My ninth-grade students are struggling with lab activities. For example, they don’t seem to know how to formulate a hypothesis or write a conclusion. When I asked them to graph the data, I saw lots of blank looks on their faces. What can I do?
—Jeff, Baltimore, Maryland
Your question brings back memories. When I started teaching, I was excited about doing inquiry-based investigations. However my middle school students were similar to yours in their understanding of hypotheses and graphing. They were also confused about observations and inferences, and their conclusions were simply summaries of their observations. I did a lot of reflecting: Am I expecting too much of middle school students? Are my students academically clueless? Are they unmotivated? Are my explanations and guidance insufficient? Am I hopeless as a teacher?
At the secondary level, it’s common for teachers to expect students to be experienced in essential science skills: questioning, observing, summarizing, formulating hypotheses, drawing conclusions, notetaking, graphing, and solving problems. If students do not measure up to these expectations, some are quick to blame the teachers in the earlier grades. So high school teachers question the middle school program, middle school teachers question the elementary program, and we all point at parents. Yet when students walk through our classroom doors, we have to take them as they are. It’s our role to set appropriate and challenging learning goals, and then work with students to meet the goals.
In situations such as you describe, it could be that in earlier grades the students did cookbook activities where the procedures were already determined and the data tables already set up. Perhaps their teachers used different vocabulary (e.g., “wrap-up” instead of summary). The equipment they used, such as balances or microscopes, may have looked different. They may have learned skills in isolation with few opportunities to apply the skills in new situations. Students moving into the school may have had different experiences in their former schools.

Once you have determined what skills your students need to develop, you can begin to “scaffold” their learning in three stages: focused instruction with examples, guided practice in a variety of contexts, followed by opportunities to choose and use the skills independently (even if they make a few mistakes).  I observed a teacher doing a “think-aloud” as she modeled how to graph data from an investigation. As she talked through the process, she showed students how to set up the graph and add data points, but it was a not a lecture. She asked herself questions and deliberately made some mistakes (and corrected them). It was as if the students could peek inside her mind as she worked through the process. When she paused in her thinking, the students volunteered their own suggestions. In the second part of the investigation, the students worked in groups to create similar graphs as the teacher monitored each group and offered suggestions and feedback.
Guiding questions, prompts, and templates can also help students focus their thinking.  For hypotheses, the template If [I do this], then  [this]  will happen can show students that a hypothesis is not just a guess. LabWrite from North Carolina State University has templates and resources for each part of an investigation. The site would probably be overwhelming for ninth graders, but it could be a valuable resource as you divide lab reporting into manageable chunks to introduce to your students. Create A Graph from the National Center for Education Statistics  is a student-friendly online tool for designing several common types of graphs. The finished graphs can be saved for additional editing, printed, or downloaded (as PDF files).
Processes or templates appropriate in younger grades may need to be “kicked up a notch” in the upper grades. For example, in the younger grades notetaking may focus on particular strategies, while at the upper grades, modeling how different strategies are appropriate for different tasks may be helpful to students. If you can project a copy of a text page, you can model how you would decide what to highlight and how you would add margin notes or questions.
Ask students to describe and reflect on their learning in science notebooks, they’ll have a record of what they did to meet the learning goals. This can be the foundation for new skills in their next course.
Graph: http://www.sciencenotebooks.org/student_work/