I saw a gang of flies kill a man! All that was left was a skeleton... —JesseSingh
I've been told that they do us no harm. Is this true? —JosephBleckman

The fall of 2005 brought incomparable pestilence upon the citizens of the fair town of Davis. Wave after wave of flies poured down upon us all. Freshmen cringed as they were besieged with whole clouds of critters that sought to land upon their flesh. Upperclassmen across campus often would too remark in surprise and disgust at this new found scourge. In the hearts of everyone dwelt one question... Why?

The pat (and unsatisfying) answer from a source in the Entomology department is that there is always an increase in flies around this time of the year, due to an abundance of dying organic material (like tomatoes) being left in fields in surrounding areas. The flies breed in the organic material, and, presumably, fly off to Davis to annoy you during lunch. This answer, while plausible, ignores the claims of several long-term Davis residents that the flies haven't been this bad in decades.

The Entomology department source denies that West Nile Virus (more specifically, the attendant death of birds) is responsible.

Aggie answer: blah blah blah weather.

Some suggest that the flies signify the coming of the Devil, or some other sort of biblical plague.

The new trash cans promulgated by Davis Waste Removal may also be to blame. The trash folks often ignore bags piled next to trash cans, creating a breeding ground. Also, sometimes random trash will fly out and land on the street when the mechanical arm rockets the trash can into the "refuse" end of the trash truck.

Fly Biology

The flies, proper, are all members of the order Diptera, meaning "two wings". This group does not include the whiteflies, mayflies or other insects which have four wings, and are members of other orders. The true flies, actually do have four wings, but the hind pair have been reduced into a pair of drumstick shaped stubs, which serve as stabilizers which help a fly to maintain direction during flight. This, along with the numerous sensory hairs and the large compound eyes on their head, is why it is incredibly difficult to kill a fly; flies are among the most agile fliers in the insect world, probably only beaten by dragonflies. Flies all develop from maggots (or wrigglers, in the case of mosquitoes), which then pupate. From the pupa, emerge the adults.

More so than probably any other insect, the flies are responsible for transmitting illness. Besides the global threat of mosquitoes, House Flies, (Muscus domesticus) can transmit many pathogens, in particular, those which can cause diarrhea or other gastrointestinal illness. The old name of the house fly used be the typhoid fly. Although the house fly is only a great danger to human health in areas with outhouses, it's still good to keep in mind that the flies still lay their eggs and feed in waste. Under certain uncommon conditions, myiasis can occurs, where maggots infest human flesh. Botflies and Warble flies, (Oestristrids) can pose problems for livestock when their maggots infest cows, horses, sheep or other animals, and cause injury.

However, flies aren't all bad. Myiasis can be beneficial, in the case of maggot therapy. The "sterile" maggots used for such treatment only eat dead flesh, and can clean a complex wound (like a messy shotgun round). Some flies and their maggots are natural enemies of plant pests (Like the Syrphids, or hover flies). Lastly, in the ecological sense, flies and their maggots are part of the overall decomposition process. Calliphorid flies, also known as blow flies, or bottle flies, are the bright green and blue iridescent flies commonly found hovering near roadkill or feces. They have keen senses, and are generally the first to find a freshly killed animal, including a human corpse. As a result, the larval stage of calliphorid larva found on a corpse is highly significant to determining the time of death for a victim, and is very useful to the forensic entomologist.

How to deal with them

First off, make sure you've got your garbage and other stuff sealed off properly and that there's no doors or windows open in your house. Of of the main elements of pest control is to limit access to food, and in this case, ovoposition sites. Otherwise, the flies are just going to keep coming in! The screen door and window were first made to prevent the House Fly from entering the home.

Aside from ignoring them, the other option is to try and kill them or get them out of your house. Everybody knows how to use a fly swatter, but it's certainly a lot of work for a lot of flies. "Fly paper" works only if the flies are concentrated in one location or continue to move through a particular location. If the flies are just all over, they have no incentive to sit down on the fly paper. Most fly papers are unscented so the flies have no reason to go to them outright.

Raid or some other toxic spray works well to immobilize large groups of flies, but it requires you to spray in potentially bad places in your house. Also, sprays don't attract flies.

The best indoor solution for flies is probably a Fly Light — a special kind of light that attracts flies and traps them. You can also just turn off your lights and open the doors, and they'll eventually fly out.

Outdoors, further away from your house, a fly zapper might be an acceptable way to deal with a continual fly problem. Keep in mind fly zappers don't just kill the flies, but also make them explode. This means a blast radius of chitin and viscera, likely infested with all sorts of unpleasant germs.