Monthly Archives: April 2015

Search, Research, and Research

When you do research, you’re not just researching your topic: you’re researching yourself, and learning how you work best. I’ve learned lab techniques this year, yes, but none is as important as these two acquired lessons: my interests are labile, and read up on lab literature before joining a lab. I want to switch labs, and I will remember these lessons when making that switch.

Research

How did I initially decide to work in Dr. Wang’s lab? “I do research in epigenetics,” said Dr. Wang on the first day, a Monday, of my BMB 251H class last fall. “I’m interested in epigenetics,” I thought, and subsequently asked if I could visit his lab. On Tuesday, I was sitting in Dr. Wang’s office, conversing about notable undergrads with whom he had previously worked, who were now in prestigious medical or graduate programs. Starting by shadowing Jinquan in September, I embarked on her research on a protein called HDGF2. However, on the penultimate day of fall semester, I took Dr. Wang out to lunch and said that I felt that I’d been in his lab for a semester but had no real responsibilities, and that I was having trouble committing to a regular schedule. He said that I could have more responsibility next semester (as in this one, almost past) and schedule weekly lab time, just as my classes are scheduled weekly. On that optimistic note, I went on winter break.

Over break, I read some of Dr. Wang’s papers to learn background information for my research this semester. But I was also searching for summer research. After realizing that my trip to China to take BMB 252 precluded me from most summer research programs, I found an email from SHC Career Development inviting undergraduates to work in Dr. Costas Maranas’s lab. His lab uses computers to design proteins which, when incorporated into bacteria, would enable them to produce biofuels and other valuable chemicals from methane and organic waste. An incentive: Dr. Maranas was offering a stipend, while Dr. Wang was not, and subletting an apartment in State College over the summer would cost money. Thus, I emailed Dr. Maranas, read two of his papers, and met with his graduate students; they informally interviewed me and judged that I would have sufficient background knowledge and programming skills by mid-June to contribute to the project. One graduate student was applying for a grant that required that two undergrads collaborate on his project, so he added me to the list, and just like that, I was committed to the lab for the summer, the day before spring semester began.

The first two weeks back in Dr. Wang’s lab were great. I had floundered the previous semester, learning (by which I mean failing, mostly) to insert a circular piece of DNA called a plasmid into E. coli, grow the E. coli to generate a lot of plasmids, and then extract the plasmids from the E. coli. The second week, though, as classes were still yawning awake, I planned how I would use every chunk of free time to do every step towards generating that DNA in E. coli. I ran to lab in the morning, set up a reaction, ran to class, to lunch, to class, and back to lab; it was stressful, like being a lab mouse in a maze. But in five days, I had two tiny tubes containing the right plasmids dissolved in water, as well as a swelling of pride: more than I had accomplished my first semester, I had done in a week. At that moment, I was quite sure I had a bright future in Dr. Wang’s lab.

That satisfaction, however, never came again. As classes accelerated, I could not manage to devote most of my non-class time in subsequent weeks to research. The plasmid extraction part of the project finished, I looked forward to the next part: putting the plasmid into bone cancer cells and measuring how it affected their gene expression via western blotting. Jinquan had to do those steps. Meanwhile, she had told me to read up on HDGF2 protein for another project, so I read some papers, but that project was on hiatus, as the mice missing one copy of the HDGF2 gene would take a month to produce mice missing both copies. (Genes are italicized; the proteins they encode are not.) I kept drifting from project to project; not committing to any one, I was not significantly learning, progressing, or feeling satisfied. The work was stressful; I never felt like I was doing well enough to please Jinquan since the week I made the plasmids. I was lonesome, working without a fellow classmate with whom I could discuss the research and have fun outside of the lab. Moreover, the specific projects of Dr. Wang and Jinquan were interesting me less and less.

What was replacing them? Microbiology, auspiciously. Before I even applied to Schreyer, I remember looking at the list of Honors courses and thinking dismissively, “Oh, I can take Honors Microbiology. Are there any classes about nutritional biochemistry?” How do you tell a good class? It changes your mind. My Microbiology 201H and Microbiology 202 lab classes have switched my interests from eukaryotic (animal, plant, fungal) to prokaryotic (bacterial, archaeal) biochemistry in only three months. Although I am still interested in human biology, I recognize now how much microbes profoundly affect human health. It startled me that our ways to identify and kill pathogenic microbes are much more tenuous than I imagined, and that resistant bacteria are on track to vitiate our last reserves of antibiotics. I thus attended a screening of The Resistance, a documentary about antibiotic resistance that would compel any biologist to switch to that field.

Microbes relate in more ways to human health. I attended a lecture here, given by University of Colorado Boulder professor Rob Knight, about how the bacteria living in our intestines profoundly affect our risk for developing obesity and other chronic diseases, but that we have only superficial knowledge of how they do this, or even what bacterial species are living there. Writing a term paper for Microbiology 201H, I learned that the microbes in our intestines even regulate our appetite. Some bacterial species not only thrive when we eat too much but also can compel us to eat too much; if they gain a stronghold, they can flourish as they make us gorge to obesity.

A little more indirectly, but no less pressingly, microbes affect human health via their potential to purify water, generate electricity, recycle waste, and produce valuable chemicals. Producing sufficient energy, water, and food are likely the three most important problems now facing humanity, even more important than cancer epigenetics (the focus of Dr. Wang’s lab), or even antibiotic resistance and obesity. If we could use unlimited energy to distribute unlimited potable water and nutritious food to everyone in the world, we would reduce malnutrition, poverty, obesity, and other chronic diseases, as well as infectious disease, which often spreads in third world nations via contaminated water, and which the aforementioned ailments exacerbate. Microbes have a role: in Microbiology 202 lab, we produced 0.3 milliwatts of electricity by packing two wires and some normal bacteria-laden dirt into a plastic jar. One Penn State professor can generate somewhat more electricity: Dr. Bruce Logan is one of the world experts on microbial fuel cells, and I am interested in visiting his lab this summer, possibly to work in his lab next fall. However, as I said at the beginning of this post, I will give his lab thought before I interview to join.

In my desire to switch labs, I have been visiting other labs and reading their background literature. Dr. Gong Chen recently made a breakthrough in repairing brain injuries; I interviewed him about and read some of his papers, but I decided that his research is not as quantitative as I would like, and that the projects his lab is moving towards—murine behavior tests—are not my passion. Dr. Miyashiro, my Microbiology 202 lab professor, is doing work with host-microbe symbiosis in squid (the human microbiome is a type of host-microbe symbiosis, too), but I visited his lab and again do not think the research is quite right. However, I am looking forward to Dr. Costas Maranas’s lab this summer. Working on a coding project this semester, I have realized that coding things on computers is one of the few activities that will keep me up until 3 AM (twice!). Add that I enjoy physics, chemistry, and biochemistry, which are integral to protein design and metabolism. Add that the mission of the lab is to design bacteria that recycle organic waste into useful chemicals, and I have more than a hunch that I will enjoy the work.

Do I know for sure? No, but I need to do research to learn if this is work I enjoy. I know my mission: make health sustainable. I do not know my approach, which is unsettling, but also exciting. As I am scoping it out, and indeed, as you too are figuring out what you want to do, I think that a good take-away message is this: always pay attention to how well the work fits you. Does it fulfill you? Aggravate you? Cut into your hours for friends, fun, or sleep? Do you have to force yourself to do it, or do other people have to pull you away from it? Don’t shoehorn yourself into something you hate, because you can find what you love. How? Search, research, and research.

Good Predictor of Achievement: GPA?

            GPA easily condenses four years of college into one number. But what does that number mean? Intelligence? Work ethic? Potential for success? As an undergraduate, I worry about maintaining a good GPA, partly because of my impression that I need a good GPA to succeed professionally, and partly because I feel pride over good grades and shame over poor grades. However, I have never believed that grades alone disclose students’ aptitudes or foretell their future successes. A number of recent events have motivated me to investigate what college GPA really means.

  1. My Microbiology 201 Honors professor gives an A or A-minus to every student in the top half of my 23-person class; my friend’s Microbiology 201 professor grades on a standard “A = 93 to 100, A-minus = 90 to 93” scale. How can you compare the grades of students from these two microbiology classes?
  2. The moderators of a seminar about scholarships that I attended said outright that if you are a senior with a 4.0, you have probably never dared to challenge yourself, or else you have spent all of your time studying and missed everything else about college. How does a GPA indicate experience and critical thinking?
  3. At the annual student awards ceremony, Penn State seniors in the top 0.5% of their class (3.99 GPA and above) were honored. Additionally, senior Chris Rae was honored for winning a Gates-Cambridge scholarship, and senior Ryan Henrici was honored for winning a Goldwater Scholarship, a Marshall Scholarship, and an Astronaut Scholarship. Neither student was in the top 0.5%. Is a student with a 4.0 and no scholarships more successful than a student who won a Gates-Cambridge scholarship with a slightly lower GPA?

Why is GPA important?

According to Roth and Bobko, there are two main reasons to use GPA: it is easy and cheap to obtain and interpret, and it is generally believed to reflect student aptitude and work ethic. Thus Caulkins, Larkey, and Wei say that colleges consider GPA in awarding financial aid, ranking students, and determining whether students have performed well enough to earn a degree. Employers use GPA to screen interviewees; indeed, students may associate GPA with their self-worth. Certain majors at Penn State, such as Mechanical Engineering, also mandate that entrants have a 3.0 cumulative GPA. GPA thus has a potentially lifelong impact on career, income, and satisfaction.

What are the flaws of GPA?

            The rationale of using GPA is that it indicates student aptitude and efficacy, according to Roth and Bobko. This is partly rational, as GPA is weakly correlated with general intelligence. However, the correlation constant (r) is somewhere between 0.3 and 0.7, which means that r2, which tells how much of the variance in GPA is due to variance in intelligence, could be between 0.09 and 0.49; that is, at most, only half of the difference in GPA between two students can be attributed to difference in intelligence. At the least: only 9%. The authors said that student conscientiousness also affects GPA (r = 0.34, r2 = 0.12), but that external factors, such as differences in grading scales, course difficulty, biased professors, and other time commitments like part-time employment, impact GPA.

Caulkins et al. illustrate that external factors in grading invalidate student-to-student GPA comparisons, especially across majors. For example, in a study of seven colleges, the average math class GPA in 1991 was 2.53, while the average English class GPA was 3.12—a difference of 0.59. Are English students that much smarter? No, say Caulkins et al.: the math classes drew higher achieving students but had more stringent grading standards, making it impossible, without adjustment, to compare the GPAs of students with substantially different course work. That GPA contains numerous factors besides intelligence and conscientiousness, such as the difficulty of classes taken, argues against using it alone to rate students.

Then what, if not GPA?

Caulkins et al. argue that no single number can accurately describe student performance. However, though GPA can never truly be accurate, it can be much more so than it is now. They evaluate five ways to adjust grades class by class to make GPAs more accurate:

  1. Calculate the difference between a student’s raw grade and the average grade in each course, and then average those differences to calculate GPA. GPA = average(student grade – course average). This method, however, does not consider that grades in some courses are clustered, while grades in other courses are widely spread.
  2. Calculate the z score of the raw grade a student received in each class, then average the z scores to find the GPA. GPA = average((student grade – course average) / course standard deviation). While this method corrects the clustered/spread problem, it does not consider that an average student will earn a lower GPA by taking classes with high-achieving students than by taking classes with low-achieving students.
  3. Instead of comparing students to the average scores of their classmates, compare students to the average historic grade of every student who has taken the class, by subtracting the average historic grade from each student’s grade. GPA = average(student grade – average historic grade).
  4. Instead of subtracting, divide each student’s grade by the average historic grade. GPA = average(student grade / average historic grade). This method and method 3, however, do not consider that in some classes, the lowest- and highest-performing students receive grades within a narrow range, while in other classes, grades are spread widely.
  5. Combine methods 3 and 4: first divide by an average historic grade, then subtract another value to adjust the grade, then average these adjusted grades to calculate GPA. GPA = average((student grade / average historic grade) – adjusting value). This method corrects for the variability in grade distribution.
  6. The Item Response Theory (IRT) method is an already-developed method that has successfully adjusted GPA to better match student aptitude.

Which method is best? Caulkey et al. studied whether these GPA-adjusting methods were better correlated with three pre-college-admission variables—high school GPA, math SAT, and verbal SAT—among Carnegie Mellon undergraduates. They found that for natural science courses, method 3 GPA correlated best with high school GPA and math SAT, and IRT GPA correlated best with verbal SAT, although not statistically significantly so. Thus the authors argue that since GPA correcting formulae are simple and more effective than raw GPA, colleges should all employ them. However, they concede that phasing in adjusted GPAs should be gradual, as a sudden change would upset colleges and employers, who use GPA so widely.

GPA inevitably has limitations

Still, a single number, even an adjusted GPA, cannot encode all that a student is or can become. Importantly, we must recognize what GPAs mean. Not only are they affected by intelligence and motivation, but also by professors, classes, classmates, extracurriculars, and dumb luck. Students should not inextricably associate these inherently flawed statistics with their self-worth, potential, or any parameter mentioned already.

Ernest William Goodpasture got a D in Latin at Johns Hopkins. Later, he pioneered growing flu vaccines in chicken eggs, a method that has saved millions of lives up to this day.

Who makes doctors look smart?

When your doctor takes a blood sample or a throat swap, then gives you the results some time later, you probably think little about who actually analyzes those samples. But without these people—clinical lab technicians—working inconspicuously, doctors would not be able to determine your blood sugar, test you for strep throat, or do any other kind of chemical test.

I toured the clinical lab at the University Health Services and observed the techniques that the clinicians use to analyze samples of all sorts. Say that you come into UHS with a sore throat. A lab technician will take your throat swap and spread it onto a Petri dish full of a type of food called MacConkey agar, then incubate the dish for several days. Only gram-negative bacteria can grow on MacConkey agar; a common cause of strep throat, Streptococcus pyogenes, is gram-positive, so growth on MacConkey agar rules out this bacterium as the infectious agent. If there is no growth, the technician will culture the bacteria on another plate containing blood agar, which is opaque red; if the bacteria make the agar transparent, they are likely S. pyogenes.

Streptococcal_hemolysis

Streptococcus growing on blood agar in section marked “β.” Y Tambe. Wikimedia Commons.

If the infection is less clear, the technicians will culture the bacteria in a plastic plate that contains over 100 wells, each filled with a different chemical, such as glucose or lactose, and a dye. As the bacteria grow, they consume specific chemicals, causing certain dyes to change color; each species produces a characteristic pattern of color changes that the technician can use to identify it. For example, most Escherichia coli strains ferment glucose, but not sucrose, producing acids that cause the dye to change color in only the glucose well, while most Pantoea ananatis strains ferment both sugars, changing the color of both wells. This way, technicians can distinguish between bacterial species.

To diagnose other conditions, infectious and not, technicians will examine almost any body fluid microscopically. Say that you are having blood work done. The clinicians will take a small amount of blood and feather it out onto a glass microscope slide. I was allowed to inspect a sample at 1000x magnification, at which point red blood cells were visible as indigo ovals with pale centers and white blood cells were purple, more irregular blobs. The white blood cells were pressing up against the red blood cells, which is indicative of mononucleosis. I also was able to inspect a urine sample that a technician had placed into the narrow gap between two plastic plates, much like in a hemocytometer. I saw tiny X-shaped crystals of calcium oxalate, which can constitute urinary or kidney stones, and thus its appearance in the urine is a warning sign.

Infectious mono

White blood cells (purple) pushing against red blood cells (pink), indicative of mononucleosis.

The heart of the diagnostics, however, is the array of test strips. To accurately test for mono, for example, the technicians take a piece of plastic that encloses a strip of paper treated with chemicals that change color upon exposure to molecules in the blood. They put a drop of blood through a hole in the plastic and onto the test strip; as the blood diffuses across the strip, it causes one or two spots to turn purple. One spot is the positive control: it should turn purple whether or not the patient has mono, and if it stays white, the test result is void. Assuming the control works, a color change in the other spot indicates mono. Technicians test for many conditions, such as pregnancy, with test strips like these.

Test Strip

A cartoon test strip, showing positive, negative, and invalid results.

When the change in color is not “Yes or no?” but rather, “How much?” technicians place the treated test strip into a machine called a colorimeter that accurately measures the color. (In the past, technicians had to estimate the colors with their own eyes.) For example, blood glucose test strips have a red circle that changes color when exposed to glucose; the more glucose, the more the color changes. A colorimeter about a meter cubed reads the test strips for glucose and triglycerides. I realized that many times in my nutrition blog and issue brief, I had talked about blood glucose and triglycerides, but never had I wondered exactly how they were measured. But seeing the colorimeter that does the job was fulfilling nonetheless.

What struck me most about the clinical lab was its reliance upon prefabricated chemical tests. Test strips, colorimeters, bacterial well plates—they all come ready to use, and this gave me new respect for the industry that mass-produces these diagnostic tools and makes them ever more efficient. The technicians told me that there are fewer schools that offer programs in clinical lab work now than there were twenty years ago, and that few people are entering this field; consequently, there will be a job shortage in ten years if trends continue. Though job prospects are promising and the median salary is about $57,000, I do not think that I would like to be a clinical lab technician. I recognize their importance in diagnostics, but I would like to go into a research career focused more on developing new technology or knowledge. But, as always, ruling against a potential career still helps me to decide what I would likely rather do.

PowerProtocol

Learning lab skills is half of the battle; I also have to learn how to learn lab skills, and learn them as time-efficiently as I can. Thus far, I have learned that simply observing Jinquan perform a procedure while asking questions occasionally is not effective. Writing down the details of the procedures helps, but is it best to write down the steps as Jinquan performs them or after she finishes? Though writing in real time minimizes the number of details that I miss, it is unfeasible for some techniques, such as exposing film in the darkroom. Ideally, I would do both, recording the details in the lab and reviewing them afterward.

So that I would better learn how to perform a western blot, Jinquan asked me to make a PowerPoint explaining the process (which you can download here). I typed out 38 slides by myself and then explained each in turn to Jinquan as she commented and corrected my errors. Creating PowerPoint slides helped me learn the details, but not as much as performing all of the steps would have.

Creating the PowerPoint was conducive to learning because I could work at my own pace and make errors. I become anxious when someone scrutinizes my performance as I am learning a new skill; at least, I do if they hastily correct my mistakes. I learn best from the innate consequences of my own failures—a protein gel that leaks out of the bottom of its mold—than I do when I am corrected before I am able to fail at all. Still, I need some sort of feedback to learn, whether it is from a leaky gel or a person. Jinquan gave me feedback on the PowerPoint, correcting my factual errors, and thus I was able to both work at my own pace and receive feedback—a plus on both accounts.

Using my time to make a PowerPoint instead of practicing an actual western blot, I did not, of course, improve my lab technique. To learn a physical task, there is no substitute for performing it; as I still have not completed a full western blot by myself; I would not say that I can perform one yet, whereas, had I instead successfully gone through a full western blot instead of making slides, I would. However, the upside was that I could practice going through the steps without the risk of wasting expensive reagents, such as antibodies.

Working in PowerPoint, I now have an accurate guide for western blotting that I can reference for future use, which could help me on subsequent western blots. The potential caveat while making the slides was the temptation to overdo the visuals. Jinquan had specifically told me to focus on content and avoid visual detail, and for the most part, I avoided fiddling with margins and fonts, but I did spend more time than I needed to making a diagram of how antibodies bind to the protein membrane.

There are definite merits of making slides to learn procedures, but I think that the most effective way in which I learn techniques is by first performing them while observing Jinquan doing them, writing down steps if possible, and later on, rewriting notes or making slides. I find both non-critical, hands-on feedback and subsequent review to be essential for learning lab procedures best.

Unhappy Valley

Jack Crean killed himself the day before his first semester at Penn State began. Introducing the deliberation “‘Blue’ & White: Addressing Depression at Penn State Common Place,” the moderators said Jack was consistently upbeat and could lighten the moods of those in his proximity. Why did he commit suicide? We may never know with certainty, but we do know that depression is a covert illness. The moderators first addressed the issue that depressed students often feel too ashamed to admit depression, as if depression is a personal failing, or a crime for which they are “guilty,” not a treatable ailment. Surveys show, they said, that about 30% of all students are depressed during some of their time at Penn State, yet few report it. Teaching students that they may become depressed at college is the first step towards preparing them to identify the signs of depression, should they develop them.

The moderators thus asked, “How can we teach students that depression is prevalent at Penn State?” We first proposed developing an online depression education module like SAFE or AWARE; however, we agreed that students would likely gloss over it, as they do SAFE and AWARE, if they completed it during the summer. Thus, we discussed having students complete it midway through their first semester, which we thought would be more effective. Integrating a lesson on depression into the first year seminar, we thought, could be effective, until someone pointed out that not all students take a first year seminar, and that first year seminars are not standardized. Therefore, we proposed that all students should take a first year seminar and that at least one class must be devoted to depression.

Once students would be wary that they or their friends could become depressed, the moderators asked, “How can we make depressed students more willing to seek help or identify students who do not willingly admit?” We brought up but quickly abandoned the possibilities of having professors or RAs take on those responsibilities. It would be entirely unreasonable for professors of large classes to identify who among their hundreds of students were depressed. Even RAs would likely not form strong enough friendships with the students on their floor to identify depressed students; Jack Crane’s own family and friends did not suspect, we said, so why would his RA? Having roommates identify depressed students is more feasible, but requires that every student know how to identify symptoms of depression. The most effective option, we agreed, would be to have friends identify depressed friends, which highlights why it is important for Penn State to teach students what the signs of depression are.

Most of the discussion focused on the next step, treating depression, through Counseling And Psychological Services (CAPS). CAPS is underfunded, the moderators lamented, and must turn down all but the most severely depressed or suicidal students (although one of my friends with moderate depression was able to get help through CAPS, so the moderators may have overstated the underfunding). Nevertheless, CAPS is underfunded, and the moderators asked, “How can we increase funding?” We proposed a small tuition increase to cover the costs, which seemed to be the most viable option. Rerouting money from highly paid organizations, such as Penn State football, seemed like it would vex the supporters of such organizations and put CAPS in a bad light. Still, CAPS provides counseling for only a limited time; then, students must seek professional help elsewhere.

Finally, then, the moderators asked “How, besides CAPS, can we help depressed students?” We proposed encouraging depressed students to seek their friends’ support and to join clubs that they would find fulfilling. However, these are broad solutions, and since depression is highly specific to each student, these solutions would likewise need to be individually tailored. The best way to help, we agreed, is to teach students that “Happy Valley” is a misnomer for 30% of students: that it is not being depressed that is shameful, but rather, it is being silent about it. Only when Penn State students accept depression will they be willing to help and seek help that they need. Depression, if treated, has an excellent prognosis.