To start things off, Amy's profession is not taken seriously. She has a PhD in neurobiology, with a research focus on addiction in primates and invertebrates. According to a study published in Neuroscience & Behavioral Reviews, the study of addiction in invertebrates is a legitimate science, but other characters (Sheldon in particular) fail to see it as such.
Her profession takes a major backseat to her developing relationship with Sheldon. It is there almost as a plot device that allows her to be part of the series. On the University of Minnesota's Feminist Film Studies Spring 2015 blog, a writer using the handle zheng556 explores Amy's profession in depth as it relates to the rest of The Big Bang Theory, rightfully observing that Amy's work is overshadowed and ignored. When she is given a big career break (an invitation to consult on a project at Caltech), the episode focuses mainly on Sheldon's reaction and its impact on their relationship. The article excuses the series' creators somewhat, saying that as a comedy, the show is not expected to address the issues of underrepresentation and obstacles in the workplace for women, but as we have seen in our series on media depiction of women in STEM, these subtle hindrances to character development add up to a greater whole that does not depict women in STEM at their fullest potential. Representation in television series and movies are tremendously important to changing the way we view women in STEM.
Amy is eventually transferred to Caltech, but Sheldon embarrasses her while she lunches with influential and established scientists. Later, he describes her work as "goofing off." Amy's work is depicted as lacking the rigour of actual scientific experimentation.