Producing new knowledge and inventions is an exciting journey that every researcher embarks upon and invests their time and energy into. However, emerging researchers and learners often lack scientific inquiry skills, particularly the skills to identify important research questions and design the responses starting from fundamental knowledge to progressively complex critical thinking. The objective of this review is to offer suggestions on how to close the learning deficiencies in scientific inquiry skills occasionally overlooked by some university faculty that impede budding researchers from effectively conducting research. Practical ways to formulate research objectives building from fundamental knowledge to advanced critical thinking skills have been suggested with the help of Bloom's taxonomy and applied to some tools used in geological research. Also, the scheme of intellectual and ethical development, reflective judgment model, and steps on better thinking have been briefly reviewed to present tools for the assessment of the researcher's learning progress. The suggested tools, data types, and objectives posed in this paper are not meant to be comprehensive but initiate a conversation in the interest of the incipient researchers and to stimulate their minds on designing and conducting research.