The Cities are the topic of the month here at Scientific American (and at least this week on the blogs), so I should chime in on an aspect of urban ecology that I am comfortable discussing - the effects of increased light at night on animals.
Not all species of animals are negatively affected by the urban environments. Even humans are not driven to insanity by the urban jungle. Some species are really thriving - rats, mice, squirrels, bats, alligators in sewers, sparrows, pigeons, starlings, crows, house flies, mosquitoes and cockroaches come to mind. Many birds have evolved (or invented) quite nifty adaptations to urban life. Of course, animals we domesticated and keep as pets, like cats and dogs, don't really care about the city vs. country, as long as they are with us and we take good care of them.
But there are definitely negative effects as well. After all, just counts and surveys of species make it obvious that many species are not thriving in dense urban ecosystems. Not all cities are the same either. A large, dense city is likely to be much less hospitable to many species than urban sprawl where much greenery and the original natural habitat are still preserved between the cul-de-sacs. Just watch the wilderness appearing on my back porch: skinks, tree frogs, Luna moths, white-tailed deer, rabbits, opossums, racoons, cicadas, endless species of birds...and I am in the middle of the Triangle, NC.
Large animals, in general, will not do well in cities, and not just because direct encounters with humans can often be deadly (imagine what would happen to a herd of bison if it tried to trek through streets of Manhattan?). Herbivores will be starved due to lack of plants, and carnivores will starve due to lack of herbivores. Thus many ecological factors affect the ability of species to adapt to the City - food, predators, shelter, and, importantly, noise.
But I will focus only on light today. Light pollution is often discussed in the context of impossibility to see the wonderful starry night, but effect of night light on wildlife is a problem beyond human esthetics - it has real-world consequences for the health of ecosystems. And the effect of light almost always involves, in some way, the circadian clock.
Circadian clock - a very, very quick primer
There is quite a lot of biological complexity in the circadian clock, but let's just remember the few key, basic points.
Circadian clock is a structure (in animals it is in the brain) that governs the daily rhythms of biochemistry, physiology and behavior.
All organisms living on or near the surface of the Earth have a circadian clock. Those that now live deep down inside the soil or rocks or caves, or on the bottom of the ocean, may have secondarily lost the clock that their ancestors once had [1,2].
Having a circadian clock is an adaptation to the cycles of day and night in the environment. Where such cycles are altered, e.g., near the poles, the animals have evolved the ability to turn their daily clocks on or off as appropriate.
Circadian clock keeps ticking in constant darkness, or constant dim light. But in many species, constant intense light disrupts the rhythm.
The clock is reset (entrained, synchronized) each day by the alternation of light and darkness. Species differ as to the intensity of light needed for this resetting to take place. While physiological laboratory experiments usually test the light intensity against the background of complete darkness (in which the sensory systems can get adapted to the dark and become more sensitive to light), it is the difference in light intensity between day and night that is of ecological relevance.
Clock is not a dictator
As much as the circadian clock is "hard-wired" in the brain and determined by the clock-work of genes turning each other on and off, there is still quite a lot of plasticity of behavior - animals can act against the signals from the clock and do stuff at odd times if needed.
For example, when hungry, nocturnal animals will hunt during the day, e.g., man-eating lions hunting at dusk and early night on moon-less night, have to hunt during the day when the moon is full.
Also, these days bats in Austin, TX are flying out earlier at dusk due to prolonged dry weather conditions decimating their food.
Two species of golden spiny mice in Israel live in the same spot - one of them is more aggressive, so the other one has evolved adaptations (including even changes in the eyes) to forage during the day instead of night. Yet, when placed in isolation in the lab, both species are strictly nocturnal, active only at night, which shows that day-time foraging goes against the clock, i.e., is not the adaptation of the clock itself .
Finally, when population of rats in a city gets too big, some individuals are displaced. They are displaced in space - foraging on the surface instead of underground - and they are displaced in time - foraging during the day instead of during the night. If you see a rat digging through the garbage bags on the street in the middle of the day, you know that the total population of rats under ground is absolutely enormous! If you are interested in learning more about the fascinating ecology of urban rats, read the wonderful book 'Rats' by Robert Sullivan.
Light at night, clocks and the outside world - behavior
One of the adaptive functions of having a clock is to synchronize one's activities to that of other players in the ecosystem . You want to go out hunting at the time when your prey is out and about and easy to catch. You want to hide (and sleep) while your predators and enemies are out on the prowl.
But what happens when the difference in the intensity of light is not very different between day and night, as in well illuminated cities? Some species will remain nicely entrained to the cycle, but others will not. Some individuals will be better entrained than others. Some will have their clocks reset over and over again and they will behave at different odd times each day, while in others all rhythms will get lost and they will be out and about all the time.
Thus, many individuals will be going about their lives at inappropriate times, perhaps when the predators are around (and predators are doing the same - one or another will be hunting at any time of day or night), or when the prey is hiding (so too much energy is wasted in looking for elusive food). As a result, many individuals will starve, or get eaten, or miss reproductive opportunities (hey, where are all the potential mates - why are they all hiding and sleeping at the time I am looking for them everywhere?).
Living in an environment in which is is hard to tell if it is day or night is similar to living without having a circadian clock at all. A couple of studies out in the field [5,6,7], with a couple of different species of rodents in which the clocks have been surgically removed from their brains, showed that such animals wonder around at unusual times and are significantly more prone to predation (this is a scientific way of saying: "they got slaughtered by wild cats within hours").
Light at night, clock and the inside world - physiology
Another adaptive function of the clock is to synchronize events happening inside the bodies, both with each other and with the outside environment. It saves energy if two compatible functions in the body happen simultaneously, while incompatible events are happening at different times. By tuning into the outside cycles of light and dark, the body allocates different biochemical and physiological functions to different times of day, thus saving energy for the animal overall.
And energy is the key. At the time when food is around, it pays to invest energy in finding it. At times when food is hard to find, it is a good idea to use less energy, to stop, hide and sleep. The rate of energy production and use by the body - the metabolism - can be measured in warm-blooded animals (the 'euthermic' animals like birds and mammals) by measuring their core body temperature. Higher the metabolism, higher the temperature.
Normally, body temperature cycles throughout the day. Circadian clock drives this cycle so, for example, our bodies are coldest at dawn, and warmest in late afternoon. In birds the difference between the low and high point during the day is routinely a whole degree Celsius. And some small birds, like swifts and hummingbirds, let their temperature drop much, much more during the night (this is called "daily torpor").
Having or not having food affects how much the body temperature will drop during the night. A hungry animal will save energy by dropping body temperature at night much more than a satiated animal . Yet, temperature will rise to its normal levels the next day in order to give the animal sufficient energy (and speed of reaction) to successfully forage again.
Light affects this: if there is no difference in light intensity between day and night, e.g., in the laboratory in constant darkness, both daytime and nighttime temperatures will fall in hungry animals  - they would become too slow and feeble to forage effectively if out in the field. But constant light has the opposite effect - keeping the body temperature artificially high at all times, i.e., not allowing the hungry animal to save energy by dropping its body temperature. The energy balance, especially in a small animal, can quickly become negative, leading to death of starvation.
Light at night, clock and reproduction
In many birds, length of day affects egg-laying in a way that helps the animal determine the total size of the clutch of eggs: how many she lays in one breeding attempt (usually one per year). Data from the laboratory (in chicken, quail and turkeys) [9,10] and from the field (bluebirds , also swallows and owls - unpublished data) suggests that this is a widespread mechanism in a variety of bird species.
If the difference between light intensities at day and night is too small for the bird's brain to integrate, the bird may be making too much of a breeding effort - laying too many eggs over a period of too many days, perhaps even throughout the year, thus exhausting her internal energy resources, while bringing too many hatchlings to life while unable to feed them all...a disaster all around.
Light at night, clock and calendar
There is a reason for the season. Many organisms do certain things at particular times of the year; breeding, molting, migration and more. The internal "calendar" they use to time such changes in behavior is dependent on the circadian clock which measures the gradually changing length of day throughout the year. The precision of such a measurement can be quite astonishing (see swallows of San Capistrano) .
So, what happens if there is not much of a difference between daytime and nighttime illumination? The clock interprets this as constant light, which is the ultimate "long day", so the animal will constantly be in the "summer mode", e.g.,. constantly breeding, or constantly trying to migrate or constantly molting its feathers or hair. All of this is energetically costly, and thus maladaptive, and will lead to exhaustion and eventual death of the animal (that is on top of not being in synchrony with other individuals of its species, see above).
Light at night, clock and orientation
When a moth wakes up in the evening and starts flying to find food, it orients by the Moon. It assumes a constant angle to the Moon and keeping that angle allows it to fly in a straight line. After all, the Moon is high and very far away, so flying along does not change the Moon's relative position in the sky. This is called "transverse" or "Y-axis" orientation.
But the Moon moves across the sky during the night. If a moth is flying for a longer time, it will use its internal clock to compensate for this movement by gradually changing the angle.
What if, instead of the Moon, the moth sees another bright light, perhaps the one on your porch? It starts using it for orientation. At first, it will fly in the straight line. But as it comes closer to the light, the angle changes - the light "moves" in relation to the moth. So the moth compensates by turning in order to keep the constant angle. And then it turns again, and again, and again, spiraling in until it hits the light itself. By that time the light is so close and so bright it looks more like the Sun than the Moon. Its clock gets reset to "day". So the nocturnal moth alights nearby and, instead of foraging for food, falls asleep. In a wrong place, where it is an easy pick for predators - bats at night, birds at dawn [13,14,15,16].
Birds also orient by celestial bodies. During the day, they orient by the Sun. Again, they use their internal clocks to compensate for the Sun's movement across the sky. At night, they may use the Moon for orienting, but they certainly use the stars . All the artificial lights become stars. Birds get disoriented, fly in all the wrong directions, and hit the windows and die.
What to do?
This post is really NOT about the solutions, but rather about the underlying science of light effects on animal behavior, physiology and health. I will leave the solutions to others who are experts on engineering or urban policy, who may use the science described above to get informed as to what kinds of solutions may work best.
From what I know, many cities are now starting to tackle the problem of light pollution. Sky lights are banned in some places or at some times of the year (e.g., times of big bird migrations). Many tall corporate buildings now instruct their tenants to turn off the lights at night. There are new designs of street lights that point down - the street below is illuminated even better, much much less light (and diffused, not pointed) goes up to the sky wasting energy and confusing the critters flying by. I am sure there are other things that people do, or things that can be done to reduce the amount of light, or at least the appearance of light sources as "points", that can be adopted by cities worldwide.
We will never make the cities completely dark at night. And that is OK. After all, the Moon and the stars make nights quite bright out in the wilderness as well. All we need is to make sure that the difference in light intensity between day and night is sufficient for animals to entrain their clocks properly to the daily cycle of bright-light and not-as-bright-light, and they should be fine.
 Lee, D.S. (1969). Possible circadian rhythm in the cave salamander Haideotriton wallacei. Bull.Maryland Herp.Soc. 5:85-88.
 Trajano, E. and Menna-Barreto, L. (2000). Locomotor activity rhythms in cave catfishes, genus Taunayia, from Eastern Brazil (Teleostei: Siluriformes: Heptapterinae). Biol.Rhythm Res. 31:469-480.
 Kronfeld-Schor, N., Dayan, T., Elvert, R., Haim, A., Zisapel, N. and Heldmaier, G. (2001). On the use of time axis for ecological separation: Diel rhythms as an evolutionary constraint. Amer.Nat.158:451-457.
 Fleury, F., Allemand, R., Vavre, F., Fouillet, P. and Bouletrau, M. (2000). Adaptive significance of a circadian clock: temporal segregation of activities reduces intrinsic competitive inferiority in Drosophila parasitoids. Proc.R.Soc.Lond.B 267:1005-1010.
 DeCoursey, P.J., Krulas, J.R., Mele, G. and Holley, D.C. (1997). Circadian performance of Suprachiasmatic nuclei (SCN)-lesioned antelope ground squirrels in a desert enclosure. Physiol.&Behav. 62:1099-1108.
 DeCoursey, P.J. and Krulas J.R. (1998). Behavior of SCN-lesioned chipmunks in natural habitat: a pilot study. J.Biol.Rhythms 13:229-244.
 DeCoursey, P.J., Walker, J.K. and Smith, S.A. (2000). A circadian pacemaker in free-living chipmunks: essential for survival? J.Comp.Physiol.A 186:169-180.
 Herbert Underwood, Christopher T. Steele and Bora Zivkovic, Effects of Fasting on the Circadian Body Temperature Rhythm of Japanese Quail, Physiology & Behavior, Vol. 66, No. 1, pp. 137-143, 1999
 Zivkovic BD, Underwood H, Siopes T., Circadian ovulatory rhythms in Japanese quail: role of ocular and extraocular pacemakers, J Biol Rhythms. 2000 Apr;15(2):172-83.
 Zivkovic, B.D., C.T.Steele, H.Underwood and T.Siopes. Critical Photoperiod and Reproduction in Female Japanese Quail: Role of Eyes and Pineal. American Zoologist 2000, 40(6):1273 (abstract).
 Caren B. Cooper, Margaret A. Voss, and Bora Zivkovic, Extended Laying Interval of Ultimate Eggs of the Eastern Bluebird, The Condor Nov 2009: Vol. 111, Issue 4, pg(s) 752-755 doi: 10.1525/cond.2009.090061
 BD Zivkovic, H Underwood, CT Steele, K Edmonds, Formal Properties of the Circadian and Photoperiodic Systems of Japanese Quail: Phase Response Curve and Effects of T-Cycles, Journal of Biological Rhythms, Vol. 14, No. 5, 378-390 (1999)
 Kenneth D. Frank, Impact of Outdoor Lighting on Moths: An Assessment, Journal of the Lepidopterists’ Society 42 (no. 2, 1988): 63-93.
 Sotthibandhu, S. & Baker, R.R. (1979). Celestial orientation by the Large Yellow Underwing Moth, Noctua pronuba L. Anim. Behav., 27, 786-800.
 Baker, R.R. (1979). Celestial and light trap orientation of moths. Antenna, 3, 44-45.
 Baker, R.R. & Sadovy, Y.J. (1978). The distance and nature of the light-trap response of moths. Nature, Lond., 276, 818-821.
 Sauer, E.G.F. and E.M.Sauer, 1960. Star Navigation of Nocturnal Migrating Birds. In Cold Spring Harbor Symposia on Quantitative Biology, Vol. 25. pp.463-473.
Images: U.S. light pollution map: NOAA; San Francisco at night, by Thomas Hawk on Flickr (part of the Ligh pollution Flickr collection); Moth attracted by porchlight from Wikimedia Commons. The rest of the images are drawn by me, including from my papers (the original raw files, not copied from final PDFs).