We last left Superhero PhD and her troop of Superhero TAs in a morass of educational glitches…
The semester had not gotten off to a smooth start. Surely this trend would change, but there was no data indicating otherwise. Then, there was a glimmer of hope. The powers that be in the department had pity on our hero’s plight and found a way to pay for a new ice machine in her teaching lab. Without hesitation, she calls the refrigeration company and orders a replacement. It is installed as the molecular biology segment of the semester is ending. Now that the traditional biochemistry experiments are set to begin, the students can be properly trained to be Fast. And. Cold. “Now, if only the hefty charge on the university-issued procurement card will clear without holding me personally liable,” thinks Superhero PhD.*
It was a great victory, but not a sign that the fortune was changing for our heroes. Meanwhile, back at the lair, a problem was waiting in Superhero PhD’s mailbox. Superhero PhD rarely checks her mailbox as it is never filled with anything of great importance, only local store ads and unwanted credit card offers. This week an official envelope is there summoning Superhero PhD to jury duty the week of midterms and that changing of the guard from Superhero TAs #1 and #2 to Superhero TAs #3 and #4. “Noooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo!” she yells shaking her fist at the sky frightening Junior PhD. Canis familiaris even howls along with her gut-wrenching cry. She composes herself as she remembers, “It’s a government agency. There’s always fine print. A way out.” She is in luck. She is within 24 hours of the deadline to fax over a postponement request to the clerk. She quickly pens the numerous specific reasons why the 19th Judicial District would have to wait until the semester break to conscript Superhero PhD into service. She calls a few hours after it has been faxed away. Success! The Clerk of Court has heard Superhero PhD’s pleas and had mercy. Her service is postponed until the semester break.
Superhero TA #4 was diligently preparing the experiments he would lead for the first time this semester, and something was terribly wrong. The first enzyme inhibition lab exercise is not matching the data in the TA Manual. There’s no inhibition. Superhero PhD invokes her first rule of biochemical troubleshooting, “Make everything fresh and repeat.” Superhero TA #4 also follows this rule with no success, and it is time to invoke the next rule, “Order new reagents, make everything fresh and repeat.” “It’s still not working.” reports Superhero TA #4. “Now it’s time to put out the ‘PhD Signal’.” Superhero PhD states. E-mails are sent to Retired Instructor and Recently-Graduated-Former-Superhero-TA detailing the problem and our futile attempts at troubleshooting. What critical step was being overlooked? Was this merely another revolt of the Teaching Lab to its new master? Over the next week, everyone tried their hand at the troublesome inhibition with no luck. A remarkably detailed e-mail outlining the experiment’s execution from Recently-Graduated-Former-Superhero-TA arrived in Superhero PhD’s inbox, but it did not illuminate any significant differences in our attempts. Late one afternoon, Superhero PhD enters the Teaching Lab only to find Retired Instructor herself performing the vexing inhibition assays. Alas, she is also unsuccessful. Inhibition could not be observed by anyone, with any reagents, nor any enzyme, nay even preparations previously showing inhibition. It is a defeat, but the lab must go on.
After midterms, the students realize that they should come to see Superhero PhD in her office. There she answers the lingering questions they had but did not ask during class. She illustrates biochemical concepts on the newly-hung white board. She calculates ways for them to improve their letter grades with the remaining graded activities. They seem to be calmed. Yet, Superhero PhD soon learns that the vast majority of students are poor project managers, relying on short bursts of intense cramming rather than steady attention to the course and its assignments. Much of their misery is of their own making. Superhero PhD also occasionally sends out e-mails with important information. It is clear that some of the students do not read them; they are unprepared for scheduling changes, oblivious to related content for exams and unaware of upcoming important dates. Superhero PhD is beginning to think that Moodle mail uses some unfortunate translation tool after she hits the ‘send’ button that rewords her carefully crafted e-mails into “Blah, blah, blah, important date, blah, blah, blah, exam info…” but she has no time to take this up with IT services.
On report due dates, Superhero PhD sighs, “Less than an hour before the listed deadline and still half of the students have yet to click the submit button, and five submitted in the last five minutes.” She muses this is not so different from real science and grant deadlines. A briefly evil thoughts cross her mind as to how to change the course to better prepare her students for a career in professional science. Of the reports submitted 10% would be sent back with no grade at all because of formatting issues, 80% would be reviewed favorably but still not receive a passing grade because of the few available to go around, and the final 10% would be both favorably graded and receive A’s. In the lab, exercises would be graded as follows: the first group to finish collecting data for the day and write it up in their notebook would receive an A (the equivalent of publishing findings first in a decent journal), second place would receive a C (because good 2nd place research could probably be dumped into some lower tier journal) and everyone else will fail. Of course, some of the later finishing groups could decide to hold onto their work, opting to file for a patent thereby subverting the advancement of the work of the 1st and 2nd place finishing groups in the future. These patent-holders would then get a guaranteed A for the course. Then Superhero PhD remembers, it’s only an undergraduate course, “They can figure out how science really works after they graduate.” Plus, this alternative system would surely negatively affect instructor evaluations at the end of the semester.
Troubles continue to plague the experiments entrusted to Superhero TAs #3 and #4. At the conclusion of the protein purification exercises, the students subject their purified enzyme to dialysis so that it will be in the most appropriate buffer for the subsequent enzymatic activity assays. This experiment takes a significant amount of time, so care must be taken to be cold. Unfortunately, the deli-cooler cold box in the lab used for this purpose died the day before Superhero PhD assumer her new role as Instructor because of course it did. Other departmental cold rooms were available, but these were less conveniently located and the buffer contained a foul-smelling reagent that would preferably be contained in a smaller space. Superhero TA #4 offers the cold box in his lab. Unbeknownst to him, the required stir plate had recently started malfunctioning such that when the necessary stirring function was initiated, so was the heating element. By the time the Superhero TAs retrieved the students’ precious enzyme samples, the solution was boiling. The first rule of biochemistry had been violated in horrific fashion. Superhero PhD and the Superhero TAs could only stare in shock at the dialysis bags containing the students’ boiled protein, looking like scrambled eggs and utterly ruined for future activity experiments. Superhero TA #3 offers, “There’s still a ton of enzyme from our previous preps and the other half of their precipitated sample for a different experiment. We could just divide that up among the groups for them to have.” “Let’s do it. They’ll never know and we won’t speak of this again,” says Superhero PhD. The lab goes on with the students none the wiser that an equipment glitch had ruined weeks-worth of their efforts. Superhero PhD also muses that this could be another opportunity for re-structuring the teaching lab to be more like real life science. When the experiment fails, go back to the beginning and repeat all of your work.
In a separate exercise, the students use a mutant enzyme to compare to the wild-type version they have meticulously purified and analyzed. This enzyme is prepared by the Superhero TAs and generally lasts for a few years before activity drops below a useful value. When Superhero TA #4 checks the activity of the purified mutant enzyme available in the freezer, it is insufficient because of course it is and by now this semester is just snake bit. Superhero PhD locates what should be the corresponding mutant DNA, but it is not useable. Attempts to locate other freezer stocks of the critical bacterial strain fail. Once again, Superhero PhD calls upon Retired Instructor, who has superior abilities at deciphering the glyphs on tubes in the bowels of the -80 freezer. A tube is found and Superhero PhD quickly determines it will express the necessary mutant protein. Superhero TA #4 isolates the enzyme and verifies that it behaves as expected. As Superhero PhD receives this news, the Hallelujah Chorus rings in the background and a bright light appears ahead- it is the light at the end of the semester. Everyone just might survive and manage to learn some biochemistry along the way.
Meanwhile in the laboratory, the students have finally entered the home stretch of their experiments- the doldrums of enzyme kinetics. It’s a greater than two week stint of exercises in which their hands must perform the same tedious assays with various reagents to understand the details of how their enzyme works. Even with the help of numerous others, Superhero TA #4 is unable to troubleshoot the problematic inhibition experiment. Superhero PhD decides to cut that experiment short and rely on data found within the Holy TA Manual for the students to analyze. It is within this series of experiments many students are reconsidering their choice of major.
The repetitious lull of kinetics assays on the spectrophotometer dulls their senses. They are less vigilant about manually recording their data in their notebooks. Inevitably, the unthinkable happens. After more than two hours of data collection, one group asks to be checked out to leave. “Do you have your data for the day? Make sure everyone in your group gets a copy of the Excel file you were working on.” says Superhero PhD. “Yes Ma’am.” they reply, but as they try to add the attachment, the file is nowhere to be found and the spectrophotometer files are woefully incomplete. They begin to panic, but Superhero PhD says, “That sucks if the computer ate your file, but you can re-enter your data from your notebook.” She is met with only blank stares and a rising sense of panic. “You did record all of your data by hand in the notebook you are keeping for the course? At least one of you did, right?” she asks. More uncomfortable silence. “Not one of the three of you wrote down any numbers today?” she asks rhetorically. “I will see if IT Services can possibly recover your file, but it appears that it has been improperly saved and no longer exists. Fortunately for you, this is the inhibition experiment for which we will be providing you with data, so you can use that. You’ve just wasted two hours of your life. If you continue to pursue a career is science, I doubt it will be your last. This is an important lesson in data management that you have learned in class instead of real life.” As it turns out, IT Services could not recover their data. There may be computer forensic scientists at the FBI that may have been able to recover the students’ file, but these methods are not routinely available to public universities. This instance has forced Dr. PhD to append the Rules of Biochemistry to include #6: Thou shalt manually record thy data. Always.
As the semester winds down, Superhero PhD can begin to think about the next semester. Some experiments will be adjusted. Also, Superhero TA #3 will transition full time into Dr. Postdoc, and at least on new TA, preferably with powers of chromatographic separation will be needed. Tenured PI’s Graduate Student is willing to take on the role, but Tenured PI is not in agreement with this decision. Graduate Student’s research is at a critical point and she won a student award that will allow her to give up her double life as a TA. Fortunately, Superhero TA #2 is able to recruit another graduate student from his lab to join the team. Superhero TA #1 will also be available for one more semester. It looks as if the team will be ready for the next semester. That is, of course, if Superhero TA #2’s visa renewal goes smoothly between semesters and he is able to travel back to the university as intended the day before classes start. “Only if my luck changes significantly,” thinks Superhero PhD. She does not underestimate the bureaucracy involved in coordinating paperwork between two sovereign nations over the holiday season. So, she writes a polite but persuasive letter addressed to the Visa Officer requesting expeditious resolution of this matter.
The battle of Semester 1 is over. All students, Superhero TAs and Superhero PhD have survived… barely. “Take that Chaos and Ignorance,” muses Superhero PhD as she indulges in the fine chocolate cookies stashed in her office.** More biochemistry majors have been indoctrinated in the practice of good laboratory techniques. The mysteries of the pKa, molecular biology and Michaelis-Menten enzyme kinetics have been unraveled for a new generation. Off they will go to Medical School, Graduate School and The Job Market empowered with this new biochemical knowledge. Superhero PhD has taught them the most important thing about biochemical research,
“It is tedious and awful both at the bench and digging through primary literature, but if you’re paying attention and you persevere, you can synthesize prior knowledge and new results into a better future.”
Stay tuned next time for new and exciting adventures in the Instructor Chronicles: A New Hope Springs. Will the new Superhero TA exhibit chromatographic supremacy? Will they ever get that one inhibition experiment to work again? Will they find a replacement for that debacle of a gel filtration lab? Will Superhero TA #1 get his visa renewal in time to return for the Spring semester? What new obstacles await our team? But before any of these questions can be answered, stay tuned for Superhero PhD: Call of Civic Duty as she serves her mandatory jury duty.
**A 2nd place prize for her ugly Christmas sweater-wear at the Departmental Holiday Party.