Keeping a Research Journal

The function of a research journal is to set down on paper your thoughts about the primary and secondary source material you are reading. It is a record of your questions about the material and your tentative answers to those questions. It documents the connections you make between the materials you read, and provides a place to record the questions this material raises.
The object of the journal is to record your thoughts about the primary and secondary material at hand. You want to do this as close to the moment of having the thought as possible, and you want to minimize anything that hampers this objective. Make your journal accessible and easy to use. Use a special computer file devoted to the purpose, or a spiral-bound notebook, or whatever device works best for you. Don't worry about correct spelling or punctuation. The journal is not for anyone's eyes but your own.
The journal should document the ways you are thinking about the material and connecting it up with other things you've thought about. What surprises you about what you are reading? For example, one journal entry might merely be an expression of personal disgust that anyone had ever held slaves:

How could anyone have ever done this? How could they have ever considered it ok to hold HUMAN BEINGS as property? And the wierd thing is that some of these slaveholders look just like normal people -- they have families, they seem concerned about other humans elsewhere. How do I understand this!!!?

Such thoughts are extremely valuable. At first, they might seem like "non-academic" thoughts because they are personal feelings. But every historian relies upon such feelings at some level; they tell us what is important to consider. In this case, the thought above suggests a thesis question: "We tend to vilify slaveholders as inhuman monsters, yet in many ways they looked just like people we do not vilify. How did slaveholders reconcile the practice of slaveholding with their own humanity?"
The journal is not a place to take notes on your sources. A journal entry may begin with, contain references to, or discuss notes, but the notes themselves should be kept elsewhere. The function of the journal is to discuss your notes, not record them. Take your notes elsewhere; if you use the journal to take them, the journal will be of less value.
Before and while writing your paper draft, go back over the journal. How has your thinking evolved on specific issues? By keeping in mind the intellectual journey you have made through the material, you are reminded that your readers will be making a similar journey, through which you must guide them. Oftentimes, properly-edited journal entries may even form the basis of paragraphs. Editing and expanding journal material may help you make the difficult transition from researching to writing.
Here is an example of one of my journal entries:

11/9/95: reading No Chariot Let Down intro (p. 11). speak of respectability demanded of free blacks in the south. check also black masters for this, as well as Berlin. idea of respectability common to free blacks North and South. free blacks of charleston, when faced with resentment of white workers who competed against them, fell back upon personal relationships with white elites. placed them among white aristocrats, because associating with slaves was dangerous. in North, blacks often Federalist, then Whig. (that Clay etching/cartoon demonstrates this.) piersen mentions it, too. black elites had closer ties to white elites than to white working class. this is the claim, anyway. dificult to test, especially at the lower level. was the boy in the clay etching representative of anything else? also, I can see former slaves maintaining their whig alliances with old masters, but what about the free elite who sought to distance themselves from associations with slavery? would this desire change things?

A few comments on this entry:

(1) I start with the date. This is the only kind of formatting rule I am concerned with, and I do it only because it helps me trace how I thought about an idea. Other than that, I am totally unconcerned with making the entry look good. I'm just thinking thoughts on paper.

(2) There are many references here that no one but me will understand. That's fine -- the important thing is that I will understand later what I was talking about. In the present case, I'm thinking about other sources that apply to my argument.

(3) In the entry, I'm making connections. I wrote the entry because I was reading a book about free blacks in antebellum Charleston, SC, and it triggered some thoughts about free blacks in the antebellum North. My entry thus makes connections between the kinds of material I've read. Ask yourself, how does what I'm reading bear on the work I'm doing?

(4) The entry also raises questions that are left unanswered. This is the most important thing I can stress about the journal. Good historical writing is the result of a process of asking questions and pondering answers (even if it looks like the historian had all the answers from the start). You simply cannot develop good papers without engaging in this process. The journal is a way to record these internal conversations, and use them to develop your paper.

You probably engage in this process anyway. Whenever you read, you ask yourself questions ("why are they representing slave speech like they are," or "what the heck was the Nullification Crisis, anyway?"). Most of us, however, don't respect our internal questions; we are taught that if we have to ask them we must be deficient, and we therefore ignore them. The journal process is about becoming comfortable with our own questioning. It is about respecting our internal (and external) discussions about what we read, and elevating our trained intuitions to the center around which we build our writing.

The point behind all of this is to develop interesting and worthwhile papers. Too many papers focus on simple, easy-to-answer, "fact"-based questions, such as "How did slaves escape their masters?" These are valid questions, but they tend not to lead to interesting papers. Rather, they produce rather dry narratives or recitations of facts. In the above case, the paper might merely relate the different ways that different slaves escaped.

Such papers lack interest. Your paper is not primarily an opportunity to relate the "facts" about something; it should be a chance for you to explore interesting questions. These are the kinds of questions that don't have simple answers; they are the ones historians and other scholars deal with constantly. With such questions, you may not arrive at the "right" answer, because there is no right answer. Instead, your paper will focus on helping us understand how we might think about a particularly troublesome issue.

Students often shy away from considering such questions because they think they cannot "prove" their point. Yet it is precisely this ambiguity which makes the questions worth asking in the first place; if the answer was easy, it wouldn't be worth asking. In the above case, it is fine to start with the question, "how did slaves escape their masters?" but at some point the issue should get more complicated. For instance, what was the meaning of slave escape? Did it reflect a revolutionary challenge to the system? Or in some ways did it actually support the slave regime? What were the causes of escapes, and what do these causes have to do with the meaning of escape in a larger sense? The list of possible questions is nearly endless; formulating and asking them is one of your first and most important task!

This process of honing-in on a good thesis question can only take place when you listen to your own thoughts about the material you read. For instance, you might start with one of those straight-forward, "fact"-based questions, like "How did masters control their slaves?" In the process of finding out how, you look up slave narratives published in the North in the 1850s. And what you find there -- among many other things -- is tale after tale of female slaves being beaten savagely, often after being stripped of their clothing. You wonder about this, but don't really know what to make of it, so you move on, ignoring it in your search for "real" answers to your question.

You have just missed a golden opportunity. Instead of ignoring your thought, you might have pulled out your journal and jotted a quick note:

on reading solomon northups narrative: All this violence in the slave narrative -- it seems also lurid, so sexual. was this a kind of entertainment as well as antislavery propaganda? What's going on here??

The mere act of writing down this question gives credibility and substance to your thought. Once it is on paper, you may see it again later. Perhaps you will read a similar passage in another narrative, and something will click in your head. You are on your way to developing a fascinating thesis question: What is the role of violence and sexuality in the antebellum slave narrative?