The adage “seeing is believing” has relevance in biology as evidenced by years of Nobel prizes awarded to scientists who contributed advances to microscopy and other imaging modalities. Whether Magnetic Resonance Imaging, light microscopy, electron microscopy, or X-ray crystallography, these technologies have given us new views of ourselves beyond sensory capacities and opened new possibilities to explore and understand nature herself. As Marty Chalfie stated in his 2008 Nobel Prize address: “Scientific inquiry starts with observation; the more we can see, the more we can investigate”. Chalfie’s introduction of Green Fluorescent Protein as a method to probe the molecular machinery of organismal and cellular biology has had an enormous impact on what we can observe in living tissue. Today’s advanced microscopes and visualization techniques are providing unprecedented opportunity to observe and describe all the molecular constituents of an organism. Yet, if a large number of proteins are present in the cell, viewing them individually becomes a challenge on the sheer multitude; how do our limited minds remember each localization pattern in relation to each other and not let our expectations of the data bias our view of these patterns?
Documenting and analyzing complex systems is being addressed in the field of genomics/systems biology where methods of recording our visual experiences involve a systematic analysis using formalized language that further allows quantitative comparisons between subjects. This method has been a boon to the analysis of RNA interference phenotypes and phenotypic differences in nematode species, and it seems only logical to employ this method for localization patterns. Foremost, such methods have only yet been employed in single cells. For multicellular organisms systematic analysis of localization is terra incognita. In my thesis, I apply these methods to the most basic and fundamental model of multicellularity, early embryogenesis of the nematode worm, C. elegans.