Complex Insight - Understanding our world
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# Space net used to control robot

DTNP is go... Astronauts on the International Space Station use an experimental version of interplanetary internet (more correctly the Disruption Tolerant Networking (DTN) Protocol)  to control a robot on Earth. Vint Cerf proposed this the basis of DTN over 10 years ago and the demonstration shows how communciations using the store and forward protocol are increasingly possible over very large distances. (a previous test was conducted with image transmition between earth and a remote satellite, 20 million miles away.).  Click on the image or title to learn more via the BBC Technologiy article.

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# Complex Insight - Understanding our world

News and notes on complex systems in life sciences, engineering, education and government
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## Complexity research in Nature Communications

This web collection showcases the potential of interdisciplinary complexity research by bringing together a selection of recent Nature Communications articles investigating complex systems. Complexity research aims to characterize and understand the behaviour and nature of systems made up of many interacting elements. Such efforts often require interdisciplinary collaboration and expertise from diverse schools of thought. Nature Communications publishes papers across a broad range of topics that span the physical and life sciences, making the journal an ideal home for interdisciplinary studies.

Via Complexity Digest
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## Influenza: A viral world war

The 1918 influenza pandemic probably infected one-third of the world's population at the time — 500 million people. It killed between 50 million and 100 million; by contrast, Second World War deaths numbered around 60 million. Why is this catastrophe

Via Ed Rybicki, Chris Upton + helpers
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## Viral vectors travel longer distances than previously thought

Gene transfer is seen as a hopeful therapy for Alzheimer's and Parkinson's patients. The approach involves using harmless laboratory-produced viruses to introduce important genes into the brain cells. In a study on mice

Via Gilbert C FAURE, Kenzibit
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## What a Fish Knows: The Inner Lives of Our Underwater Cousins

There are more than thirty thousand species of fish―more than mammals, birds, reptiles, and amphibians combined. But for all their breathtaking diversity and beauty, we rarely consider how fish think, feel, and behave. In What a Fish Knows, the ethologist Jonathan Balcombe takes us under the sea and to the other side of the aquarium glass to reveal what fishes can do, how they do it, and why. Introducing the latest revelations in animal behavior and biology, Balcombe upends our assumptions about fish, exposing them not as unfeeling, dead-eyed creatures but as sentient, aware, social―even Machiavellian. They conduct elaborate courtship rituals and develop lifelong bonds with shoal-mates. They also plan, hunt cooperatively, use tools, punish wrongdoers, curry favor, and deceive one another. Fish possess sophisticated senses that rival our own. The reef-dwelling damselfish identifies its brethren by face patterns visible only in ultraviolet light, and some species communicate among themselves in murky waters using electric signals. Highlighting these breakthrough discoveries and others from his own encounters with fish, Balcombe inspires a more enlightened appraisal of marine life.

An illuminating journey into the world of underwater science, What a Fish Knows will forever change your view of our aquatic cousins.

Via Complexity Digest
ComplexInsight's insight:
One for the reading list - looks fascinating.
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## Host and viral traits predict zoonotic spillover from mammals

The majority of human emerging infectious diseases are zoonotic, with viruses that originate in wild mammals of particular concern (for example, HIV, Ebola and SARS). Understanding patterns of viral diversity in wildlife and determinants of successful cross-species transmission, or spillover, are therefore key goals for pandemic surveillance programs. However, few analytical tools exist to identify which host species are likely to harbour the next human virus, or which viruses can cross species boundaries. Here we conduct a comprehensive analysis of mammalian host–virus relationships and show that both the total number of viruses that infect a given species and the proportion likely to be zoonotic are predictable. After controlling for research effort, the proportion of zoonotic viruses per species is predicted by phylogenetic relatedness to humans, host taxonomy and human population within a species range—which may reflect human–wildlife contact. We demonstrate that bats harbour a significantly higher proportion of zoonotic viruses than all other mammalian orders. We also identify the taxa and geographic regions with the largest estimated number of ‘missing viruses’ and ‘missing zoonoses’ and therefore of highest value for future surveillance. We then show that phylogenetic host breadth and other viral traits are significant predictors of zoonotic potential, providing a novel framework to assess if a newly discovered mammalian virus could infect people.

Via Ed Rybicki, Chris Upton + helpers
ComplexInsight's insight:
Understanding zoonotic potential will be key to health planning and epidemic prevention in the 21st century.  This paper has key insights such as major hosts (bats) and key geographic zones for observation. If you are involved in health planning or disease modeling - very worthwhile reading.
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## A Safety and Efficacy Study of TALEN and CRISPR/Cas9 in the Treatment of HPV-related Cervical Intraepithelial Neoplasia

This is an open-label and triple cohort study of the safety and efficacy of TALEN and CRISPR/Cas9 to possibly treat HPV Persistency and human cervical intraepithelial neoplasiaⅠwithout invasion.

Via Gerd Moe-Behrens
ComplexInsight's insight:
If your tracking CRISPR/Cas9 applications - this is worth reviewing.
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## Models and people: An alternative view of the emergent properties of computational models

Computer models can help humans gain insight into the functioning of complex systems. Used for training, they can also help gain insight into the cognitive processes humans use to understand these systems. By influencing humans understanding (and consequent actions) computer models can thus generate an impact on both these actors and the very systems they are designed to simulate. When these systems also include humans, a number of self-referential relations thus emerge which can lead to very complex dynamics. This is particularly true when we explicitly acknowledge and model the existence of multiple conflicting representations of reality among different individuals. Given the increasing availability of computational devices, the use of computer models to support individual and shared decision making could potentially have implications far wider than the ones often discussed within the Information and Communication Technologies community in terms of computational power and network communication. We discuss some theoretical implications and describe some initial numerical simulations.

Models and people: An alternative view of the emergent properties of computational models
Fabio Boschetti

Complexity

Volume 21, Issue 6
July/August 2016
Pages 202–213

http://dx.doi.org/10.1002/cplx.21680

Via Complexity Digest
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## Adaptive Computation: The Multidisciplinary Legacy of John H. Holland

John H. Holland's general theories of adaptive processes apply across biological, cognitive, social, and computational systems.
ComplexInsight's insight:
I first came across John Holland's work in a an article while I was at High School some 30 years ago. A few years later he kindly answered my questions in an out of the blue phone call and then over the years in conversations at conferences and in emails.  I have always been in awe of the breadth of his vision and interests, intrigued by his ideas and appreciated the fact he would take time to encourage research and passionate discussion. Sadly with his passing last year - we lost a truly original insight. Stephanie Forrest and Melanie Mitchells article for the ACM captures the breadth of his interests, his wonderful legacy of ideas and perhaps more importantly  the example he set in his humanity and generosity. Well worth reading.
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## A Bird’s-Eye View of Nature’s Hidden Order | Quanta Magazine

Scientists are exploring a mysterious pattern, found in birds’ eyes, boxes of marbles and other surprising places, that is neither regular nor random.
ComplexInsight's insight:
If you want to understand why AI is beginning to make major breakthroughts - it helps to understand the physics underpinning our world. This article gives a good overview of one such physical property - hyperuniform that is neither regular or random but a distribution that reflects the constrained reality that biological systems evolve within. Very much worth reading.
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## Engineering and Assembly of Protein Modules into Functional Molecular Systems

Synthetic biology approaches range from the introduction of unique features into organisms to the assembly of isolated biomacromolecules or synthetic building blocks into artificial biological systems with biomimetic or completely novel functionalities. Simple molecular systems can be based on containers on the nanoscale that are equipped with tailored functional modules for various applications in healthcare, industry or biological and medical research. The concept, or vision, of assembling native or engineered proteins and/or synthetic components as functional modules into molecular systems is discussed. The main focus is laid on the engineering of energizing modules generating chemical energy, transport modules using this energy to translocate molecules between compartments of a molecular system, and catalytic modules (bio-)chemically processing the molecules. Further key aspects of this discourse are possible approaches for the assembly of simple nanofactories and their applications in biotechnology and medical health.

Via Gerd Moe-Behrens
ComplexInsight's insight:
The concept  of assembling native or engineered proteins and/or synthetic components into functional systems is a key goal of synthetic biollogy and this paper gives  a good overview of current state of the art . Worth reeading
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## ‘Robot scientist’ Eve could speed up search for new drugs

Robot scientist Eve can perform a wide range of biological assays, screening at a moderately high throughput rate (credit: Kevin Williams et al./J. R. Soc.
Via Gerd Moe-Behrens
ComplexInsight's insight:
Though it will take time, the combination of automated biological assay screening with synthetic biology and goal driven targetting will be a key development in personalized medicine, targetted drug development and disease treatments in the  21st century.
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## Whatever happened to 'bans' on GM produce in British supermarkets? - Conversation (2015)

In the late 1990s, Sainsbury’s and Safeway... both offered GM tomato purée... GM and non-GM cans of purée stood side by side on their shelves, the former some 18% cheaper... The cans were conspicuously labelled and pamphlets explaining what GM was all about were to hand nearby. But when the stock ran out and it was time to re-order, the anti-GM food balloon had gone up and the product was discontinued...

In 1999 Marks & Spencer announced that it was removing all GM foods from its shelves. (In a House of Lords inquiry at that time, M&S said their customers demanded it. When asked by their lordships how many customers that meant, it turned out to have been rather a small percentage. But those who positively wanted GM were, it seems, even fewer in number)...

All the other retailers followed suit: the UK’s retail industry was to be GM-free – or was it? In fact some GM products... were always to be found... Then there is the question of GM fodder for animals.... retailers said that they would not sell any products from pigs or poultry that had been exposed to GM feeds...

Until, that is, when Asda became the first of the leading UK supermarkets to abandon its commitment to eggs and poultry fed with GM in 2010... But by then public opinion on the issue had become almost completely mute... GM-feed for pigs and poultry was no longer to be excluded... there appears to have been no noticeable consumer rejection of products from animals fed GM...

More than half the world’s cotton is GM, so this is likely to be the case with products on sale in the UK. There is no obligation to label GM cotton so one cannot be sure, but nobody seems to ask and few seem to care...

Public interest in this subject has largely waned... Though one can never be quite sure, it does begin to look as though the GM issue will fade away in the fullness of time, in England at least, even if it takes a while. I suspect GM food and crops will become commonplace and the protesting community will veer off in another direction, chasing new demons.

https://theconversation.com/whatever-happened-to-bans-on-gm-produce-in-british-supermarkets-51153

Via Alexander J. Stein
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## The role of environmental biotechnology in exploring, exploiting, monitoring, preserving, protecting and decontaminating the marine environment - Kalogerakis &al (2014) - New Biotechnol

In light of the Marine Strategy Framework Directive (MSFD) and the EU Thematic Strategy on the Sustainable Use of Natural Resources, environmental biotechnology could make significant contributions in the exploitation of marine resources and addressing key marine environmental problems. In this paper 14 propositions are presented focusing on (i) the contamination of the marine environment, and more particularly how to optimize the use of biotechnology-related tools and strategies for predicting and monitoring contamination and developing mitigation measures; (ii) the exploitation of the marine biological and genetic resources to progress with the sustainable, eco-compatible use of the maritime space (issues are very diversified and include, for example, waste treatment and recycling, anti-biofouling agents; bio-plastics); (iii) environmental/marine biotechnology as a driver for a sustainable economic growth.

http://dx.doi.org/10.1016/j.nbt.2014.03.007

Via Alexander J. Stein
ComplexInsight's insight:

late publishing this - but been on track list for some time. Also worth looking at the 2015 report on protection zones - where some progress has been made. See http://ec.europa.eu/environment/marine/eu-coast-and-marine-policy/implementation/pdf/marine_protected_areas.pdf

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## A decade of discovery: CRISPR functions and applications

This year marks the tenth anniversary of the identification of the biological function of CRISPR–Cas as adaptive immune systems in bacteria. In just a decade, the characterization of CRISPR–Cas systems has established a novel means of adaptive immunity in bacteria and archaea and deepened our understanding of the interplay between prokaryotes and their environment, and CRISPR-based molecular machines have been repurposed to enable a genome editing revolution. Here, we look back on the historical milestones that have paved the way for the discovery of CRISPR and its function, and discuss the related technological applications that have emerged, with a focus on microbiology. Lastly, we provide a perspective on the impacts the field has had on science and beyond.

Via Gerd Moe-Behrens
ComplexInsight's insight:
Great insight and perspective on CRISPR  developments and applications - worth reading.
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## The Types Of Cancer You Can Get From HPV

New study suggests HPV-related genital infection can cause cervical, anal, vulvar, and vaginal cancers.

Via Kenzibit
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## [1706.05043] The thermodynamic efficiency of computations made in cells across the range of life

Biological organisms must perform computation as they grow, reproduce, and evolve. Moreover, ever since Landauer's bound was proposed it has been known that all computation has some thermodynamic cost -- and that the same computation can be achieved with greater or smaller thermodynamic cost depending on how it is implemented. Accordingly an important issue concerning the evolution of life is assessing the thermodynamic efficiency of the computations performed by organisms. This issue is interesting both from the perspective of how close life has come to maximally efficient computation (presumably under the pressure of natural selection), and from the practical perspective of what efficiencies we might hope that engineered biological computers might achieve, especially in comparison with current computational systems. Here we show that the computational efficiency of translation, defined as free energy expended per amino acid operation, outperforms the best supercomputers by several orders of magnitude, and is only about an order of magnitude worse than the Landauer bound. However this efficiency depends strongly on the size and architecture of the cell in question. In particular, we show that the {\it useful} efficiency of an amino acid operation, defined as the bulk energy per amino acid polymerization, decreases for increasing bacterial size and converges to the polymerization cost of the ribosome. This cost of the largest bacteria does not change in ancells as we progress through the major evolutionary shifts to both single and multicellular eukaryotes. However, the rates of total computation per unit mass are nonmonotonic in bacteria with increasing cell size, and also change across different biological architectures including the shift from unicellular to multicellular eukaryotes.

The thermodynamic efficiency of computations made in cells across the range of life
Christopher P. Kempes, David Wolpert, Zachary Cohen, Juan Pérez-Mercader

Via Complexity Digest
ComplexInsight's insight:
The concept of computation as it occurs in biology is fascinating and this paper is likely to become a-classic - worth reading.
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## Africa health: Rotavirus vaccine could save 500,000 children a year

The Indian vaccine, which protects against gastroenteritis caused by rotavirus, was tested in Niger.

Via Ed Rybicki, Chris Upton + helpers
ComplexInsight's insight:
As if we need a reminder on the importance of vaccinations.
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## Genetics may lie at the heart of crop yield limitation - EurekAlert (2017)

You might think that plants grow according to how much nutrition, water and sunlight they are exposed to, but new research... shows that the plant's own genetics may be the real limiting factor.

"This could have potentially big implications for the agricultural industry... Our model plant is in the same family as cabbages, so it's easy to imagine creating giant cabbages or growing them to the desired market size faster than at present."

It was previously assumed that plant growth was generally resource-limited, meaning that plants would only grow as large and fast as they could photosynthesise. However, Dr Pullen and his team present evidence that plant growth is actually "sink-limited", meaning that genetic regulation and cell division rates have a much bigger role in controlling plant growth than previously thought:

"We are proposing that plant growth is not physically limited by Net Primary Productivity (NPP) or the environment, but instead is limited genetically in response to these signals to ensure they do not become limiting."

By genetically altering the growth repressors in Arabidopsis, Dr Pullen and his team were able to create mutant strains. They identified the metabolic rates of the different plant strains... as well as comparing the size and weight of the plants... also grew the mutant plant strains at different temperatures to see if this changed their results: "When grown at different temperatures we still find a difference in size"...

The impact of these results is wide-reaching, and... it may even change how we think about global climate data: "Climate models need to incorporate genetic elements because at present most do not, and their predictions would be much improved with a better understanding of plant carbon demand."

Via Alexander J. Stein
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## CRISPR-Cas Genome Surgery in Ophthalmology

Genetic disease affecting vision can significantly impact patient quality of life. Gene therapy seeks to slow the progression of these diseases by treating the underlying etiology at the level of the genome. Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated systems (Cas) represent powerful tools for studying diseases through the creation of model organisms generated by targeted modification and by the correction of disease mutations for therapeutic purposes. CRISPR-Cas systems have been applied successfully to the visual sciences and study of ophthalmic disease - from the modification of zebrafish and mammalian models of eye development and disease, to the correction of pathogenic mutations in patient-derived stem cells. Recent advances in CRISPR-Cas delivery and optimization boast improved functionality that continues to enhance genome-engineering applications in the eye. This review provides a synopsis of the recent implementations of CRISPR-Cas tools in the field of ophthalmology.

Via Gerd Moe-Behrens
ComplexInsight's insight:
While the promise of CRISPR was not that it would change how genetics and biology behaved its quickly becoming hyped that way in popular press.  The fact that the Cas9 protein can be used as a cheap and fast technique to co-localize with specific DNA sequences is undoubtedly incredibly useful. As researchers discover mechanisms where they can exploit co-localization and modification at specific sites using DNA cleavage capabilities it is important we get well informed reviews of actual applications as well as coverage of potential ones.  This paper gives a good summary of recent developments and insights to applications of CRISPR-CAS in ophthalmology  for both better understanding visual systems and potential treatments for ophthalmic disease.
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## Mapping the patent landscape of synthetic biology for fine chemical production pathways

A goal of synthetic biology bio-foundries is to innovate through an iterative design/build/test/learn pipeline. In assessing the value of new chemical production routes, the intellectual property (IP) novelty of the pathway is important. Exploratory studies can be carried using knowledge of the patent/IP landscape for synthetic biology and metabolic engineering. In this paper, we perform an assessment of pathways as potential targets for chemical production across the full catalogue of reachable chemicals in the extended metabolic space of chassis organisms, as computed by the retrosynthesis-based algorithm RetroPath. Our database for reactions processed by sequences in heterologous pathways was screened against the PatSeq database, a comprehensive collection of more than 150M sequences present in patent grants and applications. We also examine related patent families using Derwent Innovations. This large-scale computational study provides useful insights into the IP landscape of synthetic biology for fine and specialty chemicals production.

Via Gerd Moe-Behrens
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## Organisms might be quantum machines

Few of us really understand the weird world of quantum physics – but our bodies might take advantage of quantum properties
ComplexInsight's insight:
Interesting article on the increasingly suspected role of quantum physics in everyday biological systems including photosynthesis and migratory bird navigation. A fun read.
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## Samsung pours $1.2 billion into the Internet of Things Samsung is willing to put its money where its mouth is when it comes to the Internet of Things. The electronics giant is spending$1.2 billion on Io
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## MIT Engineers Developed a Super Strong Artificial Skin

Engineers from MIT have developed a substance that could be used as an artificial skin, long-lasting contact lens, drug-delivering bandage, and more.
Via Gerd Moe-Behrens
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## Battling the Zika virus, one old tyre at a time

From Canada, the ovillanta is a clever — and highly effective — mosquito trap made from the pests' favourite breeding spot.
ComplexInsight's insight:
Dr. Gerardo Ulibarri, PhD, an associate professor of medicinal chemistry and eco-health at Laurentian University in Sudbury, Ontario, had a  brilliant insight recycling tyres to create an effective mosquito trap that may provide an easy to build and effective mosquito management solution. Made from recycled tyres the bottom half of the device gets filled with about 2 litres of water, topped with so-called “landing strips” – pieces of Pellon or germinating paper, for example – on which the female mosquitoes lay eggs. Mosquitoes weed moisture to hatchso the landing paper if white easily shows the eggs. About once per week the user empties the device destroy the eggs, pour the water back into the ovillanta (topping it off with fresh water) and install two new landing strips. “It’s important to recycle the water because after the eggs hatch, they release a pheromone into the water that tells other mosquitoes it’s a good, safe place to lay eggs,” says Ulibarri, who’s work is funded by Grand Challenges Canada. BBC article very worth reading
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## Chemicals That Make Plants Defend Themselves Could Replace Pesticides - Elsevier (2015)

Chemical triggers that make plants defend themselves against insects could replace pesticides, causing less damage to the environment. New research... identifies five chemicals that trigger rice plants to fend off a common pest – the white-backed planthopper, Sogatella furcifera

Pesticides are used around the world to control insects that destroy crops... One of the problems with many pesticides is that they kill indiscriminately. For rice plants, this means pesticides kill the natural enemies of one of their biggest pests, the white-backed planthopper... This pest... causes the plants to wilt and can damage the grains. It also transmits a virus disease... which stunts the plants’ growth and stops them from “heading,” which is when pollination occurs.

Left untreated, many of the insects’ eggs would be eaten, but when pesticides are used these hatch, leading to even more insects on the plants. What’s more, in some areas as many as a third of the planthoppers are resistant to pesticides... “Therefore, developing safe and effective methods to control insect pests is highly desired”...

Because of the problems of using pesticides, it’s vital to find new solutions to help protect rice plants from infestation. Plants have natural self-defense mechanisms that kick in when they are infested with pests like the planthopper. This defense mechanism can be switched on using chemicals that do not harm the environment and are not toxic to the insects or their natural enemies...

Researchers... developed a new way of identifying these chemicals. Using a specially designed screening system, they determined to what extent different chemicals switched on the plants’ defense mechanism... The researchers used bioassays to show that these chemicals could trigger the plant defense mechanism and repel the white-backed planthopper. This suggests that these chemicals have the potential to be used in insect pest management...

“This new approach to pest management could help protect the ecosystem while defending important crops against attack.”

The next step for the research will be to explore how effective the chemicals are at boosting the plants’ defenses and controlling planthoppers in the field.

Original article: http://dx.doi.org/10.1016/j.bmcl.2015.10.041

Via Alexander J. Stein
ComplexInsight's insight:

Its good to see more research in these areas - but it would be good if in parallel we looked at potential impact of activated and elevated triggers and response  in terms of ecosystems and human health.  Multi-systemic approaches are going to be increasingly needed, which is worrying given how limited funding in this area already is..

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