Habitat

From Wikipedia, the free encyclopedia

This coral reef in the Phoenix Islands Protected Area is a rich habitat for sea life.

 

Few creatures make the ice shelves of Antarctica their habitat.

 

Ibex in alpine habitat

In ecology, a habitat is the type of natural environment in which a particular species of organism lives. It is characterized by both physical and biological features. A species' habitat is those places where it can find food, shelter, protection and mates for reproduction. 

The physical factors are for example soil, moisture, range of temperature, and light intensity as well as biotic factors such as the availability of food and the presence or absence of predators. Every organism has certain habitat needs for the conditions in which it will thrive, but some are tolerant of wide variations while others are very specific in their requirements. A habitat is not necessarily a geographical area, it can be the interior of a stem, a rotten log, a rock or a clump of moss, and for a parasitic organism it is the body of its host, part of the host's body such as the digestive tract, or a single cell within the host's body. 

Habitat types include polar, temperate, subtropical and tropical. The terrestrial vegetation type may be forest, steppe, grassland, semi-arid or desert. Fresh water habitats include marshes, streams, rivers, lakes, ponds and estuaries, and marine habitats include salt marshes, the coast, the intertidal zone, reefs, bays, the open sea, the sea bed, deep water and submarine vents. 

Habitats change over time. This may be due to a violent event such as the eruption of a volcano, an earthquake, a tsunami, a wildfire or a change in oceanic currents; or the change may be more gradual over millennia with alterations in the climate, as ice sheets and glaciers advance and retreat, and as different weather patterns bring changes of precipitation and solar radiation. Other changes come as a direct result of human activities; deforestation, the ploughing of ancient grasslands, the diversion and damming of rivers, the draining of marshland and the dredging of the seabed. The introduction of alien species can have a devastating effect on native wildlife, through increased predation, through competition for resources or through the introduction of pests and diseases to which the native species have no immunity.

Definition and etymology

The word "habitat" has been in use since about 1755 and derives from the Latin habitāre, to inhabit, from habēre, to have or to hold. Habitat can be defined as the natural environment of an organism, the type of place in which it is natural for it to live and grow. It is similar in meaning to a biotope; an area of uniform environmental conditions associated with a particular community of plants and animals.

Environmental factors

The chief environmental factors affecting the distribution of living organisms are temperature, humidity, climate, soil type and light intensity, and the presence or absence of all the requirements that the organism needs to sustain it. Generally speaking, animal communities are reliant on specific types of plant communities.

Some plants and animals are generalists, and their habitat requirements are met in a wide range of locations. The small white butterfly (Pieris rapae) for example is found on all the continents of the world apart from Antarctica. Its larvae feed on a wide range of Brassicas and various other plant species, and it thrives in any open location with diverse plant associations. The large blue butterfly is much more specific in its requirements; it is found only in chalk grassland areas, its larvae feed on Thymus species and because of complex lifecycle requirements it inhabits only areas in which Myrmica ants live.

Disturbance is important in the creation of biodiverse habitats. In the absence of disturbance, a climax vegetation cover develops that prevents the establishment of other species. Wildflower meadows are sometimes created by conservationists but most of the flowering plants used are either annuals or biennials and disappear after a few years in the absence of patches of bare ground on which their seedlings can grow. Lightning strikes and toppled trees in tropical forests allow species richness to be maintained as pioneering species move in to fill the gaps created. Similarly coastal habitats can become dominated by kelp until the seabed is disturbed by a storm and the algae swept away, or shifting sediment exposes new areas for colonisation. Another cause of disturbance is when an area may be overwhelmed by an invasive introduced species which is not kept under control by natural enemies in its new habitat.

Types

Rich rainforest habitat in Dominica

 

Terrestrial habitat types include forests, grasslands, wetlands and deserts. Within these broad biomes are more specific habitats with varying climate types, temperature regimes, soils, altitudes and vegetation types. Many of these habitats grade into each other and each one has its own typical communities of plants and animals. A habitat may suit a particular species well, but its presence or absence at any particular location depends to some extent on chance, on its dispersal abilities and its efficiency as a coloniser.

Wetland habitats in Borneo

Freshwater habitats include rivers, streams, lakes, ponds, marshes and bogs. Although some organisms are found across most of these habitats, the majority have more specific requirements. The water velocity, its temperature and oxygen saturation are important factors, but in river systems, there are fast and slow sections, pools, bayous and backwaters which provide a range of habitats. Similarly, aquatic plants can be floating, semi-submerged, submerged or grow in permanently or temporarily saturated soils besides bodies of water. Marginal plants provide important habitat for both invertebrates and vertebrates, and submerged plants provide oxygenation of the water, absorb nutrients and play a part in the reduction of pollution.

Marine habitats include brackish water, estuaries, bays, the open sea, the intertidal zone, the sea bed, reefs and deep / shallow water zones. Further variations include rock pools, sand banks, mudflats, brackish lagoons, sandy and pebbly beaches, and seagrass beds, all supporting their own flora and fauna. The benthic zone or seabed provides a home for both static organisms, anchored to the substrate, and for a large range of organisms crawling on or burrowing into the surface. Some creatures float among the waves on the surface of the water, or raft on floating debris, others swim at a range of depths, including organisms in the demersal zone close to the seabed, and myriads of organisms drift with the currents and form the plankton.

Desert scene in Egypt

A desert is not the kind of habitat that favours the presence of amphibians, with their requirement for water to keep their skins moist and for the development of their young. Nevertheless, some frogs live in deserts, creating moist habitats underground and hibernating while conditions are adverse. Couch's spadefoot toad (Scaphiopus couchii) emerges from its burrow when a downpour occurs and lays its eggs in the transient pools that form; the tadpoles develop with great rapidity, sometimes in as little as nine days, undergo metamorphosis, and feed voraciously before digging a burrow of their own.

Other organisms cope with the drying up of their aqueous habitat in other ways. Vernal pools are ephemeral ponds that form in the rainy season and dry up afterwards. They have their specially-adapted characteristic flora, mainly consisting of annuals, the seeds of which survive the drought, but also some uniquely adapted perennials. Animals adapted to these extreme habitats also exist; fairy shrimps can lay "winter eggs" which are resistant to desiccation, sometimes being blown about with the dust, ending up in new depressions in the ground. These can survive in a dormant state for as long as fifteen years. Some killifish behave in a similar way; their eggs hatch and the juvenile fish grow with great rapidity when the conditions are right, but the whole population of fish may end up as eggs in diapause in the dried up mud that was once a pond.

Many animals and plants have taken up residence in urban environments. They tend to be adaptable generalists and use the town's features to make their homes. Rats and mice have followed man around the globe, pigeons, peregrines, sparrows, swallows and house martins use the buildings for nesting, bats use roof space for roosting, foxes visit the garbage bins and squirrels, coyotes, raccoons and skunks roam the streets. About 2,000 coyotes are thought to live in and around Chicago. A survey of dwelling houses in northern European cities in the twentieth century found about 175 species of invertebrate inside them, including 53 species of beetle, 21 flies, 13 butterflies and moths, 13 mites, 9 lice, 7 bees, 5 wasps, 5 cockroaches, 5 spiders, 4 ants and a number of other groups. In warmer climates, termites are serious pests in the urban habitat; 183 species are known to affect buildings and 83 species cause serious structural damage.

Microhabitats

A microhabitat is the small-scale physical requirements of a particular organism or population. Every habitat includes large numbers of microhabitats with subtly different exposure to light, humidity, temperature, air movement, and other factors. The lichens that grow on the north face of a boulder are different to those that grow on the south face, from those on the level top and those that grow on the ground nearby; the lichens growing in the grooves and on the raised surfaces are different from those growing on the veins of quartz. Lurking among these miniature "forests" are the microfauna, each species of invertebrate with its own specific habitat requirements.

There are numerous different microhabitats in a wood; coniferous forest, broad-leafed forest, open woodland, scattered trees, woodland verges, clearings and glades; tree trunk, branch, twig, bud, leaf, flower and fruit; rough bark, smooth bark, damaged bark, rotten wood, hollow, groove and hole; canopy, shrub layer, plant layer, leaf litter and soil; buttress root, stump, fallen log, stem base, grass tussock, fungus, fern and moss. The greater the structural diversity in the wood, the greater the number of microhabitats that will be present. A range of tree species with individual specimens of varying sizes and ages, and a range of features such as streams, level areas, slopes, tracks, clearings and felled areas will provide suitable conditions for an enormous number of biodiverse plants and animals. For example, in Britain it has been estimated that various types of rotting wood are home to over 1700 species of invertebrate.

For a parasitic organism, its habitat is the particular part of the outside or inside of its host on or in which it is adapted to live. The life cycle of some parasites involves several different host species, as well as free-living life stages, sometimes providing vastly different microhabitats. One such organism is the trematode (flatworm) Microphallus turgidus, present in brackish water marshes in the southeastern United States. Its first intermediate host is a snail and the second, a glass shrimp. The final host is the waterfowl or mammal that consumes the shrimp.

Extreme habitats

An Antarctic rock split apart to show an endolithic lifeform showing as a green layer a few millimetres thick

Although the vast majority of life on Earth lives in mesophyllic (moderate) environments, a few organisms, most of them microbes, have managed to colonise extreme environments that are unsuitable for most higher life forms. There are bacteria, for example, living in Lake Whillans, half a mile below the ice of Antarctica; in the absence of sunlight, they must rely on organic material from elsewhere, perhaps decaying matter from glacier melt water or minerals from the underlying rock. Other bacteria can be found in abundance in the Mariana Trench, the deepest place in the ocean and on Earth; marine snow drifts down from the surface layers of the sea and accumulates in this undersea valley, providing nourishment for an extensive community of bacteria.

Other microbes live in habitats lacking in oxygen, and are dependent on chemical reactions other than photosynthesis. Boreholes drilled 300 m (1,000 ft) into the rocky seabed have found microbial communities apparently based on the products of reactions between water and the constituents of rocks. These communities have been little studied, but may be an important part of the global carbon cycle. Rock in mines two miles deep also harbour microbes; these live on minute traces of hydrogen produced in slow oxidizing reactions inside the rock. These metabolic reactions allow life to exist in places with no oxygen or light, an environment that had previously been thought to be devoid of life.

The intertidal zone and the photic zone in the oceans are relatively familiar habitats. However the vast bulk of the ocean is unhospitable to air-breathing humans, with scuba divers limited to the upper 50 m (160 ft) or so. The lower limit for photosynthesis is 100 to 200 m (330 to 660 ft) and below that depth the prevailing conditions include total darkness, high pressure, little oxygen (in some places), scarce food resources and extreme cold. This habitat is very challenging to research, and as well as being little studied, it is vast, with 79% of the Earth's biosphere being at depths greater than 1,000 m (3,300 ft). With no plant life, the animals in this zone are either detritivores, reliant on food drifting down from surface layers, or they are predators, feeding on each other. Some organisms are pelagic, swimming or drifting in mid-ocean, while others are benthic, living on or near the seabed. Their growth rates and metabolisms tend to be slow, their eyes may be very large to detect what little illumination there is, or they may be blind and rely on other sensory inputs. A number of deep sea creatures are bioluminescent; this serves a variety of functions including predation, protection and social recognition. In general, the bodies of animals living at great depths are adapted to high pressure environments by having pressure-resistant biomolecules and small organic molecules present in their cells known as piezolytes, which give the proteins the flexibility they need. There are also unsaturated fats in their membranes which prevent them from solidifying at low temperatures.

Dense mass of white crabs at a hydrothermal vent, with stalked barnacles on right

Hydrothermal vents were first discovered in the ocean depths in 1977. They result from seawater becoming heated after seeping through cracks to places where hot magma is close to the seabed. The under-water hot springs may gush forth at temperatures of over 340 °C (640 °F) and support unique communities of organisms in their immediate vicinity. The basis for this teeming life is chemosynthesis, a process by which microbes convert such substances as hydrogen sulfide or ammonia into organic molecules. These bacteria and Archaea are the primary producers in these ecosystems and support a diverse array of life. About 350 species of organism, dominated by molluscs, polychaete worms and crustaceans, had been discovered around hydrothermal vents by the end of the twentieth century, most of them being new to science and endemic to these habitats.

Besides providing locomotion opportunities for winged animals and a conduit for the dispersal of pollen grains, spores and seeds, the atmosphere can be considered to be a habitat in its own right. There are metabolically active microbes present that actively reproduce and spend their whole existence airborne, with hundreds of thousands of individual organisms estimated to be present in a cubic metre of air. The airborne microbial community may be as diverse as that found in soil or other terrestrial environments, however these organisms are not evenly distributed, their densities varying spatially with altitude and environmental conditions. Aerobiology has been little studied, but there is evidence of nitrogen fixation in clouds, and less clear evidence of carbon cycling, both facilitated by microbial activity.

There are other examples of extreme habitats where specially adapted lifeforms exist; tar pits teeming with microbial life; naturally occurring crude oil pools inhabited by the larvae of the petroleum fly; hot springs where the temperature may be as high as 71 °C (160 °F) and cyanobacteria create microbial mats; cold seeps where the methane and hydrogen sulfide issue from the ocean floor and support microbes and higher animals such as mussels which form symbiotic associations with these anaerobic organisms; salt pans harbour salt-tolerant microorganisms and also Wallemia ichthyophaga, a basidomycotous fungus; ice sheets in Antarctica which support fungi Thelebolus spp., and snowfields on which algae grow.

Habitat change

Twenty five years after the devastating eruption at Mount St. Helens, United States, pioneer species have moved in.

Whether from natural processes or the activities of man, landscapes and their associated habitats change over time. There are the slow geomorphological changes associated with the geologic processes that cause tectonic uplift and subsidence, and the more rapid changes associated with earthquakes, landslides, storms, flooding, wildfires, coastal erosion, deforestation and changes in land use. Then there are the changes in habitats brought on by alterations in farming practices, tourism, pollution, fragmentation and climate change.

Loss of habitat is the single greatest threat to any species. If an island on which an endemic organism lives becomes uninhabitable for some reason, the species will become extinct. Any type of habitat surrounded by a different habitat is in a similar situation to an island. If a forest is divided into parts by logging, with strips of cleared land separating woodland blocks, and the distances between the remaining fragments exceeds the distance an individual animal is able to travel, that species becomes especially vulnerable. Small populations generally lack genetic diversity and may be threatened by increased predation, increased competition, disease and unexpected catastrophe. At the edge of each forest fragment, increased light encourages secondary growth of fast-growing species and old growth trees are more vulnerable to logging as access is improved. The birds that nest in their crevices, the epiphytes that hang from their branches and the invertebrates in the leaf litter are all adversely affected and biodiversity is reduced. Habitat fragmentation can be ameliorated to some extent by the provision of wildlife corridors connecting the fragments. These can be a river, ditch, strip of trees, hedgerow or even an underpass to a highway. Without the corridors, seeds cannot disperse and animals, especially small ones, cannot travel through the hostile territory, putting populations at greater risk of local extinction.

Habitat disturbance can have long-lasting effects on the environment. Bromus tectorum is a vigorous grass from Europe which has been introduced to the United States where it has become invasive. It is highly adapted to fire, producing large amounts of flammable detritus and increasing the frequency and intensity of wildfires. In areas where it has become established, it has altered the local fire regimen to such an extant that native plants cannot survive the frequent fires, allowing it to become even more dominant. A marine example is when sea urchin populations "explode" in coastal waters and destroy all the macroalgae present. What was previously a kelp forest becomes an urchin barren that may last for years and this can have a profound effect on the food chain. Removal of the sea urchins, by disease for example, can result in the seaweed returning, with an over-abundance of fast-growing kelp.

Habitat protection

The protection of habitats is a necessary step in the maintenance of biodiversity because if habitat destruction occurs, the animals and plants reliant on that habitat suffer. Many countries have enacted legislation to protect their wildlife. This may take the form of the setting up of national parks, forest reserves and wildlife reserves, or it may restrict the activities of humans with the objective of benefiting wildlife. The laws may be designed to protect a particular species or group of species, or the legislation may prohibit such activities as the collecting of bird eggs, the hunting of animals or the removal of plants. A general law on the protection of habitats may be more difficult to implement than a site specific requirement. A concept introduced in the United States in 1973 involves protecting the critical habitat of endangered species, and a similar concept has been incorporated into some Australian legislation.

International treaties may be necessary for such objectives as the setting up of marine reserves. Another international agreement, the Convention on the Conservation of Migratory Species of Wild Animals, protects animals that migrate across the globe and need protection in more than one country. However, the protection of habitats needs to take into account the needs of the local residents for food, fuel and other resources. Even where legislation protects the environment, a lack of enforcement often prevents effective protection. Faced with food shortage, a farmer is likely to plough up a level patch of ground despite it being the last suitable habitat for an endangered species such as the San Quintin kangaroo rat, and even kill the animal as a pest. In this regard, it is desirable to educate the community on the uniqueness of their flora and fauna and the benefits of ecotourism.

Monotypic habitat

A monotypic habitat is one in which a single species of animal or plant is so dominant as to virtually exclude all other species. An example would be sugarcane; this is planted, burnt and harvested, with herbicides killing weeds and pesticides controlling invertebrates. The monotypic habitat occurs in botanical and zoological contexts, and is a component of conservation biology. In restoration ecology of native plant communities or habitats, some invasive species create monotypic stands that replace and/or prevent other species, especially indigenous ones, from growing there. A dominant colonization can occur from retardant chemicals exuded, nutrient monopolization, or from lack of natural controls such as herbivores or climate, that keep them in balance with their native habitats. The yellow starthistle, Centaurea solstitialis, is a botanical monotypic-habitat example of this, currently dominating over 15,000,000 acres (61,000 km²) in California alone. The non-native freshwater zebra mussel, Dreissena polymorpha, that colonizes areas of the Great Lakes and the Mississippi River watershed, is a zoological monotypic-habitat example; the predators that control it in its home-range in Russia are absent and it proliferates abundantly. Even though its name may seem to imply simplicity as compared with polytypic habitats, the monotypic habitat can be complex. Aquatic habitats, such as exotic Hydrilla beds, support a similarly rich fauna of macroinvertebrates to a more varied habitat, but the creatures present may differ between the two, affecting small fish and other animals higher up the food chain.

Google AI Princeton: Current and Future Research

Tuesday, December 18, 2018  

Posted by Elad Hazan and Yoram Singer, Research Scientists, Google AI and Princeton University

Original link:  https://ai.googleblog.com/2018/12/google-ai-princeton-current-and-future.html

Google has long partnered with academia to advance research, collaborating with universities all over the world on joint research projects which result in novel developments in Computer Science, Engineering, and related fields. Today we announce the latest of these academic partnerships in the form of a new lab, across the street from Princeton University’s historic Nassau Hall, opening early next year. By fostering closer collaborations with faculty and students at Princeton, the lab aims to broaden research in multiple facets of machine learning, focusing its initial research efforts on optimization methods for large-scale machine learning, control theory and reinforcement learning. 

Below we give a brief overview of the research progress thus far.Large-Scale Optimization Imagine you have gone for a mountain hike and have run out of water. You need to get to a lake. How can you do so most efficiently? This is a matter of optimizing your route, and the mathematical analogue of this is the gradient descent method. You therefore move in the direction of steepest descent until you find the nearest lake at the bottom of your path. In the language of optimization, the location of the lake is referred to as a (local) minimum. The trajectory of gradient descent resembles the path, shown below, a thirsty yet avid hiker would take in order to get down to a lake as fast as she can.

Gradient descent (GD), and its randomized version, stochastic gradient descent (SGD), are the methods of choice for optimizing the weights of neural networks. Stacking all of the parameters together, we form a set of cells organized into vectors Let us take a simplistic view and assume that our neural net merely has 5 different parameters. Taking a gradient descent step amounts to subtracting the gradient vector (red) from the current set of parameters (blue) and putting the result back into the parameter vector.

Going back to our avid hiker, suppose she finds an unmarked path that is long and narrow, with limited visibility as she gazes down. If she follows the descent method her path would zig-zag down the hill, as shown in the illustration below on the left. However, she can now make faster progress by exploiting the skewed geometry of the terrain. That is, she can make a bigger leap forward than to the sides. In the context of gradient descent, pacing up is called acceleration. A popular class of acceleration methods is named adaptive regularization, or adaptive preconditioning, first introduced by the AdaGrad algorithm devised in collaboration with Prof. John Duchi from Stanford while he was at Google.

The idea is to change the geometry of the landscape of the optimization objective to make it easier for gradient descent to work. In order to do so, preconditioning methods stretch and rotate the space. The terrain after preconditioning looks like the serene, perfectly spherical lake above on the right, and the descent trajectory is a straight line! Procedurally, instead of subtracting the gradient vectors from the parameters vector per-se, adaptive preconditioning first multiplies the gradient by a 5×5 multicell structure, called a matrix preconditioner, as shown below.

This preconditioning operation yields a stretched and rotated gradient which is then subtracted as before, allowing much faster progress toward a basin. However, there is a downside to preconditioning, namely, its computational cost. Instead of subtracting a 5-dimensional gradient vector from a 5-dimensional parameter vector, the preconditioning transformation itself requires 5×5=25 operations. Suppose we would like to precondition gradients in order to learn a deep network with 10 million parameters. A single preconditioning step would require 100 trillion operations. In order to save computation, a diagonal version in which preconditioning amounts to stretching sans rotation was also introduced in the original AdaGrad paper. The diagonal version was later adopted and modified, yielding another very successful algorithm called Adam. This simplified diagonal preconditioning imposes only a marginal additional cost to gradient descent. However, oversimplification has its own downside: we are no longer able to rotate our space. Going back to our hiker, if the deep-and-narrow canyon runs from southeast to northwest, she can no longer take large westward leaps. Had we provided her with a “rigged” compass in which the north pole is in the northwest, she could have followed her descent procedure as before. In high dimensions, the analog of compass rigging is full-matrix preconditioning. We thus asked ourselves whether we could devise a preconditioning method that is computationally efficient while allowing for the equivalent of coordinate rotations. At Google AI Princeton, we developed a new method for full-matrix adaptive preconditioning at roughly the same computational cost as the commonly-used diagonal restriction. 

Details can be found in the paper, but the key idea behind the method is depicted below. Instead of using a full matrix, we replace the preconditioning matrix by a product of three matrices: a tall, thin matrix, a (small) square matrix, and a short, fat matrix. The vast amount of computation is performed using the smaller matrix. If we have d parameters, instead of a single large d × d matrix, the matrices maintained by GGT (shorthand for the operation Gradient Gradient^T), the proposed method, are of sizes d × k, k × k, k × d respectively.

For reasonable choices of k, which can be thought of as the “window size” of the algorithm, the computational bottleneck has been mitigated from a single large matrix, to that of a much smaller kkmatrix. In our implementation we typically choose k to be, say, 50, and maintaining the smaller square matrix is significantly less expensive while yielding good empirical performance. When compared to other adaptive methods on standard deep learning tasks, GGT is competitive with AdaGrad and Adam.Spectral Filtering for Control and Reinforcement Learning Another broad mission of Google’s research group in Princeton is to develop principled building blocks for decision-making systems. In particular, the group strives to leverage provable guarantees from the field of online learning, which studies the robust (worst-case) guarantees of decision-making algorithms under uncertainty. An online algorithm is said to attain a no-regret guarantee if it learns to make decisions as well as the best "offline" decision in hindsight. Ideas from this field have already enabled many innovations within theoretical computer science, and provide a mathematically elegant framework to study a widely-used technique called boosting.

We envision using ideas from online learning to broaden the toolkit of modern reinforcement learning. With that goal in mind, and in collaboration with researchers and students at Princeton, we developed the algorithmic technique of spectral filtering for estimation and control of linear dynamical systems (see severalrecentpublications). In this setting, noisy observations (e.g., location sensor measurements) are being streamed from an unknown source. The source of the signal is a system whose state evolves over time following a set of linear equations (e.g. Newton's laws). To forecast future signals (prediction), or to perform actions which bring the system to a desired state (control), the usual approach starts with learning the model explicitly (a task termed system identification), which is often slow and inaccurate. Spectral filtering circumvents the need to model the dynamics explicitly, by reformulating prediction and control as convex programs, enabling provable no-regret guarantees. A major component of the technique is that of a new signal processing transformation. The idea is to summarize the long history of past input signals through convolution with a tailored bank of filters, and then use this representation to predict the dynamical system’s future outputs. Each filter compresses the input signal into a single real number, by taking a weighted combination of the previous inputs.

A set of filters depicted in a plot of filter amplitude versus time. With our technique of spectral filtering, multiple filters are used to predict the state of a linear dynamical system at any given time. Each filter is a set of weights used to summarize past observations, such that combining them in a weighted fashion, over time allows us to accurately predict the system. 

The mathematical derivation of these weights (filters) has an interesting connection to the spectral theory of Hankel matrices. Looking Forward We are excited about the progress we have made thus far in partnership with Princeton’s faculty and students, and we look forward to the official opening of the lab in the coming weeks. It has long been Google’s view that both industry and academia benefit significantly from an open research culture, and we look forward to our continued close collaboration.AcknowledgmentsThe research and results discussed in this post would not have been possible without contributions from the following researchers: Naman Agarwal, Brian Bullins, Xinyi Chen, Udaya Ghai, Tomer Koren, Karan Singh, Cyril Zhang, Yi Zhang, and visiting professor Sham Kakade. Since joining Google earlier this year, the research team has been working remotely from both the Google NYC office as well as the Princeton University campus, and they look forward to moving into the new Google space across from the Princeton campus in the weeks to come.

Mapping the brain, cell by cell

MIT researchers used their new tissue preservation technique to label and image neurons in a brain region called the globus pallidus externa. Neurons that express a protein called parvalbumin are labeled in red, and neurons labeled blue express a protein called GAD1. Image: Young-Gyun Park, Changho Sohn, Ritchie Chen, and Kwanghun Chung

Technique for preserving tissue allows researchers to create maps of neural circuits with single-cell resolution.

Anne Trafton | MIT News Office | December 17, 2018
Original link:  http://news.mit.edu/2018/cell-neural-circuit-brain-map-1217 

MIT chemical engineers and neuroscientists have devised a new way to preserve biological tissue, allowing them to visualize proteins, DNA, and other molecules within cells, and to map the connections between neurons.

The researchers showed that they could use this method, known as SHIELD, to trace the connections between neurons in a part of the brain that helps control movement and other neurons throughout the brain.

“Using our technique, for the first time, we were able to map the connectivity of these neurons at single-cell resolution,” says Kwanghun Chung, an assistant professor of chemical engineering and a member of MIT’s Institute for Medical Engineering and Science and Picower Institute for Learning and Memory. “We can get all this multiscale, multidimensional information from the same tissue in a fully integrated manner because with SHIELD we can protect all this information.”

Chung is the senior author of the paper, which appears in the Dec. 17 issue of Nature Biotechnology. The paper’s lead authors are MIT postdocs Young-Gyun Park, Chang Ho Sohn, and Ritchie Chen.

Chung is now leading a team of researchers from several institutions that recently received a National Institutes of Health grant to use this technique to produce three-dimensional maps of the entire human brain. “We will be working with the Matthew Frosch group at MGH, the Van Wedeen group at MGH, the Sebastian Seung group at Princeton, and the Laura Brattain group at MIT Lincoln Lab to generate the most comprehensive brain map yet,” he says.

Preserving information

Brain tissue is very delicate and cannot be easily studied unless steps are taken to preserve the tissue from damage. Chung and other researchers have previously developed techniques that allow them to preserve certain molecular components of brain tissue for research, including proteins or messenger RNA, which reveals which genes are turned on.

However, Chung says, “there is no good method that can preserve everything.”

Chung and his colleagues hypothesized that they might be able to better preserve tissue using molecules called polyepoxides — reactive organic molecules that are often used to produce glues. They tested several commercially available polyepoxides and discovered one that had distinctive structural traits that made it ideally suited for their purposes.

The epoxide they chose has a flexible backbone and five branches, each of which can bind to certain amino acids (the building blocks of proteins), as well as other molecules such as DNA and RNA. The flexible backbone allows the epoxides to bind to several spots along the target molecules, and to form cross-links with nearby biomolecules. This renders individual biomolecules and the entire tissue structure very stable and resistant to damage from heat, acid, or other harmful agents. SHIELD also protects key properties of biomolecules, such as protein fluorescence and antigenicity.

To protect large-scale brain tissues and clinical samples, the researchers combined SHIELD with SWITCH, another technique they developed to control chemical reaction speed. They first use the SWITCH-OFF buffer, which halts chemical reactions, to give the epoxides time to diffuse through the entire tissue. When the researchers move the sample to SWITCH-ON condition, the epoxides begin to bind to nearby molecules.

To speed up the clearing and labeling process of SHIELD-protected tissue, the researchers also applied a randomly changing electric field, which they have previously shown increases the transport rate of the molecules. In this paper, they showed that the entire process from preservation to labeling of biopsy tissue could be performed in just four hours.

“We found that this SHIELD coating keeps proteins stable against harsh stressors,” Chung says. “Because we can preserve all the information that we want, and we can extract it at multiple stages, we can better understand the functions of biological components, including neural circuits.”

Once the tissue is preserved, the researchers can label a variety of different targets, including proteins and mRNA produced by the cells. They can also apply techniques such as MAP, which Chung developed in 2016, to expand the tissue and image it at different size scales.

In this paper, the researchers worked with Byungkook Lim’s group at the University of California at San Diego to use SHIELD to map a brain circuit that begins in the globus pallidus externa (GPe), part of the brain’s basal ganglia. This region, which is involved in motor control and other behaviors, is one of the targets of deep brain stimulation — a type of electrical stimulation sometimes used to treat Parkinson’s disease. In the mouse brain, Chung and his colleagues were able to trace the connections between neurons in the GPe and in other parts of the brain, and to count the number of putative synaptic connections between these neurons.

Better biopsies

The speed of SHIELD tissue processing means that it also holds promise for performing rapid, more informative biopsies of patient tissue samples, Chung says. Current methods require embedding tissue samples with paraffin, slicing them, and then applying stains that can reveal cell and tissue abnormalities.

“The current way of doing tissue diagnosis hasn’t changed in many decades, and the process takes days or weeks,” Chung says. “Using our technique, we can rapidly process intact biopsy samples and immuno-label them with really specific, clinically relevant antibodies, and then image the whole thing at high resolution, in three dimensions. And everything can be done in four hours.”

In this paper, the researchers showed that they could label mouse kidney tumor with an antibody that targets proliferating cancer cells.

“The stabilization and preservation of biological information within tissue samples is essential in experiments for optical microscopy,” says Liqun Luo, a professor of biology at Stanford University, who was not involved in the research. “The achievement of SHIELD is not a large advance in just one category, but rather marked improvements across the board, in preserving proteins, transcripts, and tissue structure, as samples are processed through the harsh techniques prescribed by today's best labeling and imaging protocols.”

The MIT team hopes to make this technology widely available and has already distributed it to more than 50 labs around the world. The research was funded by the Burroughs Wellcome Fund Career Award at the Scientific Interface, the Searle Scholars Program, the Packard Award in Science and Engineering, the NARSAD Young Investigator Award, the McKnight Foundation Technology Award, the JPB Foundation, and NCSOFT Cultural Foundation, and the National Institutes of Health.

Thorium vs. Molten Salt Reactor

Market Intelligence | 12/18/2018 | By Canon Bryan

Original link:  http://4thgeneration.energy/thorium-vs-molten-salt-reactor/?fbclid=IwAR0OXSkaAGq2MuY3X-AiEdIFOT9p8qIGreEuslpwHqrF4t5XSa60IGwCB7k 

 

To a limited group of technophiles and nuclear technology enthusiasts, thorium has become a unicorn. But does thorium really represent nuclear innovation?

Back in the 1950s and 1960s, the scientists at Oak Ridge National Laboratory in the USA developed the Molten Salt Reactor design – a liquid salt fueled and cooled nuclear reactor system. They designed it, they prototyped it, and they operated it. The experiment was called the Molten Salt Reactor Experiment, or MSRE. The MSRE used a thorium fuel cycle.  It used a lithium beryllium fluoride coolant salt mixture, called FLiBe. It used a graphite moderator. It used a special material called Hastelloy N – a nickel alloy developed specifically to withstand the harsh environment.

The experiment was a great success. It proved that this liquid fuel system could facilitate nuclear fission, and that it was tremendously stable, and easy to operate. Dick Engel, the project manager, even called it “boring” because the engineers had virtually nothing to do while it operated.

At the rudiments of the technology lay the liquid fuel. Liquid nuclear fuel-coolant, the MSRE discovered, was a much more efficient mechanism for capturing the immense heat from fission than solid fuel/water coolant. Salt coolant was a much more versatile coolant, with a huge thermal range, compared to a water coolant, and capable of storing and easily conveying that immense heat from fission.

The thorium-232/uranium-233 fuel cycle that was used in the MSRE was a departure from the uranium-235/uranium-238/plutonium-239 fuel cycle that was being used in the Light Water Reactor design, also invented by the Americans. The LWR was being used in the US Navy submarine program, and by the mid-1950s, started to be used in commercial power plants. Thorium, it was projected, could have some advantages over uranium, particularly in a liquid fuel application.

In order to make thorium fuel, Th232 must either be blended with U235 or Pu239, or it must be bombarded with neutrons to make a supply of U233, which is also fissile. The Th232 and U233 is then blended to create a fuel that is capable of achieving criticality. Since the dawn of the atomic age, there have been a small handful of commercial applications of a thorium fuel cycle.

In order to make commercial nuclear fuel, U235, which is about 0.7% of naturally-occurring uranium, must be concentrated to between 3% and 5% of the uranium fuel element. This is not so easily achieved either, but there is a multi-decade legacy of uranium enrichment. The fuel cycle is well-understood by regulators, operators and the supply chain.

What are the advantages of thorium?

Thorium is abundant. That is certainly an advantage it has over uranium. It is abundant and broadly geographically dispersed and easy to extract from nature. Unlike uranium, thorium is found in great concentrations right on the surface of the earth, most commonly, in black sand beaches.

Thorium is not fissile, which means that thorium by itself could never possibly be weaponized. However, because it is not fissile, it means that thorium always requires fissile material to make fuel, and that creates new proliferation risks.

This is where the actual advantages of thorium end.  All the other advantages commonly attributed to thorium are actually advantages of a Molten Salt Reactor – not of thorium itself. These virtues became conflated with the Molten Salt Reactor design. Because of the fact that thorium fuel was used, enthusiasts rediscovering this technology 40 years later have misplaced the rudiments of the innovation.

Molten Salt Reactors have tremendous safety, waste and proliferation virtues, which translate into substantial commercial virtues.  The following is a non-exhaustive list:

• Fluoride salts have an approximately 1,000C range in which they stay liquid – neither freezing nor boiling;
• Fluoride salts operate naturally at high temperature, obviating the need for immense pressure in a reactor vessel;
• Fluoride salts are chemically very stable and inert, eliminating the risk of chemical explosions in a reactor system;
• A liquid fuel is inherently easier and cheaper to chemically process, thereby creating a pathway for total nuclear waste elimination.

There are many others. These advantages are specific to Molten Salt Reactors, and not to thorium fuel.

The thorium enthusiasts will certainly find this controversial. However, if the goal is eliminating energy poverty and pollution, one must accurately assess the source terms of nuclear innovation.  The mystical nature of thorium has served its purpose by attracting all walks of life to develop an interest in advanced nuclear technology – including myself.  Now the market must focus on the most pragmatic way of commercializing true nuclear innovation.

About the author

Canon Bryan

Mr. Bryan has served as officer and director for private and public companies in Canada and the USA. Mr. Bryan has considerable experience providing financial management services to clients in various industries. He has focused primarily on energy and natural resources industries. Mr. Bryan was a co-founder of: Terrestrial Energy, a developer of commercial advanced nuclear power plants; NioCorp (NB: TSXV), a company developing the largest niobium deposit in North America; Uranium Energy Corp (UEC: NYSE), a producer of ISR uranium in the USA. Mr. Bryan was senior financial analyst for Lasik Vision Corporation (LSK: CDNX), which was the world’s largest provider of laser refractive surgical services. Mr. Bryan completed his studies in accounting and finance at the University of British Columbia.

Urban ecology

From Wikipedia, the free encyclopedia

Central Park represents an ecosystem fragment within a larger urban environment.

Urban ecology is the scientific study of the relation of living organisms with each other and their surroundings in the context of an urban environment. The urban environment refers to environments dominated by high-density residential and commercial buildings, paved surfaces, and other urban-related factors that create a unique landscape dissimilar to most previously studied environments in the field of ecology.

Urban ecology is a recent field of study compared to ecology as a whole. The methods and studies of urban ecology are similar to and comprise a subset of ecology. The study of urban ecology carries increasing importance because more than 50% of the world's population today lives in urban areas. At the same time, it is estimated that within the next forty years, two-thirds of the world's population will be living in expanding urban centers. The ecological processes in the urban environment are comparable to those outside the urban context. However, the types of urban habitats and the species that inhabit them are poorly documented. Often, explanations for phenomena examined in the urban setting as well as predicting changes because of urbanization are the center for scientific research.

History

The creation of an important stream water garden in Metz's centre during the early 70s was one of the materializations of Jean-Marie Pelt's works on urban ecology.

Ecology has historically focused on "pristine" natural environments, but by the 1970s many ecologists began to turn their interest towards ecological interactions taking place in, and caused by urban environments. Jean-Marie Pelt's 1977 book The Re-Naturalized Human, Brian Davis' 1978 publication Urbanization and the diversity of insects, and Sukopp et al.'s 1979 article "The soil, flora and vegetation of Berlin's wastelands" are some of the first publications to recognize the importance of urban ecology as a separate and distinct form of ecology the same way one might see landscape ecology as different from population ecology. Forman and Godron's 1986 book Landscape Ecology first distinguished urban settings and landscapes from other landscapes by dividing all landscapes into five broad types. These types were divided by the intensity of human influence ranging from pristine natural environments to urban centers. 

Urban ecology is recognized as a diverse and complex concept which differs in application between North America and Europe. The European concept of urban ecology examines the biota of urban areas, while the North American concept has traditionally examined the social sciences of the urban landscape, as well as the ecosystem fluxes and processes.

Methods

Since urban ecology is a subfield of ecology, many of the techniques are similar to that of ecology. Ecological study techniques have been developed over centuries, but many of the techniques use for urban ecology are more recently developed. Methods used for studying urban ecology involve chemical and biochemical techniques, temperature recording, heat mapping remote sensing, and long-term ecological research sites.

Chemical and biochemical techniques

Chemical techniques may be used to determine pollutant concentrations and their effects. Tests can be as simple as dipping a manufactured test strip, as in the case of pH testing, or be more complex, as in the case of examining the spatial and temporal variation of heavy metal contamination due to industrial runoff. In that particular study, livers of birds from many regions of the North Sea were ground up and mercury was extracted. Additionally, mercury bound in feathers was extracted from both live birds and from museum specimens to test for mercury levels across many decades. Through these two different measurements, researchers were able to make a complex picture of the spread of mercury due to industrial runoff both spatially and temporally. 

Other chemical techniques include tests for nitrates, phosphates, sulfates, etc. which are commonly associated with urban pollutants such as fertilizer and industrial byproducts. These biochemical fluxes are studied in the atmosphere (e.g. greenhouse gasses), aquatic ecosystems and soil vegetation. Broad reaching effects of these biochemical fluxes can be seen in various aspects of both the urban and surrounding rural ecosystems.

Temperature data and heat mapping

Temperature data can be used for various kinds of studies. An important aspect of temperature data is the ability to correlate temperature with various factors that may be affecting or occurring in the environment. Oftentimes, temperature data is collected long-term by the Office of Oceanic and Atmospheric Research (OAR), and made available to the scientific community through the National Oceanic and Atmospheric Administration (NOAA). Data can be overlaid with maps of terrain, urban features, and other spatial areas to create heat maps. These heat maps can be used to view trends and distribution over time and space.

Remote sensing

Remote sensing allows collection of data using satellites. This map shows urban tree canopy in Boston.

Remote sensing is the technique in which data is collected from distant locations through the use of satellite imaging, radar, and aerial photographs. In urban ecology, remote sensing is used to collect data about terrain, weather patterns, light, and vegetation. One application of remote sensing for urban ecology is to detect the productivity of an area by measuring the photosynthetic wavelengths of emitted light. Satellite images can also be used to detect differences in temperature and landscape diversity to detect the effects of urbanization.

LTERs and long-term data sets

Long-term ecological research (LTER) sites are research sites funded by the government that have collected reliable long-term data over an extended period of time in order to identify long-term climatic or ecological trends. These sites provide long-term temporal and spatial data such as average temperature, rainfall and other ecological processes. The main purpose of LTERs for urban ecologists is the collection of vast amounts of data over long periods of time. These long-term data sets can then be analyzed to find trends relating to the effects of the urban environment on various ecological processes, such as species diversity and abundance over time. Another example is the examination of temperature trends that are accompanied with the growth of urban centers.

Urban effects on the environment

Humans are the driving force behind urban ecology and influence the environment in a variety of ways, such as modifying land surfaces and waterways, introducing foreign species, and altering biogeochemical cycles. Some of these effects are more apparent, such as the reversal of the Chicago River to accommodate the growing pollution levels and trade on the river. Other effects can be more gradual such as the change in global climate due to urbanization.

Modification of land and waterways

Deforestation in the Amazon rainforest. The "fishbone pattern" is a result of the roads in the forest created by loggers.

Humans place high demand on land not only to build urban centers, but also to build surrounding suburban areas for housing. Land is also allocated for agriculture to sustain the growing population of the city. Expanding cities and suburban areas necessitate corresponding deforestation to meet the land-use and resource requirements of urbanization. Key examples of this are Deforestation in the United States and Brazil.

Along with manipulation of land to suit human needs, natural water resources such as rivers and streams are also modified in urban establishments. Modification can come in the form of dams, artificial canals, and even the reversal of rivers. Reversing the flow of the Chicago River is a major example of urban environmental modification. Urban areas in natural desert settings often bring in water from far areas to maintain the human population and will likely have effects on the local desert climate. Modification of aquatic systems in urban areas also results in decreased stream diversity and increased pollution.

Trade, shipping, and spread of invasive species

A ship navigates through the Firth of Clyde in Scotland, potentially carrying invasive species.

 

Invasive kudzu vines growing on trees in Atlanta, Georgia, USA

Both local shipping and long-distance trade are required to meet the resource demands important in maintaining urban areas. Carbon dioxide emissions from the transport of goods also contribute to accumulating greenhouse gases and nutrient deposits in the soil and air of urban environments. In addition, shipping facilitates the unintentional spread of living organisms, and introduces them to environments that they would not naturally inhabit. Introduced or alien species are populations of organisms living in a range in which they did not naturally evolve due to intentional or inadvertent human activity. Increased transportation between urban centers furthers the incidental movement of animal and plant species. Alien species often have no natural predators and pose a substantial threat to the dynamics of existing ecological populations in the new environment where they are introduced. Such invasive species are numerous and include house sparrows, ring-necked pheasants, European starlings, brown rats, Asian carp, American bullfrogs, emerald ash borer, kudzu vines, and zebra mussels among numerous others, most notably domesticated animals. In Australia, it has been found that removing Lantana (L. camara, an alien species) from urban greenspaces can surprisingly have negative impacts on bird diversity locally, as it provides refugia for species like the superb fairy (Malurus cyaneus) and silvereye (Zosterops lateralis), in the absence of native plant equivalents . Although, there seems to be a density threshold in which too much Lantana (thus homogeneity in vegetation cover) can lead to a decrease in bird species richness or abundance .

Human effects on biogeochemical pathways

Urbanization results in a large demand for chemical use by industry, construction, agriculture, and energy providing services. Such demands have a substantial impact on biogeochemical cycles, resulting in phenomena such as acid rain, eutrophication, and global warming. Furthermore, natural biogeochemical cycles in the urban environment can be impeded due to impermeable surfaces that prevent nutrients from returning to the soil, water, and atmosphere.

Graphical representation of the carbon cycle.

Demand for fertilizers to meet agricultural needs exerted by expanding urban centers can alter chemical composition of soil. Such effects often result in abnormally high concentrations of compounds including sulfur, phosphorus, nitrogen, and heavy metals. In addition, nitrogen and phosphorus used in fertilizers have caused severe problems in the form of agricultural runoff, which alters the concentration of these compounds in local rivers and streams, often resulting in adverse effects on native species. A well-known effect of agricultural runoff is the phenomenon of eutrophication. When the fertilizer chemicals from agricultural runoff reach the ocean, an algal bloom results, then rapidly dies off. The dead algae biomass is decomposed by bacteria that also consume large quantities of oxygen, which they obtain from the water, creating a "dead zone" without oxygen for fish or other organisms. A classic example is the dead zone in the Gulf of Mexico due to agricultural runoff into the Mississippi River. 

Just as pollutants and alterations in the biogeochemical cycle alter river and ocean ecosystems, they exert likewise effects in the air. Smog stems from the accumulation of chemicals and pollution and often manifests in urban settings, which has a great impact on local plants and animals. Because urban centers are often considered point sources for pollution, unsurprisingly local plants have adapted to withstand such conditions.

Urban effects on climate

Urban environments and outlying areas have been found to exhibit unique local temperatures, precipitation, and other characteristic activity due to a variety of factors such as pollution and altered geochemical cycles. Some examples of the urban effects on climate are urban heat island, oasis effect, greenhouse gases, and acid rain. This further stirs the debate as to whether urban areas should be considered a unique biome. Despite common trends among all urban centers, the surrounding local environment heavily influences much of the climate. One such example of regional differences can be seen through the urban heat island and oasis effect.

Urban heat island effect

Graphical representation of the rising temperature in Kanto, Japan due to urban heat island.

The urban heat island is a phenomenon in which central regions of urban centers exhibit higher mean temperatures than surrounding urban areas. Much of this effect can be attributed to low city albedo, the reflecting power of a surface, and the increased surface area of buildings to absorb solar radiation. Concrete, cement, and metal surfaces in urban areas tend to absorb heat energy rather than reflect it, contributing to higher urban temperatures. Brazel et al. found that the urban heat island effect demonstrates a positive correlation with population density in the city of Baltimore. The heat island effect has corresponding ecological consequences on resident species. However, this effect has only been seen in temperate climates.

Greenhouse gases

Greenhouse gas emissions include those of carbon dioxide and methane from the combustion of fossil fuels to supply energy needed by vast urban metropolises. Other greenhouse gases include water vapor, and nitrous oxide. Increases in greenhouse gases due to urban transport, construction, industry and other demands have been correlated strongly with increase in temperature. Sources of methane are agricultural dairy cows and landfills.

Acid rain and pollution

Smokestacks from a wartime production plant releasing pollutants into the atmosphere.

Processes related to urban areas result in the emission of numerous pollutants, which change corresponding nutrient cycles of carbon, sulfur, nitrogen, and other elements. Ecosystems in and around the urban center are especially influenced by these point sources of pollution. High sulfur dioxide concentrations resulting from the industrial demands of urbanization cause rainwater to become more acidic. Such an effect has been found to have a significant influence on locally affected populations, especially in aquatic environments. Wastes from urban centers, especially large urban centers in developed nations, can drive biogeochemical cycles on a global scale.

Urban environment as an anthropogenic biome

The urban environment has been classified as an anthropogenic biome, which is characterized by the predominance of certain species and climate trends such as urban heat island across many urban areas. Examples of species characteristic of many urban environments include, cats, dogs, mosquitoes, rats, flies, and pigeons, which are all generalists. Many of these are dependent on human activity and have adapted accordingly to the niche created by urban centers.

Biodiversity and urbanization

Research thus far indicates that, on a small scale, urbanization often increases the biodiversity of non-native species while reducing that of native species. This normally results in an overall reduction in species richness and increase in total biomass and species abundance. Urbanization also reduces diversity on a large scale.

Urban stream syndrome is a consistently observed trait of urbanization characterized by high nutrient and contaminant concentration, altered stream morphology, increased dominance of dominant species, and decreased biodiversity The two primary causes of urban stream syndrome are storm water runoff and wastewater treatment plant effluent.

Changes in diversity

Diversity is normally reduced at intermediate-low levels of urbanization but is always reduced at high levels of urbanization. These effects have been observed in vertebrates and invertebrates while plant species tend to increase with intermediate-low levels of urbanization but these general trends do not apply to all organisms within those groups. For example, McKinney’s (2006) review did not include the effects of urbanization on fishes and of the 58 studies on invertebrates, 52 included insects while only 10 included spiders. There is also a geographical bias as most of the studies either took place in North America or Europe. 

The effects of urbanization also depend on the type and range of resources used by the organism. Generalist species, those that use a wide range of resources and can thrive under a large range of living conditions, are likely survive in uniform environments. Specialist species, those that use a narrow range of resources and can only cope with a narrow range of living conditions, are unlikely to cope with uniform environments. There will likely be a variable effect on these two groups of organisms as urbanization alters habitat uniformity.

Cause of diversity change

The urban environment can decrease diversity through habitat removal and species homogenization - the increasing similarity between two previously distinct biological communities. Habitat degradation and habitat fragmentation reduces the amount of suitable habitat by urban development and separates suitable patches by inhospitable terrain such as roads, neighborhoods, and open parks. Although this replacement of suitable habitat with unsuitable habitat will result in extinctions of native species, some shelter may be artificially created and promote the survival of non-native species (e.g. house sparrow and house mice nests). Urbanization promotes species homogenization through the extinction of native endemic species and the introduction of non-native species that already have a widespread abundance. Changes to the habitat may promote both the extinction of native endemic species and the introduction of non-native species. The effects of habitat change will likely be similar in all urban environments as urban environments are all built to cater to the needs of humans.

The urban environment can also increase diversity in a number of ways. Many foreign organisms are introduced and dispersed naturally or artificially in urban areas. Artificial introductions may be intentional, where organisms have some form of human use, or accidental, where organisms attach themselves to transportation vehicles. Humans provide food sources (e.g. birdfeeder seeds, trash, garden compost) and reduce the numbers of large natural predators in urban environments, allowing large populations to be supported where food and predation would normally limit the population size. There are a variety of different habitats available within the urban environment as a result of differences in land use allowing for more species to be supported than by more uniform habitats.

Civil engineering and sustainability

Cities should be planned and constructed in such a way that minimizes the urban effects on the surrounding environment (urban heat island, precipitation, etc.) as well as optimizing ecological activity. For example, increasing the albedo, or reflective power, of surfaces in urban areas, can minimize urban heat island, resulting in a lower magnitude of the urban heat island effect in urban areas. By minimizing these abnormal temperature trends and others, ecological activity would likely be improved in the urban setting.

Need for remediation

Urbanization has indeed had a profound effect on the environment, on both local and global scales. Difficulties in actively constructing habitat corridor and returning biogeochemical cycles to normal raise the question as to whether such goals are feasible. However, some groups are working to return areas of land affected by the urban landscape to a more natural state. This includes using landscape architecture to model natural systems and restore rivers to pre-urban states.

Sustainability

Pipes carrying biogas produced by anaerobic digestion or fermentation of biodegradable materials as a form of carbon sequestration.

With the ever-increasing demands for resources necessitated by urbanization, recent campaigns to move toward sustainable energy and resource consumption, such as LEED certification of buildings, Energy Star certified appliances, and zero emission vehicles, have gained momentum. Sustainability reflects techniques and consumption ensuring reasonably low resource use as a component of urban ecology. Techniques such as carbon recapture may also be used to sequester carbon compounds produced in urban centers rather continually emitting more of the greenhouse gas.

Summary

Urbanization results in a series of both local and far-reaching effects on biodiversity, biogeochemical cycles, hydrology, and climate, among many other stresses. Many of these effects are not fully understood, as urban ecology has only recently emerged as a scientific discipline and much more research remains to be done. Research on cities outside the US and Europe remains limited. Observations on the impact of urbanization on biodiversity and species interactions are consistent across many studies but definitive mechanisms have yet to be established. Urban ecology constitutes an important and highly relevant subfield of ecology, and further study must be pursued to more fully understand the effects of human urban areas on the environment.