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Latest news on complex systems in life sciences, engineering, education and government
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Toward a unifying framework for evolutionary processes

The theory of population genetics and evolutionary computation have been evolving separately for nearly 30 years. Many results have been independently obtained in both fields and many others are unique to its respective field. We aim to bridge this gap by developing a unifying framework for evolutionary processes that allows both evolutionary algorithms and population genetics models to be cast in the same formal framework.

 

Toward a unifying framework for evolutionary processes
Tiago Paixão, et al.

Journal of Theoretical Biology
Volume 383, 21 October 2015, Pages 28–43

http://dx.doi.org/10.1016/j.jtbi.2015.07.011


Via Complexity Digest
ComplexInsight's insight:

Interesting paper - however any paper discussing an approach to a unifying evolutionary process that discusses genetic algorithms is somewhat of a remis when doing a recap and missing John H Holland's pioneering work.   That said still worth reading.

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Are fish far more intelligent than we realize?

Are fish far more intelligent than we realize? | Complex Insight  - Understanding our world | Scoop.it
They don't have a three-second memory. And one researcher thinks we've been dramatically underestimating their intelligence all along.
ComplexInsight's insight:

Culum Brown's research into fish behaviour is deeply revealing both for the insights into aquatic life and into human prejudice regarding other species capabilities.  Good article on vox.com regarding fish sentience, perception and behavioural evolution - worth reading.

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Ancient Fossils Suggest Complex Life Evolved on Land | Simons Foundation

Ancient Fossils Suggest Complex Life Evolved on Land | Simons Foundation | Complex Insight  - Understanding our world | Scoop.it
Evidence from Southwestern deserts suggests that oxygen-breathing organisms arose on land rather than in the seas.
ComplexInsight's insight:

Understanding prehistoric evolution is at best a game of educated guesses. Paul Knuath's research has helped revolutionize our perspective of possible evolutionary pathways and this is a great article putting that research in perspective.

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Self-Assembling Molecules Like These May Have Sparked Life on Earth - Wired Science

Self-Assembling Molecules Like These May Have Sparked Life on Earth - Wired Science | Complex Insight  - Understanding our world | Scoop.it
Scientists have discovered building blocks similar to those in modern RNA that can effortlessly assemble when mixed in water and heated.
ComplexInsight's insight:

Easily accessible article on the research of Nicholas Hud and team at Georgia Institute of Technology. Hud's research group are searching for the evolutionary precursor to RNA and after 20 years of research are finding promising results.

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Human Deaths and Third-Generation Cephalosporin use in Poultry, Europe - Vol. 19 No. 8 - August 2013 - Emerging Infectious Disease journal - CDC

Human Deaths and Third-Generation Cephalosporin use in Poultry, Europe - Vol. 19 No. 8 - August 2013 - Emerging Infectious Disease journal - CDC | Complex Insight  - Understanding our world | Scoop.it

Globally, antimicrobial drug resistance is rapidly rising, with resultant increased illness and death. In Europe, increasing proportions of bloodstream infections caused by E. coli are resistant to third-generation cephalosporins...

ComplexInsight's insight:

Antibiotic use in agriculture tends to be a tension filled debate.  Farmers  want healthy stock and the use of antibiotics as with people has had a major impact. However use of antiobiotics in farming helps accelerate bacterial evolution and antibiotic resistance. The debate around antibiotic overuse on farms or over perscription in human medicine and the relation to antibiotic-resistant bacteria, how antibiotic resistant strains migrate from farms to elswhere is ongoing. The human and financial impact and cost of antiobiotic overuse  in agriculture has until now been a grey area of discussion.  A multi-national team of researchers recently published their findings to these questions in the open journal Emerging Infectious disease published by CDC. They found  number of avoidable deaths and the costs of health care potentially caused by third-generation cephalosporin use in food animals is a staggering 1,518 deaths and 67,236 days in the hospital, every year, which would not otherwise have occurred. Considering those factors, they recommend the ongoing use of these antimicrobial drugs in mass therapy and prophylaxis should be urgently examined and stopped, particularly in poultry.  The article and technical appendix are worth reading.

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New virus 'not following Sars' path'

New virus 'not following Sars' path' | Complex Insight  - Understanding our world | Scoop.it
The new Mers virus, which has killed half of those infected, is "unlikely" to reach the same scale as Sars, ministers in Saudi Arabia say.
ComplexInsight's insight:

The source of the Mers virus is still unknown. Given that Mers is from the same group of viruses as Sars and Common Cold - understanding the genotype and phenotype differences and how they relate to pathogenic and vector pathways  in its related family could help to better understand both Mers and related groups and perhaps indicate a source. Viral evolution is something we still know relatively little about - and understanding of how they coevolve and relate to microbial habitat are becoming increasingly important to health planning and treatments.

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The Case of the Missing Human Ancestor

The Case of the Missing Human Ancestor | Complex Insight  - Understanding our world | Scoop.it
DNA from a cave in Russia adds a mysterious new member to the human family.
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Interesting article on the discovery of Denisovan DNA by the evolutionary genetics team at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. 

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Evolution of Mammalian Diving Capacity Traced by Myoglobin Net Surface Charge

Evolution of Mammalian Diving Capacity Traced by Myoglobin Net Surface Charge | Complex Insight  - Understanding our world | Scoop.it
Evolution of Mammalian Diving Capacity Traced by Myoglobin Net Surface Charge
ComplexInsight's insight:

A new study published in Science shows marine mammals evolutionary adaptations to store oxygen for deep dives.  Extended breath-hold endurance enabled marine mammals to expand their range and ecological niche. However to achieve this their bodies have had to evolve mechanisms to store elevated body oxygen and use it hyper efficiently.The new study highlights the molecular and biochemical adaptations to marine mammal muscle myoglobin to enable extended dive capacity. Worth reading

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Fossil shows how turtle got a shell

Fossil shows how turtle got a shell | Complex Insight  - Understanding our world | Scoop.it
How the turtle shell evolved has puzzled scientists for years, but new research sheds light on how their hard shells were formed.
ComplexInsight's insight:

The discovery of a translational fossil has helped identifiy the series of evolutionary steps and small changes that gradually add up to the evolution of the turtle shell. 

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Gene Sequencing Pinpoints Antibiotic Resistance Moving From Livestock to Humans | Wired Science | Wired.com

Gene Sequencing Pinpoints Antibiotic Resistance Moving From Livestock to Humans | Wired Science | Wired.com | Complex Insight  - Understanding our world | Scoop.it
A new study of Danish farmers and their livestock uses genetic sequencing to show that antibiotic-resistant bacterial infections travel from animal to human. Maryn McKenna describes the evidence.
ComplexInsight's insight:

Another awesome article by Maryn McKenna. If the analysis presented in the article is correct, then it indicates several sources of potential trouble.  The article highlights potential for animal-to-human transmission of resistant bacteria  even by animals that are not routinely receiving antibiotics. Finally the potential host range for resitant bacteria that is, the species detected to be carrying mecCMRSA, now mostly being called CC130  extends past farm breeds to include host range to include not just cows and sheep, but horses, rabbits, cats, dogs, deer, seals, rats and wild birds. Worth reading the entire article so click on the image or the title to learn more.

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'Visionary' leadership needed on TB

'Visionary' leadership needed on TB | Complex Insight  - Understanding our world | Scoop.it
Plans to tackle tuberculosis are failing and a new visionary approach is needed, according to an international group of doctors and scientists.
ComplexInsight's insight:

In Eastern europe up to a third of TB ccases are multi-drug resitant and a more extensively drug resistant form of tuberculosis has now been found in 84 countries. Scary set of implications given rate of evolution of multiresistant strains.

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OneZoom: A Fractal Explorer for the Tree of Life

OneZoom: A Fractal Explorer for the Tree of Life | Complex Insight  - Understanding our world | Scoop.it

Our knowledge of the tree of life—a phylogenetic tree summarizing the evolutionary relationships among all life on Earth—is expanding rapidly. “Mega-trees” with millions of tips (species) are expected to appear imminently ( for example, see http://www.opentree.wikispaces.com ). Unfortunately, there has so far been no practical and intuitive way to explore even the much smaller trees with thousands of tips that are now being routinely produced. Without a way to view megatrees, these wondrous objects, representing the culmination of decades of scientific effort, cannot be fully appreciated. The field really needs a solution to this problem to enable scientists to communicate important evolutionary concepts and data effectively, both to each other and to the general public. Just like Google Earth changed the way people look at geography, a sophisticated tree of life browser could really change the way we look at the life around us. Our advances in understanding evolution are moving really fast now, but the tools for looking at these big trees are lagging behind. Displaying large trees is a hard problem that has so far resisted solution. We are still waiting for the equivalent of a Google Maps. However, trees with millions of tips, richly embellished with additional data, can now be easily explored within the web browser of any modern hardware with a zooming user interface similar to that used in Google Maps.


Via Sakis Koukouvis, Dr. Stefan Gruenwald, Robin Lott
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Bringing genes and fossils together in evolutionary biology | Genome Engineering

Bringing genes and fossils together in evolutionary biology | Genome Engineering | Complex Insight  - Understanding our world | Scoop.it

While the links between the study of rocks and fossils and the high-tech field of genetics are not necessarily obvious at first glance, a recent review in the Journal of Vertebrate Paleontology shows that the connection is perhaps closer than you. often think. The case studies illustrate how the understanding of paleontology can be supported by research from developmental biologists. One case study looks at the relatively small genetic changes that have led to dramatic differences, for example the steps from a four-legged ancestor to a dolphin with two forelimbs and a tail, or a snake with no limbs at all, supported by paleontological findings of transitional fossils that bridge the gaps. Fascinating article and review. click on the image or title to learn more.

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Why HIV Virions Have Low Numbers of Envelope Spikes: Implications for Vaccine Development

Why HIV Virions Have Low Numbers of Envelope Spikes: Implications for Vaccine Development | Complex Insight  - Understanding our world | Scoop.it
From molecules to physiology
ComplexInsight's insight:

Interesting paper on structural protien envelope spikes in HIV related viruses and their relation to autoimmune response and implications for vaccine development by John Schiller and Bryce Chackerian. 

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Dinosaurs shrank for 50 million years to become birds - life - 31 July 2014 - New Scientist

Dinosaurs shrank for 50 million years to become birds - life - 31 July 2014 - New Scientist | Complex Insight  - Understanding our world | Scoop.it
The meat-eating theropod dinosaurs shrank 12 times in a row, going from over 200 kilograms to less than a kilogram, until they were small enough to fly
ComplexInsight's insight:

Evidence in a study by  Mike Lee of the South Australian Museum in Adelaide and colleagues has shown that a gradual wave of evolution led theropods to evolve into modern birds. Great article from New Scientist on Mike Lee's research work.

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The world’s most endangered food

The world’s most endangered food | Complex Insight  - Understanding our world | Scoop.it
Many varieties of fruit, meat and vegetable are disappearing from our plates, says Rachel Nuwer. Why is this happening, and can we stop the rot?
ComplexInsight's insight:

 Its probably not often we stop to think of the impacts of agriculture on the evolution of foodstuffs and what varieties of plants are being lost, along with their distinct tastes, benefits and properties. Compared to pre 1900 agriculture an estimated 75% of global farmed plant diversity is now gone and lost. Diversity is key to sustainable agriculture over the long term, so the points made in the article are particularly worrying. Thought provoking article from the BBC / worth reading.

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Viewpoint: Human evolution, from tree to braid

Viewpoint: Human evolution, from tree to braid | Complex Insight  - Understanding our world | Scoop.it

If one human evolution paper published in 2013 sticks in my mind above all others, it has to be the wonderful report in the 18 October issue of the journal Science. The article in question described the beautiful fifth skull from Dmanisi in Georgia. Most commentators and colleagues were full of praise, but controversy soon reared its ugly head.

ComplexInsight's insight:

Nice article from Prof.Clive Finlayson on 2013 archeology discoveries adn the implications for how we interpret human evolution. 

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'Fossil' protein clue to early life

'Fossil' protein clue to early life | Complex Insight  - Understanding our world | Scoop.it
New reconstructions of the genetic code of an ancient protein provides clues to the origins of life on Earth.
ComplexInsight's insight:

The resurrected protein is thought to have existed almost four billion years ago in single-celled organisms linked to the earliest ancestor of all life. The protein survives in the extreme environments of high acidity and temperature expected on early Earth and, intriguingly, also Mars.

Spanish and US scientists reported their study in the journal Structure. 

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Life as we know it

This paper presents a heuristic proof (and simulations of a primordial soup) suggesting that life—or biological self-organization—is an inevitable and emergent property of any (ergodic) random dynamical system that possesses a Markov blanket. This conclusion is based on the following arguments: if the coupling among an ensemble of dynamical systems is mediated by short-range forces, then the states of remote systems must be conditionally independent. These independencies induce a Markov blanket that separates internal and external states in a statistical sense. The existence of a Markov blanket means that internal states will appear to minimize a free energy functional of the states of their Markov blanket. Crucially, this is the same quantity that is optimized in Bayesian inference. Therefore, the internal states (and their blanket) will appear to engage in active Bayesian inference. In other words, they will appear to model—and act on—their world to preserve their functional and structural integrity, leading to homoeostasis and a simple form of autopoiesis.

 

Life as we know it
Karl Friston

J. R. Soc. Interface 6 September 2013 vol. 10 no. 86 20130475

http://dx.doi.org/10.1098/ rsif.2013.0475


Via Complexity Digest
ComplexInsight's insight:

one for reading list for later.

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Evolutionary Information Theory

Evolutionary information theory is a constructive approach that studies information in the context of evolutionary processes, which are ubiquitous in nature and society. In this paper, we develop foundations of evolutionary information theory, building several measures of evolutionary information and obtaining their properties. These measures are based on mathematical models of evolutionary computations, machines and automata. 

 

Evolutionary Information Theory
Mark Burgin

Information 2013, 4(2), 124-168; http://dx.doi.org/10.3390/info4020124


Via Complexity Digest
ComplexInsight's insight:

This looks very promising - one for reading list for holidays. 

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Tiny, insect-eating animal becomes earliest known primate

Tiny, insect-eating animal becomes earliest known primate | Complex Insight  - Understanding our world | Scoop.it
Archicebus achilles lived 55m years ago in what is now China and is the ancestor of all monkeys, apes and humans
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Researchers seek fresh approach to HIV vaccine

Researchers seek fresh approach to HIV vaccine | Complex Insight  - Understanding our world | Scoop.it
Last month's cancellation of the largest ongoing HIV vaccine trial stopped yet another promising candidate. The growing pool of clinical failures shows that a new approach is needed. This past week, academia offered up two new angles of attack.
ComplexInsight's insight:

FierceVaccines is a great source of info on new research. The summary of work published in Nature Structural & Molecular Biology from The Scripps Research focus on an area of the HIV virus where mutation is limited is worth reading and shows new approaches towards researching vaccines for HIV.

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Something Other Than Adaptation Could Be Driving Evolution | Wired Science | Wired.com

Something Other Than Adaptation Could Be Driving Evolution | Wired Science | Wired.com | Complex Insight  - Understanding our world | Scoop.it
What explains the incredible variety of life on Earth? It seems obvious. Evolution, of course! But perhaps not the evolution most people grew up with.
ComplexInsight's insight:

While the headline is slightly sensationalist and misleading, the article is worth reading. In a March 13 Proceedings of the National Academy of Sciences paper, Bar-Yam and his co-authors, Brazilian ecologists Ayana Martins at the University of Sao Paulo and Marcus Aguiar at the University of Campinas, modeled the evolution of greenish warblers living around the Tibetan plateau.  The warblers are what’s known as a ring species, a rare phenomenon that occurs when species inhabit a horseshoe-shaped range. Genes flow around the ring, passing between neighboring populations — yet at the ring’s tips, the animals no longer interbreed with one another. Bar-Yam and co's model generarted a similar distribution based on continual evoluation and genetic drift rather than localised adaptation. The model echoes of Stephen Hubbell's concepts of neutral genetic drift where  random genetic variations that emerge in individuals and spread through populations, can be ‘neutral,’ having no biological function but still drive evolution of species. Good article and interesting ideas that continue to drive the healthy debate on how evolution and speciation work.

  
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Dung beetles guided by Milky Way

Dung beetles guided by Milky Way | Complex Insight  - Understanding our world | Scoop.it
Scientists show how the lowly dung beetle will use the Milky Way's band of light in the night sky as a compass.
ComplexInsight's insight:

Possibly my favourite science article of 2013 so far. It makes sense in terms of evolutionary adaption since astral light sources would be an evolutionary environmental constant so adapting to utilize them makes a lot of sense. Proving that dung beetles do this - is just a wow. cool artile worth reading. 

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Cancer can teach us about our own evolution

Cancer can teach us about our own evolution | Complex Insight  - Understanding our world | Scoop.it

Charles Lineweaver ( Australian National University) and Paul Davies(Beyond Center for Fundamental Concepts in Science at Arizona State University.) have proposed a theory of cancer based on its ancient evolutionary roots. We think that as cancer progresses in the body it reverses, in a speeded-up manner, the arrow of evolutionary time. Increasing deregulation prompts cancer cells to revert to ever earlier genetic pathways that recapitulate successively earlier ancestral life styles. We predict that the various hallmarks of cancer progression will systematically correlate with the activation of progressively older ancestral genes. The most advanced and malignant cancers recreate aspects of life on Earth before a billion years ago. Click on image or title to learn more.

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