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Civilian GPS units are often not particularly accurate, especially older or cheaper models. Sometimes accuracy to 56 feet under optimum conditions just doesn't cut it, say, if you're mountaineering in the clouds and 56 feet is the difference between a cliff and a gully. Furthermore, GPS units cannot get decent coverage in a huge variety of conditions, from densely packed forests to deep valleys to the lobbies of buildings.
GPS units are steadily improving, however; as better techniques are developed for both receiving satellite signals and adjusting for error.
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GPS units also take a few moments to triangulate their position, which may not be fast enough for a pilot relying on an airplane GPS unit. This latency is mostly caused by the time it take for signals to go from (near) the Earth's surface all the way up to the GPS satellites and back again. That is a rather long distance. Indeed, the difference in signal reception is part of how GPS units work! Obviously, there's no way to cut down on the distance between the GPS units and the satellites, nor a way for the signal to move faster than the speed of light, so there's really not much to be done on this front.
Some latency is caused by a slow CPU within the GPS unit. This is improving along with processors technology, so expect a (slightly) faster lock on your signal.
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The satellite network that GPS depends on is beginning to break down. They're old, after all, and the US Air Force simply hasn't been investing capital in this system for a while now. They won't be breaking down all at once, and there's enough discussion within the government to fix this problem that likely something is going to be done about it.
Other countries are dreaming up GPS systems of their own, everyone from India to the EU. This will provide for greater options and flexibility, as the proliferation of GPS will bring about competition which will in turn bring about better performance. But by the same token, many people falsely believe that each GPS system put into place will be compatible, allowing for superb accuracy.
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The cases are starting to trickle in: accidents caused by car GPS units. Well, not directly caused by them, but by people depending on their GPS unit so much to guide them that they end up driving down dangerous roads, pedestrian-clogged residential districts, and even over cliffs, things marked on the GPS maps that really aren't suited for driving. People are losing the ability to use their own common sense in navigation and often can't tell for themselves how to tell that the device is giving them bad advice.
While GPS units are improving in leaps and bounds with regards to how good their maps are, the problem of potential over dependence remains, and looks to continue on as GPS navigation becomes ever more ingrained in our daily lives.
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Tracking and Privacy Issues
One of the most powerful and controversial uses of GPS units is for tracking people and their things, from cell phones to cars. While this can help you get your stolen stuff back or track down a kidnapped child, it can just as easily allow someone to stalk you from afar. The US and other governments already uses the GPS system for many questionable purposes, from warrantless tracking of cars to personal tracking GPS units for sex offenders. While many of these uses have good intentions, there are those who argue that the ends here do not justify the means if the means is such a deep invasion of privacy.
There are many civil rights organizations that are constantly in the courts challenging many of these uses of GPS units and fighting for privacy rights, in addition to trying to rouse the general public to these threats. So, Big Brother might not be looking over your shoulder too closely in the future, or at least not with GPS.