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. ↩︎

Pyramid of Biochemistry Greatness

As I mentioned in my previous post, there’s at least one person in the world searching the internet with the phrase ‘everything aspiring biochemists should know.’ I feel obligated to share my pyramid for biochemist success. It’s based on Ron Swanson’s perfectly calibrated recipe for personal achievement. Click this link for context if you are not familiar with Parks and Rec.

Here is a link to the PDF with a little better resolution. Now, go achieve your dreams. I would say good luck, but as Ron says, “Luck is a concept created by the weak to explain their failures.”

Johnna

The Twelve Days of Christmas Plants

If you’re looking for a holiday related diversion, here’s a linkfest of my posts from last year on the Twelve Days of Christmas plants. Understand the plant science behind the traditions. Use these random facts to quickly change the subject when nosy but well meaning friends and family ask you uncomfortable questions.

The Twelve Days of Christmas Plants

1. The Christmas Tree

2. Chestnuts

3. Poinsettias

4. Holly

5. Peppermint

6. Mistletoe

7. Grapes

8. Greens and Black-eyed Peas

9. Sugarcane

10. Oranges

11. Pomegranates

12. Boswellia sacra and Commiphora myrrha

 

If you’re craving even more holiday nerdery or you’ve already used my random facts as diversion tactics last year, check out The 2014 Chemistry Advent Calendar over at the Compound Interest blog. Or check out these Yuletide plants gone global you’ve probably never heard of from the John Innes SVC blog.

 

Johnna

The Grinch Who Stole Science

The Grinch may be green, but he’s not photosynthetic.* However, here’s a grinchy science parody that fits just perfectly on this blog.

 

Every Sci down in Sci-ville liked Science a lot… But The Grinch, who lived just North of Sci-ville, Did NOT! The Grinch hated Science! The whole research season! Now, please don’t ask why. He just wouldn’t listen to reason. It could be that his head wasn’t screwed on quite right. It could be, perhaps, that his ties were too tight. But I think that the most likely reason of all may have been that his brain was two sizes too small. But, whatever the reason, his brain or his ties, he stood there on the funding committee, hating the Scis.

Staring down from his office with a sour, Grinchy glower at the warm lighted windows below in their tower. For he knew every Sci was preparing their aims, busily now supporting their claims. “And they’re gathering their data!” he snarled with a sneer. “Deadline’s tomorrow! It’s practically here!” Then he growled, with his grinch fingers nervously drumming, “I MUST find a way to keep Science from coming!” For, tomorrow, he knew… …All the Sci girls and boys would wake up bright and early. They’d rush for their grants! And then! Oh, the experiments! Oh, the experiments! Experiments! That’s one thing he hated! The Experiments! Then the Scis, young and old, would sit down to a bench. And they’d research! And they’d research! And they’d research! Research! Research! They would start on the -omics, and screens on yeast which was something the Grinch couldn’t stand in the least!

And THEN They’d do something he liked least of all! Every Sci in the tower, the tall and the small, would stand close together, with hypotheses greeting. They’d stand hand-in-hand. And the Scis would start meeting! They’d meet! And they’d meet! AND they’d meet! Meet! Meet! Meet! And the more the Grinch thought of the Sci’s Annual Meeting, The more the Grinch thought, “I must stop this whole thing! “Why for fifty-three years I’ve put up with it now! I MUST stop Science from coming! …But HOW?” Then he got an idea! An awful idea! THE GRINCH GOT A WONDERFUL, AWFUL IDEA!

“I know just what to do!” The Grinch laughed in his throat. And he made a quick Scientist lab coat. And he chuckled, and clucked, “What a great Grinchy ploy! “With this coat, I’ll look just like a PhD decoy!” “All I need is a postdoc…” The Grinch looked around. Since postdocs are cheap, one could easily be found. But they wanted benefits? No! The Grinch simply said, “If I have to pay a postdoc, I’ll make one instead!” So he called his dog Max. Then he took some red thread and he tied a big hood on top of his head. THEN He loaded some bags and some old empty sacks on a research vessel and he hitched up old Max. Then the Grinch said, “Giddyap!” And the vessel started down toward Sci-ville where the Scis lay a-snooze in their labs.

All their windows were dark. Quiet snow filled the air. All the Scis were all dreaming sweet dreams without care when he came to the first lab in the square. “This is stop number one,” The old Dr. Grinchy hissed and he climbed to the roof, empty bags in his fist. Then he slid down the fume hood, a rather tight pinch, but if phenol could do it, then so could the Grinch. He got stuck only once, for a moment or two. Then he stuck his head out of the fume hood flue where the little Sci flasks all hung in a row. “These flasks,” he grinned, “are the first things to go!” Then he slithered and slunk, with a smile most not nice, around the whole room, and he took every device! Beakers! And pipettors! Stir plates! Tris! Sequencers! Manuscripts! Timers! UV-Vis! And he stuffed them in bags. Then the Grinch, very nimbly, stuffed all the bags, one by one, up the fume hood! Then he slunk to the freezer. He took the Scis’ box! He took all the strains! He took the lab stocks! He cleaned out their chem shelf as quick as can be. Why, that Grinch even took their last can of LB!

Then he stuffed all the data up the fume hood with a rant. “And NOW!” grinned the Grinch, “I will stuff up the grant!” And the Grinch grabbed the grant, and he started to shove when he heard a small sound like donning a glove. He turned around fast, and he saw a small Sci! Little Cindy-Vi Sci, who’s qual exams were nigh. The Grinch had been caught by this little Sci daughter who’d got out of lab for a cup of DI-water. She stared at the Grinch and said, “Reviewer, why, “Why are you taking our R01 grant? WHY?” But, you know, that old Grinch was so smart and so slick He thought up a lie, and he thought it up quick! “Why, my sweet little tot,” the fake PhD lied, “There’s a fatal flaw in this aim that’ll kill the whole grant. “So I’m taking it home to triage, my dear. “I’ll fix it up there. Then I’ll bring it back here.” And his fib fooled the child. Then he patted her skull and he sent her to rethink of her hypothesis null. And when Cindy-Vi Sci went away with her thoughts, HE killed the grant until their funding was naught! Then the last thing he took was the log for their data. Then he went up the fume hood himself, the old hater.

On their walls he left nothing but hooks, and some wire. And the one speck of media he left in the lab was a crumb that was even too small for a stab. Then He did the same thing to the other Scis’ labs leaving crumbs much too small for the other Scis’ stabs! It was quarter past dawn… All the Scis, still a-bed all the Scis, still a-snooze when he packed up his vessel, packed it up with their instruments! Reagents! The tweezers! The tape! And the shakers! The centrifuges! The freezers! Three thousand feet up! Up the side of Mount Rejectit, He rode to the tiptop to eject it! “Bye-bye to the Scis!” he was grinch-ish-ly humming. “They’re finding out now that no research is coming! “They’re just waking up! I know just what they’ll try! “Their mouths will hang open a minute and sigh “Then all the Scis down in Sci-ville will all cry Why-why!”

“That’s a noise,” grinned the Grinch, “That I simply must hear!” So he paused. And the Grinch put a hand to his ear. And he did hear a kick-starter rising over the snow. It started in low. Then it started to grow… But the sound wasn’t sad! Why, this sound sounded rational! It couldn’t be so! But it WAS full of hope! No dope! He stared down at Sci-ville! The Grinch popped his eyes! Then he shook! What he saw was a shocking surprise! Every Sci down in Sci-ville, the tall and the small, was researching! Without any grants at all! He HADN’T stopped Science from coming! IT CAME! Somehow or other, it came just the same! And the Grinch, with his grinch-feet ice-cold in the snow, stood puzzling and puzzling: “How could it be so? It came without R01s! It came without panels! “It came without fellowships or reviews through normal channels!” And he puzzled three hours, `till his puzzler went can’t. Then the Grinch thought of something he hadn’t before! “Maybe Science,” he thought, “doesn’t come from a grant.”

Maybe Science…perhaps…means a little bit more!” And what happened then…? Well…in Sci-ville they say that the Grinch’s small brain grew three sizes that day! And the minute his brain didn’t feel quite so tight, He whizzed with his load through the bright morning light and he brought back the equipment! And the laserjet toner! And he… …HE HIMSELF…! The Grinch became a top donor!

 

Johnna

*I just wanted to clearly state that since I know at least one person stumbled upon my blog with the search term “Is the Grinch Photosynthetic?”

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.

A Green Deal for Black Friday

It’s Black Friday. The blog may have been dark for the last couple of weeks while I’ve been busy with my day job, but today I have a special deal for all my readers. I’ve been writing about the holiday plants we use in our celebrations for the past year and now you can have all of those posts to yourself in convenient downloadable PDF format*. All this plant science for the low, low price of absolutely free! How’s that for a green Black Friday Deal?

Here is the link to download:

Holiday Plants: An Autotrophic Almanac

 

Johnna

*Sorry, the Youtube video links don’t work any more, but the rest of the links are still hot.

Plant Skulls

If you didn’t know this was a plant science blog, you might think these were macbre trophies of some ancient tribe. This isn’t so much an appropriate plant costume for Halloween as it is an interesting confluence of floral anatomy and human propensity for recognizing facial forms.

Snapdragons or Antirrhinum sp. are a colorful staple of summer gardens. We’re more used to seeing them look like this image with tall inflorescences boasting clusters of ruffled flowers in a variety of color schemes.

Antirrhinum majus Credit: Michael Apel via Wikimedia Commons

What’s responsible for this spooky transition from delicate flowers to haunting faces? It all comes down to the snapdragon’s flower structure and its bilateral symmetry. The skulls are really the seed pods of the plant after the flowers have been pollinated and the petals have withered away. Dissecting the flowers in their prime shows the ovary at the base of the bloom. The pollen-containing stamens and the style emerge from the orifices in the ovary. These structures leave behind gaping holes that look like a mouth and eye sockets.

Snapdragon flower anatomy

The striking resemblance of these seed pods to human skulls has led to their association with supernatural powers. They were purported to help women stay young and beautiful as well as protect humans of all ages from witchcraft and evil spirits. I don’t have any scientific evidence of that, but if you’re looking for new ideas for botanical Halloween decorations that go beyond cucurbits and mums, dried snapdragon stems with seed pods make a wicked wreath.

Johnna

Links and References:

http://en.wikipedia.org/wiki/Antirrhinum_majus

http://en.wikipedia.org/wiki/Antirrhinum

http://www.missouribotanicalgarden.org/PlantFinder/PlantFinderDetails.aspx?kempercode=a561

http://www.kuriositas.com/2013/07/the-dragons-skull-macabre-appearance-of.html

http://www.waitwow.com/snapdragons-make-cute-flowers-die-turn-skulls/

http://gardenofeaden.blogspot.com/2014/02/the-dragons-skull-seed-pod.html

http://weirdworldwonders.com/the-dragons-skull-snapdragon-seed-pods/

https://s10.lite.msu.edu/res/msu/botonl/b_online/library/snapdragon/flower.html

http://www.flowersplans.com/snapdragon-flower-dry/

http://www.gardenguides.com/126335-history-snapdragons.html

Ophrys: Bee Costumes

Now, let’s really kick off the plant costume series with an easy one that you may have seen before- bee costumes. The bee form is a staple of Halloween costumes for all ages. There are adorable and rotund onesies complete with antennae’d hoodies for the 18 months and under set. At the other end of the spectrum there are ‘sexy’ bee costumes that get much tighter, leave little room for stripes and would otherwise lead one to believe Halloween is celebrated in July not October. Finally, let’s not forget this gem of a throwback from Blind Melon*:

Plants also dress up as bees as well. While the orchid genus Orphys may sound more like a Mardi Gras krewe, their specialty is their bee costumes. Take another look at some of these images. They’re not flowers with a bee rooting around for nectar in the middle- it’s just the flower. Don’t feel too bad if you were fooled, Orphys species fool actual bees too. You see, this is what a sexy bee costume looks like if you were designing it for a bee.

Orphys apifera by Hans Hillewaert via Wikipedia

Ophrys bomybliflora by Orchi via Wikipedia

Orphys fusca by Orchi via Wikipedia

Why would a plant wear a sexy bee costume? To attract unsuspecting male bees over to shake up some pollen. The technical term for this pollination strategy is pseudocopulation. If you haven’t connected the dots yet, the male bees have sex or try to have sex with the bee form of the flower becoming covered in flower pollen in the process. The frustrated bees can then move on to another orchid bearing an attractive female bee form. This transfers the pollen from the first orchid to the second thereby allowing sexual reproduction for the plants from the fake experience of the bees. Of course, the bees are not as likely to be fooled twice (shame on them, right?) so the actual pollination rate via this mechanism is estimated to be ~10%. The orchid makes up for this by producing about 12,000 tiny seeds.

Disguises are not limited to visual cues in the plant kingdom. In another devious trick, the orchids employ their extensive repertoire of biochemical tools to produce chemicals that mimic the smell of female bees. These alkene molecules released by the plant closely match the species-specific pheromones for their bee pollinators. It may look like a bee and smell like a bee, but it’s still just a flower.

Johnna

*What do you know, another plant reference.

References and Links:

http://en.wikipedia.org/wiki/Ophrys

http://en.wikipedia.org/wiki/Ophrys_apifera

http://www.bioone.org/doi/abs/10.1111/j.1558-5646.2009.00712.x

http://en.wikipedia.org/wiki/Allomone

http://www.visualphotos.com/image/1×6046906/eucera_bee_pollinating_ophrys_scolopax_orchid

http://www.biomedcentral.com/1471-2148/8/27

Marijuana disguised as okra. Wait, What?!?

This wasn’t the topic that I wanted to use to kick off the subject of plant costumes, but when plants make the national news, I really feel compelled to write about it. In a most unfortunate case of mistaken identity, a drug task force in Georgia raided a farmer’s property only to find okra. It seems that a helicopter fly-over mistook his okra for Cannabis plants. This information was used as the basis for a raid by law enforcement.

Upon realizing that it had dispatched officers to confiscate a popular gumbo ingredient, the Georgia State Patrol, which operates the task force, issued an apology, both to Perry and publicly.

The farmer did not appreciate being confronted at gunpoint over his choice of garden plants. However, common sense prevailed without any damage to humans or property (botanical or otherwise). As part of the news article on CNN.com, the following graphic was used and now ranks among my favorite captions of all time.

Indeed. Pop culture has led me to believe the above plant is more suitable for dessert recipes. The corollary is probably also true- don’t try to smoke okra.

The reason for the mix-up lies in the following statement:

“It did have quite a number of characteristics that were similar to a cannabis plant,” Georgia State Patrol Capt. Kermit Stokes told WSB.

Really?!? Well, they are both green and have leaves and can grow to quite tall. Generally, the leaves of the two plants look nothing alike. Okra plants have broad leaves with 5-7 lobes on them, while Cannabis leaves are compounds leaves with 7-13 thin serrated leaflets each.

Okra by Federix via Wikipedia

Cannabis plant by Pavel Sevela via Wikipedia

So, there could be some overlapping features in terms of leaf shape. But the flowers are completely different and okra produces distinct fruit pods.

It seems that law enforcement groups could benefit from remedial botany classes.

Johnna

References and Links:

http://www.cnn.com/2014/10/07/us/georgia-okra-marijuana-raid/index.html?hpt=hp_t2

http://en.wikipedia.org/wiki/Okra

http://en.wikipedia.org/wiki/Cannabis