Darwinian Ascension
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Metazoan opsin evolution reveals a simple route to animal vision

Of course this should not be seen as evidence for a single lineage of development of eyesight. It appears that "All known visual pigments in Neuralia (Cnidaria, Ctenophora, and Bilateria) are composed of an opsin (a seven-transmembrane G protein-coupled receptor), and a light-sensitive chromophore, generally retinal." and that all opsins share the same common ancestor but that is only part of the deal. ZME has a nice further tutorial on the development of eye sight: http://www.zmescience.com/medicine/genetic/evolution-of-vision-from-700-million-years/

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A simple model clarifies the complicated relationships of complex networks

Researchers have discovered many types of complex networks and have proposed hundreds of models to explain their origins, yet most of the relationships within each of these types are still uncertain. Furthermore, because of the large number of types and models of complex networks, it is widely thought that these complex networks cannot all share a simple universal explanation. However, here we find that a simple model can produce many types of complex networks, including scale-free, small-world, ultra small-world, Delta-distribution, compact, fractal, regular and random networks, and by revising this model, we show that one can produce community-structure networks. Using this model and its revised versions, the complicated relationships among complex networks can be illustrated. Given that complex networks are regarded as a model tool of complex systems, the results here bring a new perspective to understanding the power law phenomena observed in various complex systems.

 

A simple model clarifies the complicated relationships of complex networks

Bojin Zheng, Hongrun Wu, Jun Qin, Wenhua Du, Jianmin Wang, Deyi Li

http://arxiv.org/abs/1210.3121


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Low fertility increases descendant socioeconomic position but reduces long-term fitness in a modern post-industrial society

Adaptive accounts of modern low human fertility argue that small family size maximizes the inheritance of socioeconomic resources across generations and may consequently increase long-term fitness. This study explores the long-term impacts of fertility and socioeconomic position (SEP) on ...


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Selectively altering belief formation in the human brain

Humans form beliefs asymmetrically; we tend to discount bad news but embrace good news. This reduced impact of unfavorable information on belief updating may have important societal implications, including the generation of financial market bubbles, ill preparedness in the face of natural disasters, and overly aggressive medical decisions. Here, we selectively improved people’s tendency to incorporate bad news into their beliefs by disrupting the function of the left (but not right) inferior frontal gyrus using transcranial magnetic stimulation, thereby eliminating the engrained “good news/bad news effect.” Our results provide an instance of how selective disruption of regional human brain function paradoxically enhances the ability to incorporate unfavorable information into beliefs of vulnerability.

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Understanding the placebo effect from an evolutionary perspective

Understanding the placebo effect from an evolutionary perspective | Darwinian Ascension | Scoop.it
Evolution & Human Behavior, Volume null, Issue null, Pages null, null, Authors:Pete C. Trimmer; James A.R. Marshall; Lutz Fromhage; John M. McNamara; Alasdair I.
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Ready steady slow: action preparation slows the subjective passage of time

Professional ball game players report the feeling of the ball ‘slowing-down’ before hitting it. Because effective motor preparation is critical in achieving such expert motor performance, these anecdotal comments imply that the subjective passage of time may be influenced by preparation for action. Previous reports of temporal illusions associated with action generally emphasize compensation for suppressed sensory signals that accompany motor commands. Here, we show that the time is perceived slowed-down during preparation of a ballistic reaching movement before action, involving enhancement of sensory processing. Preparing for a reaching movement increased perceived duration of a visual stimulus. This effect was tightly linked to action preparation, because the amount of temporal dilation increased with the information about the upcoming movement.

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On the evolutionary origins of the egalitarian syndrome

The evolutionary emergence of the egalitarian syndrome is one of the most intriguing unsolved puzzles related to the origins of modern humans. Standard explanations and models for cooperation and altruism—reciprocity, kin and group selection, and punishment—are not directly applicable to the emergence of egalitarian behavior in hierarchically organized groups that characterized the social life of our ancestors. Here I study an evolutionary model of group-living individuals competing for resources and reproductive success. In the model, the differences in fighting abilities lead to the emergence of hierarchies where stronger individuals take away resources from weaker individuals and, as a result, have higher reproductive success. (...)

 

On the evolutionary origins of the egalitarian syndrome
Sergey Gavrilets

http://dx.doi.org/10.1073/pnas.1201718109


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Wisdom of groups promotes cooperation in evolutionary social dilemmas

Whether or not to change strategy depends not only on the personal success of each individual, but also on the success of others. Using this as motivation, we study the evolution of cooperation in games that describe social dilemmas, where the propensity to adopt a different strategy depends both on individual fitness as well as on the strategies of neighbors. Regardless of whether the evolutionary process is governed by pairwise or group interactions, we show that plugging into the "wisdom of groups" strongly promotes cooperative behavior.(...)

 

Wisdom of groups promotes cooperation in evolutionary social dilemmas

Attila Szolnoki, Zhen Wang, Matjaz Perc

http://arxiv.org/abs/1208.4091


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Neuroscience: Genes and human brain evolution. [Nature. 2012] - PubMed - NCBI

Neuroscience: Genes and human brain evolution. [Nature. 2012] - PubMed - NCBI | Darwinian Ascension | Scoop.it

Several genes were duplicated during human evolution. It seems that one such duplication gave rise to a gene that may have helped to make human brains bigger and more adaptable than those of our ancestors.

 

 

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Task-switching costs promote the evolution of division of labor and shifts in individuality

Task-switching costs promote the evolution of division of labor and shifts in individuality | Darwinian Ascension | Scoop.it

Does the ability to improve group efficiency through the reduction of task-switching costs promote the evolution of division of labor? Our results demonstrate that as task-switching costs rise, groups increasingly evolve division of labor strategies. We analyze the mechanisms by which organisms coordinate their roles and discover strategies with striking biological parallels, including communication, spatial patterning, and task-partitioning behaviors.

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Consciousness Is Everywhere

Consciousness Is Everywhere | Darwinian Ascension | Scoop.it

The belief in human exceptionalism, so strongly rooted in the Judeo-Christian view of the world, flies in the face of all evidence for the structural and behavioral continuity between animals and people.


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ScienceDirect.com - Biosystems - The genetic code and its optimization for kinetic energy conservation in polypeptide chains

ScienceDirect.com - Biosystems - The genetic code and its optimization for kinetic energy conservation in polypeptide chains | Darwinian Ascension | Scoop.it

Why is the genetic code the way it is? Concepts from fields as diverse as molecular evolution, classical chemistry, biochemistry and metabolism have been used to define selection pressures most likely to be involved in the shaping of the genetic code.

Here minimization of kinetic energy disturbances during protein evolution by mutation allows an optimization of the genetic code to be highlighted. The quadratic forms corresponding to the kinetic energy term are considered over the field of rational numbers. Arguments are given to support the introduction of notions from basic number theory within this context. The observations found to be consistent with this minimization are statistically significant. The genetic code may well have been optimized according to energetic criteria so as to improve folding and dynamic properties of polypeptide chains.

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Evolution, Creation, and The Sting of Death: A Response to John Laing, Part 3 | BioLogos

Evolution, Creation, and The Sting of Death: A Response to John Laing, Part 3 | BioLogos | Darwinian Ascension | Scoop.it
It is one thing to say that death is primordial; it is another to view it not just as an ancient byproduct, but as the central means of creation.
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Mesoscale symmetries explain dynamical equivalence of food webs

A goal of complex system research is to identify the dynamical implications of network structure. While early results focused mainly on local or global structural properties, there is now growing interest in mesoscale structures that comprise more than one node but not the whole network. A central challenge is to discover under what conditions the occurrence of a specific mesoscale motif already allows conclusions on the dynamics of a network as a whole. In this paper, we investigate the dynamics of ecological food webs, complex heterogeneous networks of interacting populations.

 

Mesoscale symmetries explain dynamical equivalence of food webs

Helge Aufderheide, Lars Rudolf and Thilo Gross

New J. Phys. 14 105014

http://dx.doi.org/10.1088/1367-2630/14/10/105014


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Slimed! Scientists Discover that Evolution of Memory Started by Feedback from Chemicals

Slimed! Scientists Discover that Evolution of Memory Started by Feedback from Chemicals | Darwinian Ascension | Scoop.it
Although They only have a single cell and no brain, slime molds, Physarum polycephalum, remember where they’ve been by constructing a form of spatial memory by avoiding areas it has previously explored, according to researchers at University of...
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Artificially Intelligent Game Bots Pass the Turing Test on Turing’s Centenary | News

Artificially Intelligent Game Bots Pass the Turing Test on Turing’s Centenary | News | Darwinian Ascension | Scoop.it
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Evolution of cooperation and skew under imperfect information

The evolution of cooperation in nature and human societies depends crucially on how the benefits from cooperation are divided and whether individuals have complete information about their payoffs. We tackle these questions by adopting a methodology from economics called mechanism design. Focusing on reproductive skew as a case study, we show that full cooperation may not be achievable due to private information over individuals’ outside options, regardless of the details of the specific biological or social interaction. Further, we consider how the structure of the interaction can evolve to promote the maximum amount of cooperation in the face of the informational constraints. Our results point to a distinct avenue for investigating how cooperation can evolve when the division of benefits is flexible and individuals have private information.

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Why the bigger live longer and travel farther: animals, vehicles, rivers and the winds : Scientific Reports : Nature Publishing Group

Why the bigger live longer and travel farther: animals, vehicles, rivers and the winds : Scientific Reports : Nature Publishing Group | Darwinian Ascension | Scoop.it
Here we show that constructal-law physics unifies the design of animate and inanimate movement by requiring that larger bodies move farther, and their movement on the landscape last longer.
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Network Context and Selection in the Evolution to Enzyme Specificity

Enzymes are thought to have evolved highly specific catalytic activities from promiscuous ancestral proteins. By analyzing a genome-scale model of Escherichia coli metabolism, we found that 37% of its enzymes act on a variety of substrates and catalyze 65% of the known metabolic reactions. However, it is not apparent why these generalist enzymes remain. Here, we show that there are marked differences between generalist enzymes and specialist enzymes, known to catalyze a single chemical reaction on one particular substrate in vivo. Specialist enzymes (i) are frequently essential, (ii) maintain higher metabolic flux, and (iii) require more regulation of enzyme activity to control metabolic flux in dynamic environments than do generalist enzymes. Furthermore, these properties are conserved in Archaea and Eukarya. Thus, the metabolic network context and environmental conditions influence enzyme evolution toward high specificity.

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Computational social science: Making the links

Computational social science: Making the links | Darwinian Ascension | Scoop.it

The emerging field of computational social science is attracting mathematically inclined scientists in ever-increasing numbers. This, in turn, is spurring the creation of academic departments and prompting companies such as the social-network giant Facebook, (...) to establish research teams to understand the structure of their networks and how information spreads across them.

 

Computational social science: Making the links

Jim Giles

Nature 488, 448–450 (23 August 2012) http://dx.doi.org/10.1038/488448a


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Abiotic Self-Replication - Accounts of Chemical Research (ACS Publications)

Abiotic Self-Replication - Accounts of Chemical Research (ACS Publications) | Darwinian Ascension | Scoop.it

The key to the origins of life is the replication of information. Linear polymers such as nucleic acids that both carry information and can be replicated are currently what we consider to be the basis of living systems. However, these two properties are not necessarily coupled. The ability to mutate in a discrete or quantized way, without frequent reversion, may be an additional requirement for Darwinian evolution, in which case the notion that Darwinian evolution defines life may be less of a tautology than previously thought.

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Proto-genes and de novo gene birth. [Nature. 2012] - PubMed - NCBI

Novel protein-coding genes can arise either through re-organization of pre-existing genes or de novo. Processes involving re-organization of pre-existing genes, notably after gene duplication, have been extensively described. In contrast, de novo gene birth remains poorly understood, mainly because translation of sequences devoid of genes, or 'non-genic' sequences, is expected to produce insignificant polypeptides rather than proteins with specific biological functions. Here we formalize an evolutionary model according to which functional genes evolve de novo through transitory proto-genes generated by widespread translational activity in non-genic sequences. Testing this model at the genome scale in Saccharomyces cerevisiae, we detect translation of hundreds of short species-specific open reading frames (ORFs) located in non-genic sequences. These translation events seem to provide adaptive potential, as suggested by their differential regulation upon stress and by signatures of retention by natural selection. In line with our model, we establish that S. cerevisiae ORFs can be placed within an evolutionary continuum ranging from non-genic sequences to genes. We identify ~1,900 candidate proto-genes among S. cerevisiae ORFs and find that de novo gene birth from such a reservoir may be more prevalent than sporadic gene duplication. Our work illustrates that evolution exploits seemingly dispensable sequences to generate adaptive functional innovation.

 

 

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Computing in the net of possibilities

Computing in the net of possibilities | Darwinian Ascension | Scoop.it

(Phys.org) -- Scientists at the Max Planck Institute for Dynamics and Self-Organization in Göttingen have developed an entirely new principle for information processing.

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Epidermis architecture and material properties of the skin of four snake species

Epidermis architecture and material properties of the skin of four snake species | Darwinian Ascension | Scoop.it

Snakes are highly specialized legless animals, which have evolved around 150 Million years ago. Although without extremities their body is exposed to constant friction forces. The PhD-Student Marie-Christin Klein and Professor Stanislav Gorb of Kiel University found out how snake skin is adapted to legless locomotion. The skin is stiff and hard on the outside and becomes soft and flexible towards the inside, independent of habitat. Klein and Gorb are publishing their current results in today’s issue of the Journal of the Royal Society Interface.

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Surprising finding: Tree's leaves genetically different from its roots

Surprising finding: Tree's leaves genetically different from its roots | Darwinian Ascension | Scoop.it

Black cottonwood trees (Populus trichocarpa) can clone themselves to produce offspring that are connected to their parents by the same root system. Now, after the first genome-wide analysis of a tree, it turns out that the connected clones have many genetic differences, even between tissues from the top and bottom of a single tree. The variation within a tree is as great as the variation across unrelated trees. Such somatic mutations — those that occur in cells other than sperm or eggs — are familiar to horticulturalists, who have long bred new plant varieties by grafting mutant branches onto ‘normal’ stocks. But until now, no one has catalogued the total number of somatic mutations in an individual plant.

 

In one tree, the top buds of the parent and offspring were genetically closer to each other than to their respective roots or lower branches. In another tree, the top bud was closer to the reference cottonwood genome than to any of the other tissues from the same individual.The tissue-specific mutations affected mainly genes involved in cell death, immune responses, metabolism, DNA binding and cell communication. Olds think that this may be because many of the mutations are harmful, and the tree reacts by destroying the mutated tissues or altering its metabolic pathways and the way it controls its genes, which leads to further mutations.

 

The findings have parallels to cancer studies, which have recently shown that separate parts of the same tumor can evolve independently and build up distinct genetic mutations, meaning that single biopsies give only a narrow view of the tumor’s diversity.


Via Dr. Stefan Gruenwald, Complexity Digest
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