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4/1/02: Also note a couple of pieces of information that I've decided it's necessary to give out:
4/2/02: You can take a look at an example plasmid (no, we're not telling you which one it is; if you know, don't tell anyone) on the right-hand whiteboard up in Lipman Hall 202. (The plasmid in the lab manual is not the plasmid you got, or anything close to it. The plasmid that is up on the board, on the other hand, is mostly the same as your plasmid. It's part of your job to figure out what the differences are, and - moreover - to show me that you understand how the example one was worked out (don't just copy from it, in other words - you have to use your own data).) Note that the room in question is occupied by classes 2:50-4:10 Tuesday and Thursday, and that I will be occupying it and distinctly adverse to being disturbed (if you bother me while I am studying for the Biochem exam or am taking it (I need extra time and no distractions due to Attention Deficit Disorder), I am very likely to throw something at you!) Tuesday night and probably much of Wednesday. If you need to ask someone about the plasmid lab during this time period, check with Dr. Chase or with John Campor (firstname.lastname@example.org), the Wednesday lab TA.
4/3/02: (I am writing this before I fully wake up (I will be studying instead once that happens), so sorry if it isn't as clear as it should be.) Two things:
4/4/02: OK, I am now available again (including until quite late). Do keep in mind that there is a class in 202 from 2:50-4:10, so I will not be in there during those hours (try 119 or 325). Contrary to some rumors, I will take labs turned in after Friday - although if there's anyone who hasn't had an exam this week (and doesn't have any other valid excuse), I may be somewhat irked - especially if you make mistakes that I could have helped you with and you don't come and ask me. I will accordingly be available this weekend to help with labs. I'll try to email this out to everyone; if there's anyone I miss, please tell them!
4/5/02: I will (unless overriden by Dr. Chase) be counting labs turned in before midnight Sunday as in on time (although the (two) people who got theirs in on Friday will get some brownie points). In the instructions regarding how to do the lab report:
4/7/02: I will be here until at least 1 AM Monday morning, although anything that comes in after midnight will be treated as late. On Monday, I will be available in the evening after General Biochemistry, and may be available prior to General Biochemistry (but after 12:00 noon) - email or call to be sure before coming over.
4/10/02: I am still available for consultation; email me to ask about when. Please note that on the RNA labs, you should use the bottom 4 standard bands only - the 9.49 and 7.46 BP bands are not going to work for you, from what I've seen. You may need to use the 2 bands from the E. coli rRNA (in the rightmost lane) along with the info in the introduction to the lab on prokaryotic rRNA sizes to get a sufficiently accurate standards graph. Come and ask if you have any more questions on either the plasmid or the RNA labs - but note that I am not grading the RNA labs, so can't give you as much of an answer on many things as I can on the plasmid labs.
4/12/02: Sorry about people who were looking for me yesterday - I wound up having to spend the afternoon getting my car fixed (muffler problems (that would have made it illegal to drive!) and running low on oil). I should be available for at least part of the afternoon on Friday (try between 4:30PM and 6:00PM - before then, I am either waking up or taking care of what's due Monday, April 15th (taxes)), although there's a dinner Friday night that I will be at, and the rest of the celebration of the department's 175th anniversary on Saturday.
4/13/02: I am available for consultation on plasmid and RNA labs, and should be also tomorrow evening after General Biochemistry. In addition to the above and below regarding the RNA labs, note that you don't need to worry about what the physical distance was on the original gel, just on the picture - I have checked with Dr. Chase on this. He has also said that you can use the end of the picture (away from the wells) as the "dye front".
4/15/02: I am available this evening until 12-1AM or so, and should be tomorrow afternoon after the lab (do allow time for me to take a break after the lab, though!). I've spoken to Dr. Chase regarding the RNA lab again, and he says:
4/16/02: RNA lab due date has been pushed back by one day due to confusion on whether people were supposed to measure the other plant's bands (and that Dr. Chase, who will be grading them, is busy grading Proteins and Enzymes take-home exams!). The sequencing labs, which it looks like I will be grading, are due in two weeks also, not the one week that it says in the lab schedule. (We don't actually have a lab two weeks from today (4/30/02, a Tuesday), nor one on that Wednesday (5/1/02), but it's still during the class-time part of the semester, as opposed to the exam-time part.) When the PCR lab (which is a much shorter lab report) is due has not changed, partially because it's already pushed back about as far as we can do so.
4/19/02: I will probably be working on grading the plasmid labs (that I've gotten, that is) this weekend, starting off with revising the grading master that Dr. Chase gave me earlier this week. My availability for helping people with lab reports (plasmid or RNA or other) will therefore be limited - do not disturb me when I am actually doing the grading (other times I may be available), unless you're really not interested in having a high GPA... My need not to be disturbed while grading is aggravated by that I normally use the PC in 118 to do my grading (with a spreadsheet), but those rooms are having power fluctuation problems (making using the computers in them unsafe) and (to me, at least) currently have inadequate air conditioning (likewise due to power problems) - I therefore may be in 214, the PC computer lab on the teaching lab side of Lipman, to do the grading.
4/22/02: OK, I am available this evening (after I wake up, that is - try 6:10 PM or later) for assisting people. I'll be working some more on grading the plasmid labs later this week sometime (plus I have a paper due May 1st in Advanced Cell Biology, a graduate-level course I'm taking over on Busch), however - I did revisions to the grading master and a preliminary pass (through the 26 I've gotten) this past weekend.
4/24/02: Sigh... I am getting a considerable amount of feedback that the reason people weren't asking questions of Dr. Zylstra during the sequence lab was that they were completely lost (this may be happening during General Biochemistry lectures at times also...). There seems to be a rather thorough lack of background given people on this - genetics and computers - for biochemistry majors... and this isn't something that Dr. Zylstra - or Dr. Chase and myself (especially when I was talking to people during the lab about what I expected - sorry about that!) - took into account with this lab. I will be grading the sequencing lab, which is due slightly later than earlier announced - see below. What I will be looking for in regard to the analysis (4 and 5 in the lab manual page 8):
PCR Gels, for use by people who can't use theirs for some reason:
4/26/02: I should have the plasmid labs (which have been turned in - 8 have not been) graded after this weekend. Note that I will not take any (plasmid labs) after next Tuesday/Wednesday, which is when the Sequencing labs are due... and if you get a zero on a lab because you didn't turn it in, you flunk the course.
4/29/02: Due to an electrical power outage, and subsequently waiting for the computer UPSes to recharge (1.5 hours), on Sunday evening, plus disruptions on Saturday due to Ag Field Day, a paper that I have due on Wednesday (in a graduate-level course), etcetera, I am afraid that I don't have the labs quite done yet - I had hoped to have them ready to hand back this morning - but I'm doing my best, and might have them done by this evening. If I am, I will be available for consultation this evening for help with the labs, although I'll need Tuesday evening (at the minimum) for doing the rest of the paper I have due (that we don't have lab tomorrow will help on this, of course).
Update: Sigh... I am not done yet (I wrote the above at about 4AM, and left here for a class on Busch at 9:30AM, went to sleep from noon until 3:30PM or so, then came back here), but am nonetheless available for a couple of hours or so this evening (starting at 6:00PM) for consultation. If it's after 8:00PM, email before coming over.
4/30/02: It's almost 1:00AM when I'm writing this, BTW. I expect to be here working on the labs - don't disturb me! - until I put them in Dr. Chase's office for him to pick up before he goes over to give the ExpBio lecture. Then I'll go home and sleep, but I should be back - and available for assisting people, at least for a few hours (keep in mind the paper I have due Wednesday morning) - by 4:00PM.
5/1/02: Due to that my availability was rather limited yesterday, and may be today until 4:00PM or so (before which I'll be working on the paper I have due today, then getting some sleep!), I have decided to accept plasmid labs for one extra day. This doesn't mean you won't have today counted off on their lateness, of course! To answer a question someone had, this deadline is for the plasmid labs only - not for the sequencing labs. The last date I'll take those is the due date of the PCR labs, May 6th. 8:14 PM: My apologies to anyone who was looking for me this afternoon; I wound up working on my Advanced Cell Biology paper until 11:20, dropped it off, went home and collapsed, then slept rather longer than I had intended - not unsurprising given cumulative sleep debt (average of 4 hours of sleep a night for the past week or so!). Given this, I will be willing to push back the due dates for the plasmid and sequencing labs by a day:
5/2/02: I will be here until about 10-11AM, then will need to go home to sleep. I'll be available again this evening (probably around 7-8PM).
8:45PM: OK, I'm here and available, and should be until at least 4-6AM - email to let me know if you are needing to come by after then, and I should be able to be available until 10-11AM (if you don't email me, I might decide to go get something to eat or whatever). On question 2 in the sequencing lab:
5/4/02: I am here and available for helping with labs and/or turning them in, provided people keep in mind that I will be grading both the remaining plasmid labs and what sequencing labs I have received this weekend - probably sometime around 3-4AM Sunday and Monday mornings. (I will post up later when exactly this is - don't disturb me between those times!) See below for how to contact me to get into the building, since the doors are locked. Incidentally, if I took off because you said on the question on the plasmid lab about what the prehybridization does that the prehybridization solution binds to the blot (as opposed to the DNA on the blot, which is what is actually the case), come by and ask - you may have points coming back, depending on why you put that.
5/5/02: It's almost 1:00PM; I've been here since 11:00PM yesterday (helping people with the sequencing and PCR labs, then grading the remaining plasmid labs (all except for a couple that I need to ask Dr. Chase about are now ready to be handed back - I've put them in Dr. Chase's office). I'm going home and going to bed. I should be back sometime around 10-11PM, and plan on grading the sequencing labs (I will try to have them all graded and ready to give back by 8AM Monday morning) starting at about 3AM Monday (again, don't disturb me while I'm doing this). People may wish to come by and take a look at the info I've put up on the boards in 202, BTW, mainly on sequencing - keep in mind that that could be on, say, the General Biochemistry final (Dr. Zylstra did go over it this term). The plasmid lab drawings have been removed; if anyone is curious, the ones on the side whiteboard were the "trial run" that Zaher (Tuesday lab) and I worked out with his data (taking something like 20 hours, including false starts - I was learning about this also!), and the (longest-lasting) ones on the front board were the second group to be worked out (taking somewhat less time), namely that of Henry, Matt, and Amit (also Tuesday lab). I had previously asked people not to reveal this information, but since I won't be accepting any more plasmid labs, I thought it was appropriate to give proper credit to the people who effectively helped everyone else - both with the drawings and with giving me practice in interpreting and explaining restriction mapping!
5/6/02: It's just after midnight, and I am here and available until 3 or 4 AM, when I'll be grading the sequencing labs that I've gotten. Note that on the PCR lab that you were using genomic, not plasmid DNA, for purposes of answering part 3.
3:30 PM: Yes, I'm still here, obviously (I don't have a computer connected up to a phone line at my apartment). I will be available until at least after General Biochemistry to do things like signing labs as being in; while I will do my best to answer questions and give other help, I make no guarantees as to the accuracy of my responses, given how sleep-deprived I am. The plasmid labs are all graded, and almost all are available (see Dr. Chase). I also have graded the sequencing labs that I've gotten and have made up an info sheet on said grading, which I have attached to the labs and will put up on here (for usage in exam study - note that Dr. Chase's webpage now has the spring 1998, 1999, and 2001 exams up with answers (unlike the copies on electronic reserve); he was on sabbatical in 2000 and thus doesn't have that exam up) after the time has passed when I will take sequencing labs (namely midnight tonight, or later if I'm still here (if need be, email to make sure I will be, within reason!)). In regard to whether there will be a restriction mapping question on the final, which there has been some confusion about - including on my part (sorry about that), Dr. Chase has now stated:
[I am] not guaranteeing not to have a restriction map question on the exam - only that, since the digests will be complete and the measurements clean, it will be easier than the actual values they had to deal with!What people appear to have misinterpreted was his commenting that he'd never give people on an exam (at least for this course and an in-class exam) one with partial digests, uncertain measurements, missing data, etcetera. BTW, I have not curved either the plasmid or the sequencing labs, mainly because I'd need to curve down (unless I include late points and, for the latter, people who haven't turned theirs in (as zeros)).
8:10PM: Do Not Disturb.
5/14/02: I learned yesterday about the extremely sudden and unexpected death (23 years old; died of a cerebral aneurysm within 12 hours of the onset of symptoms Sunday evening) of a very close friend. Do Not Disturb - I am really not feeling like talking to anyone, especially about your grades. Speaking of those, Dr. Chase should have them figured up by tommorrow morning. While I wasn't feeling anything like doing any grading yesterday, to put it mildly (even before I learned of her death, I had an exam in Advanced Cell Biology that afternoon), I managed to pull myself together enough to produce quiz, subjective, and prelab grades for Dr. Chase this evening, plus grade the sequencing problem on the exam of two people who'd taken the exam (due to conflicts) on Monday. He should have the grades for pretty much everyone (modulo a few T grades) tomorrow morning. Bug him about them, not me, or I may ask to retroactively change your subjective grades to a negative number...
5/16/02: The grades are posted outside Dr. Chase's office.
5/24/02: I do hope I'll see people who are graduating today. I'm feeling... somewhat better.
I am also not enthused about the amount of memorization required for the final exam. (Dr. Chase is not of the opinion that it is that heavy on memorization - but he has an extremely good memory, so perhaps does not fully realize how difficult memorization can be, especially for those of us like me who have a bad memory.) My disapproval of memorization where not absolutely necessary is one reason that I don't give in-class, closed-book quizzes except on safety matters - things that people do need to know things off the tops of their heads, to avoid endangering anyone.
People frequently say that the lab takes more time than a 2.5 credit course should. You are correct; Dr. Chase and I agree with you. Unfortunately, it appears to be University policy, probably due to the various humanities departments lobbying, to not count laboratory hours as much as classroom hours - even if the laboratory in question has, like Experimental Biochemistry, lab reports that require lots of time outside of class. On the other hand, do realize that this is one of the more thorough biochemistry (and related areas) laboratory courses that undergraduates might ever take, and definitely gives people lots of experience - experience that has meant the difference between getting a job and not getting a job for some.
I have suggested to Dr. Chase that the Rutgers Genetics course (as variable in quality as I've heard it is - some report it being better-taught in the summertime, BTW), or some equivalent, be prerequisites or corequisites for the second semester of Experimental Biochemistry - and may suggest this also for the second semester of General Biochemistry - in light of the many people coming to me needing help on what I, as a geneticist, would consider very basic aspects of the plasmid, RNA, sequencing, and PCR labs. While this would take too much wrangling to get through for next year, he is planning on adding a strong recommendation for such a course to the description of Experimental Biochemistry in the course catalog.
My background: My primary background is in biology, specifically molecular genetics. I am mainly qualified for this lab due to:
Getting in touch: The best means of getting in touch with me is to come by Lipman Hall room 202 (the SGI computer lab), then try Lipman Hall 119. (If the building is locked up, try the phone number given below - use the 202 number first in that case.) The second best is to email me (see below for the address), since I check my email several times most days. (Note the points on my tutorials page about not sending me email that's something other than plain text.) The third best is to call me at 932-9255 extension 118 (202 if that doesn't work). (Do not assume that I'll receive voicemail; only use this method if I (or someone else) answers the call.) The fourth best is to put a note in my box; it is on the first floor of Lipman Hall. (By the way, if you are turning in a lab report other than directly to a TA or to Dr. Chase, be sure to get someone - a secretary, professor, graduate student, whoever, just someone other than another undergraduate - to sign and date it so we don't have to count off for lateness (or for any more lateness than you should have been counted off for).) If you are trying to get in touch with me and Lipman Hall is locked up, do not try yanking on the doors to open them. (As should be obvious to anyone with enough brains that they should be allowed into a college, this will damage the doors. I will not accept lab reports from anyone who has done this, much less give them other help, and may well call the cops to have them arrested for vandalism.)
Office Hours: I will not be available on Mondays or Wednesdays unless I specifically tell you otherwise, since I have both a graduate course over on Busch and Biochemistry 403-404 (or, actually, the graduate-level version of the course); I _may_ be contactable after the latter lectures if you're also in that course. (I say "may" because by that point I may be feeling like simply going home (or to the computer lab in Lipman Hall Room 202) and taking a break...) I will try to let you know what times I will be available; the best thing to do is to simply ask whether I will be available at a given time - people who've had me before can tell you that I am willing (unless other obligations, including my own academics, conflict) to work with people at quite odd times and/or for very long hours.
Quizzes: My quizzes have as their primary purpose encouraging you to have read over the lab before you come in and making sure that you know, in particular, safety-related information. I do not expect you to have memorized all of it; my own memory isn't that good, and I will generally consult the lab manual before answering questions - but I will have read over the lab. I expect you to know in general terms what we are supposed to be doing that day and about any safety precautions that you need to take, particularly those which can affect other people. I may - I generally don't unless I get inspired or feel that you aren't reading over things - give you a take-home, open-library quiz (or at least a question or two, if not a full quiz) that is for the next week's lab, again mainly to encourage you to read it over. Except for take-home quizzes and safety quizzes, given the prelabs you are being asked to do, I will not ask for any further quiz-taking.
Subjective Grade: How I do the subjective grade is to note down when you do something good, and when you do something bad. I will fix a particular starting grade, and doing something bad will decrease your subjective grade below this; doing something good will increase it above this. The starting grade and amount up/down will be determined by whatever gives a final mean of 85 and a high of 100. Examples of good and bad things:
I normally find I have more +'s than -'s by the end of a semester. This means that those who do get significant minuses (e.g., a lab group a bit back that left lots of gunk in the pig kidney centrifuge bottles...) will get a rather low subjective grade, and that those who simply don't do much either positive or negative won't get a particularly good one.
Nametags: I have problems remembering people's names (including close friends, BTW!), especially in a class of 18+ people. This sometimes causes problems with assigning subjective grades. Something I'm trying out this year is to have everyone fill out and wear a nametag. These should be left in the lab, to avoid losing them. At least for the fall semester, if you forget to wear it, that will be subjective points off; if you lose yours, that will be even more subjective points off - especially since I bought them with my own money!
Curving: I normally will try to curve to a mean of 85 and a high of 100. On lab reports and quizzes, I'll circle the final grade that you'll get for each of them. Such curving does not include extra credit points or points taken off for lateness.
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