Field of Science

Manifestation of Prof Stress

The Spring semester has ended, which means something from a teaching perspective but not from a research perspective. At least that's true for me. I know others can vary in their teaching/research mileage. For me, teaching is basically a fall/spring semester concern. I do teach a couple of weeks during the summer, but this requires little prep work so I don't count it. Research is a year long venture, but does suffer during the fall/spring, especially the fall, because of my teaching duties. A couple of weeks ago on consecutive nights, I woke up around 2 am from bad dreams. These dreams, I won't say nightmares because they were stress inducing but not terrifying, related to these two big areas of my professional life.

The first night it was a research related dream and the focus was on grants, big surprise to people in the field I expect. The dream actually started out on a good note as I was just awarded an R21 grant from NIH! The happiness and relief of having some money to conduct the research I want to do, quickly transitioned to stress as I began thinking about how quickly I could get someone hired and trained to do the research successfully. I became increasingly stressed because the R21 is only a two year grant. If it takes 6 months to hire and get someone well trained (a stretch in my opinion), I basically have 6 more months before we need to be generating most of the data in order to write a larger grant. For those not in the know, it takes a few months to write a proposal (for me at least) and then ~ 9 months before funding decisions are made. Thus, in order to maintain constant funding from the onset of the R21, I basically have 12 months to get most of the work done with an untrained person. I woke up a mix of happiness combined with a whirlwind of stress. I was up about 2 hours before going back to sleep.

The second night it was a teaching related dream. In real life I had just completed final grades for my Spring semester course and was breathing a sigh of relief to have ~3 months to focus on experiments and writing (papers and grants). In my dream, I felt like I was in the same place and at work setting up experiments when I realized my Fall semester classes were starting in a couple hours and I hadn't set up the course website, planned any lectures, etc. I was running around trying to get together some slides for the introduction and to print off some worksheets for the students but couldn't find a printer. To make things worse I couldn't find out where my class was meeting and time was ticking down to the point where I was figuring out how late I would be. Basically this was my adult version of the 'just realizing you have a final in a class you didn't know you were enrolled in all semester' nightmare. Again up for a couple of hours without being able to sleep.

Haven't had anymore repeats of the stressmares™, but apparently my sleep schedule basically requires waking up at 2 am. I do get some reading done I guess, but would rather get a straight 7-8 hours of sleep. Stupid brain.

What I Read (2017)

(Grade A-F, no E's) Title-Author Additional thoughts

C+     The Man in the High Castle by Philip K. Dick. An alternate history where the axis wins WWII and life in the US under oppression. Many story lines that were linked, but he connections seemed weak. Still not sure about the importance of the man in the high castle (although he moved) other than to imply the strange twist at the end. I guess that keeps the story in the sci-fi genre.
      Lost Gods by Gerald Brom. Didn't know what to expect, but I liked the cover. Fun story merging horror and fantasy. 
C       Island in the Sea of Time by S.M. Stirling. I enjoyed the premise of this story and it got better in the final two acts. There were many clunky technical details in the beginning that did not fit in with the narrative well. Seemed like the Stirling learned a lot about schooner ships for research and tried to jam it in.
C       Wytches vol 1 by Scott Snyder. Meh, but not as Meh as God Country.
B       And Then There Were None by Agatha Christie. Ok this was fun. Glad Christie included an epilogue how the hell everything happened.
D      God Country by Donny Cates & Geoff Shaw. Meh. American Gods is a great book and would make a great graphic novel. This was not American Gods.
B+    The Stone Sky by N.K. Jemisin. I did not enjoy the second story in this series, by the final entry is a winner. The story came to a solid conclusion tying up many loose ends.
B       The Walking Dead Compendium Two by Robert Kirkman et. al. A good follow up to the first one. The survivors discover a idyllic community only to have everything go the shit. People suck.
B      Breakfast of Champions by Kurt Vonnegut. I understood this book better than Slaughterhouse V and thus enjoyed it more. Satirical book touches on many aspects of life in the US. Author drawings throughout the book is interesting.
B      The Black Elfstone by Terry Brooks. The first Shannara story I read was Elfstones, shortly after it came out. I've had a fondness for this world for decades and while some stories have felt repetitive, this one is starting out on familiar territory but is introducing some new complexities and territory. A solid beginning for a new quadrilogy (and a change from the trilogy form Brooks has generally used).
C      Grave Peril by Jim Butcher. See Fool Moon below.
A      It Can't Happen Here by Sinclair Lewis. A timely book, incredibly timely. How a populist can come to power in the US and quickly devolve into fascism. Although written in 1935 the populist plank could be written (and much of it has) by today's tea party. This is my required reading book choice for the year.
C      Fool Moon by Jim Butcher. Another easy read to pass some time. Didn't add much to the Harry Dresden's character which was something I was looking for.
B      Storm Front by Jim Butcher. Recommended to me by a prince of assholes, a fun read before bed. Look forward to reading more about Harry Dresden. Wish there was more character development in the book, but a good first story.
A     To Green Angel Tower part 2 by Tad Williams. Rereading this series in preparation for the Witchwood Crown, originally read this series during graduate school when I took some time off to mentally relax after writing the initial draft of my thesis.
B+   To Green Angel Tower part 1 by Tad Williams. Rereading this series in preparation for the Witchwood Crown, originally read this series during graduate school when I took some time off to mentally relax after writing the initial draft of my thesis.
A        Coraline by Neil Gaiman. A story of a not very nice mother, the other mother. Not really a children's book although I would have read this to my son when he was younger anyway. The world's not all kittens and puppies.
B+     The Stone of Farewell by Tad Williams. Rereading this series in preparation for the Witchwood Crown, originally read this series during graduate school when I took some time off to mentally relax after writing the initial draft of my thesis.
A       The Dragonbone Chair by Tad Williams. Rereading this series in preparation for the Witchwood Crown, originally read this series during graduate school when I took some time off to mentally relax after writing the initial draft of my thesis.
A       End of Watch by Stephen King. A great ending to the series. Intertwines with the first story well, but each of the trilogy is a stand alone story.
B       Weaponized Lies by Daniel J. Levity. Good book, but covers some ground I'm quite familiar with.
C       Blade Reforged by Kelly McCullough. I enjoy this series and the flawed protagonist but this story was entertaining yet fleeting. It provided more backstory for Aral and the war amongst the gods in this world.
 B      Tripwire by Lee Child. An easy fun read. f the three books I've read so far, the villain in this story is the most developed and interesting and all around evil.
B-     Injustice: Gods Among Us Year 2 The Complete Collection by Tom Baylor, Bruno Redondo, and Mike S. Miller. A decent follow up on the initial story. Lags because the first collection established the world and key problem of Superman becoming an authoritarian. This is developed further and the two sides more fleshed out.
B      Paycheck and Other Classic Stories by Philip K. Dick. Has any short story sci-fi author had as many movies made out of their work? I doubt it. Some of the stories in this anthology I enjoyed, others were just so-so, but thats to be expected.
A      The Walking Dead: Compendium One by Robert Kirkman et. al. Great first compilation of the graphic novels. It's hard to read these stories and not give up on humanity. Basically a reasonable analysis of the human condition.

26 books read this year. Below average by a few books, not going to count the 4 rereads against myself since it was a good 20 years since I read before. 
Of the 26 books: 5 were graphic novels, 1 was philosophy, 4 were older books.

Eukaryotic Microbiology: The Blogs Are Coming

Despite my desire to keep updating the blog with course information, which has been an abject failure in regards to updates, I still want to post when I can. To be fair, I'm behind on grading, so I can't in good conscience be blogging about the course when assignments need to be graded.

However, I'll take a minute to make this brief post. It's getting to my favorite time of year: Student Blog Posts at Traveling Small with a Nucleus! I know for many students this is a writing assignment they truly enjoy. (Of course I'm sure some students do not like this assignment, but I have yet to hear from them.)
S0, I invite you to check out some previous students posts in the interim. The majority are quite good and there are some real gems in there. It's possible TSw/aN may be invaded with some organisms lacking a nucleus too. I'll keep you posted. 

Eukaryotic Micro: Week 3 the last of the fungi

So this week (actually last week) we covered what is probably the last unit concerning fungi: Cryptococcus neoformans. The first two weeks covered two ascomycetes, Candida albicans and Fusaruim species, and now we move over to the basidiomycetes, otherwise known as 'if I asked you to draw a fungus this is what you would draw'.

The primary research papers were:
This is an interesting point in the semester. Upon completion of this week, we are ~25% of the way through the semester and exactly 25% of the way through the 12 modules. This is the point where students have completed the short writing assignment four times now, so hopefully they are comfortable with what I am looking for. I lay out the guidelines on day 1, and then model what I expect. There are two difficulties. 1: Getting students to explain a dataset of their choosing such that someone would walk away knowing what was done, what it showed, and most importantly be able to ask informed questions about the data set. Students are reasonably good at explaining the data after a week or two, but struggle to give enough experimental information such that you would know how the data was obtained. 2: Identifying limitations with the data set. This is in fact difficult, but it is an important skill to foster if we really want people who are critical thinkers. I ask them that their limitation answers the question 'how does this affect the authors' conclusions or interpretations?' This latter issue usually takes a couple more weeks to get better at for most of the class.
It's also interesting because Cryptococcus follows up the ascomycetes we already discussed extremely well. Like Candida albicans, C. neoformans is a budding yeast, which is distinct from Fusarium, which although more closely related to C. albicans, is a filamentous fungus. However, like Fusarium, C. neoformans forms dikaryotic filaments during sexual reproduction and grows in a filamentous form during asexual spore production. 

I like these two papers (this is the first year I've used the Gerstein paper) because they deal with different aspects of development/differentiation in different ways.  The Gerstein paper is focused on a role titan cells play using primarily genomic approaches; the Huang paper is focused on spore formation and development using classical genetic approaches.

Gerstein et al ties in conceptually with the Selmecki and Ma papers from the Candida and fusarium modules respectively. All are centered on the acquisition of additional genetic information and the outcomes of this. I'm certain creationists always talk about the inability for an organism to acquire new 'information'. Well here are three independent examples.

Huang et al ties in, slightly, with the Lui paper from the Fusarium module by dealing with cellular differentiation and development. This is something we will come back to in the future frequently and is a biological concept I think is often underappreciated in microbes.  

Eukaryotic Microbiology: Two Weeks In

Have the second week of Eukaryotic Microbiology in the books (except for some residual grading to complete). So far we've covered Candida albicans and two Fusarium spp. Last week was C. albicans and we discussed two papers. (I'm not including the review articles students read at the beginning of each week.):
And this week was Fusarium and we discussed:

While I planned to discuss each week individually, these end up going well together, plus this is a difficult time of the semester for me guaranteeing I can't write as frequently as I would like.

So we stay within the ascomycota for the first two weeks. Some things that I wanted to emphasize in class and that came from the students:
  • What does it mean to be 'wild-type'? This came up with regards to a 'wild-type' genomic sequence. Is the CFTR mutation (the allele that causes cystic fibrosis when homozygous) a mutant genotype? Does the fact that in the caucasian population a cystic fibrosis causing mutation in the CFTR gene occurs with a frequency of 0.025 make a difference? What about the allele that causes sickle cell anemia when homozygous? People who have a 'mutant' allele and a 'normal' allele are more resistant to malaria, so this mutation is potentially beneficial.
  • How is phenotypic diversity generated in asexual organisms? This is an important question because sexual reproduction is promotes phenotypic diversity in many eukaryotes. However, there are significant issues associated with sexual reproduction that prevents using it as a simple explanation for phenotypic diversity.
  • How do organisms adapt to their environment and is a pathogen really any different from any other organism (short answer is 'no')?
  • How do duplicated genes evolve? This (Lui paper) goes hand-in-hand with the Candida Selmecki et al paper and the Fusarium Ma paper.
We'll be revisiting many of these issues throughout the semester. We spend a fair amount of time dealing with specific aspects of the papers, but I try to highlight some of these broader issues. This week we tackle Cryptococcus neoformans and will highlight at least one of the above issues again.

First Eukaryotic Microbiology Classes

Since we do not start classes until after Labor Day, the first week represents a Wednesday, Friday week for my writing intensive Eukaryotic Microbiology course. I designed the course to run on a M/W/F cycle, so this first W/F week might seem problematic, but it is not. In fact, it works out extremely well.

The first day of class (today), involves discussing what is going on in the course and going over the syllabus. Similar to last year, in the first class I try getting students involved by having describe their goals and defining plagiarism. This year I focused the first lecture on the structure of the course and less time going in detail on the syllabus. It was only partially successful because I didn't get through the course set up but got through most of it. Luckily there's time to finish on Friday.

Although I don't get too deep into the syllabus (the students can read), I do cover grades and how they are determined because this is an issue that cuts to the heart of many students. One thing I started doing last year in another class, is determining the course GPA. That is the GPA for the course, determined by the student grades. The last two years my Eukaryotic Microbiology course had a GPA of 3.0 and 2.7. I'm pretty happy with these GPAs overall, it means I am not giving out a ton of A's but the GPA is higher than one might expect for an introductory class (this is not an introductory class and is taken primarily by seniors in the major with a smattering of graduate students).

The class is generally set up as follows:

  • Monday: I give a standard lecture introducing the students to an organism and the relevant topics for the week.
  • Wednesday: Students present primary research papers. However, they don't actually present the paper, I have them answer some specific questions:
    • A. What question is the paper addressing and why do we care?
    • B. Which conclusion do you think is the most interesting/important and why?
    • C. Pick one figure that you think best supports your favorite conclusion and explain in detail how the data support the conclusion.
    • D. What are the limitations of the data?
    • E. Why are the conclusions important?
Questions A and E are only answered by the presenters, which is why they are struck out. These questions are derived from a document by Little and Parker (no longer available online, but they were at the University of Arizona). I like these because they focus the students in on a specific aspect of the paper, their favorite conclusion, which may be completely different than the press release or authors' overall conclusion.

The students then focus in on the data that supports that conclusions and not the entirety of the paper. Essentially, I do not want the presenters to reiterate the paper to the class, everyone is required to read the papers so there is no need to reiterate them.

The most difficult part is finding limitations or some issue(s) with the data/interpretation of data. I think students are trained to accept the literature and not rigorously go after the authors and their arguments, which, is in a nutshell, how science works. This one takes time and experience to get good at. Even excellent papers can have issues and I think one of my jobs is to get students comfortable with finding issues.

One thing I haven't told the students about is that the presenters have to give a 30 second elevator talk about the paper. I started doing this several years ago and I think it is extremely important. Basically, if you were an author and someone in the grocery store asked you about your work, how do you explain cogently and succinctly such that they are impressed and glad their tax dollars are supporting the work.
  • Friday: Discussion of things. This varies markedly and is dependent on the students. I have a discussion board for them to ask questions, raise issues, provide feedback, etc. I do not post to these boards unless things are going off the rails and try to keep it a student oriented discussion board. (Once a prof posts a comment, all additional comments cease in my experience.)
On Friday, the second day of class, I will model what I expect out of the student presentations. We are reading "Complementary Adhesin Function in C. albicans Biofilm Formation' by Nobile et al. I also provided a review article 'Adhesion in Candida spp.' by Paula Sundstrom.

I will give a 30" elevator talk and then give an oral presentation that covers answers to the above questions A-E. Students are required to provide written responses to questions B-D to get us started.

Starting Monday we really kick into gear, although we will stay with Candida albicans. FYI the topics we are covering are drug resistance and host environmental adaptation.

My goal is to keep blogging about the course throughout the semester.

How to Study: Repetition is good (which is why I post this every year)

With the onset of a new semester and a new crop of students having arrived or shortly arriving at college, here are some words of advice from someone who had to learn to study the hard way...

Here is an advice column for students looking for some techniques to improve their study habits. I am not an expert in learning, but I am an expert in being a college student with no fucking idea how to study and had to figure it out over the course of a year or two. I was one of those students who didn't have to do much to maintain an A/B average in high school. Although I was exposed to study skills and habits while in high school, none of it stuck because I really didn't need to study to do reasonably well. So here is what I learned that worked for me. If you have your own successful techniques, please feel free to add them in the comments.

Learning is an active process, it requires energy. It may not be as physically taxing as a 45 minute work out, but then again you may not be doing it right. What I discovered is that I learn when I do things, when I engage the material, when I'm an active participant. If it's a couple of days before the big exam and you're wondering to yourself 'What's the best way I can study? I know, I'll take some time to search online and get some tips.' Well, if this is you, you're fucked or at least I don't have anything for you. Come back after your upcoming exam, my advice might help you for the next exam. Right now, you are in cram mode, so you better start cramming and not wasting your time reading blogs. I will admit that cramming works, to a degree. Cramming is a short term solution, getting enough material under you belt to survive or even succeed at the exam. But it's a long-term problem. Are you really in college to survive exams and classes? That was really high school wasn't it? Cramming is problematic because the material is never actually learned, it may come up again on the final, it will likely be important next semester or the semester after that in your more advanced classes. Learning and cramming both take energy, but the former is far less stressful and provides both short-term and long-term gains.

Step 1. Find an environment to study in. Ultimately this became at my desk in the bedroom of my apartment. I also kept my stereo close by set at police notification level. I learned quickly that I could ignore the music, but sounds from the street, from the kitchen/dining/living room area, or from anywhere outside my room were distracting. To this day, when I'm working on grants or papers and do not want to be disturbed, I  close my office door and crank up some music. Although I am a chaotic person by nature, my desk was neat and organized. I needed a place to work comfortably and that was it. My textbooks and notebooks were stacked in/on some milk crates I used for shelves. (These of course were the store bought kind of 'milk crates' not the easily available sturdy and inexpensive milk crates available behind 7/11s, like the one across the street of my apartment. Although if they were the illicit version, which they weren't, they would have been returned when I moved to go to graduate school.)

$0.69 for 3 in 1989
Step 2. Get a bunch of notebooks. I used spiral bound notebooks available for next to nothing at drug stores. Of course these notebooks will have absurd cover designs or pictures you would never in a million years gravitate towards (see picture of my Molecular Biology notebook). That's not the point. The point is what's inside the notebook, and that will be gold. I mixed up the designs on the notebooks I bought so I could easily identify which one I wanted. The alternative is to be flipping through them wondering if this is the black notebook Im looking for. Get one notebook for every class you take (except maybe for the golf/tennis/etc classes). Any class that has a lecture has its own notebook. No cheating by getting a three-subject notebook. Also, get a couple of additional notebooks.

These things are evidence of evil
Since you're at the drug store already, get some pens and pencils. I love pens, but despise cheap ass ball point pens. You'll be using these a lot, so get pens/pencils you are comfortable with. Make sure you get a variety of colors. I survived with black, blue, and red, but there is a veritable palate of colored inks now. Get what you love or at least can tolerate. I prefer mechanical pencils, but if you get classic ones, you better kick in for a decent pencil sharpener or two. Also grab some highlighters also in assorted colors.

Step 3. Do the readings strategically. Chapter 3 is covered Wednesday? Read it through by Tuesday night. That isn't very strategic is it? The strategy is to skim read the text. Get a sense of what's in there and what will be the likely topics and points for the upcoming lecture. You don't need to be more than familiar with the material. (In the case of labs, this is not true. You must be intimately aware of the material, because you will be using that information in the lab. Hell, there may even be a quiz on the lab manual!)

Step 4. Go to class. Although you probably couldn't pass a quiz on the readings material, the vocabulary is familiar. Now you already know a bit about the upcoming lecture. Gather up your pens and pencils and one of the extra notebooks. Leave your textbooks at home, along with the highlighters, and other notebooks. You don't need much.

Get to class on time and get a good seat. In large classes, I recommend a seat near to the front and in the middle where the professor can actually see you. Why? Psychology that's why. Take two students doing equally well, one student the professor recognizes, even if there is no name associated with the face, and one student the professor has barely, if ever, seen. If both come to discuss an issue regarding an examination or writing assignment, which one will have at least a sub-conscious advantage?

Open your notebook to page 1 get out a couple of writing implements and get ready. If the professor has handouts or, god forbid, print outs of the slides, then definitely pick them up, but DONT use them during the lecture (with rare exception). Your job is to take a shit ton of notes. Don't worry about neatness and perfection, just get the stuff written down. Write down the points on the slides, the drawings, incorporate what the professor is saying. The very act of writing things down is helping you learn the material! 'But we have the slide print outs, so why write stuff down?' you ask. In my more youthful days I would have responded with 'Because we didn't have the material presented to us, so stop being so fucking needy.' But in my dotage I think an example is better. What is another name for a television? Did 'idiot box' spring to mind? There's a reason for that. Some people watch tons of TV, these are not inherently the most educated people in the world. My mother loved to watch soap operas during the 70s, hours of soap operas. She was not an expert in social interactions because of this nor was she an expert story teller, she just watched a lot of soap operas. This is one of the biggest impediments to learning, fucking handouts. Remember I said learning was an active process. Lectures are not television. You should be doing something not just watching. The problem with handouts is that it facilitates the TV watching mentality. There are reasons to hand out the notes, which is why you are collecting them, but wait until later to use them. For now, take a shit ton of notes.  Do not be tempted to put notes in the margin of the print outs, you bought the cheap ass notebook, so use it. (Plus you'll want a pristine copy of those hand outs for later.) So, you were in class sitting in a strategic location, you took a shit ton of notes, now what? Go to your next class and repeat using the same notebook.

Notes on chromosomal
melting temps.
Step 5. THE MOST IMPORTANT STEP: The next day. So you went to all your classes, even the ones you think are boring, and you took a bunch of notes, even on things you think you know already. Now what? Hang out with friends, watch TV, play some PlayStation, then go to bed and the next day go to all your other classes. At some point on this second day, you need to carve out some studying time. When depends on your schedule. I did this in the mid-late-afternoon, because I was generally done with classes then. Go to your studying environment, get out your notes from yesterday, one of the fresh notebooks that will be specific for a specific class, any handouts, and your textbook. Now you will rewrite your notes in a more organized and legible manner. As you rewrite, you will refer to the text for additional points, and in your class-specific notebook you can either incorporate the textbook material or simple refer to the page numbers/figure numbers. Either redraw or cut out the handout figures you need and add them to your notebook. This could take as long as the original lecture, but probably won't. Regardless, you are now learning some serious material. The act of rewriting helps embed the information into your memory, by organizing the material in a manner that works for you (which is probably like it was presented) you are thinking about the material in total not simply one fact after another. You are also reading the text in a more in depth way, which is easier because you already skimmed it and went to the lecture. Do this for those boring easy classes too. It helps maintain good study habits and instead of simply learning the material, you'll own it. Another benefit is that if you do this, you will know before the next lecture what material you may not understand. This gives you a ton of time to meet with your colleagues, TAs, professor to get things straight.

Step 6. When you finish going through the crappy notes, rip out the page(s) and throw them away. You don't need them anymore because they are rewritten and you'll feel good about the progress you made.

I won't guarantee these steps will improve your grade, but I do guarantee that they will improve your understanding and knowledge of the material.

Additional thoughts:

A. Write in your textbooks, at least highlight important information. I used different colored highlighters for different purposes. Red was for definitions, blue was for what I thought were key concepts, green was for things referring to my class notebook. Will writing in your textbook reduce its value when you resell it? Well hopefully you will not resell it. Having that chemistry textbook could come in handy when you need to revisit something you forgot in your molecular biology class. If you absolutely do not want the book, why buy it in the first place? Probably you could borrow one from a colleague or use the library.

B. Scheduling. You need to prepare ahead of time when things are getting done. If you don't, you will almost certainly get behind or not have enough time. If you want to go to that party or game, you may need to start rewriting your notes earlier than normal to make sure you have enough time to finish before going out. Also, there will be several big assignments due for other classes throughout the semester, you'll need to be prepared for catching up on those notes you couldn't rewrite the day after class. (Don't get more than a class or two behind or you'll defeat the purpose of rewriting.)

C. Turn off your phone. You can survive an hour or two without reading all those awesome texts and tweets coming in. A 30 second distraction actually amounts to much longer, because it takes time to get back to where you were before you were distracted. Every time you break focus, you are back to a more superficial level of learning and it takes some time to get back to that deeper level.

D. When it's test time, you'll find it much easier to study. The material is already there in your mind because you've been through it at least twice already. You may have to pull an occasional all-nighter, but it will be different than the cramming you did previously.

Notes for a recently submitted grant
from a relevant paper.
E. For the record, I still use these techniques to prepare grants and papers (see photo). I do a lot of background reading and have notebooks dedicated to taking notes on the papers, complete with different colored pens. This allows me to make connections and think about the material in a much deeper way than I would be able to otherwise. Same for seminars I attend, I bring a notebook.


With those words of advice,
Good luck and have a great semester!