Category Archives: Peer Reviewed Article Review

designing ecosystem complexity

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This article in Ecological Engineering is about measuring and purposely designing complexity into ecosystems to support biodiversity. I like this idea – certainly grass and trees are a step up from concrete in cities, but there might be some relatively simple design choices that could improve conditions for both wildlife and people without adding effort or cost. We actually expend enormous amounts of time, effort, and money maintaining our grass and trees, whereas natural ecosystems manage to maintain themselves while being more beautiful, diverse, and productive. The first step is to understand the systems better, the second would be to understand what variables we can manipulate, then the third and most difficult step is always translating that new understanding to actions on the ground and getting people to actually take them.

Simplification of natural habitats has become a major conservation challenge and there is a growing consensus that incorporating and enhancing habitat complexity is likely to be critical for future restoration efforts. Habitat complexity is often ascribed an important role in controlling species diversity, however, despite numerous empirical studies the exact mechanism(s) driving this association remains unclear. The lack of progress in untangling the relationship between complexity and diversity is partly attributable to the considerable ambiguity in the use of the term ‘complexity’. Here, we offer a new framework for conceptualizing ecological complexity, an essential prerequisite for the development of analytical methods for creating and comparing habitat complexity. Our framework distinguishes between two fundamental forms of complexity: information-based complexity and systems-based complexity. Most complexity–diversity studies are concerned with informational complexity which can be measured in the field through a variety of metrics (e.g. fractal dimensions, rugosity, etc.), but these metrics cannot be used to re-construct three-dimensional complex habitats. Drawing on our operational definition of informational complexity, it is possible to design habitats with different degrees of physical complexity. We argue that the ability to determine or modify the variables of complexity precisely has the potential to open up new lines of research in diversity theory and contribute to restoration and reconciliation by enabling environmental managers to rebuild complexity in anthropogenically-simplified habitats.

“robot scientist”

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This article is about a robot that can somehow develop its own experiments to test new drugs.

There is an urgent need to make drug discovery cheaper and faster. This will enable the development of treatments for diseases currently neglected for economic reasons, such as tropical and orphan diseases, and generally increase the supply of new drugs. Here, we report the Robot Scientist ‘Eve’ designed to make drug discovery more economical. A Robot Scientist is a laboratory automation system that uses artificial intelligence (AI) techniques to discover scientific knowledge through cycles of experimentation. Eve integrates and automates library-screening, hit-confirmation, and lead generation through cycles of quantitative structure activity relationship learning and testing. Using econometric modelling we demonstrate that the use of AI to select compounds economically outperforms standard drug screening. For further efficiency Eve uses a standardized form of assay to compute Boolean functions of compound properties. These assays can be quickly and cheaply engineered using synthetic biology, enabling more targets to be assayed for a given budget. Eve has repositioned several drugs against specific targets in parasites that cause tropical diseases. One validated discovery is that the anti-cancer compound TNP-470 is a potent inhibitor of dihydrofolate reductase from the malaria-causing parasite Plasmodium vivax.

Planetary Boundaries 2

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Johan Rockstrom and company have published a sequel to their original “planetary boundaries” work. Here’s a summary from the Stockholm Resilience Center:

Four of nine planetary boundaries have now been crossed as a result of human activity, says an international team of 18 researchers in the journal Science (16 January 2015). The four are: climate change, loss of biosphere integrity, land-system change, altered biogeochemical cycles (phosphorus and nitrogen).

Two of these, climate change and biosphere integrity, are what the scientists call “core boundaries”. Significantly altering either of these “core boundaries” would “drive the Earth System into a new state”.

“Transgressing a boundary increases the risk that human activities could inadvertently drive the Earth System into a much less hospitable state, damaging efforts to reduce poverty and leading to a deterioration of human wellbeing in many parts of the world, including wealthy countries,” …

Nine planetary boundaries
1. Climate change
2. Change in biosphere integrity (biodiversity loss and species extinction)
3. Stratospheric ozone depletion
4. Ocean acidification
5. Biogeochemical flows (phosphorus and nitrogen cycles)
6. Land-system change (for example deforestation)
7. Freshwater use
8. Atmospheric aerosol loading (microscopic particles in the atmosphere that affect climate and living organisms)
9. Introduction of novel entities (e.g. organic pollutants, radioactive materials, nanomaterials, and micro-plastics).

And for the video watchers, here is Mr. Rockstrom himself on Youtube:

Exxon’s 2015 Outlook for Energy

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Here is Exxon’s 2015 Outlook for Energy report. They talk about the importance of fossil fuels in the progress in living standards over the past couple centuries. They talk about the rise of the middle class in developing Asia, and how that is going to lead to rising living standards and health, but also big increases in demand for energy, food and materials. Now, you can’t begrudge people rising living standards and health, which are wonderful things. However, I wouldn’t equate progress just with more traffic, concrete and shopping malls full of designer hand bags. I would equate it more with things like safe drinking water, affordable food and health care. And air conditioning – I would never begrudge any human being in the tropics air conditioning.

They make a crucial logical error – using the rate of carbon emissions, rather than accumulation of emissions in the atmosphere, as a proxy for ecological footprint. They say the rate of global emissions is expected to peak around 2030.

While every country faces a unique set of priorities and resource
constraints, we expect that most every nation, regardless of circumstance, will seek solutions that help curb emissions without harming the prospects of greater prosperity for its own citizens.
Toward this objective, two of the most effective solutions are improving energy efficiency across the economy (also referred to as reducing energy intensity) and reducing the CO2 content across the energy mix. Through 2040, each will play a powerful role in slowing emissions growth, and ultimately reversing what had been a decades-long rise in global CO2 emissions. In fact, we expect global energy-related CO2 emissions will rise
by about 25 percent from 2010 to 2030 and then decline approximately 5 percent to 2040.

In absolute terms, global CO2 emissions are expected to be about 6 billion tonnes higher in 2040 than they were in 2010. While that increase is significant, it is only about half the level of emissions growth seen from 1980 to 2010. This is all the more remarkable considering the growth in economic output from 2010 to 2040 will be about 150 percent more than the prior 30-year period.

Stabilizing the rate of emissions will not do the trick, unless the rate of emissions is below the rate the atmosphere can absorb without permanent harm to the environment or economy. That’s like saying the amount of credit card debt you add each month is the same each month. You are still spending more than your income, and one day this is going to “harm your prospects of greater prosperity”.

We will have really turned the corner if our rate of emissions is reduced to the point where the concentration in the atmosphere is stable or declining. And even if we manage to do that, we need to think about other impacts – nutrient pollution, soil depletion, groundwater and glacier loss, biodiversity and habitat loss, ocean acidification, and the list goes on.

open source street noise model

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Here’s an open-source code for modeling street noise propagation. It’s written in R and open source database and GIS tools.

This paper describes the development of a model for assessing TRAffic Noise EXposure (TRANEX) in an open-source geographic information system. Instead of using proprietary software we developed our own model for two main reasons: 1) so that the treatment of source geometry, traffic information (flows/speeds/spatially varying diurnal traffic profiles) and receptors matched as closely as possible to that of the air pollution modelling being undertaken in the TRAFFIC project, and 2) to optimize model performance for practical reasons of needing to implement a noise model with detailed source geometry, over a large geographical area, to produce noise estimates at up to several million address locations, with limited computing resources. To evaluate TRANEX, noise estimates were compared with noise measurements made in the British cities of Leicester and Norwich. High correlation was seen between modelled and measured LAeq,1hr (Norwich: r = 0.85, p = .000; Leicester: r = 0.95, p = .000) with average model errors of 3.1 dB. TRANEX was used to estimate noise exposures (LAeq,1hr, LAeq,16hr, Lnight) for the resident population of London (2003–2010). Results suggest that 1.03 million (12%) people are exposed to daytime road traffic noise levels ≥ 65 dB(A) and 1.63 million (19%) people are exposed to night-time road traffic noise levels ≥ 55 dB(A). Differences in noise levels between 2010 and 2003 were on average relatively small: 0.25 dB (standard deviation: 0.89) and 0.26 dB (standard deviation: 0.87) for LAeq,16hr and Lnight.

 

green infrastructure, happiness, and the ginkgo-stinkgo tree

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Do trees make people happy? Well yes, I think most people subjectively just have a sense this is true. But for the cynics out there, there is also hard scientific evidence. People have tried all sorts of economic approaches – correlations with real estate markets and willingness-to-pay surveys – for example, to try to estimate the value people place on trees. (Can you measure happiness in dollars? The average man on the street might say no, but the average economist might say it’s the best of many imperfect options for measuring value.) Medical researchers have tried having people walk around cities with brain scanners on their heads. This is a new one to me though – correlating tree coverage with antidepressant prescriptions. And the correlation is there.

Growing evidence suggests an association between access to urban greenspace and mental health and wellbeing. Street trees may be an important facet of everyday exposure to nature in urban environments, but there is little evidence regarding their role in influencing population mental health. In this brief report, we raise the issue of street trees in the nature-health nexus, and use secondary data sources to examine the association between the density of street trees (trees/km street) in London boroughs and rates of antidepressant prescribing. After adjustment for potential confounders, and allowing for unmeasured area-effects using Bayesian mixed effects models, we find an inverse association, with a decrease of 1.18 prescriptions per thousand population per unit increase in trees per km of street (95% credible interval 0.00, 2.45). This study suggests that street trees may be a positive urban asset to decrease the risk of negative mental health outcomes.

And in other urban tree news, you can collect ginkgo berries, take out the nuts, roast them and eat them. The only problem being that they stink to high heaven and are mildly poisonous. Ginkgos are very interesting trees though, sort of an ancient cross between trees and ferns if you believe this article.

Believed to be truly indigenous to only a single province in China , this 270 million year old species belongs to an ancient lineage of species that have since disappeared for one reason or another over the past few millennia, making Ginkgo biloba (known as a ‘living fossil’) the sole extant representative of what was once a vast and diverse group of organisms. In fact, the ginkgo tree is so unlike any other living plant species that this tree has it’s own genus, family, order, class and division. To put this into terms that may be easier to conceptualize: the only thing that ginkgo trees have in common with other plants is they are also plants. This means that pretty much everything about their genetic make-up, physiology, general behavior, reproductive strategies (including their mobile sperm; a trait particular to ferns, cycads and algae) and even their ability to photosynthesize is anywhere between slightly-off to fundamentally different from any other living plant. Oh, and you can eat it’s seeds…

It’s a bit of a messy operation collecting the seeds which are often produced profusely by female trees and lie unmolested by fungi, insects or most pests of any kind save for some adventurous squirrels which occasionally eat the seeds. I find some rubber or latex gloves and a plastic bag are your best bet for collecting the seeds in addition to some grubby clothes that you don’t mind smelling cheesy for a little while. The scent from the fruit tends to linger when it gets on fabric or clothing and so you might want to try extra hard to remember not to wear anything that you are particularly fond of when engaging in the participatory act of ginkgo seed collecting.

I think it’s cool that some people do this, but I personally am not going to take up this hobby right now.

A realistic leverage point for one-planet living: more compulsory vacation in the rich world

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This article in System Dynamics Review advocates requiring more vacation time as a tool to decelerate growth in humanity’s ecological footprint. The idea is logical enough, but politically very hard if you ask me. The only way it might be politically possible is in the wake of a crisis, like a famine or sudden shift in climate, that is big enough to be a major wakeup call to the rich countries but small enough that it doesn’t kill a big fraction of humanity (which would decrease our ecological footprint footprint of course, but at an obviously horrible cost.)

As envisioned by Keynes in Economic Possibilities for our Grandchildren, reducing work hours could make sense if it is done in parallel with productivity and wealth increases, and policies that address a fair distribution of the new wealth created by those productivity increases. This brings us back to trying to steer economic and technological growth in a more sustainable direction, trying to at least postpone and limit the next crisis, but having some ideas on how we might take advantage of the next crisis when it happens, while hoping it is not the one that wipes us out.

William Lazonick vs. Wally

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Still thinking about my William Lazonick post from yesterday. One of his arguments is that it is not just stockholders that deserve a part of corporate returns, because they are not the only ones taking risk. As he explains in his working paper, taxpayers and employees also take risk:

Then I show how and why MSV [maximizing shareholder value] is a theory of value extraction that, when applied to corporate resource allocation in the United States, has undermined the social conditions of innovative enterprise and resulted in employment instability and income inequity. I refute the fundamental economic assumption of MSV that of all participants in the business corporation it is only shareholders who bear risk and hence have a claim on profits if and when they occur. Taxpayers in funding government spending on productive resources that are essential to the innovation process and workers in supplying effort to the processes of organizational learning that are the essence of innovation make productive contributions to the enterprise without guaranteed returns. Indeed I argue that public shareholders do not in general invest in the innovation process but just extract value from it, and hence bear little, if any, risk of the failure of that process. I summarize a growing body of empirical research that shows that since the 1980s, backed by MSV ideology, financial interests, including top corporate executives, have been able to extract vast amounts of value from US industrial corporations in excess of value that they may have helped to create.

I contacted Future Yada Yada workplace effort correspondent Wally from Dilbert, who offered the following. (sorry, you have to click – I’m a huge Scott Adams fan but I don’t see an easy, unambiguously 100% legal way to embed his graphic here)

a 1200-year drought

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How bad is the drought in California? So bad that based on historical data, you would only expect it to happen once in 1200 years, on average, according to Geophysical Research Letters.

For the past three years (2012-2014), California has experienced the most severe drought conditions in its last century. But how unusual is this event? Here we use two paleoclimate reconstructions of drought and precipitation for Central and Southern California to place this current event in the context of the last millennium. We demonstrate that while 3-year periods of persistent below-average soil moisture are not uncommon, the current event is the most severe drought in the last 1200 years, with single year (2014) and accumulated moisture deficits worse than any previous continuous span of dry years. Tree-ring chronologies extended through the 2014 growing season reveal that precipitation during the drought has been anomalously low but not outside the range of natural variability. The current California drought is exceptionally severe in the context of at least the last millennium and is driven by reduced though not unprecedented precipitation and record high temperatures.

There are some eye-opening pictures of dry farm fields here.

more on automated data synthesis

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Here’s another article from Environmental Modeling and Software about automated synthesis of scattered research results:

We describe software to facilitate systematic reviews in environmental science. Eco Evidence allows reviewers to draw strong conclusions from a collection of individually-weak studies. It consists of two components. An online database stores and shares the atomized findings of previously-published research. A desktop analysis tool synthesizes this evidence to test cause–effect hypotheses. The software produces a standardized report, maximizing transparency and repeatability. We illustrate evidence extraction and synthesis. Environmental research is hampered by the complexity of natural environments, and difficulty with performing experiments in such systems. Under these constraints, systematic syntheses of the rapidly-expanding literature can advance ecological understanding, inform environmental management, and identify knowledge gaps and priorities for future research. Eco Evidence, and in particular its online re-usable bank of evidence, reduces the workload involved in systematic reviews. This is the first systematic review software for environmental science, and opens the way for increased uptake of this powerful approach.