Semester

From the Tortured Biochemists Department

It’s the end of the semester. Here’s a song parody for some much-needed levity.

I was supposed to graduate

But degree audit said biochemistry

I was a [insert relevant degree]

And there was a degree requirement

All of this to say I hope you’re okay

But I’m the reason

And no one here’s to blame

But what about procrastination?

And for one semester, we were biochemists

Email you sometimes, ask about the enzymes

Now you’re moving on, turned into engineers

Dr. Roose’s exams, I wanna kill her¹

All those assignments stuck on a single protein structure²

I only crammed for Exam 1, the effects were temporary

Biochemistry, it’s ruining³ my life

Biochem, it’s ruining my life

I taught you for one semester

I learned you, but I learned you

And for a semester, we were biochemists

Email you sometimes, ask about the enzymes

Now you’re moving on, turned to engineers

Dr. Roose’s exams, I wanna kill her

And for a semester, we were biochemists

Email you sometimes, ask about my pathway

Now you’re at Himes Hall, which answer is it?

My students aren’t cheating, I wanna pass them

Biochem, it’s ruining my life

Biochem, it’s ruining my life

I taught you for one semester

I learned you, I learned you

Biochem, it’s ruining my life

Biochem, it’s ruining my life

I taught you for one semester

I learned you, I learned you

Thought of emailing ya but you won’t respond

‘Nother semester passed at LSU

Graduate and have the life you want

But it won’t begin til I learn biochem

Thought of emailing ya but you won’t respond

‘Nother semester passed at LSU

Graduate and have the life you want

But it won’t begin til I learn biochem

For your reference:

1. I’m perfectly safe. It’s a parody. We joke in class about my evil multiple choice questions. ↩︎
2. Hopefully, I’ll have time to write about this soon. ↩︎
3. Hopefully too strong a word, but again, it’s a joke. ↩︎

Could you, would you teach online?

By Dr. Roose

 

Could you, would you teach online?

Really? I just had to whine.

 

Yes, from a social distance.

It’s really university insistence.

 

I like my students in the lab,

I must generate data for them to grab.

 

It will be great, you’ll all see!

You will still learn biochemistry.

 

I can teach it here or there,

With Coronavirus everywhere.

 

I can teach near or far,

I can teach it from a car.

 

I can teach it from my house

If my dogs can be quiet as a mouse.

 

If you’ll all connect to Zoom,

I can teach from my living room.

 

Everyone plug in your machine,

We can all learn during quarantine.

 

With this virus so concerning,

We all so love online learning.

 

It will be great and you will see,

Still getting your degree.

 

Dr. Roose can teach online.

Stay calm. It will be just fine.

The Instructor Chronicles: Semester 1, Part 2

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 19^th 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 2^nd 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 1^st and 2^nd 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.

Johnna

*It did.

**A 2^nd place prize for her ugly Christmas sweater-wear at the Departmental Holiday Party.

The Instructor Chronicles: Semester 1, Part 1

We last left Superhero PhD leaving the funeral of her research career for a new adventure in biochemistry laboratory instruction…

The course she was entrusted with has a really great structure- starting from cloning a gene to expressing a protein to enzymology and protein crystallization. There was just precious little time between Superhero PhD’s start date and the first day of class. She just really needed an electronic version of the manual to get it churned out for the students or instead of alcohol dehydrogenase, biochemistry majors would be working on Photosystem II* (Dr. PhD’s forte). Fortunately, Retired Instructor was willing to be incredibly helpful, she had just been out of town visiting grandchildren. There was no time for significant edits, but it was much better than the other nightmarish scenarios that flashed through Superhero PhD’s brain.

With the lab manual in hand, Superhero PhD felt confident in her prospects for successfully completing the semester’s lab exercises. There was only one thing standing in her way, the thing that stands in the way on anyone that’s ever walked into a new lab- finding out where the hell everything is. The room was lined with benches containing identical equipment, tons of cabinets filled with God knows what, and freezers and refrigerators possessing an uncalled-for amount of previous years’ samples.** If only X-ray vision were one of Superhero PhD’s superpowers! Alas, she had to rely on the lesser power she did possess- painstakingly opening each cabinet and drawer, taking an inventory and labeling the contents on lab tape.

Of course, Superhero PhD was not alone in this new quest. The class came with 4 Superhero TAs with tons of experience running the lab exercises. Thankfully, they knew the location of everything Superhero PhD couldn’t find. However, there was one major concern held among all the TAs. The great secret to their power resided in a trilogy of binders they reverently called the ‘TA Manuals.’*** These holy books were nowhere to be found since the teaching lab had been vacated by Retired Instructor. “By the power invested in me by the search committee, I swear I shall deliver these holy texts to you by the start of class.” promised Superhero PhD. So she embarked on a crusade to acquire the TA manuals. It turned out that another e-mail to Retired Instructor specifically requesting them and coordinating delivery of the precious relics between Retired Instructor’s visits to her grandchildren was all that was required. With that, the Superhero TAs set about prepping for the semester’s labs.

The first day of class started with a strange omen. As Superhero PhD was driving on campus to her usual parking spot, she nearly hit two cyclists that thought it was appropriate to blow through a 4 way stop as if they were not vehicles. It was a sign of other obstacles to come. All seemed to be well with the TAs until Dr. PhD’s second day on the job when Superhero TA #3 mentioned he was trying to graduate and had, in fact, found a local postdoc job starting immediately. Superhero PhD isn’t one to begrudge anyone with a PhD finding gainful employment, but on the inside she felt like this. On the outside, her panic was probably only a brief eye-twitch. The next day, while she was still thinking of the lies she would have to tell to recruit another TA on such short notice, a miracle of miracles happened. Since Superhero TA #3 had not yet defended, he still qualified to be a TA and his new employer was willing to accommodate his schedule such that he could be both a Superhero TA and a Dr. Postdoc simultaneously. At this news, Superhero PhD smiled and began breathing again. “Now, we are really ready for the semester,” she thought naively.

As part of her new role in the Department, Dr. PhD actually got her own office. The space was glorious by postdoc standards- 4 walls, a small window with a view of the stadium, and a door. Even when she first laid eyes on it, filled as it was with file cabinets that seemed to be holding up the walls, flood damage along the exterior wall, and ductwork to who knows where in the corner. Her eyes welled up with tears and not solely due to the decades’ worth of dust that had accumulated. Nothing comes without a price of some kind and this room came with a whole other to-do list to manage: painting, sheet-rocking, cleaning, a computer, a printer, a phone, a phone number, a key, transferring all those file cabinets to surplus property. Each job meant a separate person handling it.

The office was not move-in ready on the first day of class, but it didn’t take too long before 90% of things were in place. Surplus furniture was moved into the hallway. A better desk chair was inherited from the Departmental Office. The whiteboard was not re-hung, but Superhero PhD owns a drill and a Home Depot card, so no big deal. Someone else a Facility Services even fixed the interior side of the door knob (Superhero PhD had some concerns that she would accidentally become trapped inside when it fell off). Surely at any moment, her new students would come pouring in for office hours seeking biochemical laboratory guidance. Alas, the only person to visit her office in the first month was Tenured PI.

As the semester began, chaos ensued. Superhero PhD received a minor in Chaos Management at the Evening Academy of My Family Circus, so most of the instances about to be described in no way affected the learning environment for the students, but nevertheless took years off of Superhero PhD’s life.

Critical reagents needed to be ordered for the lab, reagents with a hefty price tag for special expedited handling. In one case, the shipping company failed to deliver the package on time and in another, the reagent was backordered indefinitely. Superhero PhD managed to get a refund of the shipping charges for the late package and Superhero TA #3 suggested doing away with the backordered reagent entirely for the other experiment.

The teaching lab uses an ancient glass still to produce the dH₂O necessary for experiments. It is a finicky contraption whose secrets were relayed to Superhero PhD by Retired Instructor. The plumbing connections are not to be trusted. Sure enough, the first day Superhero PhD started it running, the tubing for the cooling water jacket source blew off as she dropped off her laptop in her office. It was a mess, but luckily no damage was done to any equipment or labs on lower floors. Dr. PhD did not even enlist the help of janitorial staff.

On the first lab exercise doing molecular biology work, Superhero TA #1 opened the ice machine to find it empty. This ice machine that had worked perfectly for all prep work until then was now broken. Again, if only Superhero PhD had more traditional superpowers like Elsa’s freezing powers she and Superhero TA #1 and #2 would not have had to cart ice from the common equipment room for every class thereafter. Perhaps it was just a maintenance error light. Superhero PhD’s power of randomly pressing buttons failed to resurrect the ice machine. The refrigeration serviceman was contracted to revive the ice machine. It was not in need of routine maintenance. It needed a completely new motor and a new unit was the most cost effective way of doing that.

Another experiment was giving us more trouble than it should have. The second transformation by electroporation to generate the expression cell line was not working. After re-making reagents and new competent cells, it turned out to be the electroporator. Luckily again, the lab had another fully functional back-up instrument.

Now that Superhero PhD’s schedule was more inflexible due to class schedules, all manner of personal emergencies seemed to occur. In her spare time, Dr. PhD’s life involves a lot of child-, pet-, and elder-care. And honestly, for someone who’s not-that-kind-of-doctor, she still ends up dealing with more bodily fluids than one can imagine. Nevertheless, quick texting allowed her to communicate with other caregivers and coordinate emergency room situations from the classroom. If only the superpower of being in two places at once was something Superhero PhD possessed, she’d have tenure a Nobel Prize by now. Since she does not possess this power, she is just ecstatic to have made it through so far without having to pay per minute overage charges for Junior PhD’s after care.

At some point Superhero PhD decided that her office was in fact stable enough without half a dozen file cabinets crammed in it. There was no way she wanted another piece of furniture in it and it was time to rid the hallway of the extras. The proper forms had to be filled out detailing the property inventory numbers for each. One perk of Superhero PhD’s new position is a handful of undergraduate minions to help with support tasks. With the forms filled out and sent away to the appropriate university office, the months-long wait for retrieval began. Upon inspection of the copies of the forms, Superhero PhD notices that her undergraduate minion was a little overzealous in listing items- not all of the furniture in the hallway was her surplus. Neighboring lab had a nice lunch table and other cabinet in the hallway for their convenience. Superhero PhD was their neighbor for less than a month and she’s already giving away their property. “I’ll just have to be on the lookout for Facility Services again.” she thinks. The next day there is a crash outside her office, the sound of metal being unceremoniously moved about. “They’re here already?!?” she thinks. She walks into the hallway to explain the mistake on the paperwork. Speaking quickly to the man in the hallway, he appears to listen briefly before signing that he is deaf. Finally, a situation appears for which Superhero PhD can summon one of her lesser-used powers- a basic understanding and use of ASL. She manages to point to the paper and the misidentified furniture and sign, “Wrong. Must Stay. Thank You.” It worked! “Now that the hallway is clear, my students will surely come to my office hours,” she thinks to herself.

Just when Superhero PhD thinks all office-related work has been completed, other workmen from Facility Services show up to replace a 6 ft stretch of plastic baseboard along the back wall where sheet rock had been replaced. Every little bit helps. While they are there, they notice that no one has re-hung Superhero PhD’s white board. They just so happen to have the appropriate clips and bolts in the truck and hang it up for her. “This will really come in handy when I have to explain biochemistry to my students during office hours,” thinks Superhero PhD.

In some ways, research labs can be like the Mafia- they never really let you leave The Family. Superhero PhD still attends the lab meetings of Tenured PI to keep tabs on the research projects she left behind, offer insightful experimental suggestions and tell others in the lab where to find things. One week both Tenured PI and Lab Manager will be absent and Superhero PhD is called upon to preside over lab meeting. Experiments are reported without much incident. Superhero PhD and the Research Team retire back to the lab. Just as she is leaving, Superhero PhD hears the one sound that strikes fear into every researcher- the piercing cry of the high temperature alarm of the -80 F freezer. Graduate Student says, “By the way, this alarm was going off before lab meeting, but it doesn’t seem to be getting better after being shut for another hour.” Superhero PhD can sense the precious biochemical samples thawing and decades of freezer stocks becoming perilously warm. There’s no way Tenured PI or Lab Manager will be around to handle this. Superhero PhD and the Research Team**** spring into action securing additional freezer space in other departmental labs’ freezers. All samples are safely stored in time. Scientific crisis averted.

Stay tuned for the next installment of Superhero PhD’s inaugural semester in the Instructor Chronicles. How can she be Fast. And. Cold. without a functional ice machine? What will become of Tenured PI’s freezer? Will students ever come to her office hours? Is anybody really learning anything about biochemistry? What new slings and arrows of outrageous fortune await Superhero PhD and her TAs for the remainder of the semester? All of these questions will be answered in the next episode of the Instructor Chronicles.

Johnna

*Working with a large membrane protein complex whose substrates are water and light definitely qualifies as the deep end of the biochemistry techniques pool, so it’s probably not the best place to start.

**They took Rule #2 to the extreme, even for molecular biology samples and cultures that could never hope to be resurrected.

***The TAs were awesome apart from the TA Manual, but it contains all manner of useful information for managing the course that makes their lives a lot easier.

****Collectively, the new name for the group is the Chlorophyll-a Team. Homage to @AmeliaRWright who came up with that gem for #ScienceAMovieTitle. When I have spare time, I’ll write a spin-off with this title.

Superhero PhD: Nike!

We last left Superhero PhD and her labmates in a state of noncompliance with the system that is supposed to support them. Fortunately, their misdeeds did not attract the attention of accountants higher up in the matrix. Even the recently purchased equipment from e-bay works just fine. These small triumphs make the days in the lab pass easier, which was good since several more days passed beyond the funding agency’s deadline for divulging the fate of tenured PI’s latest grant renewal. Finally, the e-mail from the Program Manager arrives… victory! The grant is renewed for another three years. Tenured PI must send a flurry of additional e-mails as slight adjustments to budgets must be made, but these are a welcome burden given the possible alternatives.

Superhero PhD takes a break from benchwork to battle with the peers who reviewed her latest manuscript submission. She has spent the last months painstakingly repeating experiments to satisfy their demands for MOAR DATA! Now is the time to revise, remake figures and resubmit. Tenured PI submits a more appropriately censored version of the responses to reviewers’ comments to the editor than the first draft provided by Superhero PhD. It’s probably for the best. It will be another few weeks before the next battle with reviewers over this manuscript.

Back to the routine of research Superhero PhD focuses on projects that have been on the sidelines. A new mutant is giving unexpected results, but our heroine knows better than to get too excited. DNA samples are submitted for sequencing analysis to check for possible errors in the intended sequence. It seems like an easy task, but the new on-line system for submitting the samples and payment information requires more steps and approvals than acts of congress to approve federal budgets. Tenured PI even gets automated and unrecognizable e-mails from the system requesting approvals. Finally, the analysis is complete and Superhero PhD receives the results. “Nooooooo!” she cries, shaking her fist at the screen. The construct has a point mutation in addition to the complex construct she has pieced together. The mutant is unusable because it runs afoul of a central tenet of scientific experimentation- only change one variable at a time. These results sentence Superhero PhD to weeks of molecular biology work to remake a clean version of the mutant. In all truthfulness, Superhero PhD already had a stint of molecular biology ahead of her with other constructs and mutants to be made for her new project. For biochemists, molecular biology is a necessary evil.

Despite the occasional sequencing error, Superhero PhD also has molecular biology superpowers as well. She sets out to spend her days tediously pipetting PCR reactions, restriction enzyme digests and running agarose gels. To visualize these gels, she must rely on departmental common equipment whose other users can be less than meticulous. Today, she finds something even more unusual. An unexpected power outage overnight has forced the computer to restart, a computer still running WindowsXP that probably hasn’t restarted in three years. Sigh. Login required. The password is not written anywhere in the area of the computer. Superhero PhD summons her powers of clairvoyance to divine the password, and she is correct.* She captures the image of her gel on the screen. Print. But something again is wrong. “Damn, the printer is out of the special thermal paper. Chances of other users reporting it to the Departmental Coordinator in charge of ordering the replacement- zero.” But Superhero PhD is prepared for such instances; she keeps a secret stash in her lab for just these occasions. “Incomplete lab notebook, I think not.” she chuckles. “However, I will have to step up my notes describing the proper procedures for acquiring more paper from passive-aggressive to full-on aggressive.” Superhero PhD muses.

Another consequence of molecular biology work is defrosting the frost-free freezer. For those of you wondering why a sophisticated modern research lab would have a frost-free freezer, it is because the precious enzymes used for these projects must not endure the temperature cycles of a typical modern freezer. They must remain cold at all times and fluctuations too warm will diminish their activity. Superhero PhD’s lab has still-active molecular biology enzymes whose purchases pre-date the births of many undergrads working there. However, after about a year of opening and closing the door of a frost-free freezer, the ice build-up inside necessitates the removal of all contents and a manual defrost. Superhero PhD uses her skills of organization to temporarily store all of the contents of the full size frost-free freezer, taking special note to remember where each item must be returned. It would be nice to say that Superhero PhD then uses her laser vision to melt the excess ice on all of the shelves and coils, but alas, that is one superpower she lacks. Instead, she and Graduate Student use a hair dryer** and spatula to melt and hack away at the ice for about an hour.

Elsewhere in the departmental common equipment room, Research Technician is battling with the ultracentrifuge, an expensive and formidable foe. “The imbalance error light is on, but there is no imbalance. I cannot get it to start.” he says. Superhero PhD gives him a hard, disbelieving look. “No, really. It’s balanced.” he retorts. Instances of imbalanced ultracentrifuges are the stuff of scientific research legends. The instruments turn rotors at such high speeds that failures in components or user error like imbalanced samples can turn these metal rotors into dangerous projectiles that penetrate walls and kill unsuspecting graduate students down the hall. “Did you turn it off and turn it back on?” she asks. “Yes, the error is still there.” Research Technician says exasperated. Superhero PhD then uses her superpower of pressing seemingly random buttons on the control panel (SET, IMBALACE, CLEAR, ENTER) and the imbalance error is cleared. The instrument will now be able to start the run. “What buttons did you push? I’ve been pushing buttons too!” he says even more exasperated. Superhero PhD’s fingers fly too fast in that mode, “I’m not sure.” is all she can answer. She shrugs, “But wait until I leave the room to start the run.” She’s not completely convinced there may be an imbalance. For the record, there wasn’t.

There are other problems in the lab. She senses trouble immediately because Research Technician and Undergraduate Researcher bombard her with their pleas as soon as she opens the door. “Something is wrong with the cooler! The blotter won’t work! What do we do?” they cry.*** These things only happen when Tenured PI and Lab Manager are out of the lab for the day. Superhero PhD assesses the situation. Indeed, the deli cooler is a mess. It seems to have cycled much cooler than normal at some point overnight causing the coils to ice up. This caused the case to stop trying to keep the temperature low and the ice build-up was currently dripping all over the contents inside. “What a mess.” she thinks. However, experiments must be salvaged. “Remove the blotter from the cooler. We need to get it to work or borrow a replacement.” she decides. The blotter screen wasn’t giving a reading of the output voltage, but the electrodes appeared to be responsive to the controlling knob. Superhero PhD estimates the correct setting based on her perception of the rate of bubbling along the wires (and the transient flashing of a reading on the LED screen). “Take it to the cold room, and run it for two hours. Turn off the cooler. Take everything out of it. Turn it back on in the morning and monitor the temperature.” she orders. The blots are saved. The blotter screen miraculously starts working during the run. The cooler works normally after the reset. Another crisis averted.

Later that week, Tenured PI receives an e-mail from the editor regarding Superhero PhD’s latest manuscript. The verdict is favorable. Finally, acceptance! We can put that research behind us. He comes to share the news with Superhero PhD. He says only one word, “Victory!” She is having her lunch at the moment, so she only gives him a puzzled look. “What are you talking about?” she asks. He responds, “When the Greek messenger Pheidippides ran from Marathon to Athens to announce the victory over the Persians, he exclaims ‘Victory!’ Well, ‘Nike!’, in the Greek language. Your paper was accepted, so I said ‘Victory.’” Superhero PhD smiles to herself at the triumph, then says, “But in the legend, Pheidippides falls over dead after that exclamation.” Tenured PI answers, “Yes, that’s how I feel!” Superhero PhD agrees. So she announces, “Me too. I’ll be taking that Biochemistry Instructor teaching position in the Department.” At that moment, Tenured PI fell over dead.

NOT REALLY, but his heart probably stopped for a few beats to mourn the death of Superhero PhD’s research career.****

What will happen to the research projects that were on Superhero PhD’s to-do list? Will Tenured PI find a replacement SuperPostDoc to work on the recently renewed federal grant? Does Superhero PhD have instructional super powers? Stay tuned next time for the answers to these questions in the continued adventures of Superhero PhD: The Instructor Chronicles.

 

Johnna

*It’s the same as the login ID BTW.

**Yes, our lab has a deluxe model hair-dryer with a very powerful temperature and speed output. If your lab doesn’t have one for this purpose, you should get one, but good luck justifying the purchase with accounting.

***If you read the footnotes of my last post carefully enough, you know how critical the blotter instrument is for our research.

****He really should have written his reference letter more carefully.

Superhero PhD vs. The System

Uncertainty and The Unknown are constant adversaries of Superhero PhD. Careful application of the scientific method keeps them at bay. It is a battle that never ends. However, other enemies can come from within the Ivory Tower- well-intentioned policies band together to create formidable bureaucracies that mire progress. At times, Dr. PhD, her crew and common sense run afoul of the system. This is one of those stories.

A good deed…

Graduate Assistant needed some spinach to prepare samples for her experiments, but her lack of transportation prevents her from going to the MegaLowMart to get what she needs in sync with her experimental schedule. Fortunately, Superhero PhD can easily stop by there at any time in her PhDMobile. The wall-o-produce at the MegaLowMart has what she is looking for- bagged spinach, not that baby stuff but mature leaves full of PSII. Mission accomplished. Dr. PhD thinks to herself, “What else was on the lab shopping list?” Ah yes, batteries. Tenured PI had used up the lab’s supply when changing out the batteries in the portable light meter last week. The battery kiosk is next to the checkout, and batteries are added to Dr. PhD’s cart. She pays with her institution-issued credit card aka TheCard, making sure to alert the cashier to the purchase’s tax-exempt status and keep the receipt to file the appropriate accounting paperwork. All this productivity and efficiency before 8 a.m. One would hardly think a rule had been broken.

Doesn’t go unpunished

The spinach is turned into samples for useful experiments in the lab by a grateful Graduate Assistant. The stash of batteries is full so the next time one of the small electronics in the laboratory dies, it can immediately be resurrected without inconveniencing any experiments. The original receipt, signed and labeled with the appropriate account number to be charged, is turned in to the accountant. Lab life goes on… Until… Superhero gets an e-mail from Departmental Accountant asking for clarification. Every transaction is audited to prevent fraudulent purchases and he needs to know what “the salad spinners and batteries” were used for. Superhero PhD, “Huh?” Oh, yes. The abbreviation on the receipt was ‘salad spin’ for salad spinach not spinner and it was turned into PSII. Batteries are used to power small electronics in the lab. (No, there isn’t a non-snarky way to describe what we use batteries for in the lab, especially not on a Friday afternoon.) Later, another e-mail; this one is a warning from Departmental Business Manager. Her superpower is generally keeping the system from negatively interfering with laboratory science. Sometimes even she can’t keep the system from impeding research. Departmental Business Manager informs Dr. PhD that batteries are available at a cheaper price with next day delivery from WorkplaceSupplySupreme via the Online Institutional Ordering System. “That’s great! Anything to keep me away from MegaLowMart.” thinks Dr. PhD. Well, there’s more to it than that explains Departmental Business Manager. Our institution is contractually obligated to buy them from WorkplaceSupplySupreme, and elders in the main institution accounting office may deny the transaction and send Dr. PhD a ‘Noncompliance’ form. Sigh. In the meantime, Dr. PhD will wear a scarlet ‘N’ on her lab coat and be prepared to personally pay for the illegal transaction. This will teach our hero to think of WorkplaceSupplySupreme the next time random consumables are needed for the lab.

Additional noncompliance and other rebellions

Apparently, Superhero PhD is the bad apple spoiling the whole bunch because the other individuals in the lab have also been fiscally rebellious. Research Technician bought spinach at a produce stand that did not provide a receipt with detailed item descriptions, such that there is no way for accountants to tell if he really purchased $6.00 worth of spinach for the lab or a few bananas for his own consumption. Laboratory Manager had to replace the lab’s blender, which is used to grind the spinach for PSII preparations. Scientific supply companies will sell versions of this appliance with features the lab doesn’t need for exorbitant fees, but a decent kitchen supply outlet will sell the basic model for less than half the price. Lab Manager had to spend a lot of time responding to e-mail correspondence from institution accountants as to why she purchased a food blender on her TheCard and federal grant funds. Sometimes there are unexpected difficulties when your model organism is also a common food. Tenured PI also decided to join in the fun of noncompliance by ordering a piece of lab equipment from e-bay using his TheCard. If it were new, it would cost $5000.00, but by shopping victoriously it was only $100.00. Tenured PI has not technically gotten a noncompliance notice, but his transaction makes too much financial good sense to be legitimate, and notification is likely to be imminent.

Schrodinger’s grant*

All of this fiscal (ir)responsibility is amplified by the fact that Tenured PI has not received notice on the funding status of his federal grant renewal submission. For months now, it has been in the pipeline being checked, reviewed, discussed and ranked. Federal Agency Officers can give no information on the status of submissions. Since they have significant power over amounts of funds and release dates, Tenured PI knows not to press the issue. The only response, “No new information will be provided until 2 weeks from this date.” Tenured PI’s grant exists only as Schrodinger’s grant. It is the superposition of both the funded and non-funded states. There is no way to really know at this time which state it really is, and thus it can exist as both states simultaneously. Ultimately, the e-mail from Federal Agency Officer is the black box that entangles both states. When this e-mail arrives in Tenured PI’s mailbox, he can click on it to collapse the superposition of dual states and make the observation to know for sure whether the grant is truly funded or not funded. Until then, the lab waits, conjuring ideas for alternative funding strategies and sources for lab consumables.

Slow River Honky Tonk Extravaganza

Our hero’s lab isn’t the only place feeling the squeeze of governmental budgets. It’s a state-wide problem, and Dr. PhD’s institution has discovered how profitable it is to rent out our MegaStadium for a weekend’s-worth of country music. No one knows for sure how the money is split, but with seating for just under 100,000 it can’t be a bad racket. Of course, an event of this size has logistical implications and repercussions for Superhero PhD and other institutional employees. Weeks in advance the police department sends out e-mails describing the parking situation. Even though Superhero PhD pays for a parking permit, the spaces will be sold or made available to concert goers. The specifics are unclear, but what would normally be restricted-access will be publicly available starting at 1pm. The concert doesn’t start until 530pm, but our state accounts for a requisite four-hour window for the public consumption of alcoholic beverages prior to large events such as this. Vehicular navigation on campus will be such a cluster&@#% that commercial delivery services will not run their normal routes. Outgoing packages will just have to wait until Tuesday. Superhero PhD arrives to a campus that appears business-as-usual in the morning and is not asked for additional payment for parking. However, by 330pm there is a steady influx of buzzed women in tank tops and cowboy boots- all Reba’s biggest fans, no doubt. Their escorts all have crisp new cowboy hats. Superhero PhD wraps up her experiments earlier than usual and the roads appear to be moving reasonably well. Just like that she disappears from the Ivory Tower and begins her escape from campus. Half of the intersection is blocked where she normally makes her left turn, but a car in the oncoming lane is disabled. There are no pedestrians to yield to for the left turn. Dr. PhD thinks, “Here’s your one chance PhDMobile, don’t let me down!” Fancy that, the rest of the commute to the PhD lair is smooth sailing.

Stay tuned for the continuing adventures of Superhero PhD and the rest of the lab. Will they all be relegated to noncompliance and have their purchasing privileges revoked? Will Tenured PI’s grant get renewed so there will even be money to spend? The answers to these burning questions will be in the next episode.

 

Johnna

*I can’t take credit for this bit. It was all Tenured PI’s idea.

Also, for the record, better judgement and common sense has prevailed regarding noncompliance. While time was wasted by all in terms of e-mail correspondence, no lab members were held personally liable for the purchases described here.

Sidekick (Cont’d Adventures of Superhero PhD)

Science doesn’t stop for holidays, so Superhero PhD must always be vigilant- even if the Ivory Tower is officially closed. For biology research labs, something is always growing and can’t be left unattended for two weeks or more. For these working holidays in the lab, Superhero PhD has a special sidekick- PhD Junior. No really, he is a literal sidekick. One of his superpowers is stealthily climbing into bed with Superhero PhD and SuperChef whereupon he flops and kicks the both of us until it is approximately 30 minutes before the alarm clock buzzes (Yes, just enough time to slip back into such a deep sleep state so as to achieve maximum aggravation by the alarm). Below is his character fact sheet:

Alter ego: Deuce* (4 yr old male)

Tag line: If I have to come to the lab today, we’re going to see Mike the Tiger. It’s really not as much like Monster’s University as Superhero PhD promised.

Special powers: Pushing elevator buttons, adorable pronunciations of Chlamydomonas and Thermosynechococcus

Transportation: A booster seat with cup holder in the backseat of the PhD-mobile

Sidekicks and Associates: Legos, Zoobooks and a Kindlefire loaded with StarWars Angry Birds and Netflix

Nemeses: stairwells, vegetables

Backstory (read with the gravitas of a movie-trailer voice-over): PhD Junior is the spark of chaos in Superhero PhD’s life that pushes her to be increasingly efficient. His sense of wonder and non-stop questions about the world around are an inspiration of Superhero PhD.

Skills Breakdown:

Speed 20

Endurance 20

Stealth 30

Agility 30

During one short visit to check on cultures, Superhero PhD and PhD Junior approach the locked Ivory Tower. It is practically abandoned on the cold holiday, but bacterial cultures must be checked. But first, a potty break. As the mission resumes, Superhero PhD makes for the stairwell. The growth chambers are in the basement and it is only one floor down. PhD Junior balks at the dim and somewhat sinister-looking stairwell. Apparently, they are like kryptonite to him. Anyway, PhD Junior’s special skills include pushing elevator buttons. Superhero PhD says, “Of course we can take the elevator.” But silently calculates how long it might be before someone could come extricate them from the elevator on a holiday (Superhero was stuck for a while on said elevator once when she was still pregnant with PhD Junior). Fortunately, today the elevator functions without incident.

Since PhD Junior only makes rare appearances in the lab, his skill set it not often helpful for the experiments at hand. However, he is honing his own superpowers of logic, reasoning and knowledge by incessantly inquiring, “What’s that? What’s this? Why did you do that?” Superhero PhD is able to answer all of these questions with ease as she carries out her tasks. She peers at the plates of cyanobacteria evaluating their growth. Deep in thought for just a moment, then she snaps back quickly because the questions have stopped from PhD Junior. Silence is always suspicious. Out of the corner of her eye, there is a sudden dimming, and she focuses her attention like a laser on PhD Junior who is now very close to the fluorescent light banks and shaking cultures of Chlamydomonas that belong to the Moroney lab. “Did you just pull the chain on those lights?” asks Superhero PhD. A shy smile broadens across PhD Junior’s face as he nods. Superhero PhD turns the bank of lights back on. “Don’t touch anything” becomes the mantra of the mission.

When PhD Junior is in the lab, Superhero PhD must kick her superpowers up a notch to channel his excess energy and dangerous curiosity. For longer missions, “Don’t touch anything” and “Do you need to potty” become regular utterances for Superhero PhD. Monday was a longer mission fraught with danger. OK, not as dangerous as if he would have gone to work with SuperChef where everything in the kitchen is hot and sharp, but pouring gradient acrylamide gels and silver staining another gel are not small tasks in the presence of a 4 year old. Supplies are brought in to keep PhD Junior occupied- books, legos, snacks in a T-rex lunchbox, cash for the vending machine on the first floor, a Kindle fire loaded with apps for Netflix and Star Wars Angry Birds (Pro tip: Turn off one-click ordering for Amazon.com and the appstore if a preschooler will be using your Kindle fire unattended for long periods of time.)

PhD Junior is first taken aback when Superhero PhD dons her uniform (lab coat). “Don’t be a Dr.!” PhD Junior pleads. In his defense, the only people wearing lab coats that he interacts with are medical professionals of some kind trying to give him a shot or look down his throat or ears with an uncomfortable instrument. Superhero PhD quickly diverts his attention with the Kindle and bag of distractions. He plays Angry Birds for an hour. Superhero PhD dives into her experiments with lightning speed, arriving at a critical moment just as PhD Junior wanders over to her bench. Let’s just say that loading an acrylamide gel while fending off a 4 year old playing ninja fight is now one of Superhero PhD’s superpowers.** The critical gel was loaded. No one was exposed to any toxins.

Superhero PhD successfully manages to again divert PhD Junior’s attention with games and Scooby Doo on Netflix as other experiments are done. However, just as a critical stage is reached in silver-staining an acrylamide gel, PhD Junior announces, “I’m hungry!” Superhero PhD  is at first taken aback by this because one of her superpowers is working without eating (or going to the bathroom) for hours on end as experiments are executed. Nevertheless, she materializes food from the lunchbox and sets up lunch time just outside the open door of the lab (no food or drink allowed inside of course). Superhero PhD’s experiment continues.

By mid-afternoon the mission is almost complete, which is perfect timing because PhD Junior has eaten through all of the provisions packed by Superhero PhD. The last thing that must be done is scan the stained gel. This must be done in a separate lab room, but PhD Junior is happily assembling Legos in the main lab room. Superhero PhD explains the dilemma to PhD Junior and offer options- stay with Legos or go with Superhero PhD. “I’m building a Lego car!” is the terse reply. After 10 minutes of scanning and saving the image, Superhero PhD’s work is done for the day. She returns to the lab, but PhD Junior is nowhere to be seen. It is quiet. Superhero PhD nervously calls for PhD Junior. No answer, she detects the slightest movement out of the corner of her eye. Then she sees small grey tennis shoes under the bench where the Legos are. First Middle Last Name (redacted)! PhD Junior sheepishly emerges from under the lab bench and says, “I was hiding for you.” Superhero PhD is relieved that PhD Junior is found and her anxiety is eased only slightly by PhD Junior’s misuse of prepositions. They have a serious discussion about Not. Hiding. Evar.

Mission accomplished, it is time to leave the lab. It takes 20 minutes to pack all of PhD Junior’s gear. This includes finding a way to hand-carry the Lego Car and House constructed by PhD Junior. He adamantly refused to disassemble them (ala Johnny Five) and place the pieces back in their case. Everything makes its way back to the PhD mobile and PhD Junior is sleeping before they reach their secret lair.

Johnna

*For those of you paying attention his nickname is Deuce Roose.

**Remind me to update my CV and LinkedIN profile.

The continued adventures of Dr. PhD

Today, in the continued adventures of Superhero Dr. PhD…

From high in her ivory tower, Dr. PhD senses something ominous and dreadful. Something is hanging in the foggy fall air. Death.* No it’s Deadlines! Just after coming down from post-summer meeting euphoria and getting into the routine of the new semester, there they are. Deadlines looming every other week.

The most obvious of deadlines this time of year in academia (and beyond) are job application deadlines. Fortunately, Dr. PhD has a few finely honed superpowers essential for this process. She can update her CV and research plan in a flash. She can tailor cover letters for any position. She provides her references with meticulously curated lists of requirements and submission dates for letters, and then relentlessly hounds them until all letters have been e-mailed away. Each week more applications are due. Her fingers fly across the keyboard to finalize submissions to online systems. PDFs of application materials are compiled in a snap. Her entire professional persona is neatly and persuasively bundled in tidy electronic packages and clicked away into the oblivion of the internet. Goodbye, hope to hear from you soon.

Speaking of hearing back- the reviews are in on Dr. PhD’s latest manuscript. While not completely dead, more experiments are needed to bring it to life in the reviewers’ eyes. The clock is ticking on the resubmission timeline. With Dr. PhD’s prescient super-sense for this kind of response, precious samples are already waiting in the freezer. More antisera will have to be ordered, but alas, one critical antiserum is not commercially available. Superhero PhD will have to send out a signal to the international community for help. (OK, really it’s just an e-mail to the only other person that has used this antiserum in a publication a number of years ago.)

While Dr. PhD spends her days experimenting to revive her manuscript, her labmates have their own deadlines. She’s only seen glimpses of Undergrad Minion since midterms- his time in the lab waning in the face of other deadlines in his last semester of classes. Dr. PhD-β is leaving the country at the end of the year and is a flurry of activity to finish up critical projects. Graduate Assistant has a handful of key presentations to give this semester to fulfill her degree requirements. However, she is still cultivating her superpower of putting together Powerpoint presentations. Dr. PhD, Dr. PhD-β, Tenured PI and Research Associate painstakingly pore over her slides offering mountains of editorial corrections until every typo, inconsistent capitalization and un-credited figure are refined by fire into pure presentation gold.**

This deadline season has also been hectic for Tenured PI as well. There’s a grant submission deadline looming on the horizon, and the lab only speaks of it in hushed whispers. Before we can worry about any new money, Tenured PI must give his own presentation for our current funding overlords. It is not a meeting one can miss. Slides are put together. Additional data is analyzed. More slides are put together. The margin is slim on this timeline and Research Associate doesn’t get to use her scrutinizing superpower on all of them. Nevertheless, Tenured PI gives an entertaining performance with captivating data and a joke about a dual colored laser pointer that only biophysicists will get. It went over well and let’s just say that’s one deadline he killed- in a good way.

Of course, the absence of Tenured PI on a weekday in the semester means that Superhero PhD must come to the rescue as a substitute teacher. Slides are quickly transferred to Dr. PhD. She looks through them. Ugh. Tenured PI always sticks me with lectures that involve some kind of ∆G calculation. It takes all of her superpowers to create a stimulating lecture on the Na/K Pump and Bacteriorhodopsin.*** The students are hung over from their recent exam (No, I did not have those results.), but they are especially attentive during the explanations of enzyme mechanisms (Yes, you have to be able to explain those from memory.). Of course, not all deadlines are met perfectly. The lecture went well, but 36 hrs later Dr. PhD thinks of an awesome active learning exercise to do for the Bacteriorhodopsin mechanism. Next time Biochemistry I, next time.

View from inside a gorge, Turkey Run State Park, Indiana, 6-2005 (Photo credit: Wikipedia)

The final deadline of the season is our annual regional meeting on photosynthesis- The Midwest**** Photosynthesis Conference at Turkey Run State Park Indiana. Yes, it is as exciting as it sounds and an annual culinary experience that will test any scientist’s digestive superpowers. This means more lab presentations must be churned out. Travel accommodations and associated departmental forms must be filled out. Accounting paperwork is another one of Dr. PhD’s superpowers. Yes, Graduate Assistant you will need to fill out this form if you have never used that card for travel before or it will be denied. Don’t listen to what the other coordinators tell you! But also this year, Tenured PI is Co-Chair of coordinating this meeting. Abstracts must be catalogued. Registrations must be done. A program must be scheduled. A program booklet must be assembled, printed and shipped to the meeting location. Deadlines, deadlines, deadlines. Don’t worry, we made all of them. The program looks to be interesting, so stay tuned for upcoming posts with breaking photosynthesis research from the meeting.

But what will become of the other deadlines? What about all those applications? Will the reviewers appreciate the additional experiments and give life to Dr. PhD’s manuscript? Will the lab get additional funding? Stay tuned for the continuing saga of Superhero PhD.

Johnna

*No, that’s just the unfortunate feral kitten that met an untimely end under the hood of the PhD mobile. Alas, feline detection is not one of Dr. PhD’s superpowers. Bang on your hoods on cold mornings for God’s sake people!

**She did an awesome job on her talk and will again soon.

***That one is basically primitive photosynthesis, so it’s fine.

The continued adventures of Dr. PhD

From the top of her ivory tower (well, really the 6^th floor is only the penultimate level), Dr. PhD gazes down at the sidewalk below. It’s teeming with undergraduates trying to find their way to their fall classes. They move from their dorms and commuter parking lots in mass migrations correlated with the half-hour chime of the clock tower. This herd pays little attention to pedestrian traffic signals as they focus on the small glowing screens of their smartphones, adjusting their playlists and texting other students also migrating a mere hundred feet away. They are a mix of self-absorption and optimism. It smells like exotic coffee flavors, stale beer, too much body spray and naïve dreams.

Many of them are biology majors intent on one day entering Medical School. But Dr. PhD knows the statistics. If they only knew how much Dr. PhD doesn’t enjoy seeing their dreams crushed. It’s all been spelled out in their syllabi. If they would only heed the instructions, then they could keep their precious points. Despite all admonitions by Tenured PI and Grad Assistant on their first day of classes, the undergraduates only value points once they’ve been taken away. Sigh. Tenured PI approaches, but something looks different. “Why are you wearing a shirt with buttons and pants? And what’s with all the black?” Dr. PhD asks. “To convey my seriousness to the new students and my mourning for their hopes of an easy grade.” he says. “Now where is the revised draft of that manuscript?”

Dr. PhD spins suddenly on her heel and with a twirl of white lab coat she disappears back into the laboratory. She pores over font sizes, line widths and object spacing in her figures. She spends the day clarifying the arguments in the discussion section of her latest manuscript. She anxiously reads it through one last time before sending it over to Research Associate, whose superpower is English grammar and usage. May God have mercy on the comma that should be a semicolon, dangling participles, and the incorrect use of the subjunctive because Research Associate sure won’t have any. Dr. PhD’s manuscript is returned, bleeding with corrections. Once these are fixed, a PDF file is sent to Tenured PI, and it disappears into the realm of peer review. Dr. PhD lets out a brief sigh. “Now we wait.” It will be another few weeks before she’ll have to do battle with Reviewers’ Comments.

When she retreats to her PhD-mobile at the end of the day, something is awry on the street. There are barricades at either end and ‘No Parking’ signs at every spot where the vehicles have left for the day. The PhD-mobile is one of the last on the street. There was an e-mail from parking and transportation earlier in the day. What did it say, again? She double checks quickly… road closures, parking permits, roundabouts, blah, blah, blah, ivory tower street will become a pedestrian-only zone this fall and street parking will no longer be available. “Nooooooooooooooo!” she cries, shaking her fist at the sky. The back-up camera of the PhD-mobile and Dr. PhD’s lack of shame to try-try-again at parallel parking made street parking just outside the ivory tower a glorious time-saver in her quest to rush back and forth in her commute without being late to pick-up Jr. PhD. Someone higher up in the university administration was going to hear about this. Surely, they knew that street parking is a critical family-friendly policy for her.

What is Dr. PhD to do now? The wait-time to get a spot in a gated lot with guaranteed parking is longer than the lab’s current funding for Dr. PhD’s salary and even if it weren’t she’d have to sell plasma every other week to afford it! The other option is to migrate with the undergrad commuters from the shadowlands beyond the ivory tower. Shudder. The next morning Dr. PhD rises before the sun and coerces Jr. PhD to get ready early; they leave the house 15 minutes earlier. Dr. PhD is able to find parking around the corner from the ivory tower. “Victory is mine!” Ironically, while searching for a new parking place and getting on and off campus by a slightly different route, she very nearly runs over more than a couple of migrating undergrads. Pedestrian safety indeed. Let’s just say Dr. PhD and the undergrads will have to agree to disagree about what constitutes a crosswalk.

Stay tuned to find out what happens next with Dr. PhD’s manuscript and life in the ivory tower, next time on the continued adventures of Dr. PhD!

Johnna

If you enjoyed this installment of the adventures of Dr. PhD, you can find the other episodes by searching ‘superhero’ in the search box on the blog homepage.

The continued adventures of Superhero Dr. PhD

A man clutches his chest in a busy restaurant. He slumps. A vase crashes to the floor. His wife screams. The waiter cries, “Is there a doctor in the house?” Dr. PhD cringes, then raises her hand, “Check please!” M’eh, this is a job for superhero Dr. MD.

Dr. PhD startles awake. Of course it was just a dream. When would Dr. PhD be at restaurant expensive enough to have vases on the tables? Scavenging free pizza after a seminar, picking up take-out from the Whole Foods deli, or at the bar on trivia night- those are all more realistic scenarios for Dr. PhD. One day a situation will arise when Dr. PhD’s expertise is needed in an emergency. Surely someday knowing the electron transfer pathway within Photosystem II and its protein components will come in handy, right? Yes, Dr. PhD is one you’d want on your team for trivia night.

Today: the continued adventures of Dr. PhD…

We find Dr. PhD busy in the lab washing western blots. Before she can trek downstairs to the dark room with the x-ray developer, Tenured PI approaches her. “I’m going on vacation for two weeks with Research Associate,*” he says. “You’ll be in charge while I’m gone. If you’re not here, Dr. PhD-β will be in charge. If she’s not around, hopefully Grad Assistant’s VISA will come through so she can come back to the U.S. Don’t leave Undergraduate Pre-med Minion** on his own. My cat Sigma falls before him in the chain of command.” “But, PI, Sigma’s been dead for 20 years,” says Dr. PhD. Tenured PI only shoots back an icy stare between his thick-lensed glasses and even thicker eyebrows. Fortunately, Dr. PhD has worked with him long enough to understand his humor. He’s not being that serious, besides he knows reanimation is not one of Dr. PhD’s superpowers. Dr. PhD shakes her head and smiles, “Understood.”

And so Dr. PhD assumes her watch over the lab. The other lab members had been given their instructions. In theory, they knew what to do, but the onslaught of questions starts not long after Tenured PI and Research Associate have boarded their plane. Minion has to probe his western blots with a new antibody, well really an old one that hasn’t been used for a decade. “Where is the antibody?” Minion asks. Dr. PhD uses her superpowers to decipher the lab’s antibody list and cross-reference this with the freezer box notations. From the frosty depths, a tube is found; its contents are older than Minion. Dr. PhD explains how to perform the control experiment, but the thought of running extra gels dismays Minion. Returning from the dark room several days later, he looks distraught. “It just doesn’t work. Look.” Dr. PhD looks at the film in the portrait orientation as it is handed to her. Indeed, the film does not seem to show any signal that could be construed as protein bands. Dr. PhD summons her analytical superpowers by squinting. “Wait, could the orientation be this way (landscape)? And could you have possibly gotten the orientation of the middle panel upside down?” she asks. “Yes!” replies Minion. “Then those are your bands down there.” asserts Dr. PhD. Crisis averted.

Meanwhile, Grad Assistant has successfully navigated the governmental bureaucracy required for her VISA renewal and has returned to the lab. At first there are only rare sightings and traces of physical evidence that she has been in the lab, but then as the jetlag wears off she keeps ‘normal’ hours that overlap with the rest of the group. She gears up for experimentation that has been on hold for six weeks. In consultation with Dr. PhD, she has questions. Dr. PhD summons all of her memory superpower to provide answers. When data from preliminary experiments come in, there is another consultation. This time Dr. PhD channels her attention-to-detail superpower, “Of course, I remember exactly what your samples were from your multistep biochemical preparation and the order you ran them on your gel.”

On top of this, the on-campus scientific store stopped re-stocking its inventory as the University launches their new on-line procurement system for ordering supplies. Yes, Dr. PhD can attend a three hour training session. Will the lab be OK? Dr. PhD is concerned because Minion has another experiment to set up and needs supervision. “Where is that Minion?” Undoubtedly, feeding Tenured PI’s cats (not Sigma, of course, but the current feline family). Well, he knows when Dr. PhD is available and has been warned how long the experiment will take for all of his samples. Upon her return, Dr. PhD finds Minion in the lab preparing his samples for the experiment. Hours pass; calculations are completed and double checked. Dr. PhD begins to show minion how to perform a routine measurement on the fluorometer. Upon returning from the other lab room to get a reagent, Dr. PhD senses something is terribly wrong. Where is the data that should have been collected and waiting on the computer screen? The instrument is not working with the default parameters. Dr. PhD-β is consulted, since she was the last one to use it without problems. No, this is something new. Other protocols are tried. Some work. Some fail. The one Minion needs still fails. At this point Dr. PhD feels her superpowers fading. Damn. Her kryptonite is closing in- the hour in which she must leave to commute back in time to pick up Jr-PhD before his daycare starts charging by the minute. All of their efforts fail. “I will contact technical support and deal with this later. Just put your samples in the freezer, Minion,” Dr. PhD says. In a flash, Dr. PhD is gone, out of the door, morphed from her academic superhero status into superhero mommy mode as she races away in her crossover vehicle littered with cheap plastic toys and empty juice boxes.

In the final days at the helm, Dr. PhD summons all of her powers to focus on writing a manuscript of her latest data and transforming a lab notebook’s-worth of other data into a poster presentation for a meeting. Tenured PI and Research Associate will be ready to proof the drafts upon their return. Dr. PhD must also lead the Journal Club discussion this week- finding a suitable article and converting it into a coherent presentation by Friday. There is more troubleshooting of that dysfunctional fluorometer. Just then, Tenured PI phones the lab, “I’m back. Bring the cart down to pick up the repaired computer tower and bring it back to the office.” “I’m on my way,” Dr. PhD replies. It seems that feats of strength are required even for a Superhero PhD.

“So how were things here?” Tenured PI asks as he scans the lab for evidence of catastrophe. He finds none. “Oh, pretty normal. The fluorometer is not completely functional, but I’m in contact with technical support.” replies Dr. PhD. Tenured PI grumbles then asks, “Fine, now where is Minion? I need the other data he was working on for my poster presentation.”

What will happen next? Where is that Minion?*** Will the fluorometer be fixed? Will the manuscript be accepted for publication? Stay tuned for the continued adventures of Dr. PhD.

Johnna

*It’s not that scandalous, they have been married for their entire working career. The implication is just that the lab will be without decades of expertise for the next two weeks.

**OK, well he’s been converted such that he isn’t Pre-med any more. Let the record show that Minion was never Pre-med.

***Good luck on the GRE next week Minion. You’ll fit into graduate school and the wider research world just fine.