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Malformed Frogs
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This activity (on page 2 of the PDF under SciGirls Activity: Malformed Frogs) is a full inquiry investigation into using indicator species to assess the health of an environment.

Destination Tidepool
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In this activity (page 7 of pdf), learners research tide pool ecosystems, and then create brochures that "advertise" these environments.
Butterflies in Space
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The Butterflies in Space Teacher's Guide uses "life in space" to encourage learners to conduct their own open-ended scientific investigations.