At present two ways come to my mind- if the outcomes of education have been scoped down to scientific literacy, this can be evaluated by -

1. Ethnographic study- prolonged interaction and observation with the students, followed by thick rich description. During analysis, the aspects will come up.

2. Control group experiments (or type of group activities) can be conducted and their discussions, outcome of activity can be reported.

Is the purpose to research the issue for yourself or to develop methodologies for assessing the students?

My purpose of research is to examine secondary school students' scientific literacy levels longitudinally (for 3 years). I would like to use mixed methods. In literature there are lots of scales about it, so I can use one of them. However in qualitative method section I don't know what to do.

Ankur Joshi and Paulo Matos Graça Ramos thank you for your suggestions...

you can have a pre-post method and see how much they are improving. It means students are challenged to answer some question (it can be questionnaire that makes your study quantitative) or it can be interview or open ended questions that make your study qualitative!

I hope it helps.

I have some colleagues that have used mixed methods in science education studies. We have discussed this extensively. One way is to use project based group science problems and tape/video record their processes (pre and post). After they have completed the science problem/project, you can do a follow up interview to ask them to about what they did to solve the problem and why.

You can then use discourse analysis. By having them work in groups, you would be able to get a better idea of the language they are using and their understanding of the science concepts. You can also use linguistic analysis (quantitative) to identify patterns of interaction/vocabulary use. There is a lot of literature in the science education journals on the use of language in assessing science literacy.

Have you considered self-reported data from the students expect from using think-aloud protocols in followed interviews, to use textual comments of theirs in a progressive scheme i.e. a diary? when you are reffering to scientific literacy..  which skills-set exactly  are you aiming to evaluate?  

The issue is not getting clear. Quantitative measurement of scientific literacy or comparing scientific literacy of one nation with other, If someone can suggest scientific articles or any book, will be highly appreciated.

Ahsan Beetay, Brilliant answer. Actually, I have proposed a study to evaluate scientific literacy of Ras Al Khaimah, Emirates region and then extend to the Arab World. If anyone has sample questionnaire, would love to see that. So pleased to see answer from the IUB.