First Observation:

The Scientific Method is not really a set of steps to answer a question, though it is often useful to think of it that way.  The steps we identify in the Scientific Method are our way of making the cyclical and complex process of Scientific Thought simple enough to be able to see the bigger picture pattern; like a topographical map, it gives you the general lay of the land.  The question is actually part of the process and ,while specific questions may be answered, many more questions are usually created.

So where does it really begin?  Many sources begin the process with a question.  "Ask/Identify A Question"  But this is not how Scientific Thought really begins.  Scientists don't invent questions to answer.  They see something; think about it, want to know more, wonder if ... 

The process of scientific thought begins with observations that the observer can't totally reconcile with current knowledge.  This tension creates the curiosity to do something.  The first something to occur is the formation of a question.  That is why it shows up at the beginning of the Scientific Method, because it is the first thing you can do.  But why isn't the first step to observe?  Well, I say it is...

The evolution of a question:

In the Ohio River Fresh Water Mussels were in significant decline

It was shown that wastewater treatment processes do not break down some pharmaceuticals (Aspirin was the first to be discovered)

• What pharmaceuticals might be in the Ohio River from the myriad wastewater treatment plants along it and it's tributaries?

Researchers in the mid West identified trace amounts of Prozac, and 22 other pharmaceuticals in the water and sediments of the Ohio River

• Does a trace amount of Prozac impact the survival of Fresh Water Mussels?

Researchers discovered trace levels Prozac consistently caused female Fresh Water Mussels to release larvae too immature to survive.  

I did not know the Fresh Water Mussels were in decline in the Ohio River and its tributaries, but I did know they were in decline in Lake Champlain.  It wasn't until they discovered pharms in the Ohio River that I became aware of the issue.  By then, scientists knew some pharms were not being broken down, and that there were measurable amounts of them in the water and sediments of the Ohio River.  The research on the effects of Prozac on Fresh Water Mussels was already underway, though no results were available yet.

The population of Fresh Water Mussels in Lake Champlain appear to be in significant decline

Turbidity, general pollution and invasive species, most notably the zebra mussel, are identified causes

Now I wanted to know...

• What pharmaceuticals might be in Lake Champlain from the wastewater treatment plants on the lake and it's tributaries?

• Does the water and sediments in areas of Lake Champlain have sufficient levels of Prozac to effect the Fresh Water Mussel population?

• Can a similar chemical be used to control zebra mussels in infested area of the lake?

See?  I didn't just make these questions up out of thin air!  I had data, observations and many others' questions before mine.  This is the stuff of Background Research.

Now we have to narrow our question down to something we can test.  The first question seems testable, but really it needs to be refined  because we can't possibly test every pharm in the world, and detecting the prescence of a substance is different than measuring the concentration.  Do we want to look at just prozac, or the top 10 most likely drugs, or a certain class of pharms, such as seratonin uptake inhibitors?  Are we testing water near tributaries, sediments, or zebra mussels for the drugs?  More information is needed to design the experiement.  What kind of containers should be used?  Do the samples require special preservation or handling?  How are we going to detect trace amounts?  How sensitive do our measurements need to be to confirm the prescence of a substance?  Has anything like this been done before on Lake Champlain?  How did they do it on the Ohio River?

Wow! So many answers needed just to ask a single question!  All of the information you look up to help you narrow your question down and design your experiment is also Background Research.