Some Suggestions for Studying

Since a new semester is about to begin I think a post on how to study would be apropos. So 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 didnt 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 my not be doing it right. What I discovered is that I learn when I do things, when I engage the material, when Im an active participant. If its a couple of days before the big exam and you're wondering to yourself 'What's the best way I can study? I know Ill take some time to play 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 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 to 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 Im 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 all ready, 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 Xbox, 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, red 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 facebook postings 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!

Precision: why we should not submit

An On Scientific Writing post.


One aspect of scientific communication that is essential in both oral and written modes is precision. Scientific writing should be precise. Of course, we know have to define what it means to be precise and maybe the best way to do that is to use some examples. As you read each sentence below picture the image the sentence conveys to you.

1. "An animal went into a building," is a fairly vague sentence.
2. "A cat went into the brick building," is a lot more specific.
3. "A Siberian tiger went into the brick hospital," is more specific still.
4. "A sick Siberian tiger went into the brick animal hospital on 4th St," is the most specific example to date.

Now I expect you imagined something completely different with the different sentences, particularly sentences #3 and #4.

One of the points I want to emphasize is that words have meaning. Depending on the word choices we make, we can communicate effectively or we can communicate in a much less efficiently. This is precision. In the case of science writing I prefer the 'distinguished from every other' definition of precise. You want to be clear when you write and one of the ways you do that is to use the most concrete and direct words possible, a sick Siberian tiger vs an animal, a building vs. the brick animal hospital on 4th St.

One problem in trying to be precise is the invention of fucking pronouns. Pronouns breed imprecision. In your science writing the mantra should be 'pronouns are used with extreme prejudice.'

The car was parked on the street, it was blue. What was? The car? The street? Fucking pronoun.

Another problem in trying to be precise is that the meaning of a word is somewhat fluid, words exist in cultural contexts, and the definition of a given word can evolve. Our language conspires against us. Now we could take the relativistic approach, throw up our hands, and give up. I prefer to take the bit by the teeth, get my hands dirty, and actually try to communicate. (This latter approach is generally worthwhile if you happen to live amongst other humans.) The point is that we have to be vigilant and thoughtful by the time we have completed our writing (the emphasis on the finished product is intended because, if we worry about 'perfect' word choices while we are drafting, then we will never get out of the starting gate).

Jack and I went to the gay parade yesterday. Meant something slightly different in 1911 than it does in 2011.

which brings us to 'submissive'. When you read the following, what does 'submissive' mean?

"Tax law? I hate taxes," she [Michele Bachmann] continued. "Why should I go into something like that? But the lord says, be submissive. Wives, you are to be submissive to your husbands.'" CBSNEWS. 

In the universe Michele Bachmann inhabits, submissive = respect. In my universe, submissive means something a little different. Things like relinquishing power to another, compliance, to be subservient to, cowed come to mind. Respect? not so much.





In my quest to obtain the Bachmann quote, I stumbled across a site that provided the following opinion regarding Bachmann's submissiveness respect.

According to Karen Seat, a religious studies professor at the University of Arizona, some conservative evangelicals argue that women’s deference is itself empowering, because it’s what God intends, and because it is the fullest expression of womanhood. In this world of opposites, submission is strength and inequity is proof of equality. It’s quite possible that a President Bachmann would primarily define herself not as the first female president of the United States, but as a wife and mother. And she would not see that as anything less than progress.

But of course we have always been at war with Eurasia.

On scientific writing

In science, communication, both oral and written, is a critical skill. I know the stereotypical scientist is some extremely awkward asocial geek or nerd (at least when they aren't maniacally evil). Of course this is not true¹. Although an argument can be made that scientists are not necessarily good at communicating with the general public, to be a successful scientist you need to be able to discuss your work and the work of others and to write papers/grants/etc effectively. Unfortunately scientific communication is skill that is often developed on the fly.

¹OK, Ill admit physicists really are awkward.

I argue that we should be teaching scientific writing early, at the undergraduate level. But unfortunately for undergraduate students, at least in the life sciences, a few stock lab reports, the occasional 10-20 page essay, and maybe a research project thesis represents their 4 year scientific writing experience. More problematic however is that there often little instruction given to the writing apart from the different sections that you need to include (abstract, introduction, etc.). As instructors, we rely on the English department, at best, or high schools, at worst, to teach students how to write. This generally leads to failure. The failure is not due to poor instruction by the English department, but due to the fact that the mission of the English department is not to teach scientific communication. The College of Biological Sciences (CBS) wants to rectify this issue by promoting student writing at the undergraduate level and providing some cohesion in writing instruction throughout the college.

CBS tries to get faculty cohesion in writing instruction.

To date I have been involved in a number of meetings (we're good at that) with colleagues to define the goals for CBS student writing. In part, we developed a list of the characteristics of science writing, realizing that a review paper and lab report have some different characteristics. Over the last two years, I have been introducing more writing and writing instruction into my fall semester course and I am continuing that trend this year. So with a few years of experience plus a small number of 'student writing' focused meetings under my belt, I will be posting (yet another probably never finishing) series regarding science writing.

This was supposed to be the first post in that series, but my introduction got so long the point was going to be buried. So I decided to make this an introductory post, another will follow shortly.

2011 Cartoon Contest Contestants | Union of Concerned Scientists

Check out the 12 entries to the UCS editorial cartoon contest (2011 edition) AND VOTE. I'll add my favorites later, but they are all winners.

2011 Cartoon Contest Contestants | Union of Concerned Scientists

Here are three of my favorites, although it was tough to pick just three.

I'll update this later with my thoughts on these and the other entrants and add my rationale behind choosing these three. Can you guess which I voted for?

Fair questions?

Sure he does.

You know, I realize that in order to be nominated for a major elected office in this country you need to actively wrap yourself in the blanket of christianity. But there are differing degrees in which a candidate can do this. For example, a candidate could simply use the word 'faith' along with family, parents, children, work, education when talking about what is important to them. Or a candidate could tell you that during discussions with god almighty, they were informed that they were anointed to be the winner of the election. Many of the republican candidates for president of the US have taken the latter approach (Rick Perry, Michele Bachmann, Rick Santorum, and even Herman Cain). Since these candidates are in direct communication with one of the numerous gods worshiped in this country, I think the following questions are completely fair game.

1. If god tells you to nuke a foreign country that attacked us or our interests, would you do it?

2. If god tells you to nuke a foreign country that hasn't done anything to us or our interests, would you do it?

3. If god told you to nuke a US city because it was time to pull another Sodom for the history books, would you do it?

4. If god told you to imprison US citizens because they loved the same sex would you do it? If so, would you also imprison all the fishermen/women? What if god told you to do that too?

5. If the vast vast vast majority of experts in a particular field told you something that contradicted your beliefs, how would you reach a decision? If you discounted the vast vast vast majority of experts, how would you justify your decision to the general citizenry?

Personally, I think that hearing voices in your head telling you to do things should absolve you from government office. Just for the record, here are some other people that were absolutely convinced god spoke to them and they were doing gods work.

By what criteria do we say that these three men were delusional, psychotic, and/or sociopathic, but separate out the republican candidates? Obviously, the consequences/actions of following these three men is a great criteria (see below).

While I do not doubt that the republican candidates are relatively sane compared to these psychos, Im not comfortable wondering what kind of bat shit crazy consequences/actions the majority of republican candidates may decide to carry out. What shocks me most is that many others don't seem to worry about it.

Name that Scientist Quiz

How did you fair? Check out the NYTimes Name that Scientist Quiz.

Name that Scientist

I scored 8/10, missed #6 and #8.


H/T WEIT

Student blogs to check out, part II

Oh goodie, 2 more student blogs you should check out. Oh, and anyone coming from AbC needs to play nice on these sites.

That Voice in My Head

The first just started and has decided to post everyday for 30 days. To help him out, you should go encourage him (and by help I mean add a bunch of external pressure).

You know this beast is jut waiting for the sun to set.

The second I discovered by way of the first. It has two things I love on the front page: sloths and blood (anyone else envisioning vampire sloths?). You'll notice the author has not posted recently, but maybe all she needs is some encouragement to keep up the good work.

Statistics ≠ Checking Your Brain at the Door

As part of an endeavor to improve undergraduate writing, I was involved in a day long session of reading senior level writing assignments.  Basically, a group of us had a list of criteria and ranked each assignment as meeting or not meeting the criteria. We were not grading or assessing the worth of the assignments simply whether a given criteria was met or not met. I learned a few things during the 7 hours of reading 16 assignments (~20-30 pages each), one of which I want to touch on here.

COLLEGE SENIORS DO NOT UNDERSTAND STATISTICS!!!

Now I am not a statistician nor do I have any real expertise in statistical analysis. In fact, I turn to statisticians when I need to do statistical analyses beyond student T-tests or analysis of variance. However, I think I know enough about statistics to not make the error of the p-value.

The p-value essentially tells you the probability that some event, data, occurrence is due to chance (generally referred to as the null hypothesis). So if you are hoping that the effect you are looking at is not due to chance you want a small p-value. The question, of course, then becomes 'how small'? The scientific community has generally agreed that a p-value of < 0.05 is a rigorous cut-off. A p-value > 0.05 is considered to be reasonable odds that your effect may be due to chance. However, this cut-off of 0.05 is arbitrary and indeed higher and lower cut-offs are used in some fields.

To be clear, p-values can range from 0 - 1, so you can consider a p-value of 0.05 to be analogous to a 5% chance that the effect you are looking at to be due to chance. That also means that your p-value of 0.06 means there is a 6% chance your data is due to chance and that is too high for most scientists to consider your data significant.

xkcd's take

Now we come to the error of the p-value. By way of example, you should check out xkcd's acute take on the problem (well several problems, but the one we care about is central). If we look at a lot of different data under a given condition, then we should expect a data set to show a p-value < 0.05 on average 1/20 times (5%) that is strictly due to chance. This does not mean that we should discount a result that comes with a p-value of 0.05. It means there is only a 5% chance the result is due to chance. However, if there is additional data to back this result up, we can increase our confidence even more. If there is not additional data, hopefully the scientists (aka senior undergraduate students) will at least acknowledge the limitation of the many data points. Sadly, both of these were lacking in a couple of cases that I observed, although I admit I do not know if this represents a statistically significant (p < 0.05) result.

Tormenting the Students

My Teaching Mentor?

This represents my 5th year teaching at Nature of Life. This is an outstanding program for incoming first year students in the biological sciences. For three days, these soon to be college students (I guess they are now technically) take three 4 hour laboratory classes some of which include some field work, have a number of workshops, listen to some guides for success in college, and get to know each other. Oh, did I mention there's an exam?

I teach a module on environmental sensing and how environmental conditions can affect morphogenesis. However, I mostly try to expose them to ideas and/or concepts of critical thinking. About an hour before a module begins I get the cells going and then write something on the board for the students to see when they show up. I arrive about a minute before the module is supposed to start.

This year I did some variations on themes I've used in the past. For example:

Several times I simply wrote 'Skepticism' on the board. When we start I ask the students what connotations the word 'skepticism' has. Invariably the results are negative. One of my modules I asked 'What's the opposite of skepticism?' after the students told me skepticism was a negative thing. I heard 'gullibility', 'taken advantage of', 'trust', and of course 'faith'. I expected trust and faith, but after these students told me that skepticism was kind of a bad thing, the first thing antonym out of their collective mouths was gullibility!!! Regardless, I make a point that they are scientists, or at least training to be scientists, and they should embrace skepticism. I suggest they need it to be good scientists, but even if they decide that they do not want that kind of career, skepticism will serve them well if they are to be productive members of society.

Once, just to screw with the students, I put an obnoxious completely bogus formula on the board. I started by writing 'As you will recall from your biology course(s) growth of an organism in a given environment can be defined as:' then a bunch of formulaic BS. 'However, this is clearly only valid for spherical cells in static conditions. In nutrient rich environments,' slightly altered formulaic BS. 'What is the formula in nutrient poor environments?' Since I arrive just before the module begins, they can stew on it for awhile. Most students realize it's bullshit, but there is still a bit of concern.

Finally, several times I wrote 'Critical Thinking' and left it at that. We then briefly discuss what they think it means. Interestingly, though not surprisingly, most students have heard the phrase and can use it in conversation, but if you ask them to define it......I tell them critical thinking is the way to evaluate truth statements/claims.

During the module we keep coming back to the concepts of skepticism and critical thinking. We talk about controls, predictions, assumptions, bias, and whatever is relevant based on how the discussions go. While I mess with the students a lot and force them to play along, overall the students have seemed to get a lot out of it. (We'll see this year, once I get the evaluations.)