organization and behavior of these fish is primarily explained by predation risk and related ecological factors. Remarkably, ecology affects group structure more strongly than group size, with predation inversely affecting small and large group members. High predation and shelter limitation leads to groups containing few small but many large members, which is an effect enhanced at low population densities. Apparently, enhanced safety from predators by cooperative defense and shelter construction are the primary benefits of sociality. This finding suggests that predation risk can be fundamental for the transition toward complex social organization, which is generally undervalued.
(Edited by 唐璐)
Facebook和YouTube用户的极化 （Users Polarization on Facebook and Youtube）
April 13, 11:18 PM
BY Alessandro Bessi, Fabiana Zollo, Michela Del Vicario, Michelangelo Puliga, Antonio Scala, Guido Caldarelli, Brian Uzzi, Walter Quattrociocchi
(Translated by - dan)
Algorithms for content promotion accounting for users preferences, might limit the exposure to unsolicited contents. In this work, we study how the same contents (videos) are consumed on different platforms -- i.e. Facebook and YouTube -- over a sample of 12M of users. Our findings show that the same content lead to the formation of echo chambers, irrespective of the online social network and thus of the algorithm for content promotion. Finally, we show that the users' commenting patterns are accurate early predictors for the formation of echo-chambers.
(Edited by 唐璐)
城市地区拥堵的全球分析（ A global take on congestion in urban areas）
April 14, 3:38 PM
BY Marc Barthelemy
(Translated by -余思瑶)
We analyze the congestion data collected by a GPS device company (TomTom) for almost 300 urban areas in the world. Using simple scaling arguments and data fitting we show that congestion during peak hours in large cities grows essentially as the square root of the population density. This result, at odds with previous publications showing that gasoline consumption decreases with density, confirms that density is indeed an important determinant of congestion, but also that we need urgently a better theoretical understanding of this phenomena. This incomplete view at the urban level leads thus to the idea that thinking about density by itself could be very misleading in congestion studies, and that it is probably more useful to focus on the spatial redistribution of activities and residences.
(Edited by 唐璐)
手机通话的邓巴数（Calling Dunbar's Numbers）
April 14, 5:40 PM
BY Pádraig MacCarron, Kimmo Kaski, Robin Dunbar
(Translated by - 卢罡)
The social brain hypothesis predicts that humans have an average of about 150 relationships at any given time. Within this 150, there are layers of friends of an ego, where the number of friends in a layer increases as the emotional closeness decreases. Here we analyse a mobile phone dataset, firstly, to ascertain whether layers of friends can be identified based on call frequency. We then apply different clustering algorithms to break the call frequency of egos into clusters and compare the number of alters in each cluster with the layer size predicted by the social brain hypothesis. In this dataset we find strong evidence for the existence of a layered structure. The clustering yields results that match well with previous studies for the innermost and outermost layers, but for layers in between we observe large variability.
(Edited by 唐璐)
进化中的复杂系统的时间尺度探测 （Detection of timescales in evolving complex systems）
April 14, 7:43 PM
BY Richard K. Darst, Clara Granell, Alex Arenas, Sergio Gómez, Jari Saramäki, Santo Fortunato
(Translated by -张皓)
Most complex systems are intrinsically dynamic in nature. The evolution of a dynamic complex system is typically represented as a sequence of snapshots, where each snapshot describes the configuration of the system at a particular instant of time. Then, one may directly follow how the snapshots evolve in time, or aggregate the snapshots within some time intervals to form representative "slices" of the evolution of the system configuration. This is often done with constant intervals, whose duration is based on arguments on the nature of the system and of its dynamics. A more refined approach would be to consider the rate of activity in the system to perform a separation of timescales. However, an even better alternative would be to define dynamic intervals that match the evolution of the system's configuration. To this end, we propose a method that aims at detecting evolutionary changes in the configuration of a complex system, and generates intervals accordingly. We show that evolutionary timescales can be identified by looking for peaks in the similarity between the sets of events on consecutive time intervals of data. Tests on simple toy models reveal that the technique is able to detect evolutionary timescales of time-varying data both when the evolution is smooth as well as when it changes sharply. This is further corroborated by analyses of several real datasets. Our method is scalable to extremely large datasets and is computationally efficient. This allows a quick, parameter-free detection of multiple timescales in the evolution of a complex system.
A Possible Link Between Pyriproxyfen and Microcephaly
April 14, 8:36 PM
BY Dan Evans, Fred Nijhout, Raphael Parens, Alfredo J. Morales, Yaneer Bar-Yam
(Translated by -)
The Zika virus is the primary suspect in the large increase in microcephaly cases in 2015-6 in Brazil, however its role is unconfirmed despite individual cases of viral infections found in neural tissue. Here we consider the alternative that the insecticide pyriproxyfen, used in Brazilian drinking water for mosquito control, may actually be the cause. Pyriproxifen is an analog of juvenile hormone, which corresponds in mammals to regulatory molecules including retinoic acid, a vitamin A metabolite, with which it has cross-reactivity and whose application during development causes microcephaly. Methoprene, another juvenile hormone analog approved as an insecticide has metabolites that bind to the retinoid X receptor, and causes developmental disorders in mammals. Isotretinoin is another example of a retinoid causing microcephaly in human babies via activation of the retinoid X receptor. Moreover, tests of pyriproxyfen by the manufacturer, Sumitomo, widely quoted as giving no evidence for developmental toxicity, actually found some evidence for such an effect, including low brain mass and arhinencephaly--incomplete formation of the anterior cerebral hemispheres--in rat pups. Finally, the pyriproxyfen use in Brazil is unprecedented--it has never before been applied to a water supply on such a scale. Claims that it is not being used in Recife, the epicenter of microcephaly cases, do not distinguish the metropolitan area of Recife, where it is widely used, and the municipality, where it is not. Given this combination of information we strongly recommend that the use of pyriproxyfen in Brazil be suspended pending further investigation.
时间片：感知的过程是什么？ Time Slices: What Is the Duration of a Percept?
时间片：感知的持续时间是什么？ Time Slices: What Is the Duration of a Percept?
PLOS April 14, 11:49 PM
BY Michael H. Herzog, Thomas Kammer, Frank Scharnowski
(Translated by -dan)
We experience the world as a seamless stream of percepts. However, intriguing illusions and recent experiments suggest that the world is not continuously translated into conscious perception. Instead, perception seems to operate in a discrete manner, just like movies appear continuous although they consist of discrete images. To explain how the temporal resolution of human vision can be fast compared to sluggish conscious perception, we propose a novel conceptual framework in which features of objects, such as their color, are quasi-continuously and unconsciously analyzed with high temporal resolution. Like other features, temporal features, such as duration, are coded as quantitative labels. When unconscious processing is “completed,” all features are simultaneously rendered conscious at discrete moments in time, sometimes even hundreds of milliseconds after stimuli were presented.
通过电脑游戏探索量子速度极限 Exploring the quantum speed limit with computer games
Nature 532, 210–213 (14 April 2016) April 15, 6:57 PM
BY Jens Jakob W. H. Sørensen, Mads Kock Pedersen, Michael Munch, Pinja Haikka, Jesper Halkjær Jensen, Tilo Planke, Morten Ginnerup Andreasen, Miroslav Gajdacz, Klaus Mølmer, Andreas Lieberoth & Jacob F. Sherson
(Translated by -秦德盛)
Humans routinely solve problems of immense computational complexity by intuitively forming simple, low-dimensional heuristic strategies. Citizen science (or crowd sourcing) is a way of exploiting this ability by presenting scientific research problems to non-experts. ‘Gamification’—the application of game elements in a non-game context—is an effective tool with which to enable citizen scientists to provide solutions to research problems. The citizen science games Foldit, EteRNA and EyeWire have been used successfully to study protein and RNA folding and neuron mapping, but so far gamification has not been applied to problems in quantum physics. Here we report on Quantum Moves, an online platform gamifying optimization problems in quantum physics. We show that human players are able to find solutions to difficult problems associated with the task of quantum computing. Players succeed where purely numerical optimization fails, and analyses of their solutions provide insights into the problem of optimization of a more profound and general nature. Using player strategies, we have thus developed a few-parameter heuristic optimization method that efficiently outperforms the most prominent established numerical methods. The numerical complexity associated with time-optimal solutions increases for shorter process durations. To understand this better, we produced a low-dimensional rendering of the optimization landscape. This rendering reveals why traditional optimization methods fail near the quantum speed limit (that is, the shortest process duration with perfect fidelity)7, 8, 9. Combined analyses of optimization landscapes and heuristic solution strategies may benefit wider classes of optimization problems in quantum physics and beyond.
人们往往通过直观的方式形成低维度的简单启发式策略，从而解决具有巨大计算复杂性的问题。公民科学（或称众包）是一种通过向非专业人群提出科学研究问题来开发该能力的途径。“游戏化”——在非游戏背景下运用游戏元素——是一种非常有效的工具，它可以向公民科学家提供研究问题的解决方案。公民科学游戏Foldit、EteRNA和EyeWire已经成功地将这种方法应用于蛋白质和RNA的折叠以及神经元映射的研究当中。但是到目前为止，游戏化尚未应用于量子物理的问题研究中。在这里，我们提出了一个量子移动游戏（Quantum Moves），它是一个可以将量子物理领域中的优化问题进行游戏化的在线平台。我们发现，人类玩家可以解决量子计算领域中具有挑战意义的难题。玩家可以在纯数值优化方法失败之处取得成功，并且他们的策略可以为研究人员在优化问题上提供一种更深刻而普适的视角。凭借玩家的策略，我们已经开发出一种多参数的启发式优化方法，它明显优于现有的最优秀的数值算法。对于较短的过程来说，它的数值复杂性（与时间最优解相关）会不断增加。为了更好地理解这一点，我们生成了一个最优景观的低维渲染图，以揭示为什么传统优化方法在接近量子速度极限（即完美保真度的最短持续时间）的时候会失败。将景观优化和启发式求解策略相结合可能有利于量子物理乃至更多领域中广泛存在的优化问题的求解。 注：citizen science，直译为公民科学，也作公众科学、群智科学。
人们通常采用直观地形成启发式策略的方法来解决巨大的计算复杂性问题，这种策略是简单而低维的。公民科学（或是群体采购）是开发该能力的一种途径，它是向非专业人群提出科学研究问题。“游戏化”——在非游戏背景下运用游戏元素——是一个非常有效的工具，它可以使公民科学家提供研究问题的解决方案。公民科学游戏Foldit、EteRNA和EyeWire成功的应用于蛋白质和RNA折叠研究以及神经元映射研究当中，但是到目前为止，游戏化尚未应用于量子物理的问题研究中。在这里，我们报告一个量子移动游戏（Quantum Moves），它是一个可以将量子物理领域中的优化问题游戏化的在线平台。我们发现，人类玩家可以寻找到与量子计算挑战相关的难题的解决方案。在纯粹的数值优化失败之处，玩家却可以取得成功，分析他们的策略可以为优化问题提供一种更深刻而一般性的视角。凭借使用玩家策略，我们已经开发出一种多参数启发式优化方法，这种方法明显优于现有的优秀数值方法。较短的持续时间内，与时间优化解法相关的数值复杂性在增加。为了更好地理解这一点，我们提供了一个景观优化的低维效果图。这一效果图揭示了传统优化方法在接近量子速度极限（即完美保真度的最短持续时间）时为何失败了。景观优化和启发式解法策略的结合可能有利于量子物理以及更多领域内广泛种类的优化问题。 注：citizen science，直译为公民科学，也作公众科学、群智科学。
从大数据到重要信息（From Big Data To Important Information）
April 15, 10:34 PM
BY Yaneer Bar-Yam
(Translated by - 猪哥)
Advances in science are being sought in newly available opportunities to collect massive quantities of data about complex systems. While key advances are being made in detailed mapping of systems, how to relate this data to solving many of the challenges facing humanity is unclear. The questions we often wish to address require identifying the impact of interventions on the system and that impact is not apparent in the detailed data that is available. Here we review key concepts and motivate a general framework for building larger scale views of complex systems and for characterizing the importance of information in physical, biological and social systems. We provide examples of its application to evolutionary biology with relevance to ecology, biodiversity, pandemics, and human lifespan, and in the context of social systems with relevance to ethnic violence, global food prices, and stock market panic. Framing scientific inquiry as an effort to determine what is important and unimportant is a means for advancing our understanding and addressing many practical concerns, such as economic development or treating disease.
自适应社会网络中从个体到集体行为的连接 Linking Individual and Collective Behavior in Adaptive Social Networks
Phys. Rev. Lett. 116, 128702 April 15, 11:28 PM
BY Flávio L. Pinheiro, Francisco C. Santos, and Jorge M. Pacheco
(Translated by -高德华)
Adaptive social structures are known to promote the evolution of cooperation. However, up to now the characterization of the collective, population-wide dynamics resulting from the self-organization of individual strategies on a coevolving, adaptive network has remained unfeasible. Here we establish a (reversible) link between individual (micro)behavior and collective (macro)behavior for coevolutionary processes. We demonstrate that an adaptive network transforms a two-person social dilemma locally faced by individuals into a collective dynamics that resembles that associated with an N-person coordination game, whose characterization depends sensitively on the relative time scales between the entangled behavioral and network evolutions. In particular, we show that the faster the relative rate of adaptation of the network, the smaller the critical fraction of cooperators required for cooperation to prevail, thus establishing a direct link between network adaptation and the evolution of cooperation. The framework developed here is general and may be readily applied to other dynamical processes occurring on adaptive networks, notably, the spreading of contagious diseases or the diffusion of innovations.
多层网络上的物理 The physics of multilayer networks
April 16, 3:33 PM
BY Manlio De Domenico, Clara Granell, Mason A. Porter, Alex Arenas
(Translated by 蔡嘉文)
The study of networks plays a crucial role in investigating the structure, dynamics, and function of a wide variety of complex systems in myriad disciplines. Despite the success of traditional network analysis, standard networks provide a limited representation of these systems, which often includes different types of relationships (i.e., "multiplexity") among their constituent components and/or multiple interacting subsystems. Such structural complexity has a significant effect on both dynamics and function. Throwing away or aggregating available structural information can generate misleading results and provide a major obstacle towards attempts to understand the system under analysis. The recent "multilayer' approach for modeling networked systems explicitly allows the incorporation of multiplexity and other features of realistic networked systems. On one hand, it allows one to couple different structural relationships by encoding them in a convenient mathematical object. On the other hand, it also allows one to couple different dynamical processes on top of such interconnected structures. The resulting framework plays a crucial role in helping to achieve a thorough, accurate understanding of complex systems. The study of multilayer networks has also revealed new physical phenomena that remained hidden when using the traditional network representation of graphs. Here we survey progress towards a deeper understanding of dynamical processes on multilayer networks, and we highlight some of the physical phenomena that emerge from multilayer structure and dynamics.
edited by 傅渥成
专题：含时网络理论及应用 （Modern temporal network theory: a colloquium）
Eur. Phys. J. B (2015) 88: 234 April 16, 7:24 PM
BY Petter Holme
(Translated by -)
The power of any kind of network approach lies in the ability to simplify a complex system so that one can better understand its function as a whole. Sometimes it is beneficial, however, to include more information than in a simple graph of only nodes and links. Adding information about times of interactions can make predictions and mechanistic understanding more accurate. The drawback, however, is that there are not so many methods available, partly because temporal networks is a relatively young field, partly because it is more difficult to develop such methods compared to for static networks. In this colloquium, we review the methods to analyze and model temporal networks and processes taking place on them, focusing mainly on the last three years. This includes the spreading of infectious disease, opinions, rumors, in social networks; information packets in computer networks; various types of signaling in biology, and more. We also discuss future directions.
edited by 傅渥成
标度非线性？（Is this scaling nonlinear? ）
arXiv:1604.02872 physics.soc-ph April 16, 9:20 PM
BY J. C. Leitao, J.M. Miotto, M. Gerlach, E. G. Altmann
(Translated by - 刘清晴)
One of the most celebrated findings in complex systems in the last decade is that different indexes y (e.g., patents) scale nonlinearly with the population-x of the cities in which they appear, i.e., y∼x^β, β≠1. More recently, the generality of this finding has been questioned in studies using new databases and different definitions of city boundaries. In this paper we investigate the existence of nonlinear scaling using a probabilistic framework in which fluctuations are accounted explicitly. In particular, we show that this allows not only to (a) estimate β and confidence intervals, but also to (b) quantify the evidence in favor of β≠1 and (c) test the hypothesis that the observations are compatible with the nonlinear scaling. We employ this framework to compare 5 different models to 15 different datasets and we find that the answers to points (a)-(c) crucially depend on the fluctuations contained in the data, on how they are modeled, and on the fact that the city sizes are heavy-tailed distributed.
近10年来复杂系统研究领域中最著名的发现之一是：不同的指标y（如专利数）随着城市人口x非线性变化，呈现出某些规律，如 y∼x^β, β≠1。最近，在一些使用了新的数据库并用不同的方法定义城市边界的研究中，这个发现的普适性受到了质疑。在本文中，我们用一种概率论的框架研究了非线性标度的存在性，在研究中，我们可以将涨落明确地描述出来。特别地，我们发现这种方法不仅允许（a）估计β和置信区间，还允许（b）量化支持β≠1的证据，并且（c）检验观察数据符合非线性标度的假设。我们使用这种研究思路来比较了为15个不同的数据库建模的5个不同的模型，我们发现，数据的涨落、建模方法和城市规模为重尾分布的事实对（a）~（c）的结果是至关重要的。
edited by 傅渥成
复杂网络的控制需要结构和动态 Control of complex networks requires both structure and dynamics
Scientific Reports 6, Article number: 24456 (2016) April 19, 11:50 PM
BY Alexander J. Gates & Luis M. Rocha
(Translated by -女周瑜)
The study of network structure has uncovered signatures of the organization of complex systems. However, there is also a need to understand how to control them; for example, identifying strategies to revert a diseased cell to a healthy state, or a mature cell to a pluripotent state. Two recent methodologies suggest that the controllability of complex systems can be predicted solely from the graph of interactions between variables, without considering their dynamics: structural controllability and minimum dominating sets. We demonstrate that such structure-only methods fail to characterize controllability when dynamics are introduced. We study Boolean network ensembles of network motifs as well as three models of biochemical regulation: the segment polarity network in Drosophila melanogaster, the cell cycle of budding yeast Saccharomyces cerevisiae, and the floral organ arrangement in Arabidopsis thaliana. We demonstrate that structure-only methods both undershoot and overshoot the number and which sets of critical variables best control the dynamics of these models, highlighting the importance of the actual system dynamics in determining control. Our analysis further shows that the logic of automata transition functions, namely how canalizing they are, plays an important role in the extent to which structure predicts dynamics.
edited by 傅渥成
有重尾的符号分布频率的相似点（Similarity of Symbol Frequency Distributions with Heavy Tails）
Phys. Rev. X 6, 021009 April 21, 9:45 PM
BY Martin Gerlach, Francesc Font-Clos, and Eduardo G. Altmann
(Translated by -王与剑)
A mathematical technique for comparing large symbol sets suggests that less frequently used words are mainly responsible for the evolution of the English language over the past two centuries. 原文链接：http://journals.aps.org/prx/abstract/10.1103/PhysRevX.6.021009
Understanding how biodiversity unfolds through time under neutral theory
Philosophical transactions of the royal society B April 22, 3:38 PM
BY Olivier Missa, Calvin Dytham, Hélène Morlon
(Translated by -)
Theoretical predictions for biodiversity patterns are typically derived under the assumption that ecological systems have reached a dynamic equilibrium. Yet, there is increasing evidence that various aspects of ecological systems, including (but not limited to) species richness, are not at equilibrium. Here, we use simulations to analyse how biodiversity patterns unfold through time. In particular, we focus on the relative time required for various biodiversity patterns (macroecological or phylogenetic) to reach equilibrium. We simulate spatially explicit metacommunities according to the Neutral Theory of Biodiversity (NTB) under three modes of speciation, which differ in how evenly a parent species is split between its two daughter species. We find that species richness stabilizes first, followed by species area relationships (SAR) and finally species abundance distributions (SAD). The difference in timing of equilibrium between these different macroecological patterns is the largest when the split of individuals between sibling species at speciation is the most uneven. Phylogenetic patterns of biodiversity take even longer to stabilize (tens to hundreds of times longer than species richness) so that equilibrium predictions from neutral theory for these patterns are unlikely to be relevant. Our results suggest that it may be unwise to assume that biodiversity patterns are at equilibrium and provide a first step in studying how these patterns unfold through time.
Parasites Are Us
nautil.us April 22, 5:41 PM
BY ROBERT V. LEVINE
(Translated by -)
But if the mitochondria are me, doesn’t this mean I have two sets of genes? Aren’t I a mosaic of both my own cellular DNA and that of my mitochondria? The fact is that all of the “others”—whether they are parasitic or mutualistic, cheaters or straight-shooters, long-term residents or one-night stands—have a significant characteristic in common: They each carry their own DNA. And this means that, for however long they are inside their host’s body, two genetically distinct organisms are living under the same skin and, to one extent or another, are biologically intertwined. Deep down, at the core of our tissue, we are a gigantic, symbiotic array, a ragtag assortment of organisms. All of these are to some degree us.
Waste not, want not, emit less
Science 22 Apr 2016:Vol. 352, Issue 6284, pp. 408-409 April 22, 5:54 PM
BY Jessica Aschemann-Witzel
(Translated by -)
Ensuring a sufficient supply of quality food for a growing human population is a major challenge, aggravated by climate change and already-strained natural resources. Food security requires production of some food surpluses to safeguard against unpredictable fluctuations (1). However, when food is wasted, not only has carbon been emitted to no avail, but disposal and decomposition in landfills create additional environmental impacts. Decreasing the current high scale of food waste is thus crucial for achieving resource-efficient, sustainable food systems (2). But, although avoiding food waste seems an obvious step toward sustainability, especially given that most people perceive wasting food as grossly unethical (3), food waste is a challenge that is not easily solved.
Microbiome: Eating for trillions
Nature 532, 316–317 (21 April 2016 April 22, 7:41 PM
BY Derrick M. Chu & Kjersti M. Aagaard
(Translated by -)
Three studies investigate the bacteria in the guts of malnourished children and find that, when this microbiota is transferred into mice, supplements of certain microbes or sugars from human breast milk can restore normal growth.
An Experimental Study of Team Size and Performance on a Complex Task
PLoS ONE 11(4) April 23, 7:34 PM
By Mao A, Mason W, Suri S, Watts DJ
(Translated by -)
The relationship between team size and productivity is a question of broad relevance across economics, psychology, and management science. For complex tasks, however, where both the potential benefits and costs of coordinated work increase with the number of workers, neither theoretical arguments nor empirical evidence consistently favor larger vs. smaller teams. Experimental findings, meanwhile, have relied on small groups and highly stylized tasks, hence are hard to generalize to realistic settings. Here we narrow the gap between real-world task complexity and experimental control, reporting results from an online experiment in which 47 teams of size ranging from n = 1 to 32 collaborated on a realistic crisis mapping task. We find that individuals in teams exerted lower overall effort than independent workers, in part by allocating their effort to less demanding (and less productive) sub-tasks; however, we also find that individuals in teams collaborated more with increasing team size. Directly comparing these competing effects, we find that the largest teams outperformed an equivalent number of independent workers, suggesting that gains to collaboration dominated losses to effort. Importantly, these teams also performed comparably to a field deployment of crisis mappers, suggesting that experiments of the type described here can help solve practical problems as well as advancing the science of collective intelligence. 原文链接：http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0153048
Why Physics Is Not a Discipline
From nautil.us April 24, 1:38 AM
By PHILIP BALL
(Translated by -)
Saying that physics knows no boundaries is not the same as saying that physicists can solve everything. They too have been brought up inside a discipline, and are as prone as any of us to blunder when they step outside. The issue is not who “owns” particular problems in science, but about developing useful tools for thinking about how things work—which is what Aristotle tried to do over two millennia ago. Physics is not what happens in the Department of Physics. The world really doesn’t care about labels, and if we want to understand it then neither should we.
Why we need democracy 2.0 and capitalism 2.0 to survive
From futurict.blogspot.ch April 26, 8:34 PM
By Dirk Helbing (ETH Zurich/TU Delft)
(Translated by -)
The world is running into great trouble. The anthropocene challenges (including climate change, impending resource shortages, demographic change, conflict, financial and economic crises) call for entirely new answers. As a result, we are now seeing the emergence of data-driven societies around the globe. Feudalism 2.0, fascism 2.0, communism 2.0, socialism 2.0, democracy 2.0 and capitalism 2.0 can now be built. What framework should we choose? What would be the implications?
Estimating biologically relevant parameters under uncertainty for experimental within-host murine West Nile virus infection
From rsif.royalsocietypublishing.org April 27, 9:17 PM
By Soumya Banerjee, Jeremie Guedj, Ruy M. Ribeiro, Melanie Moses, Alan S. Perelson
(Translated by -)
West Nile virus (WNV) causes viral encephalitis in humans, and is related to viruses such as Dengue and Zika that are also of significant public health concern. We have developed a computational method to determine characteristics of WNV infection even in the face of limited experimental data. This could be applicable to other emerging diseases like Zika virus for which there is little data. It may be particularly useful to estimate the potential rate of within-host viral reproduction early in an outbreak in order to assess the epidemic potential of emerging pathogens.
A model to identify urban traffic congestion hotspots in complex networks
From arxiv.org April 28, 3:00 PM
By Albert Solé-Ribalta, Sergio Gómez, Alex Arenas
(Translated by -)
Traffic congestion is one of the most notable problems arising in worldwide urban areas, importantly compromising human mobility and air quality. Current technologies to sense real-time data about cities, and its open distribution for analysis, allow the advent of new approaches for improvement and control. Here, we propose an idealized model, the Microscopic Congestion Model, based on the critical phenomena arising in complex networks, that allows to analytically predict congestion hotspots in urban environments. Results on real cities' road networks, considering, in some experiments, real-traffic data, show that the proposed model is capable of identifying susceptible junctions that might become hotspots if mobility demand increases.
Spatial Patterns in Urban Systems
From arxiv.org April 28, 5:09 PM
By Hoai Nguyen Huynh, Evgeny Makarov, Erika Fille Legara, Christopher Monterola, Lock Yue Chew
(Translated by -)
Understanding the morphology of an urban system is an important step toward unveiling the dynamical processes of its growth and development. At the foundation of every urban system, transportation system is undeniably a crucial component in powering the life of the entire urban system. In this work, we study the spatial pattern of 73 cities across the globe by analysing the distribution of public transport points within the cities. The analysis reveals that different spatial distributions of points could be classified into four groups with distinct features, indicating whether the points are clustered, dispersed or regularly distributed. From visual inspection, we observe that the cities with regularly distributed patterns do not have apparent centre in contrast to the other two types in which star-node structure, i.e. monocentric, can be clearly observed. Furthermore, the results provide evidence for the existence of two different types of urban system: well-planned and organically grown. We also study the spatial distribution of another important urban entity, the amenities, and find that it possesses universal properties regardless of the city's spatial pattern type. This result has one important implication that at small scale of locality, the urban dynamics cannot be controlled even though the regulation can be done at large scale of the entire urban system. The relation between the distribution of amenities within the city and its spatial pattern is also discussed.
Merging evolutionary history into species interaction networks
From onlinelibrary.wiley.com April 28, 7:20 PM
By Guadalupe Peralta
(Translated by -)
The occurrence of complex networks of interactions among species not only relies on species co-occurrence, but also on inherited traits and evolutionary events imprinted in species phylogenies. The phylogenetic signal found in ecological networks suggests that evolution plays an important role in determining community assembly and hence could inform about the underpinning mechanisms.
Efficient network structures with separable heterogeneous connection costs
From www.sciencedirect.com April 28, 9:18 PM
By Babak Heydari, Mohsen Mosleh, Kia Dalili (Translated by -)
We provide the analytical solution for the efficient network with heterogeneous, separable connection costs. The efficient network has a diameter no bigger than two and exhibits a core–periphery structure. We calculate the lower bound for clustering coefficient of the efficient network. (请在此输入译文) 原文链接：http://dx.doi.org/10.1016/j.econlet.2015.06.014
Prediction of Cascading Failures in Spatial Networks
From journals.plos.org April 28, 9:18 PM
By Yang Shunkun, Zhang Jiaquan, Lu Dan (Translated by -)
Cascading overload failures are widely found in large-scale parallel systems and remain a major threat to system reliability; therefore, they are of great concern to maintainers and managers of different systems. Accurate cascading failure prediction can provide useful information to help control networks. However, for a large, gradually growing network with increasing complexity, it is often impractical to explore the behavior of a single node from the perspective of failure propagation. Fortunately, overload failures that propagate through a network exhibit certain spatial-temporal correlations, which allows the study of a group of nodes that share common spatial and temporal characteristics. Therefore, in this study, we seek to predict the failure rates of nodes in a given group using machine-learning methods. We simulated overload failure propagations in a weighted lattice network that start with a center attack and predicted the failure percentages of different groups of nodes that are separated by a given distance. The experimental results of a feedforward neural network (FNN), a recurrent neural network (RNN) and support vector regression (SVR) all show that these different models can accurately predict the similar behavior of nodes in a given group during cascading overload propagation.
From www.nature.com April 29, 2:58 PM
By Kaj-Kolja Kleineberg & Marián Boguñá
(Translated by -)
The overwhelming success of online social networks, the key actors in the Web 2.0 cosmos, has reshaped human interactions globally. To help understand the fundamental mechanisms which determine the fate of online social networks at the system level, we describe the digital world as a complex ecosystem of interacting networks. In this paper, we study the impact of heterogeneity in network fitnesses on the competition between an international network, such as Facebook, and local services. The higher fitness of international networks is induced by their ability to attract users from all over the world, which can then establish social interactions without the limitations of local networks. In other words, inter-country social ties lead to increased fitness of the international network. To study the competition between an international network and local ones, we construct a 1:1000 scale model of the digital world, consisting of the 80 countries with the most Internet users. Under certain conditions, this leads to the extinction of local networks; whereas under different conditions, local networks can persist and even dominate completely. In particular, our model suggests that, with the parameters that best reproduce the empirical overtake of Facebook, this overtake could have not taken place with a significant probabilit
Bond Percolation on Multiplex Networks
From journals.aps.org April 29, 7:20 PM
By A. Hackett, D. Cellai, S. Gómez, A. Arenas, and J. P. Gleeson
(Translated by -)
Modern society is permeated by systems with many numbers of nodes and connections (e.g., rail networks, airports). A theoretical study of the multiplex network consisting of European Union air routes and the London rail transportation system demonstrates the fragility of such a network.
Broken detailed balance at mesoscopic scales in active biological systems
From science.sciencemag.org April 29, 9:53 PM
By CHRISTOPHER BATTLE, CHASE P. BROEDERSZ, NIKTA FAKHRI, VEIKKO F. GEYER, JONATHON HOWARD, CHRISTOPH F. SCHMIDT, FRED C. MACKINTOSH
(Translated by -)
Systems in thermodynamic equilibrium are not only characterized by time-independent macroscopic properties, but also satisfy the principle of detailed balance in the transitions between microscopic configurations. Living systems function out of equilibrium and are characterized by directed fluxes through chemical states, which violate detailed balance at the molecular scale. Here we introduce a method to probe for broken detailed balance and demonstrate how such nonequilibrium dynamics are manifest at the mesosopic scale. The periodic beating of an isolated flagellum from Chlamydomonas reinhardtii exhibits probability flux in the phase space of shapes. With a model, we show how the breaking of detailed balance can also be quantified in stationary, nonequilibrium stochastic systems in the absence of periodic motion. We further demonstrate such broken detailed balance in the nonperiodic fluctuations of primary cilia of epithelial cells. Our analysis provides a general tool to identify nonequilibrium dynamics in cells and tissues.
Who's downloading pirated papers? Everyone
From science.sciencemag.org April 29, 10:45 PM
By John Bohannon (Translated by -)
In increasing numbers, researchers around the world are turning to Sci-Hub, the controversial website that hosts 50 million pirated papers and counting. Now, with server log data from Alexandra Elbakyan, the neuroscientist who created Sci-Hub in 2011 as a 22-year-old graduate student in Kazakhstan, Science addresses some basic questions: Who are Sci-Hub's users, where are they, and what are they reading? The Sci-Hub data provide the first detailed view of what is becoming the world's de facto open-access research library. Among the revelations that may surprise both fans and foes alike: Sci-Hub users are not limited to the developing world. Some critics of Sci-Hub have complained that many users can access the same papers through their libraries but turn to Sci-Hub instead—for convenience rather than necessity. The data provide some support for that claim. Over the 6 months leading up to March, Sci-Hub served up 28 million documents, with Iran, China, India, Russia, and the United States the leading requestors.
The Free Energy Requirements of Biological Organisms; Implications for Evolution
From www.mdpi.com April 30, 4:34 AM
By David H. Wolpert
(Translated by -)
Recent advances in nonequilibrium statistical physics have provided unprecedented insight into the thermodynamics of dynamic processes. The author recently used these advances to extend Landauer’s semi-formal reasoning concerning the thermodynamics of bit erasure, to derive the minimal free energy required to implement an arbitrary computation. Here, I extend this analysis, deriving the minimal free energy required by an organism to run a given (stochastic) map π from its sensor inputs to its actuator outputs. I use this result to calculate the input-output map π of an organism that optimally trades off the free energy needed to run π with the phenotypic fitness that results from implementing π. I end with a general discussion of the limits imposed on the rate of the terrestrial biosphere’s information processing by the flux of sunlight on the Earth.
From big data to important information
From onlinelibrary.wiley.com April 30, 2:28 PM
By Yaneer Bar-Yam (Translated by -)
Advances in science are being sought in newly available opportunities to collect massive quantities of data about complex systems. While key advances are being made in detailed mapping of systems, how to relate these data to solving many of the challenges facing humanity is unclear. The questions we often wish to address require identifying the impact of interventions on the system and that impact is not apparent in the detailed data that is available. Here, we review key concepts and motivate a general framework for building larger scale views of complex systems and for characterizing the importance of information in physical, biological, and social systems. We provide examples of its application to evolutionary biology with relevance to ecology, biodiversity, pandemics, and human lifespan, and in the context of social systems with relevance to ethnic violence, global food prices, and stock market panic. Framing scientific inquiry as an effort to determine what is important and unimportant is a means for advancing our understanding and addressing many practical concerns, such as economic development or treating disease.
Explaining the Prevalence, Scaling and Variance of Urban Phenomena
From arxiv.org April 30, 3:05 PM
By Andres Gomez-Lievano, Oscar Patterson-Lomba, Ricardo Hausmann
(Translated by -)
The prevalence of many urban phenomena changes systematically with population size. We propose a theory that unifies models of economic complexity and cultural evolution to derive urban scaling. The theory accounts for the difference in scaling exponents and average prevalence across phenomena, as well as the difference in the variance within phenomena across cities of similar size. The central ideas are that a number of necessary complementary factors must be simultaneously present for a phenomenon to occur, and that the diversity of factors is logarithmically related to population size. The model reveals that phenomena that require more factors will be less prevalent, scale more superlinearly and show larger variance across cities of similar size. The theory applies to data on education, employment, innovation, disease and crime, and it entails the ability to predict the prevalence of a phenomenon across cities, given information about the prevalence in a single city. (请在此输入译文)