Category Archives: Peer Reviewed Article Review

The Secret of N.I.M.H.

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I remember going to see the rats of N.I.M.H. way too young and being terrified (perhaps second only to my fear of the Wicked Witch of the West). Anyway, the secret is out…

Wong FK, Fei J-F, Mora-Bermúdez F, Taverna E, Haffner C, Fu J, et al. (2015) Sustained Pax6 Expression Generates Primate-like Basal Radial Glia in Developing Mouse Neocortex. PLoS Biol 13(8): e1002217. doi:10.1371/journal.pbio.1002217

The evolutionary expansion of the neocortex in mammals has been linked to enlargement of the subventricular zone (SVZ) and increased proliferative capacity of basal progenitors (BPs), notably basal radial glia (bRG). The transcription factor Pax6 is known to be highly expressed in primate, but not mouse, BPs. Here, we demonstrate that sustaining Pax6 expression selectively in BP-genic apical radial glia (aRG) and their BP progeny of embryonic mouse neocortex suffices to induce primate-like progenitor behaviour.

NIMH stood for “National Institute of Mental Health”. Which was, of course, secretly creating super-intelligent rats.

chemicals and cancer

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I’ve tended not to obsess over chemicals and cancer, because I think there are other risks that are much higher and much more clearly proven (like the high odds of death every time you set foot in or anywhere near a motor vehicle, to give one example.) I also tend to accept some chemicals, like water disinfectants, food preservatives, drugs, even pesticides, as somewhat necessary evils – we actually know they have a downside, but they do more good than harm on balance. In a sense, it is a “luxury” that many of us avoid violence and infectious diseases long enough to get old and die of cancer. Cancer is at least to some extent a random phenomenon. That doesn’t mean we shouldn’t be looking for safer alternatives to these chemicals that do the same good. If we don’t look we won’t find them. And then, there are chemicals that are known to be harmful, and have no positive effects. Triclosan comes to mind. The companies using cynical fear-based marketing to force these on people should be punished.

All that aside, our food, water, air, and consumer products are full of chemicals, with the result that our bodies are full of chemicals. We don’t have good information on what most of them are doing to us, and especially what combinations of them may be doing to us. Here’s an interesting article that estimates what fraction of cancers are caused by chemicals in the environment, as opposed to lifestyle choices, genetics, and plain old bad luck.

Assessing the carcinogenic potential of low-dose exposures to chemical mixtures in the environment: the challenge ahead

Lifestyle factors are responsible for a considerable portion of cancer incidence worldwide, but credible estimates from the World Health Organization and the International Agency for Research on Cancer (IARC) suggest that the fraction of cancers attributable to toxic environmental exposures is between 7% and 19%. To explore the hypothesis that low-dose exposures to mixtures of chemicals in the environment may be combining to contribute to environmental carcinogenesis, we reviewed 11 hallmark phenotypes of cancer, multiple priority target sites for disruption in each area and prototypical chemical disruptors for all targets, this included dose-response characterizations, evidence of low-dose effects and cross-hallmark effects for all targets and chemicals. In total, 85 examples of chemicals were reviewed for actions on key pathways/mechanisms related to carcinogenesis. Only 15% (13/85) were found to have evidence of a dose-response threshold, whereas 59% (50/85) exerted low-dose effects. No dose-response information was found for the remaining 26% (22/85). Our analysis suggests that the cumulative effects of individual (non-carcinogenic) chemicals acting on different pathways, and a variety of related systems, organs, tissues and cells could plausibly conspire to produce carcinogenic synergies. Additional basic research on carcinogenesis and research focused on low-dose effects of chemical mixtures needs to be rigorously pursued before the merits of this hypothesis can be further advanced. However, the structure of the World Health Organization International Programme on Chemical Safety ‘Mode of Action’ framework should be revisited as it has inherent weaknesses that are not fully aligned with our current understanding of cancer biology.

CRISPR

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Here’s some more info on CRISPR, a genetic engineering technique some people are saying will be revolutionary.

 The Bacterial Origins of the CRISPR Genome-Editing Revolution
Sontheimer Erik J. and Barrangou Rodolphe. Human Gene Therapy. July 2015, 26(7): 413-424. doi:10.1089/hum.2015.091.

Like most of the tools that enable modern life science research, the recent genome-editing revolution has its biological roots in the world of bacteria and archaea. Clustered, regularly interspaced, short palindromic repeats (CRISPR) loci are found in the genomes of many bacteria and most archaea, and underlie an adaptive immune system that protects the host cell against invasive nucleic acids such as viral genomes. In recent years, engineered versions of these systems have enabled efficient DNA targeting in living cells from dozens of species (including humans and other eukaryotes), and the exploitation of the resulting endogenous DNA repair pathways has provided a route to fast, easy, and affordable genome editing. In only three years after RNA-guided DNA cleavage was first harnessed, the ability to edit genomes via simple, user-defined RNA sequences has already revolutionized nearly all areas of biological science. CRISPR-based technologies are now poised to similarly revolutionize many facets of clinical medicine, and even promise to advance the long-term goal of directly editing genomic sequences of patients with inherited disease. In this review, we describe the biological and mechanistic basis for these remarkable immune systems, and how their engineered derivatives are revolutionizing basic and clinical research.

natural capital

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Here’s a slightly novel take on natural capital, as a charged battery.

Human domination of the biosphere: Rapid discharge of the earth-space battery foretells the future of humankind

Earth is a chemical battery where, over evolutionary time with a trickle-charge of photosynthesis using solar energy, billions of tons of living biomass were stored in forests and other ecosystems and in vast reserves of fossil fuels. In just the last few hundred years, humans extracted exploitable energy from these living and fossilized biomass fuels to build the modern industrial-technological-informational economy, to grow our population to more than 7 billion, and to transform the biogeochemical cycles and biodiversity of the earth. This rapid discharge of the earth’s store of organic energy fuels the human domination of the biosphere, including conversion of natural habitats to agricultural fields and the resulting loss of native species, emission of carbon dioxide and the resulting climate and sea level change, and use of supplemental nuclear, hydro, wind, and solar energy sources. The laws of thermodynamics governing the trickle-charge and rapid discharge of the earth’s battery are universal and absolute; the earth is only temporarily poised a quantifiable distance from the thermodynamic equilibrium of outer space. Although this distance from equilibrium is comprised of all energy types, most critical for humans is the store of living biomass. With the rapid depletion of this chemical energy, the earth is shifting back toward the inhospitable equilibrium of outer space with fundamental ramifications for the biosphere and humanity. Because there is no substitute or replacement energy for living biomass, the remaining distance from equilibrium that will be required to support human life is unknown.

 

“global renaissance of coal”

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This article from the National Academy of Sciences says that although coal use is dropping in some developed countries and China, it is exploding in many developing countries.

Coal was central to the industrial revolution, but in the 20th century it increasingly was superseded by oil and gas. However, in recent years coal again has become the predominant source of global carbon emissions. We show that this trend of rapidly increasing coal-based emissions is not restricted to a few individual countries such as China. Rather, we are witnessing a global renaissance of coal majorly driven by poor, fast-growing countries that increasingly rely on coal to satisfy their growing energy demand. The low price of coal relative to gas and oil has played an important role in accelerating coal consumption since the end of the 1990s. In this article, we show that in the increasingly integrated global coal market the availability of a domestic coal resource does not have a statistically significant impact on the use of coal and related emissions. These findings have important implications for climate change mitigation: If future economic growth of poor countries is fueled mainly by coal, ambitious mitigation targets very likely will become infeasible. Building new coal power plant capacities will lead to lock-in effects for the next few decades. If that lock-in is to be avoided, international climate policy must find ways to offer viable alternatives to coal for developing countries.

 

nature and mental health

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From the Proceedings of the National Academy of Science:

Urbanization has many benefits, but it also is associated with increased levels of mental illness, including depression. It has been suggested that decreased nature experience may help to explain the link between urbanization and mental illness. This suggestion is supported by a growing body of correlational and experimental evidence, which raises a further question: what mechanism(s) link decreased nature experience to the development of mental illness? One such mechanism might be the impact of nature exposure on rumination, a maladaptive pattern of self-referential thought that is associated with heightened risk for depression and other mental illnesses. We show in healthy participants that a brief nature experience, a 90-min walk in a natural setting, decreases both self-reported rumination and neural activity in the subgenual prefrontal cortex (sgPFC), whereas a 90-min walk in an urban setting has no such effects on self-reported rumination or neural activity. In other studies, the sgPFC has been associated with a self-focused behavioral withdrawal linked to rumination in both depressed and healthy individuals. This study reveals a pathway by which nature experience may improve mental well-being and suggests that accessible natural areas within urban contexts may be a critical resource for mental health in our rapidly urbanizing world.

vegetable rain gardens

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Growing food in rain gardens – it seems almost too obvious. But it isn’t done much, and somebody has gone to the trouble of studying it scientifically here. They planted “beetroot, onion, spinach, tomato and broad bean”. This sounds good, but it might be fun to experiment with trees and other perennial species. There are some tough plants out there that will tolerate wet and dry conditions better than your typical annual garden crops. Jerusalem artichoke comes to mind, which is a sort of invasive American prairie flower that produces enormous amounts of delicious potato-like tubers.

gators and tigers and extinction, oh my!

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The extinction rate is now 1000 times normal, says Duke University.

Not to worry, say Stanford, Berkeley, Princeton, and the University of Florida (and what would they know, those ‘gators with their beady dinosaur eyes), it’s only 114 times normal using “conservative assumptions”.

And according to a surprisingly edgy book review in my favorite special interest publication Civil Engineering (because what could be more special than my own interest), there is a new book out:

You probably don’t subscribe to Civil Engineering, so here is the Amazon description:

A growing number of scientists agree we are headed toward a mass extinction, perhaps in as little as 300 years. Already there have been five mass extinctions in the last 600 million years, including the Cretaceous Extinction, during which an asteroid knocked out the dinosaurs. Though these events were initially destructive, they were also prime movers of evolutionary change in nature. And we can see some of the warning signs of another extinction event coming, as our oceans lose both fish and oxygen. In The Next Species, Michael Tennesen questions what life might be like after it happens.

Tennesen discusses the future of nature and whether humans will make it through the bottleneck of extinction. Without man, could the seas regenerate to what they were before fishing vessels? Could life suddenly get very big as it did before the arrival of humans? And what if man survives the coming catastrophes, but in reduced populations? Would those groups be isolated enough to become distinct species? Could the conquest of Mars lead to another form of human? Could we upload our minds into a computer and live in a virtual reality? Or could genetic engineering create a more intelligent and long-lived creature that might shun the rest of us? And how would we recognize the next humans? Are they with us now?

climate change and the economy

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Here’s another modeling study in Ecological Economics that looks at the effects of climate change on the global economy.

A demand-driven growth model involving capital accumulation and the dynamics of greenhouse gas (GHG) concentration is set up to examine macroeconomic issues raised by global warming, e.g. effects on output and employment of rising levels of GHG; offsets by mitigation; relationships among energy use and labor productivity, income distribution, and growth; the economic significance of the Jevons and other paradoxes; sustainable consumption and possible reductions in employment; and sources of instability and cyclicality implicit in the two-dimensional dynamical system. The emphasis is on the combination of biophysical limits and Post-Keynesian growth theory and the qualitative patterns of system adjustment and the dynamics that emerge.