Final

This is finally demoted from the top of the page. It may very well be the last one with the "dissertation" tag. I can always hope, right?

Done!

Really, totally, completely done! After having gone back and forth a number of times with the editorial office to finalize the dissertation, they finally sent me an e-mail that I've met their requirements. It's over!

Thanks to everyone for cheering me on, from the deepest of depths to highest of peaks, thanks for all your support, advice, good wishes, and all the other things I'm too emotional to think about right now.

Special thanks to Brazen Hussy for hosting InaDWriMo 2008. Having a counter and a blog to put it on to keep you painfully aware of your (lack of) progress helped me more than I can express. I would highly recommend putting up some sort of counter to help you with your goals. It didn't hurt matters that I had some pretty solid deadlines from the university to work with, but I had options if I failed to meet those. I could have postponed graduation with a semester without having to pay additional tuition fees by submitting in early January, I could have been stuck with having to pay for 3 credits of tuition next semester and graduated in May if I had decided to not finish by early January. It might have made things tougher, but they were real options that I seriously considered.

I think ultimately what pushed me through is the support from my family. They paid a really high price in terms of my absence of the past year. I hope it was worth it. I have some major repair work to do there. Hopefully I'll have some time now.

It seems like an incredibly long road, but I did finish up in 4 years. I started this program in January 2005. That's not too bad for having 3 kids (4, if you count the husband), one of which with special needs. I sincerely hope they will be rewarded for their efforts.

Thank you so much everybody!!!

Now back to regular blogging.

Dr. Makita

Yep! I managed to convince my 4 committee members that I am worthy. I successfully defended my dissertation. I got my committee members to sign the form, and I'm not giving it back.

So, that's Dr. Makita for everyone.

Tasks ahead

Thanks for all your encouraging comments. Twelve hours after I submitted, and I'm still running on no sleep and lots of caffeine. I killed even more trees today and printed out 3 copies of my dissertation to hand out to committee members. It's not over yet. I'm starting a new counter to keep track of the tasks at hand. I think I will keep this on top for a while, so I can amend as necessary.

1. Finish statistical analysis
2. Add to chapter 3 results section and discuss
3. Maintain cultures
4. Check reference list
5. Check buffering capacity of medium
6. Schedule exit seminar
7. Reserve room for seminar
8. Prepare mini version of exit seminar for defense day
9. Prepare exit seminar
10. Work more on chapter 4, topic 1
11. Work more on chapter 4, topic 2
12. Add in table for chapter 3
13. Get paperwork together for employment authorization
14. Organize defense date (coffee and stuff)
15. Ask hubby to help pick out clothes for defense and exit seminar
16. Buy shoes for F1-2 who is getting a brand new brace for his leg
17. Start job hunting
18. Incorporate committee members comments
19. Convert dissertation to pdf with Acrobat ("save as pdf" is unacceptable)
20. Submit final dissertation
21. Update CV
22. Defend dissertation

All this needs to be done by the end of the month. So I can guess I'm still in the running for InaDWriMo 2008, with adjusted goals.

Dissertation Submitted!

Submitted

If my writing is a bit disjointed (or as F1-1 would say, discombobulated), it's because I worked through the night, and turned in the dissertation at 6:30 am this morning. Yesterday a student colleague, our labmanager and I worked all day on trying to get a statistic calculated and tested that my adviser wanted me to add. I must have killed two trees in the process. All the intermediate steps needed t be analyzed carefully for model fitting, numbers to be used in subsequent steps, and such. I had only done this exercise in a class more than 3 years ago. And the others I worked with were a bit rusty themselves, but eventually we managed to figure it out for one of my experiments. I ran out of time to finish up the second, but now that I know how it's done, it ought to go quicker. It was too late to put it in the dissertation at this time. I'll add it in before final submission.

Now I've done 2 of the 3 submissions. I have to defend it in 2 weeks, if I pass, I'll have to incorporate comments from my committee members, before final submission.

No break for me though. I have to print the dissertation up for at least one of my committee members, take care of my plants in the greenhouse, start up fungal cultures for inoculation next week, finish up model fitting and statistics, incorporate last-minute comments from my adviser. Ideally I would also start working on my exit seminar, but that seems overly ambitious at this point.

I ought to feel elated. I always thought that if my adviser said my dissertation was good enough to be sent to the rest of the committee that it was just a formality from there on end, and pretty much a done deal. But now I feel numb, edgy, and unable to estimate whether it will be good enough. There are some pretty major gaps in my work that I am very painfully aware of. I simply ran out of time. If I would start on this project now, I would do a kick-ass job in a fraction of the time that I did a shitty job on this degree. It feels so inadequate. And deep down, I'm convinced that my committee members will see through the whole farce and realize that I'm just not up to the task.

I know it sounds pessimistic, and I probably shouldn't be writing this on virtually no sleep and lots of coffee, but there you go. That's how it feels. Not good at all. Just another hurdle in a string of them.

I'll be starting up a separate counter for all the steps that need to be done from now on.

A break from your regularly scheduled dissertation writing

Important breakthrough! Autism is linked to rainfall. Finally all speculation can stop. All kids can get immunized against dangerous, deadly diseases. Move to the desert, and you children should be safe.

In other news: I worked until 3 am last night. Check out that progress meter!

InaDWriMo 2008 Update

I underestimated the number of words of this dissertation. It'll be at least 30k, so the progress meter will be updated. On the bright side, I've done a good chunk already. On the not so bright side, chapters 1-3 are about to go into the 3rd round of revisions. The second round of Chapter 4 revisions still needs to be submitted. All 3rd round submissions need to be complete by November 14 at the very latest.

I have been working very hard, but very productively, so a pat on the back for me.

Joyful!

I'm setting my progress meter to joyful right now! My adviser told me that chapter 2 is in good enough shape to send on to the rest of my committee. I'm tickled pink. This will give me enormous energy, hopefully enough to finish the last two chapters this weekend. Look at the progress meter, I must say it's good to see progress.

Update: Ok, enough joy. Back to work

Next!

I'm beat. I worked all day. It wasn't easy, but I managed to finish the second draft of my literature. The counter has been duly updated. The number of words hasn't changed appreciatively, so I kept the numbers the same. I'm going to bed now and catch some zzzzz's. I'll change my progress meter accordingly. Tomorrow: chapter 4.

Election night was good for me

Few could have imagined the impact it had on my productivity. Although I was a bit distracted by the tv, and wanting to check on election results, it did make me stay up late enough to finish the second draft of chapter 3. The counter will be updated appropriately. It turned out to be an additional 500 words, so I'll update the total number of words too, so as not to give myself an unfair advantage.

No celebration for me though, I have to move on immediately to the next one.

Also, of course, I have to eat my own words. More than a year ago, I claimed that if the US even had to ask whether they were ready for a black president, they weren't. Little did I realize that Barack Obama would fight the uphill battle, and aided by some bad choices by McCain, but most importantly (I think) by inspiring a new generation of voters, would win this battle. He fought a hard fight, and his win was well-deserved. I don't envy him his position to try and fix the damage of the last 8 years, and the enormous task to be everyone's president. He sure has poise, charisma, and the will the do just that. Time will tell.

Concentration issues

I stayed home today to write. And it's not going so well. I'm easily distracted today. I really, really need to submit this chapter today, and it looks like I might be up all night. If I could only get my act together now...

In the late afternoon, I'm going to the lab to quickly end an experiment that is a repeat of 2 previous ones. Last week I couldn't stand the idea of walking around the lab with nothing to do but water my plants every few days, so I figured I might as well start another experiment. Today is the last day for that, so I'll be going in to take the last batch of measurements, quickly run the statistics on the lab computer, then pick up the little girl and the big boy, then head back home to add the data to the chapter and send it off already.

Concentrate..... concentrate.....

Postponed

Dang! I don't think there is any way that I can turn in the next chapter today. I was really hoping that I could and working hard. But it'll have to be tomorrow, I'm afraid. That pushes everything up with a day at the very least.
So I'm hoping to do this:
Ch 2 2nd draft submitted
Ch 3 Tuesday Nov 4
Ch 1 Friday Nov 7
Ch 4 Sunday Nov 9
And then I'll have to get ready for the next round of revisions. And then another. All of these have to be finished by the end of November. It'll be really tough.

I'm working fairly productively today, it's just not enough. Back to work.

InaDWriMo 2008

Ok, I'll be participating in InaDWriMo 2008, hosted by Brazen Hussy.

Since I already submitted the first draft, I'll be counting revised chapters. I have turned in 1 first revised chapter, 4 more to go. If and when my adviser approves the chapters (with more revisions, of course), I can send them to the rest of my committee.

Because I'm doing revisions, I think I'm going to count the revised words per chapter, so if I revise chapter 1 (see below), I will count them as 3000 revised words, and count my way up to the approximately 20,000 it'll be in total. The word count is divided up as follows:
Ch 1. Literature review, currently 4000 words
Ch 2. Experiments with RGS, currently 6000 words
Ch 3. Characterize new pathogen and more RGS experiments, currently 5000 words
Ch 4. Side project, currently 3000 words
Ch 5. Overall discussion, currently 2000 words

Until this torture is over, the progress meter will be on top of the page. I submitted the revised version of chapter 2, which accounts for the 6000 words of progress made so far.

Thanks to Sciencewoman for encouraging me to do this.

It'll be a roller coaster ride. Hang on tight!

Next round

Hi everyone!!
I'm still alive. Barely.


It took several sleepless nights, and some cajoling to make the first submission deadline, but I made it. My adviser made it very, very clear though, that this is all contingent on my next experiment (which is in progress) giving the right results. So keep your fingers crossed. These plants are alive, and they do have a mind of their own. I'm coming up today for a quick gasp of air, before going back under for the next stretch of deadlines to meet.

I have to work on the experiment, analyze some more data of previously harvested experiments, revise the chapters so that they're in good enough shape to be submitted to the rest of my committee. I also have to start working on applying for a change in immigration status, and pay whopping fee. If I fail to graduate on time, I can withdraw that application, and re-apply at a later date. And re-pay the fee, of course.

Anyone want to get together for lunch, or coffee before all hell breaks loose again?

3rd down

I just sent off Chapter 4. While I was waiting for F1-3 this morning at her ballet class, I got quite a bit written for Chapter 5, so I'm hoping to wrap that up this evening. I haven't gotten any feedback yet on Chapter 3 from my adviser. I'm getting there. Not fast enough, but I can only do so much.

This afternoon we had lunch on the porch. I was feeling really drained. I'm running out of steam. After lunch I fell asleep on the porch chair. I must have slept for an hour or more. P1 didn't wake me up, he figured I needed the nap. I was furious with myself after waking up, but in retrospect it did give me the energy to finish off Chapter 4.

You know what's most frustrating about it all? That working to the pointing of killing myself now, is not by any stretch a guarantee that I'll make it on time, that my adviser will approve, that my committee will approve, that I will pass my defense, or that I will graduate. But I have no choice at this point but to go on. Ok, back to it.

It's getting harder

I may not be able to make it. Here is an overview of the dissertation:

chapter 1. Literature review
chapter 2. Really good stuff doesn't work in these cute plants
chapter 3. Really good stuff does work in this plant, and it does fantastic things
chapter 4. Data analysis of large scale experiment done by other people
chapter 5. Overall discussion

I sent off chapter 2 to my adviser two days ago, and yesterday I sent off chapter 3. He sent my chapter 2 back last night, telling me I have to add ALL my data in the dissertation, instead of writing, this experiment was performed X more times with similar results. That may be good enough for a publication in a journal, in the dissertation you need to provide everything.

It's not that I mind, really, it's not. But man, that is going to take me *Forever* with a capital F. I have to get all that data, perform statistics, prepare new table, figures, you know, the works. Can be done, but not on time!

I was hoping to submit chapter 4 today, but it's not looking promising.

After that I was hoping to write chapter 5. The BIG picture, how fabulous is all of this to the survival of the universe? Then I was going to go back and write the literature review of chapter 1. Then there are a bunch of other things that need to be written, a biographical sketch, a summary for the general public. Nothing earth shattering, just stuff that takes time. A lot of it. After proofreading and formatting, I'll consider myself lucky to turn this in anywhere near the deadline without rewriting an entire chapter.

I was hoping to get some more data gathered, finish up some stuff in the lab and the greenhouse. Pffft! No way! I'd rather get more data, than revamp old, negative data, but that's just me. You see, chapter 2 was the chapter where I summarized all my negative data, the stuff you don't want to be reminded off too much, the stuff that never went anywhere.

Anyway, enough ranting, back to chapter 4. I'm going to ignore chapter 2 for now, and get back to it when I'm further along. It just means that I will not be able to graduate this semester. And that is rather depressing.

Shortage

There may not be a enough coffee in the world to get me through the next week. Widespread shortages of coffee should be expected.

Oh no!

In my experiments I test whether an additive to the soil does good things to the plants. We'll call it RGS (Really Good Stuff) for now. When I add RGS, I also add (because it's part of the chemical) something we'll call ES (Extra Stuff). To verify that the observations are due to RGS and not ES, I have a control to which I add only ES. This is a negative control.

A while ago, I analyzed my plant material and noticed that the plants that had only gotten ES, tested positive for RGS. I had already seen that the observations weren't as expected. ES plants were behaving too much like RGS plants.

The next experiment had the same problem. As I was writing this up for the past few weeks, I had a real problem explaining my data, because the ES plants were doing weird things. I did some tests last night, and more detailed ones this morning. And the verdict is: someone must have mixed up the labels on the container and put a form of RGS in the container labeled ES. All the while I though I was putting in ES as a negative control, I was simply adding another RGS treatment.

When I started noticing these problems with my plants, I added another negative control to my experiments, to which I didn't add anything at all (no ES or RGS). Those experiments are still salvageable, because at least I have a negative control. The ones where ES was my only negative control are useless.

I now have to re-do the entire statistical analysis and go back over all my data, trying to figure out when exactly this problem occurred. On the bright side: my data makes much more sense now. ES plants were behaving like RGS plants, because that's exactly what they were. It's easier to explain, but I really didn't need to spend more time analyzing data, thank you.

I'll spend the rest of the day working on statistics, and making new graphs and tables for the chapter in question, and sadly, tossing out a bunch of experiments.

This is exactly what the negative control is supposed to do, though. Science did do it's job here, and let me know that something was up. At least I figured it out now, and not after the paper was published. I would have had a hard time explaining my data.

I also have to notify all the other people in the lab that might have used ES as a negative control. They're likely to run into problems too. If I ever get my hands on the person that mislabeled those containers....

Deadlines looming

I have been told that finishing your PhD is anti-climatic, because there is no single deadline. There are bunches of them. For example:

My first submission deadline is in 2 weeks. That means I have to submit the manuscript to the university for review of formatting issues and such. It will be incredibly difficult (if not impossible) for me to meet that deadline. There is no way I can put all my data in, and I don't have time to work on my data right now. All I can do is write. So I will hopefully submit the first draft to my adviser next week, so that he can sign off on that. This is necessary for me to do the first submission.

Once I've killed nearly myself meeting that deadline, I have to go back to the lab, gather more data, and revise the manuscript in about 2 weeks, so that I can submit the revised version to the rest of my committee too. More killing of myself to get it to them on time.

Time to sit back and relax? Hell, no! Of course, I will not manage to get all the data in on time, so there will be more crunching of data, statistics, quick repeats of experiments that need confirmation, and putting in the final data as I go along. Oh yeah, and prepare to defend. That would be the next deadline. In the third week of November I'm scheduled to defend my work. That means I have to convince a group of 5 or 6 faculty members that I am worthy of carrying the same degree they have. How am I going to fool these people into thinking that I am worthy?

Big sigh and a break after that? Hell, no! My committee members will give me a list of things to change in the final document, and I will work for a full week to implement those. There might even be some last minute data to be added. I would be surprised if there will not be any of that. The final submission deadline is in early December.

So you see, it's not one final burst of activity, culminating in this big sense of freedom. Right now, the road is blocked by 4 major hurdles, with hardly any time to breathe in between. Who ever thought this was a good idea?

Adding insult to injury, P1 is leaving for the weekend. As in: going out of town, and I'm stuck at home with a couple of little kids when I'm supposed to be working on this. Anybody want some kids for the weekend?