I've taught at four institutions so far, and all of them required me to cover the traditional formal research paper. The assumption seems to be that professors in other departments give this sort of assignment frequently, and they believe it's the job of first-year composition instructors to make sure the students can complete it well.
Setting aside the question of how realistic this belief is, I'm wondering if the research paper deserves the fire it takes from some of my colleagues. Apparently, there are concerns about whether it is an effective pedagogical tool in any department. If it's not, perhaps it should be dropped in favor of more effective assignments, which in turn would have implications for the role of FYC instructors.
Should the formal research paper be assigned at all? And if so, by whom?



Research papers.
My students wonder where on earth they will ever use MLA once they graduate. The "formal" research paper, in my humble opinion, has its use, but only among dedicated scholars - those few students who are positive they will be going on to do upper level work. Even then, MLA only seems important when it comes to a narrow portion of the Humanities (English geeks like ourselves). Perhaps if FYC courses focused, as you say, on more effective assignments and curriculum committees created a separate course, say, "Writing the Formal Research Paper," we could eliminate a lot of wasted time spent on teaching MLA to those unwilling to learn it. Rhetorically speaking, the research paper as argument should encourage students to perfect their arguments without slavish devotion to hanging indents.
MLA
That's more or less how I feel about the matter. I don't teach any long research papers unless I'm forced. Thankfully, that isn't the case here. The only thing worse than reading 1,000 words of crapola is 12,000 words of it. Heck, I think I could teach a FYC just having them work on sentences. "The first project will be a simple, then a compound..."
Seriously, though, the MLA stuff is awful. I am so glad that it's built-into the new Word. I just tell students to use that; if it doesn't look 100% right, what does that tell you about MLA? That squadrons of professional engineers couldn't get it right, either? That should really tell you something.
Most people and many journals (at least in C&W) I know are switching to APA or some variation thereof.
BTW, there's an MLA template you can download from the MS Office site that works with the old Word. It's basic, but should serve in a pinch. 2007, though, is much nicer with the built-in bib tools, though you do have to monkey with the settings to do certain things (such as suppressing the author's name if it's been mentioned in the text.) Still, it's all worth it when you can generate a bib with one key press.
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Interesting Assumption
Why are we assuming that teaching a research paper = teaching MLA style?
Assumptions
I apologize if I seem to be assuming. At USF we specifically teach MLA since a majority of the instructors (probably 90% and up) are already familiar with MLA. I do not assume that other universities follow the same guidelines.
Aside from the MLA ...
... or whatever style system a particular university chooses, I do see a lot of value in writing research papers (and, by extension, in teaching students to do it well).
Consider, for example, the case of a student who began with this as a guiding question for a research paper in a history class: "What is the long-term significance of the defeat of the Spanish Armada in 1588?" By the time she narrowed the question sufficiently, read enough material to be able to formulate a supportable thesis, found the facts necessary to support that thesis, and pulled all of that together into a persuasive piece of writing, she would know a lot more than if she had simply read the textbook and listened to a lecture. (Not to imply that textbooks and lectures are the only other options, but they do seem to be the most common ones in an academic environment.)
Are history professors--and their peers in many other departments--wrong for giving assignments like this?