Graduate School Does Not Prepare Students to Teach Effectively

Graduate School is Great

Don’t get me wrong. I enjoyed most of my experience while in graduate school working towards my Ph.D. I was paid to fuel my personal curiosities about how bacteria make choices. It was a win-win in my opinion. I was contributing to the overall knowledge of the scientific community and making connections that I never would have dreamed of years before. I could safely say no one on the planet was investigating the same phenomena I was, so I held knowledge only I knew. Pretty amazing feeling. I read some article in Science Careers long ago about advice for graduate students. One nugget was that the student needed to become the expert of their project, not their advisor. I tried to make that my goal and knew I was succeeding when my advisor would ask my advice about observations she was making in the lab.

Graduate School is Good

Don’t get me wrong. Graduate school was not all a field of lilies. It was hard, very hard. Blazing trails and keeping up with all the latest research from around the world about my topic was daunting. Then, there was the preliminary exam (aka qualifying exam); six weeks of taking on an entirely different topic, becoming an expert, devising experiments to answer research questions, writing a full grant proposal, presenting to the department, and defending your ideas for hours is not for the faint of heart. However, the prelim (I had to go through twice) is like being thrown into the ocean as an infant and told to swim the English Channel. If you make it, you are a much better scientist for it. It was HARD, but I don’t regret all the effort it took.

Graduate School is O.K.

Working in the lab can be very time consuming. Many lab bosses expect the grad students to be in the lab 60 to 80 hours a week. I should have been in the lab more, I admit, but I also had a wife and a daughter the last couple years. I had a lot of expectations of me not only as a student and a training scientist but also as a husband and father. Only one of these four expectations was I an expert at after 25 years of schooling. Being spread so thin made each facet that much harder. Needless to say, my wife (and daughter, and in-laws, and parents, and brother, and the rest of the family, and friends, etc.) were very excited when I finally saw the fruits of my indentured labor.

Graduate School is Absolutely Horrible

Don’t get me wrong. I had opportunities to ‘teach’ students during graduate school. I taught a few semesters of lower-level biology lab sections early on. I enjoyed trying to make connections for the students. I remembered when it all came together for me and the light clicked. I wanted that so badly for my students; and much earlier in their academic career.

Now I am out of school with a degree I am very proud of. At what point in graduate school was I supposed to become an expert teacher? Much emphasis is towards shaping an independent scientist who can survive in the jungle, and rightly so. But, what about an emphasis on one of the tenets that come with many job descriptions those fledgling scientists would eventually end up with: instructing? No courses, no seminars. Am I missing something? Is the arena of instructing young minds preparing them for the future jobs we need them to take and excel at not important?

I am very fortunate. I have a faculty position now. I am an expert…but not at what I am expected to do, teach. I am a novice, an infant trying to very quickly consume as much information in teaching strategies and instructing styles that I feel I should have been exposed to in school. Do the science departments and education departments of our colleges and universities know of each other’s existence and absolute need for integration?

I want to be the best instructor ever. I want my students to get it every lecture/class meeting. I want them to appreciate the world around them and make logical decisions. Is that too much to ask? It is for the current state of a majority of graduate schools.

 

Academia as an Unwieldy Vortex

Vortex of Academia

 The safety of academia

In the fall of 2012, I left the comfortableness of the lab in which I had been nestled for 6 years. It was an exciting and terrifying time. I was not going the normal tract for a new Ph.D.; a post-doctoral fellowship. Are we not steered towards a career in academia? I was warned by several professors to make my choice wisely (and for good reason). My wife and I had a life in my town and the thought of uprooting for two to 8 years did not sound appealing. I was very fortunate to take a position as a science writer helping a federal department’s program in biological and environmental research. It was new territory for me, but I knew the opportunity was too great to pass up.

Exactly one year later, I found myself out of work due to reduction in force. I had never gone through such a thing. Those words when they were spoken to me gave me a sort of out-of-body experience, a nightmare really. It took weeks for me to come to grips fully of the immense toll it would take on my family.

Back to the applicant pool

Being a Ph.D. in a mid-sized market is a daunting thing. It seemed as if I was over-qualified or in the running with about 50 other sorry Ph.D.s for each position in which I applied. One part-time position became available as I was hitting the unemployment line as an adjunct professor at a local college. I was teaching ‘Health Science Research’. A great and appealing position if I knew exactly what health science research was. My wife was not as thrilled as I in this opportunity. Who knows, I could land a full-time position soon, I thought. I gladly took the position and kept searching for something permanent and life-sustaining. By early 2014, I had found a hand full of part-time spots to keep us afloat. I was looking several times a day at career sites and every other job portal for the biggest employers in the region. My search had grown to opportunities an hour a way from home. Academia, industry, government; it did not matter to me. I had mouths to feed.

Oh boy, what luck, er tragedy

My adjunct employer asked me to teach additional courses in the summer. However, this schedule overlapped with my wife going back to her position as an elementary school teacher. This meant we would have to pay childcare for a newborn. In other words, we would have to pay the equivalent of another small mortgage monthly for me to work. A catch 22 if ever there was one, but my boss knew my incredible urge to be taken on full-time.

A few weeks after regretfully declining the offer, I received an email on a Sunday morning from my adjunct boss. A faculty member in the Science Department was on life support after a ruptured aneurysm. I was asked to step in (in the middle of the quarter) and teach three additional classes starting the next day. I had no choice but to accept out of respect and duty. The next morning, I found out the faculty member passed away. I couldn’t be happy for my good fortune. How could I? His mother had lost her husband and son within 6 weeks time.

So, here I am stepping into a full-time role with two mid-term exams and a quiz my first week to prepare; not to mention hours of lectures to prepare with no slides to reference from previous quarters. I have not, and will not, complain about my circumstance. I think of his mother and sisters often.

Home Sweet Home

18 months after leaving the world of academia, I find myself thrown back into a forceful vortex. No time to stop and think about ivory walls or effective pedagogy. I’m treading the academic waters for a few more weeks. Going one lecture/class at a time trying to give the students my best efforts, for their sake. Don’t get me wrong, I want to become increasingly effective at teaching my students and getting them curious in biology. Just let me turn in final grades for this quarter first.

Using HIV to Cure Leukemia: Mixed Emotions About the Claims

For those who don’t know, I teach a health science research course at a local college. I love teaching this class because I am allowed to give students a foundation in scientific inquiry and build upon this up to current topics in health science like personalized medicine and systems approaches. All this builds up to an article summary the students prepare based upon a journal article of their choosing.

Two of the students pairing up to present a summary of their paper showed me last night a video they found that accompanied the research they were excited about presenting [see below].

First, I was surprised the principal investigator, Carl June, when asked if he was curing cancer, said unequivocally, “Yes”. I understand this is a promotional video produced by GE, but June really took the bait.

I truly recognize the enormous potential this type of therapy has. The week before being shown this video by the students, I gave a short lecture about science and the media. The main point was to be skeptical of the message portrayed by the media. It appears, I need to revisit this subject.

This promotion of research goes beyond the “Hidden DNA Code” press release that went viral as part of the ENCODE project from the University of Washington. Not only was the wording sketchy (using ‘HIV’ to cure leukemia), but the lead researchers are touting curing cancer (leukemia in this case). A very good article about this entire subject can be found here. In small clinical trials, the therapy has found success thankfully. However, the trials have been very small thus far and we are dealing with cancer; the correct term is remission, not cure.

I urge everyone, please do not read medical breakthrough stories and go away with a warm fuzzy feeling. Please take an extra step and dig a bit deeper. You will find the warm fuzzy feeling is not for the present story you just read but from the optimism you (and everyone else for that matter) should feel about the stories to come in the future when the science has been thoroughly tested and the therapy is real.

For ‘Emma’ in the above video and only Emma, today that therapy is real.

Abstract 2.0 Is On: Help Wanted

I have sat on this long enough. It’s not like a have anything else going on right now (except the birth of a son in a  month, syllabus to write, classes to prepare, evaluations to do, data to journal, …). Introducing:

Abstract 2.0

Here are the details presently. I and anyone willing to help will scour the journals of our respective fields and choose those we feel need to be disseminated to the larger public. In a short synopsis (abstract if you will), an overview of the article and why it is important will be written and deposited here. Details will be worked out on how to submit the abstracts in the near future.

Now is the time to act (or later if now is not convenient)!

Bacterial Chemotaxis and Human Memory: Pete and Repeat

Many do not place ‘bacteria’ and ‘memory’ in the same sentence. Normal human perception does not connect the two concepts. However, Mother Nature seems to have a more profound perception. The past 50 years or so of scientific investigation has shown how our uniqueness as humans is actually commonplace across all forms of life on Earth. Case in point, how closely associated molecular memory is between bacteria and human.

Bacteria use adaptation to signals as memory

Swimming bacteria do not move randomly in their environment. This behavior would be futile and counterproductive. Instead, bacteria are constantly monitoring their environment in search of food and poisons. Moving towards the former and away from the latter. This observation was first published in the late 19th century. Bacteria, like the famous and infamous E. coli, use molecular antennae to receive these important ‘signals’ as the basis in the decision of which direction to swim. What if the bacteria find a great place to reside with lots of food but still need to receive signals to ensure they remain there? The antennae have sections that can be modified easily and reversibly. These modifications, in the form of methylation, alter the sensitivity of the antenna protein to subsequent signals. Methylation allows these antennae not to receive the number of absolute signals but relative signals. In other words, the antenna protein through fine-tuned methylation detects changes in the number of signals now versus some time in the past. This is the basis of molecular memory.

These antennae are proteins called methyl-accepting chemotaxis proteins, or MCPs. MCPs accept methyl groups from the essential cofactor S-adenosylmethionine (aka SAM or AdoMet). AdoMet is essential to both prokaryotes and eukaryotes like humans. The methyl groups are added by a protein called CheR (pronounced ‘key R’) which transfers the methyl from AdoMet to very specific amino acid side groups of glutamate. The process, called O-methylation adds the methyl group to the single-bonded oxygen on the carboxyl.

O-methylation reaction
O-methylation reaction. Courtesy of www.brenda-enzymes.org.

The length of a bacterium’s molecular memory is very short in comparison to how we perceive memory at only a few seconds. But, to bacteria it is long enough to successfully navigate the environment with similar precision when concentrations of food or poison vary (up to several orders of magnitude, or ~1000x).

Does the basis of molecular memory in humans mimic bacteria?

Eukaryotes, including humans, use a very similar mechanism in signal transduction to bacteria. Phosphorylation (transferring a phosphate group from ATP or GTP to a protein amino acid) is the basis of all signal transduction and cell regulation. Bacteria use histidine kinases and response regulators, as do plants to some degree. However, the majority of regulation through signal transduction in eukaryotes is through two types of proteins, RAS proteins and the heterotrimeric G-proteins. G-proteins interact with membrane receptors that regulate their activity. What determines which surface receptors G-proteins interact with? Isoprenylcysteine methyltransferase, or ICMT, is one of two methyltransferases that regulate signal transduction activity. ICMT is a membrane protein that uses AdoMet to add methyl groups to isoprenylcysteine, a post-translationally modified cysteine residue on both heterotrimeric and RAS-related G proteins. Methylation regulates which receptors the G-proteins interact with, thus playing a major role in connecting the initial signal to downstream regulatory pathways. The carboxyl methylation essentially modulates G-protein signalling globally.

G-protein carboxyl methylation is regulated by GPCR signaling and, as seen above, GPCR signaling is regulated by G-protein carboxyl methylation. This feedback/feed forward loop could be seen as a form of molecular memory stored in methylation patterns. Within the brain, ICMT activity is almost exclusively found in the region controlling coordination of movement. Thus, methylation could be used to modulate certain neuronal signaling pathways which result in learned patterns of sensory-motor skills.

The only other major methyltransferase is from a protein known as PPMT. PPMT interacts with a major enzyme in signal termination, the protein phosphatase PP2A. PPMT adds methyl groups to the backbone carboxyl of a specific leucine in PP2A. This carboxyl methylation helps determine which B subunit PP2A interacts with and where in the cell PP2A can be found. PPMT structurally resembles CheR in bacterial memory. Moreover, the enzyme that removes the methyl group from PP2A, PME, structurally resembles the bacterial enzyme that removes methyls from MCPs, CheB.

PP2A is one of the major regulators of pathway coordination to maintain synaptic plasticity in the brain. Interestingly, methylation defects and PP2A-PME complexes are suggested to play a role in the cause of Alzheimer’s Disease and memory loss. Methylation defects leading to defective phosphatase activity of PP2A leads to accumulation of a phosphorylated subunit of the structural protein microtubule. In this phosphorylated form, the filaments used to keep axons structurally sound collapse and lead to loss of normal synapses. Therefore, molecular memory in the form of methylation plays a vital role in promoting normal brain activity and its disruption can ultimately lead to dementia. 

Chicken, meet egg. Egg, meet chicken.

So, from bacteria to human, carboxyl methylation is necessary for memory. Did these pathways evolve individually in parallel, or did the memory we have today originate in the predominant lifeforms found within us?

 

Suggested Reading

Li and Stock. (2009) Biol. Chem. 390: 1067-1096. DOI 10.1515/BC.2009.133

Science: Solving Mysteries One Clue at a Time

This past Tuesday, something mysterious and amazing happened. My wife noticed a strange deposit into our bank account; a large deposit: $1,400. She asked when I was supposed to be paid for something I was working on and I told her not until later. This deposit piqued both our curiosities. What was it? Why was it in there? Who put it there? I started investigating; researching as much as I could. I was able to find out it was $1,400 cash, which bank branch and what time the money was put in. Paranoid it was some scam perpetrated to clean out our bank account, my wife wanted me to call the bank to inquire. So, Wednesday morning, I called. Long story short, my wife received a call Wednesday afternoon from a bank employee saying someone anonymously deposited money in our account because they thought we should have it. What? To say the least, we were humbled and astonished. The curiosity has not gone away. We are still trying to figure out who this saint(s) is.

This mystery made me think; it is eerily like the field of science. The path to discovery in any science discipline begins with something very simple, an observation. My wife observed a strange deposit into our bank account. Observations lead to curiosity and ultimately yield questions. What was this deposit? Why was it there? Who put it there? Explanations or answers to the questions are developed. These explanations, or hypotheses, have their validity tested through experiment or some action. My wife’s initial explanation was that someone deposited it to somehow gain access to our account to clean it out. My action of calling the bank to report the deposit as not originating from the wife or myself was partly to make sure the deposit was legitimate and not some clever scam. Through experiment or action, facts are gathered to support the explanations or rule them out. The fact a bank employee called to let us know the deposit was from an anonymous ‘Good Samaritan’ ruled out the hypothesis of the scam. Scientific discovery ultimately leads to more observations, curiosity, questions, and hypotheses.

For my wife and I, the discovery that someone thought so highly of us to give us any amount of money has only fueled the mystery. The main question now is, who did it? Unlike any good mystery, or science for that matter, we may never find out.

This post is dedicated to my family’s ‘Good Samaritan’. Thank you…

STORYTELLING IN SCIENCE: THE CELL AS YOUR FAVORITE RESTAURANT PART III

<img alt="Storytelling in science visualized through bacteria"      src="open-for-business.png">
Storytelling in Science visualized

Perhaps a running list of metaphors so far:

Restaurant: bacterial cell

Building: cell membrane

Doors: channels and transporters

Patrons: metabolites/compounds/substrates and products

Employees: proteins/enzymes

Managers: two-component proteins to regulate gene transcription

Employee list: genome

Copy machine: DNA replication machinery

So, in the last part our restaurant was going great and we opened up a new restaurant with the same employee list among other things. The two restaurants are now independent of each other and are free to act accordingly.

What if things change and times are not going as well? The overall number of patrons drastically decreases, not enough electricity (ATP) to run the restaurant or running water (redox potential)? What if disaster is about to strike? How can the restaurant prepare all the managers, employees, the building, the doors, the patrons for it?

Luckily the restaurant has a monitoring system that can quickly make sure the restaurant will be ready for anything that comes its way. The monitoring system can take snapshots of all data generated by the restaurant: power supply, water supply, patron count, employee count, conditions outside the restaurant like weather or competing restaurants. The monitoring system is the bacterial second messenger systems. With the support of the managers, the monitoring system can instantaneously keep track of all variables and make changes as needed.

The system is detecting the start of a drought. This drought will lower the number of patrons coming and going from the restaurant. The drought will also change the available electricity and water supply of the restaurant. The monitoring system sounds the alarm, a message is sent over the intercom for all the managers and employees to hear and react to. The intercom message alerts some managers to call in additional employees while telling others to stop their work. Some employees take on a new job in preparation for the drought. The intercom message is the bacterial second messenger cyclic-di-GMP. The entire restaurant begins preparations for the drought so it can survive until better times are present. Other than changes to managers and employees, some new employees are called in to prepare the building itself. Perhaps to change the number of doors. The employees may also change the exterior of the building to better withstand the drought like changing a wood exterior to a brick or stucco one. The brick or stucco are the exopolysaccharides, complex sugars on the exterior of the cell that can serve as protection or to help cells adhere to each other to ride out the hard times together. 

When times change, the restaurant has to be able to change with them. That is why these restaurants have been in business for ~3 billion years and still going strong.