[highlight color="blue"]Question: In the double slit experiment what is it about observation that changes the way the molecules behave? Is it the simple act of observation or a disruption from the observation equipment?[/highlight]
That experiment is one example of the observer effect. Anytime measuring (or observing) something causes a change in the original state, this is called the observer effect. Though we do have this problem in the double slit experiment, quantum mechanics is not the only place it shows up.
Outside of the context of the double slit experiment, both the equipment and the observation could change the original state to be measured. An easy example of equipment interfering is a thermometer. The mere presence of a thermometer will either raise or lower the heat of whatever you are trying to measure.
What About the Experiment Itself?
The equipment certainly has the possibility of causing the observer effect, but even if the equipment were perfect, we would still have the same problem. I once heard an excellent analogy that does a good job of explaining the principle. It goes as follows:
"Imagine that you're blind and over time you've developed a technique for determining how far away an object is by throwing a medicine ball at it. If you throw your medicine ball at a nearby stool, the ball will return quickly, and you'll know that it's close. If you throw the ball at something across the street from you, it'll take longer to return, and you'll know that the object is far away."
"The problem is that when you throw a ball -- especially a heavy one like a medicine ball -- at something like a stool, the ball will knock the stool across the room and may even have enough momentum to bounce back. You can say where the stool was, but not where it is now. What's more, you could calculate the velocity of the stool after you hit it with the ball, but you have no idea what its velocity was before you hit it.”
[Reference: How Stuff Works]
Where Things Get Tricky:
When we start working with very small amounts of energy, we notice a problem: light, the means by which we observe most things, is itself powerful enough to completely change what is going on. So light would be the medicine ball in the analogy. It is energetic enough to cause significant changes on a quantum scale.
Any attempt to measure something on the quantum scale will invariably result in altering what you were trying to measure at the start. Sometimes, this isn’t that big of a problem, but then again, sometimes it is (as seen in the double slit experiment). To be clear, having observed something doesn’t change anything, but the nature of how something is observed is what is causing the observer effect.
So in short, the equipment we use is perfectly capable of distorting our results, but we can expect a baseline of error simply by observing it in the first place.