Ahhhhhhh, that's better...

I've been feeling a little weird about my impending defense. In part because I've had zero feedback from GrAdvisor, which could mean 1) he's confident that I've got my shit together so I don't really need anything from him, 2) he's already written me off since I'll be out of here soon after so who cares, or 3) he's giving me enough rope to hang myself.

Now, 1 is the most likely answer but like most of us I'm a little neurotic. It can make for good science, but it also makes me well, a little neurotic. So I just can't dismiss options 2 and 3 out-of-hand.

Which brings me to the weird bit: I'm not freaking out about this.

Ordinarily, I would be freaking out about this. Some not-so-small part of me thinks I should be freaking out about this. I usually freak out about stuff like this, and I have well-practiced coping mechanisms for dealing with it.

I don't have coping mechanisms for not freaking out. So I don't know what to do with myself.

I had a nice relaxing holiday weekend. Great low-key meal with friends. Came to the lab only briefly to keep a few things running so I can get back to the bench when it's all over. Did some work around the house. Went running a lot with DangerDog. Took BH out to lunch. Put up the Christmas tree. Spent 2 hours putting together my talk and declared it done. Didn't freak out.

I gave a practice talk today and I will give another one tomorrow including suggested changes. It needs another run-through, but then really, truly, I'm ready. But I'm not freaking out. Which totally freaks me out.

I don't know how to deal with this. Therefore, I'm improvising. I'm not freaking out about the D-day itself, which is probably good but it feels unnatural...so instead I am freaking out about not freaking out. Phew! That feels better.

Well this is unexpected...

Since completing the dreaded dissertation, my attention has focused to preparing my public defense seminar. I have been sooooo burned out on this topic for a while and feeling rather embittered about the whole 4.5 years of my life in 200 pages thing.

But you know what? I am *excited* about this talk. I really really like the stuff I work on and it's actually very easy to capture other people's interest with it (even non-scientists). Oh hell, I'm just going let the cat out of the bag here, or maybe just a whisker out of the bag I guess: I work on stuff that has to do with sex* (that's still a pretty broad identifier so whatev). Who doesn't love to talk about sex? I'm really looking forward to giving this seminar because it's to a broad audience - most people know next to nothing about this particular aspect of sex, and even those of us who study it have a LOT more questions than answers. But since I'm giving this talk to a bunch of non-sex-scientists, and my friends and family, and whoever else wanders in off the street, I have to make it relevant to wide range of people.

Easy! Tell them about themselves! Crack few jokes, play some videos, show them just how awesome the intricacies that they've never even considered can be. A bit of time on the new stuff I've contributed to our understanding and where the field should go from here, and presto! Forty minutes over before you know it, and everyone hopefully had a good time.

I'm sure it will feel a little anti-climactic when it's over, in the sense that 4.5 years of my life can be condensed into 40 minutes, but for now I'm OK with it. It's going to be fun, not just for me but for my audience. Randy Olson, eat your heart out.

*A friend informed me last night that the flyer advertising my talk was "kinda pornographic" - HA!

Who said my day off wouldn't be exciting?

Thing1 just brought me a bird. A real one. (Awwww, thanks buddy!) He carried it in through the cat-flap and then yowled at me very insistently until I properly acknowledged his superior hunting skillz. (He yowls as a matter of course and I generally just ignore him so it took me a while to notice the bird.)

When I went to scoop up the carcass to discard it he picked it up and wouldn't let go. Fine. Be that way. So I picked him up and chucked him (with bird) out onto the second story patio and locked the door behind him. It's raining. He's informed me of how cruel I am. I could hear him from all the way across the house. Sorry mister, that bird carcass is not coming inside.

This is one smart cat though. The bird carcass did eventually come inside...in his stomach. When I went to let him in, all that was left on the patio was a few feathers.

Now taking bets on how long before he pukes it up.

IT IS FINISHED.

I am done with the effing thing. I have a title that I don't hate and 4.5 years of my life in 200 pages that nobody will ever read. Hardcopy to the bossman's desk and I am taking the day off tomorrow. Then one last push to get the seminar put together, but I already feel like the worst is over.

Soooooooo close!

Title - I HAVE ONE!!! I don't like it much, but it's a start.
Abstract - DONE
Chapter 1 (Intro) - DONE
Chapter 2 (Project 1) - DONE
Chapter 3 (Project 2/3) - DONE - just need to make sure Figure refs in the text match legends
Chapter 4 (Summary) - DONE
Figures - need scale bars on one, and to add 2 panels to another - still haven't finished this because the files borked when I downloaded off the server...waiting for time on the scope to upload the raw data again. :P
References - DONE

Still left to do: once figures are really truly finished, must annotate table of contents with appropriate page number and create PDF of figs plus text. Waiting to hear from the bossman about whether he wants to look over this again. Can't wait to send it out!!!

Crossing things off

Title - I HAVE ONE!!! I don't like it much, but it's a start.
Abstract - DONE and edited by labmate
Chapter 1 (Intro) - DONE
Chapter 2 (Project 1) - DONE
Chapter 3 (Project 2/3) - looking more like finished and passed off to labmate who is an excellent editor.
Chapter 4 (Summary) - DONE and edited by labmate
Figures - need scale bars on one, and to add 2 panels to another - still haven't finished this!
References - Salvaged - Took me the better part of an afternoon fighting with my EndNote library before admitting defeat by a corrupted file. After some tedious copy-pasting into a new document, it seems to be behaving now.

Off to do the figures now. Worried that GrAdvisor and I have miscommunicated about my submission deadline. He still hasn't read Chapter 3, but we've discussed it (last week). Not sure if when I said, "*next* Wednesday" and he said "OK", he was actually OKing the Wednesday after the one coming up.

Motivation FAIL

I was just psyching myself to finish up the last of the dissertation...when my email popped up to say that the ManuBeast was rejected "declined" (PhysioProf tells me that this is not the same thing).

Fuck.

Some of the reviewers' critiques were pretty reasonable, and I now have data in hand to address most of them.

However, the major catch-point for all of them was that they weren't convinced by one key piece of data: that a particular gene was *not* expressed in our tissue of interest. It's kind of important to our findings that this particular gene is not expressed, and I've gone to great lengths to show that it is not, complete with a very solid obvious convincing positive control. They still don't like it. Negative results are tough, but if we need to show that the gene is not expressed, then listen folks, you're going to have to be happy with a negative result. They don't seem to be unconvinced by the positive control, they just don't believe that this gene is not expressed because it makes sense that it would be. PEOPLE, LOOK AT THE FREAKIN' DATA PLEASE.

The editor has "declined" our submission based on the reviewers' critiques but offered to let us resubmit if we think that we can address the reviewers' concerns. I do have other data to bolster the central finding of the paper (which is not actually about this gene, however the non-expression of this gene is important to our conclusions), but I was hoping to put some of it into a second paper. And there is no way to demonstrate that the gene is not expressed without showing that see, it's not there. Look at the positive control - there it is! Look at the experimental samples - not there! Since this is the major sticking point, I'm not sure that I can be any more convincing about this. LOOK AT THE DATA!! I know everyone expects it to be expressed there. I did too when I started this project. BUT IT ISN'T!!! (And that's why it's interesting.) See?!?!? You can see it right here!!

What worries me is that even if we go to another journal, this field is small enough that we're likely to get the same reviewers. As I said, most of their suggestions are reasonable, but if they're going to be irrationally hung up on this gene that is not expressed, then I don't know what else I can do to show them that it is NOT EXPRESSED.

Grrrrr.

Will try to put this out of my head so I can finish Chapter 3 and get the dissertation submitted in the next couple of days. This is really hard to do right now.

Killing it slowly

Title - ???? I still got nothin'.
Abstract - DONE
Chapter 1 (Intro) - DONE
Chapter 2 (Project 1) - DONE
Chapter 3/4 (Project 2/3) - Fuck it. I'm just going to merge them. This will require writing some transitions when I stick them together but it's better than writing a whole new intro and discussion.
Chapter 5 (Summary) - DONE
Figures - need scale bars on one, and to add 2 panels to another - images are taken I just haven't had time to get to this today - tomorrow the figures will be done.
References - Salvaged - Took me the better part of an afternoon fighting with my EndNote library before admitting defeat by a corrupted file. After some tedious copy-pasting into a new document, it seems to be behaving now.

I'm afraid that I'm not going to do projects 2/3 much justice. The findings are really exciting and I'm very proud of these projects. I just. can't. write. about them anymore. I'm not loving this chapter. It's rough around the edges and not so well-organized...or maybe it's fine but I've been looking at it so long that I just can't even tell anymore. You know how if you stare at your own face in the mirror for long enough you start to look like a stranger? I'm having a very similar experience with this chapter. I should pass it off to someone else to look at for a while but I don't feel like it's good enough to even do that yet.

Dissertation Progress

Title - ???? (Seriously, why is this so difficult!?!? Maybe it will come to me in a dream tonight.)
Abstract - DONE
Chapter 1 (Intro) - DONE
Chapter 2 (Project 1) - DONE
Chapter 3 (Project 2) - all but references and 2 panels on one figure
Chapter 4 (Project 3) - all but references and 1/2 of discussion
Chapter 5 (Summary) - DONE
Figures - need scale bars on one, and to add 2 panels to another
References - BORKED!! WTF EndNote!?!?

The clock is ticking...only a few more days. And of course now GrAdvisor is suggesting that we merge Chs 3&4. Urg. I don't really want to spend any more energy on that...but maybe then I won't have to write any more discussion for Ch. 4. Fresh eyes on it tomorrow.

Fun with Fucking-with-people's-assumptions

Female Colleague: "Oh, AA, I'm glad you're here - I was just telling Male Colleague about Awesome Body-Bashing Sport and I think you're probably the only other person in the lab who knows anything about it."

Male Colleague: "What? AA doesn't know anything about Awesome Body-Bashing Sport! How could she know anything about it? She didn't grow up in [Region of this Country Where it is More-Commonly Played]." (As an aside, Male Colleague, who knows next to zero about Awesome Body-Bashing Sport, is not from that region either.)

AA: "No, I didn't grow up there, but I am interested in Awesome Body-Bashing Sport and I do know a thing or two about it."

MC: "Yeah, sure, but you only know what your boyfriend has told you about it, because he likes it."

AA: "It is true that BH is also a fan and that I have some learned some things about Awesome Body-Bashing Sport as a direct result of his interest and experience in it. However, I became interested in this sport originally in high school, long before I knew BH.*

"Furthermore, you may want to sit down because this might come as a bit of a shock to you: Surprisingly, my vapid little girly-brain is not just a vacuum to be used as a repository for BH's knowledge, interests and opinions. It actually is capable of thoughts, interests, and opinions of its very own. Even on matters of things like (gasp!) sports!** "

FC: "Yeah, you know AA actually knows more about Awesome Body-Bashing Sport than I do - I can name all the players on our national team, but AA knows more about the game."

MC: *boggles*

AA: "Dumbass."






What kills me is that MC has no problem with the fact that my girly-brain is pretty good at science; he even defers to me on professional and scientific matters. But to acknowledge that I might know about and be interested in non-"girly" stuff as opposed to just parroting whatever's been deposited in my cerebral vacuum by the men in my life is tantamount to hell freezing over.

*eyeroll*


*The local university had a women's team and I was invited to play for them since I was taking classes there - I didn't end up getting to play due to liability issues since I was still in high school but this is neither here nor there with respect to my interest in the game. My alma mater also had a men's team and I watched their games.

**Believe you me, I would not haul my ass out of bed at stupid o'clock on a Saturday to see the live broadcasts if I were not genuinely interested of my own accord.

Boring post

Appendix figures complete. So is the intro. Still need to write a (brief) discussion and add some references then I can cross it off the list completely.

I'm just noting it here to keep my motivation up.

Still have 1.5 figures to finish on chapter 3, plus part of discussion and references on that one before end of day tomorrow. Then I can cross that off, leaving me with the abstract and summary.

I'm only one day behind my self-imposed schedule which has some padding built in because I know me.

Dilemma

So this hot data set that I wanted to put into my dissertation isn't looking so hot. It looked GREAT when I took the images, but after being passed through three different processing protocols in three different software programs in order to build figures out of them...well, they don't look so awesome anymore.

Crap.

I'm not so worried about this in the long run. I can repeat the experiment (this data set was gathered under less-than-optimal conditions which affect the imaging but not the ultimate result). I will repeat the experiment since I plan to publish this result. But I can't repeat the experiment before I have to submit the dissertation. I can do it before I defend though.

I'm just not sure what to do.

One of my chapters sort of hinges on this result, so I could write it up with the not-so-great images as the important figure (ick), then have these replaced by the better images by the time I defend.

This worries me - I don't really want to give my committee something to pick at. But then, most of them probably won't read the dissertation all that carefully before the defense anyway, so they might not even notice the not-so-great looking images in the written dissertation if I present good-looking ones at the defense.

But what if my second run looks crappy too? Unlikely, but not impossible. Should I take the gamble that they'll look good? Or just toss this chapter out?

My committee hasn't seen these results before. They were not included in my asking for permission to write outline because I didn't have them then. They're not expecting these results so they won't feel like they're missing anything if I don't include them. On the other hand, they have all been fighting with me to make sure I can retain authorship of the paper from my second project - it got scooped right after my asking for permission meeting (they are aware of this), we're taking a new direction, this chapter is that new direction. I'd really like to be able to show it to them to demonstrate that their efforts on my behalf paid off.

What to do? Any advice?

Take that bitchez!

So I've got this little dataset that I've been sitting on. Not doing much with it because, well, n=3. It is possible to run stats on a sample size of n=3, but I much prefer n>6 or so due to the inherent variability in this system.

But I'm using some new statistical analysis software and decided to get myself accustomed to the data entry format I'd start with a small dataset. So I plugged in my numbers, told the software to crunch them and....

p=0.0004

!!!!!!!!!!!!!!!!!!

Double-checked to make sure I didn't screw something up. Nope. That is one sweet p-value for n=3.

Bwaahahahahahaaa!!

Got this in my inbox today (emphases in original):

Dear Blog Owner,

Our website Science.org is a informational databases and online news publication for anything and everything related to science and technology. We recently ran a poll asking our website users regarding what online informational resources they use to keep up to date or even to simply find great information. It seems many of our users have labeled your blog as an excellent source of Space information. We have reviewed your blog and must say, we absolutely love the information you have made available to the public and would love to make your blog a part of our top science blogs. After browsing your blog, our research team has decided to award you a Top science Blogs award banner.

It is a distinction we offer to the blogs that our team feels is ahead of the curve in terms of content.

Thanks again for the great information and we look forward to the great responses your blog will receive from our site. Your blog presence will be very effective for our users (top science blogs).

We have put great efforts in making this decision to give deserving with award acknowledgment. For listing please reply to request banner.

Yay, spammers! Yes, do please let me join "a informational databases and online news publication". I am so impressed with your excellent grammar that I'm sure you're running a real top-notch site.

I'm flattered and all...but I would probably be much more so if they actually bothered to read first. My blog provides great "Space Information"? It's "ahead of the curve interms of content"? Please.

There's been about fuck-all in terms of content since I started writing my disseration (and none of it has had the first damn thing to do with space, which I think is pretty cool but know nothing at all about). Which reminds me - better get back to hammering out the rest of this chapter intro.