Category Archives: Peer Reviewed Article Review

climate, economics, and agent based models

This journal article is mostly over my head, but I found the introduction interesting. It talks about the use of equilibrium models most common in economics compared to emerging research into agent based models.
Complexity and the Economics of Climate Change: a Survey and a Look Forward

Excerpt:

Mitigation and adaptation to climate change represent governance challenges of an unprecedented scale because of their long-term horizon, their global nature and the massive uncertainties they involve. Against this background, equilibrium models generally used in Integrated Assessment Models (IAM) represent the economy as a system with a unique equilibrium, climate policy as an additional constraint in the optimization problem of the social planner and consider the uncertainty of climate-related damages to be predictable enough to be factored out in the expected utility of a representative agent. There is growing concern in the literature that this picture might convey a false impression of control (seePindyck,2013; Stern, 2013, 2016; Weitzman, 2013; Revesz et al., 2014; Farmer et al., 2015, among manycontributions) and that IAMs might underestimate both the cost of climate change and the bene fits resulting from the transition to a low carbon-emission economy (Stern, 2016).

Network and agent-based models have been increasingly advocated as alternatives t to handle out-of-equilibrium dynamics, tipping points and large transitions in socio-economic systems (see e.g Tesfatsion and Judd, 2006; Balbi and Giupponi, 2010; Kelly et al., 2013; Smajgl et al., 2011; Farmer et al., 2015; Stern, 2016; Mercure et al., 2016). These classes of models consider the real world as a complex evolving system, wherein the interaction of many heterogeneous agents possibly reacting across different spatial and temporal scales give rise to the emergence of aggregate properties that cannot be deduced by the simple aggregation of individual ones (Flake, 1988; Tesfatsion and Judd, 2006). The development of agent-based integrated assessment model can overcome the shortfall of equilibrium models and ease stakeholder participation and scenario exploration (Moss et al., 2001; Moss, 2002a). Indeed, the higher degree of realism of ABMs (Farmer and Foley, 2009; Farmer et al., 2015) allows to involve policy makers in the process of the development of the model employed for policy evaluation (Moss, 2002b).

roads and railways as wildlife movement corridors?

At least, I think that is what this paper in Conservation Biology is about. The key conclusion is that biodiversity impacts (of the roads and rails themselves? it’s unclear) can be reduced by up to 75%. I am presuming this is by locating a linear park of sufficient width along the road or railway. Presumably you might need to do something to keep the animals off the road too. Could a few larger reserves located along the corridor reduce the impact to zero? I would find it very encouraging both to know that it is possible and to know that we have the quantitative tools to accurately predict the outcomes of policy and design choices.

Quantifying the conservation gains from shared access to linear infrastructure

The proliferation of linear infrastructure such as roads and rail is a major global driver of cumulative biodiversity loss. Creative interventions to minimise the impacts of this infrastructure whilst still allowing development to meet human population growth and resource consumption demands are urgently required. One strategy for reducing habitat loss associated with development is to encourage linear infrastructure providers and users to share infrastructure networks. Here we quantify the reductions in biodiversity impact and capital cost under linear infrastructure sharing and demonstrate this approach with a case study in South Australia. By evaluating proposed mine-port links we show that shared development of linear infrastructure could reduce overall biodiversity impacts by up to 75%. We found that such reductions are likely to be limited if the dominant mining companies restrict access to infrastructure, a situation likely to occur without policy to promote sharing of infrastructure. Our research helps illuminate the circumstances under which infrastructure sharing can minimise the biodiversity impacts of development.

tipping points and ecosystem collapse

This research presents seagrass meadows as an example of an ecosystem that seems to disappear suddenly, but actually reached a tipping point caused by chronic pollution.

Testing for thresholds of ecosystem collapse in seagrass meadows?

Ecological systems can be dynamic and unpredictable, with shifts from one ecosystem state to another often considered ‘surprising’. This unpredictability is often thought to be due to ecological thresholds, where small cumulative increases in an environmental stressor drives a much greater consequence than would be predicted from linear effects, suggesting an unforeseen tipping point is crossed. In coastal waters, broad-scale seagrass loss often occurs as a sudden event which is associated with human-driven nutrient enrichment (eutrophication). We tested whether the response of seagrass ecosystems to coastal nutrient enrichment represents a threshold effect. Seagrass response did follow a threshold pattern when nutrient enrichment (dissolved inorganic nitrogen) exceeded moderate levels, with a switch from positive to negative net leaf production. Epiphyte load also increased with nutrient enrichment, potentially driving this shift. Inadvertently crossing such thresholds, as can occur through ineffective management of land-derived inputs such as wastewater and stormwater on urbanised coasts, may help account for the widely observed ‘sudden’ loss of seagrass meadows. By identifying tipping points we may not only improve monitoring for adaptive management that seeks to avoid threshold effects, but also the restoration of systems that have crossed them.

glyphosate

It’s not as safe as advertised, according to Conservation Biology.

Glyphosate has become the most commonly used herbicide worldwide, with a reputation of being environmentally benign, non-toxic and safe to wildlife and humans. However, studies have indicated its toxicity has been underestimated, and that its persistence in the environment is greater than once thought. Its actions as a neurotoxin and endocrine disruptor indicate its potential to act in similar ways to persistent organic pollutants (POPs) such as the organochlorine (OC) chemicals dichlorodiphenyltrichloroethane (DDT) and dioxin. Exposure to glyphosate and glyphosate-based herbicides for both wildlife and people is likely to be chronic and at sub-lethal levels, with multiple and ongoing exposure events in both urban and agricultural landscapes. Despite this, little research attention has been given to the impact of glyphosate on wildlife populations, and existing studies appear in the agricultural, toxicology and water chemistry literature that may have limited visibility among wildlife biologists. There is a strong case for the recognition of glyphosate as an ‘emerging organic contaminant’ and significant potential exists for collaborative research between ecologists, toxicologists and chemists to quantify the impact of glyphosate on wildlife and to evaluate the role of biosentinel species in a preemptive move to mitigate downstream impacts on people.

 

reproducible research in hydrology

This October 2016 article in Water Resources Research on reproducible research got some attention.

Hutton, C., T. Wagener, J. Freer, D. Han, C. Duffy, and B. Arheimer (2016), Most computational hydrology is not reproducible, so is it really science?, Water Resour. Res., 52, 7548–7555, doi:10.1002/2016WR019285.

Reproducibility is a foundational principle in scientific research. Yet in computational hydrology the code and data that actually produces published results are not regularly made available, inhibiting the ability of the community to reproduce and verify previous findings. In order to overcome this problem we recommend that reuseable code and formal workflows, which unambiguously reproduce published scientific results, are made available for the community alongside data, so that we can verify previous findings, and build directly from previous work. In cases where reproducing large-scale hydrologic studies is computationally very expensive and time-consuming, new processes are required to ensure scientific rigor. Such changes will strongly improve the transparency of hydrological research, and thus provide a more credible foundation for scientific advancement and policy support.

using CRISPR to create new crops

This article in Trends in Plant Science (which I know you’ve seen, since it flies off the news stands) argues that CRISPR should be used to create entirely new crops out of wild plants, mimicking the process that created our most common cereal crops over thousands of years.

Of the more than 300 000 plant species that exist, less than 200 are commercially important, and three species – rice, wheat, and maize – account for the major part of the plant-derived nutrients that humans consume.

Plants with desirable traits, such as perennials with extensive root systems and nitrogen-fixing plants, are currently being domesticated as new crops…

Several traits in crops that were crucial for their domestication are caused by mutations that can be reproduced by genome-editing techniques such as CRISPR/Cas9, offering the potential for accelerated domestication of new crops.

breaking the 90 barrier

 

The Lancet has an open-access article on projected life expectancies in 35 industrialized countries by 2030. A few interesting findings are that South Korea seems to have some of the longest life expectancies and some of the largest gains in life expectancy among both sexes. South Korean women are projected to be the first to break the barrier of an average life expectancy of 90, with a 50% probability of this happening by 2030. The USA is consistently below the middle of the pack. The good news is that life expectancy is projected to increase in all countries studied, and the gap between men and women is projected to narrow. The graphics in this article are really interesting – I have picked just one below.

http://www.thelancet.com/journals/lancet/article/PIIS0140-6736(16)32381-9/fulltext

Figure 3 from Future life expectancy in 35 industrialised countries: projections with a Bayesian model ensemble

lead, crime and teen pregnancy

Leaded gasoline peaked around the year I was born, and both crime and teen pregnancy peaked while I was a teenager. I managed to steer clear of these two things (or maybe I left no evidence in either case…), but maybe I would have been the next Einstein if it weren’t for lead, we’ll never know.

Lead Exposure and Behavior: Effects on Antisocial and Risky Behavior among Children and Adolescents Jessica Wolpaw Reyes NBER Working Paper No. 20366 August 2014

It is well known that exposure to lead has numerous adverse effects on behavior and development. Using data on two cohorts of children from the NLSY, this paper investigates the effect of early childhood lead exposure on behavior problems from childhood through early adulthood. I find large negative consequences of early childhood lead exposure, in the form of an unfolding series of adverse behavioral outcomes: behavior problems as a child, pregnancy and aggression as a teen, and criminal behavior as a young adult. At the levels of lead that were the norm in United States until the late 1980s, estimated elasticities of these behaviors with respect to lead range between 0.1 and 1.0.

Maybe we learned our lesson with lead and mercury and have moved on. Or maybe something as bad or worse is hiding in plain site in our consumer products and we just haven’t figured it out yet.

Just for the archives, here is a key 2000 study by Rick Nevin on the subject: How Lead Exposure Relates to Temporal Changes in IQ, Violent Crime, and Unwed Pregnancy.

This study compares changes in children’s blood lead levels in the United States with subsequent changes in IQ, based on norm comparisons for the Cognitive Abilities Test (CogAT) given to representative national samples of children in 1984 and 1992. The CogAT norm comparisons indicate shifts in IQ levels consistent with the blood lead to IQ relationship reported by an earlier study and population shifts in average blood lead for children under age 6 between 1976 and 1991. The CogAT norm comparisons also support studies indicating that the IQ to blood lead slope may increase at lower blood lead levels. Furthermore, long-term trends in population exposure to gasoline lead were found to be remarkably consistent with subsequent changes in violent crime and unwed pregnancy. Long-term trends in paint and gasoline lead exposure are also strongly associated with subsequent trends in murder rates going back to 1900. The Andings on violent crime and unwed pregnancy are consistent with published data describing the relationship between IQ and social behavior. The Andings with respect to violent crime are also consistent with studies indicating that children with higher bone lead tend to display more aggressive and delinquent behavior. This analysis demonstrates that widespread exposure to lead is likely to have profound implications for a wide array of socially undesirable outcomes.

interspecies chimerism, or Dr. Moreau returns

I only understand a few words of this paper in Cell, like “human”, “pig”, “embryo”, and “implantation”, but they are enough to raise both my eyebrows. I’ll quote the last paragraph of the paper rather than the abstract because it contains a little less jargon. There are some understandable, or possibly hair-raising depending on your point of view, pictures in the paper too.

Interspecies Chimerism with Mammalian Pluripotent Stem Cells. Wu, Jun et al. Cell, Volume 168 , Issue 3 , 473 – 486

The procedures and observations reported here on the capability of human pluripotent stem cells to integrate and differentiate in a ungulate embryo, albeit at a low level and efficiency, when optimized, may constitute a first step towards realizing the potential of interspecies blastocyst complementation with hPSCs. In particular, they may provide a better understanding of human embryogenesis, facilitate the development and implementation of humanized animal drug test platforms, as well as offer new insights on the onset and progression of human diseases in an in vivo setting. Ultimately, these observations also raise the possibility of xeno-generating transplantable human tissues and organs towards addressing the worldwide shortage of organ donors.

Of course rich people are going to have copies of all their vital organs cloned in pigs as soon as this technology is available. And some mad dictator or Bond villain on an island somewhere is going to be breeding pig people. Now speaking of madmen on islands, there was a story about a certain Dr. Moreau…but it was only a story, right?

 “Monsters manufactured!” said I. “Then you mean to tell me—”

“Yes. These creatures you have seen are animals carven and wrought into new shapes. To that, to the study of the plasticity of living forms, my life has been devoted. I have studied for years, gaining in knowledge as I go. I see you look horrified, and yet I am telling you nothing new. It all lay in the surface of practical anatomy years ago, but no one had the temerity to touch it. It is not simply the outward form of an animal which I can change. The physiology, the chemical rhythm of the creature, may also be made to undergo an enduring modification,—of which vaccination and other methods of inoculation with living or dead matter are examples that will, no doubt, be familiar to you. A similar operation is the transfusion of blood,—with which subject, indeed, I began. These are all familiar cases. Less so, and probably far more extensive, were the operations of those mediaeval practitioners who made dwarfs and beggar-cripples, show-monsters,—some vestiges of whose art still remain in the preliminary manipulation of the young mountebank or contortionist. Victor Hugo gives an account of them in ‘L’Homme qui Rit.’—But perhaps my meaning grows plain now. You begin to see that it is a possible thing to transplant tissue from one part of an animal to another, or from one animal to another; to alter its chemical reactions and methods of growth; to modify the articulations of its limbs; and, indeed, to change it in its most intimate structure.

“And yet this extraordinary branch of knowledge has never been sought as an end, and systematically, by modern investigators until I took it up! Some of such things have been hit upon in the last resort of surgery; most of the kindred evidence that will recur to your mind has been demonstrated as it were by accident,—by tyrants, by criminals, by the breeders of horses and dogs, by all kinds of untrained clumsy-handed men working for their own immediate ends. I was the first man to take up this question armed with antiseptic surgery, and with a really scientific knowledge of the laws of growth. Yet one would imagine it must have been practised in secret before. Such creatures as the Siamese Twins—And in the vaults of the Inquisition. No doubt their chief aim was artistic torture, but some at least of the inquisitors must have had a touch of scientific curiosity.”

“But,” said I, “these things—these animals talk!”

He said that was so, and proceeded to point out that the possibility of vivisection does not stop at a mere physical metamorphosis. A pig may be educated. The mental structure is even less determinate than the bodily. In our growing science of hypnotism we find the promise of a possibility of superseding old inherent instincts by new suggestions, grafting upon or replacing the inherited fixed ideas. Very much indeed of what we call moral education, he said, is such an artificial modification and perversion of instinct; pugnacity is trained into courageous self-sacrifice, and suppressed sexuality into religious emotion. And the great difference between man and monkey is in the larynx, he continued,—in the incapacity to frame delicately different sound-symbols by which thought could be sustained. In this I failed to agree with him, but with a certain incivility he declined to notice my objection. He repeated that the thing was so, and continued his account of his work.

I asked him why he had taken the human form as a model. There seemed to me then, and there still seems to me now, a strange wickedness for that choice.

He confessed that he had chosen that form by chance. “I might just as well have worked to form sheep into llamas and llamas into sheep. I suppose there is something in the human form that appeals to the artistic turn more powerfully than any animal shape can.