The year in books

Every year, I mean to keep a list of all the books I read that year so I can look back at the end of the year and be proud of how much reading I was able to do. Every year, I forget. Will 2009 be any better? Stay tuned.

So, I have to compile this list from memory. Which makes it extremely not accurate because I’m sure I’ll forget some things and other things I can’t remember if I read them this year or last year or what.

Mostly what I read was a lot of crap. Well, not necessarily crap, but if it were food, it would be junk food. Generally speaking, I’m okay with this because I primarily read for entertainment and escape and that pretty much guarantees I’m going to read fluff of little redeeming value. It’s only when I see other people’s lists of books they read this year that I feel a little sheepish.

But, whatever, on to the list!

So, apparently, this was the year of the vampire novel for me. I had never really gotten into vampires before (I stopped reading Anne Rice after Interview with a Vampire) but for some reason, this year they spoke to me. Don’t judge me.

1-8. Sookie Stackhouse novels by Charlaine Harris. These are the vampire books I started with. I think they may be my favorites of the vampire genre.

9-24. All of the Anita Blake novels by Laurell K. Hamilton. These are much darker than the Sookie Stackhouse books. Also, much smuttier. They start out okay (that is to say, the first several books are smut-free) and I got invested in the characters and then the characters started having sex and then it got more and more graphic as a succubus got introduced, because, well, you can’t have succubi without sex, right? I don’t normally like reading about graphic sex because it embarrasses me, but, dammit, I wanted to know what happened to Anita! And, just like that I had read all 16 books. But, I just read somewhere that Anita Blake is considered “urban fantasy” which sounds way better than “vampire porn” and makes me feel slightly better about reading them. I’m still not sure I want my mother to know I read them, though.

25-28. The Twilight series by Stephenie Meyer. I know. I probably just lost the respect of at least half of you. Let me explain. I got sucked into these books because a friend of mine asked me if I wanted to go to the movie which I did and, having seen the movie, I still couldn’t understand the hoopla surrounding it, so I read the first book thinking this might give me a better idea of what the fuss is about. Then, I wanted to know what happens in the 2nd book, and, well, you get the idea. I have lots to say about these books, mostly about how I cringe to think of pre-teens reading these books because I think the main characters are really, really not good role models and also, if a boy is following you around everywhere you go and crawling into your room at night to watch you sleep (especially, especially if he is crawling into your room to watch you sleep, holy shit!), that boy is a STALKER and you need to report it to the police. That is really not okay behavior. But, hello, this is fluff. Much like cotton candy. You don’t read it with the expectation that it is going to be great literature. And, just like cotton candy, the closer you get to the end, the more you wonder why you are partaking of it, but, it’s cotton candy, you gotta keep going til it’s all gone (by the way, book 4? What.the.fuck??? Was Meyer smoking crack? Srsly). Perhaps, I should write more about this in another post.

So, that’s it with the vampires. And werewolves. Because, apparently, if you have vampires, you also have to have werewolves. At least in my experience.

29-34. The Merry Gentry novels by Laurell K. Hamilton. So, I really should have known that these books would have just as much graphic sex as the Anita Blake books (what with them having the same author), but, dudes, the main character is a faerie princess and I just could not refuse. I haven’t read the most recent one yet and I haven’t decided if I’m going to.

35-46. Riftwar books by Raymond E. Feist. Shadow of a Dark Queen, Rise of a Merchant Prince, Rage of a Demon King, Shards of a Broken Crown, Krondor: The Betrayal, Krondor: The Assassin, Krondor: Tear of the Gods, Talon of the Silver Hawk, King of Foxes, Exile’s Return, Flight of the Nighthawks, Into a Dark Realm. I still need to read Wrath of a Mad God to finish the series.

47. Ender in Exile by Orson Scott Card. Got this one for Christmas this year. Was a fun read. Wish I had reread Ender’s Game before I read this latest one, though.

48. Tales of Beadle the Bard by J. K. Rowling. Also a Christmas present. It’s just three fairy tales so it went by quickly.

49-51. The Wee Free Men, A Handful of Sky, and The Wintersmith all by Terry Pratchett. These are technically kids books, but I love me some well-written kids books. They take place in the Discworld universe and have an awesome female protagonist. Way better role model than Bella of Twilight.

52. The Best Science Writing of 2007 by Gina Kolata Cohen. I think there may be a few essays in this I still haven’t read. I’ll get around to it one of these days.

53. The Duchess by Amanda Foreman. I saw the movie so I was curious to read the book. I haven’t finished the book, but I’ve read as much as I think I’m going to. Not that it’s a bad read. It just started to depress me, and, having the problems I do with depression and so forth, I can’t be reading depressing shit.

54. The Golden Compass by Phillip Pullman. I think I actually started this in 2007 but whatever. I listened to this book rather than read it and the audiobook had a full cast so it was pretty fun. However, for reasons I haven’t entirely been able to figure out, I’m not in a hurry to read the 2nd book. I think this is partially because I’m upset about what Lord Asreal (sp?) did at the end of book 1 and I really don’t want to read more about him. Asshole.

55. Mason-Dixon Knitting: Knitting Outside the Lines by Kay Gardiner and Ann Meador Shayne. Knitting books do so count. Especially if they are full of essays. So there.

I think that may be it. I’ll add more if I think of them. Also, I reread a bunch of Terry Pratchett books but I don’t think I should count them toward the total.

So, wow. I read 55 books this year. Huh. I would have sworn it wasn’t that many. I think the key to the volume of books was that I read several series. Often, when I start reading a series, I obsessively read that series until I get through all of the books. And by obsessively, I mean, read while eating, read instead of sleeping and read while walking down the street (which works better in the summertime because it stays light later). Also, a large number of those books were low on substance which makes them quick reads.

Additionally, I started a few books that I then put down for one reason or another (probably to read a vampire book) and still intend to finish. So, I guess I’ll count those in 2009.

Before I started this list (back when I was thinking I hadn’t read a lot of books this year), I was considering making a goal to read X number of books in 2009. This seems less necessary, now. So, instead of making a goal for the total number of books, I will make it my goal to read at least 12 non-fiction books in 2009. That’s only 1 a month. That seems doable, right?

So, you guys have any suggestions for non-fiction books?  Nothing too heavy, mind you.  Also, what did you guys read this year?

Conversation with the boss

Today, I went  into my advisor’s office, sat  down and said, “I’ve never written a  paper before, I have no idea what I’m doing.”  Then, I handed him the image, figure legend, and results section for figure 1 and asked him to look them over.  The verdict?  Well, some of what I have in the results could go in the intro and he doesn’t like it when you use the word “this” without something following it (ie “To do this, we…” is bad) but otherwise, it looks “fine.”

I may be able to do this thesis thing after  all.

Back to the Grind

I didn’t really mean to take the last 5 days off from lab, it just happened.  I blame  it entirely on the fact that my husband was here and I can’t be expected to care about yeast when my husband, who is usually far, far away, is sitting in my apt.  Right?  But now he’s gone back to California, so it’s back to lab for me.

It felt really good to take a break.  Really, really good.   So good, I think I’m actually up for working and maybe even *gasp* writing.  We shall see what the day brings.



The vector I’m trying to cut my insert out of is the product of 6 subclonings.  Let me tell ya’ it was a joy trying to figure out that mess.  Anyhoo, this insert has previously been cut out from this vector (vector 1) to make a different vector (vector 2), using the exact same method I’m trying to use.  (Before you ask, I cannot just cut it out of the 2nd vector using the same method because it was cut out using XhoI, Blunted, then cut with XbaI and then ligated into Ecl136II and XbaI.  However, I just realized, I  may be able to cut it out with EcoRI and XbaI….hmm….).  So, I thought, easy peasy, I  just do the same thing as has been done before and presto changeo, I have my vector (vector 3).


First, the size of the insert and the size of the vector backbone from which I was trying to liberate it were very close in size.  So, I ran a long gel and cut out the top band, because according to my calculations, the insert was bigger than the vector.  Then I did the ligation and transformation and miniprepped them and I did a digest to identify clones with insert.  But, the digest came out sort of funky.  So, I sent some clones to have the edges of the insert sequenced and lo and behold, I had ligated two vectors together.

So, I  already know there is something slightly goofy because the sizes aren’t quite right.  I recut out my insert and this time, just to be certain, I ligated both bands into my new vector (you know, in separate reactions).  Then, I did a transformation and I miniprepped them and did a digest and goddamnit, neither possibility looked right.  It looked like the enzymes I was using to check for positive clones weren’t cutting at all, even though they linearized the parent vector just fine (which is what I expected).

So, fuck it.   I’m PCR amplifying the damn thing from a different vector (vector number two in the first paragraph; a vector I’ve actually used in an experiment so I know it’s good) with sites on the ends.  No more Ms. Nice Girl.

Except, I’m waiting on primers.  I ordered the damn things before Christmas, when will they get here?

But, I’m intrigued by my new idea of cutting the insert out of vector 2 with EcoRI and XbaI.  Maybe I’ll get started on that today.

Dedication or Stupidity?

It is the week of Christmas.

The weather has turned seven shades of ridiculous.

The boss is out of town for the week.

My entire lab is here working (except for, you know, the boss).

And, just on a personal level, my husband is in town and I still don’t have all of my Christmas shopping done.

What the hell are we doing here?



So, my advisor already made CPP’s suggestion of doing all of the figures and figure legends first.  However, after spending hours of time moving images miniscule distances to the right or left and changing the font on the figures several times, I had to accept that I was procrastinating.  So, I thought I should start writing the text of the Results.  I still have a couple of figure legends I could write, though.  Maybe I should do that.  Especially since all I’ve really done is change forms of procrastination.

I’m not even thinking about the introduction.  There is no introduction in my fantasy world.  Panic does not even come close to describing how I feel about the introduction.  I’m just going to get through the results first.



I’ve got the sleeping pills.  They helped me get to sleep, but I didn’t stay asleep for the first couple of nights I took it.   Then, I started sleeping through the night and needing to sleep through half of the day, too.


No sleeping pills = no sleep, tired all the time

+ sleeping pills = lots of sleep, sleepy all the time

Not sure this is an improvement.  I think I’m going to try a different sleeping pill and see if that’s any better.



If someone could make my super simple subcloning work right, I’d appreciate it.  I really don’t understand what the problem is.   Cut fragment out of vector 1, ligate into vector 2, transform, miniprep.  But, then I do a digest to check if it’s right and the digest comes out all wrong.  On all of them.  This is the second time I done this damn cloning.  If I have to do it a third time, I’m going to be wicked pissed.

Sheer idiocy

Despite my myriad mood and sleeping problems, my benchwork has been coming along just fine. So much so, that I do not have so much of it left and, while I’m waiting for a digestion or a gel or something or other, I have no other benchwork to do.

Now, you might imagine, then, that I would use this suddenly available free time to do something really productive, like, I don’t know….write my thesis, maybe?

You would be wrong.

It seems that this free time is perfect for me to read some blogs, wander around the lab talking to people and, at the height of responsible behavior, download and read an unfinished manuscript in the Twilight series. Yes, that’s right, read trashy teenage vampire romance during normal business hours.

WTF is wrong with me???

I want to graduate, I swear I do, but everytime I sit down to start writing my thesis, I start to hyperventilate and end up coming up with something way more interesting to do like reading all the comments on the latest Drugmonkey post ,or going to go buy tea, or commenting on the status of various friends on Facebook.

Or, you know, writing a blog post.

The few times I have actually started to write, I have written nothing but pure, unadulterated, grade A crap. Absolute crap. Crap that is so crappy I couldn’t possibly show it to my advisor because of its craptacularness. I completely and totally suck at academic writing.

I’m not even trying to write the intro, this is the results section for crying out loud. It really shouldn’t be that hard. But, I’ve never done this before–never written so much as a short correspondence–and now, I’m stuck writing the most important document in my life with no experience whatsoever in this kind of writing, a time limit, and a really bad case of nerves.

Excuse me while I go breathe into a paper bag for awhile.

Everyday, I haul my laptop into lab with the promise to myself that I will write. Just a little bit. Just a couple of paragraphs. Just a few damn sentences. I swear up and down to myself and on the Bible, cross my heart and hope to die, that I will write just one measly little sentence on my thesis and by the end of the day, I’ve read every blog on my blogroll three times, cleaned up my bench, checked my email a billion times, and gone shopping for yarn on the internet. And updated my wish list.

I am so screwed.



Now, if only I could get my brain to turn off

So, I started taking the medicine for restless leg syndrome and it’s helping.  My legs aren’t totally comfortable, but I don’t have to move them around like crazy either.  Stretching helps.   Thanks to whoever suggested that.

And, I seem to be emerging from my depression, too.  I’ve been feeling happier and more motivated.  Things are going well.


I. Still. Can’t. Sleep!!!!!!

It takes me forever to fall asleep.  And then I sleep for a couple of hours and I’m wide awake again.  My brain will just not shut off.  So, I end up staying awake for  a few hours before I can finally fall asleep again.  I think I haven’t had a decent night’s sleep in a month.

So, it’s back to the doctor for me.  Hopefully she can give me something that will let me sleep through the night.


One of the reasons my labwork is suffering right now is because I haven’t gotten enough sleep.  Why haven’t I gotten enough sleep?  Restless legs.

Restless legs syndrome is a little hard to describe well.  It’s really hard to say what the actual feeling in your legs is, exactly.  The best I can do is to say that it reminds me of what your legs feel like if you have been trapped in a car for many hours.  They don’t so much ache or itch or anything, they just feel…uncomfortable.  And the thing that makes them comfortable is moving them around.  Constantly.

Generally speaking this feeling is muted when I’m doing something else–anything else.  Even just sitting and reading.  It’s like it distracts that part of my mind that makes my legs want to move.   However, when I am sleeping, or trying to get to sleep, my mind isn’t distracted anymore and the restlessness begins.  It’s not so bad  when I first lay down, so if I’m really tired, I can fall asleep quickly and it’s not a problem.  The problem is, it wakes me up and then I can’t get back to sleep.  The other night, I actually resorted to jumping jacks (at 2:30AM) to get my legs to feel better and then read for awhile, and then was able to go back to sleep.  But, it wasn’t very restful sleep.

Before you ask, I’ve tried sleeping aids–they haven’t worked.

It’s getting to the point that my legs feel tired and achy during the day, probably from all the moving around they’re doing during the night (on the plus side, maybe I’ll lose a few pounds with all the calories I’m burning moving my legs around all night).  An even bigger problem is that I’m having difficulty functioning during the day.  I’m kind of wandering around in a daze.  I walked right past the stairs when I was trying to go to lunch earlier, and I left my backpack at the cafe.  And, I have this little headache over my right eye.

And I’m supposed to get some labwork done.

This has to be one of the worst medication side effects that I’ve endured.  Well, okay, that extreme anxiety and panic attack was not much fun, I’ve got to admit.  But, I could deal with the overwhelming fatigue.  I could handle the nausea, the dizziness, the shaking hands, the dry mouth.    This is different.  This has taken the one thing I could do when I felt like crap, the one activity that I knew I would feel better after–sleep–and made it torturous (okay, maybe torturous is a slight exaggeration, perhaps unpleasant is a better description).  Whenever I’m upset, if I’m having a bad day, or the depression is just too bad, or I’m having panic attacks, or I’m angry about something, I go home and go to bed.  If it’s during the day, I just take a nap.  There are some nights that I really, honestly feel the best thing for me to do is quit grad school because I’m so miserable and I think there’s no way I can go to lab the next day, and I go to bed and when I wake up, it doesn’t seem all that bad anymore.  My bed is the one place I always feel comfortable, always feel like I can cope.  Now, if I go lay in the bed, I have to get up pretty quickly because my legs start driving me nuts.  On the one hand, its helping me get out of bed in the morning, on the other hand, there’s absolutely no place I can go that I feel at peace.

My doctor and I are working on it.  We’re switching the medication around, trying to see if we can get the restless legs to go away.  If that doesn’t work, there’s medication for restless leg syndrome that I can take.  I mean, what’s another pill?  But, I’m really starting to lose my patience and I don’t know how much longer I can go without real, good, 8 hours of sleep


Re:  Wellbutrin and alcohol.  Thanks for the input.  When I was at lower doses of that and my other medication, I had a glass of wine in the evening and my psychiatrist thought that was okay (well, actually, I think she didn’t like the idea of alcohol being in integral part of my life, I think because she was afraid I would abuse it).  But, when I started taking much higher doses of my medication, my doctor told me it was too risky for me to drink.  She may be slightly paranoid because she actually did have a patient have a seizure while taking Wellbuttrin, but I’m going to take her advice anyway.


The last several weeks have been pretty miserable for me. I just feel down, unmotivated, tired all the time. I’ve had a pretty bad case of writer’s block (No! Really?) and getting myself to do labwork has been a real struggle. Frankly, if I can manage to be in lab every weekday for 8 hours, I’m impressed with my accomplishment.

I get like this sometimes, I know I suffer from major depression (I’ve been officially diagnosed and am medicated and everything) and that I’m bound to have relapses, but each one comes hard. There’s never a good time to be mind-numbingly depressed but I think it’s safe to say that when you are finishing your thesis work is really not a good time. I need to be pushing hard, working long hours, in lab on weekends but instead I’m fighting not to get back into bed every morning.

It sucks.

My psychiatrist and I are working on this problem from the medication aspect. The side effects I’ve encountered so far have been: crushing fatigue (discontinued that med), severe anxiety including the worst panic attack I’ve had in years (went back to a lower dosage on that med) (that was while riding in a car with R; and I’ve got to say that it doesn’t help matters to go crazy in front of your friends–really doesn’t help with the taming of the panic attack; I would really rather be all by myself when those things happen), restless legs when I’m trying to sleep so bad that it wakes me up (caused by the med that caused the anxiety) which went away when I went down on that med, but then we increased a different med and now I have trouble falling asleep because of restless legs. And I’ve had to give up all alcohol because the the increased risk of seizure with the high dosages of meds that I’m taking.

That’s right, seizure.

Giving up alcohol is not such a big deal, because I’m not the kind of person who goes out drinking. But, I did like sipping a glass of wine in the evenings. I like the taste of wine and in my family we only had wine on holidays so having wine for no reason at all was a luxury. It made me feel like I was treating myself. Now, I have hot chocolate with whipped cream, but it’s really not the same.

And to top it off, I had a bit of a kerfluffle with the insurance company and my pharmacy and a medication change that took hours to fix with much calling between me and my psychiatrist and the psychiatrist and the pharmacy that resulted in me walking 10 blocks in the cold when I was so sick with a cold all I did that day was sleep at 9pm so I could get my damn prescription.  On the Friday after Thanksgiving.  And I’m not sure it was worth it because the medication change doesn’t seem to be helping and I’ve got my restless legs back.

I’ve gotta say, it’s a good thing I’m not suicidal because that little episode might have pushed me over the edge.

My lab work suffers when I have these relapses.  My motivation is so low, my outlook so dismal, it’s difficult for me to do anything at all, let alone troubleshoot troublesome experiments.  And my concentration is crap.  I make stupid mistakes–the kind of mistakes that I don’t make when I’m well.  My psychiatrist once said I’m one of the highest functioning depressives she’s ever met, and given the very little that I’m able to accomplish, I would hate to see what a low-functioning depressive looks like.

These little episodes lead to very interesting conversations with my advisor where I go in, shut the door and basically say, “Hey, I’m crazy again, and you know how I can’t get any good labwork done when I’m like this, but I’m adjusting my meds and I should be sane any day now and then it will be business as usual.”  I don’t envy him.  There’s not much he can say.  “Well, I hope things get better soon,” is about the extent of it.

And yet, how reasonable is it to expect me to be mentally healthy at this point in my life?  My husband lives a long plane ride away.  My thesis project has been subjected to an unreasonable amount of bad luck (my advisor actually speculated that the universe hates me).  I feel trapped with no good options.  Option 1:  stay in this miserable existence until I finally, finally get all of my labwork done.  Option 2:  quit, but do so knowing that I’m about 1 month of hard work away from having all of the experiments done.  Option 3:  stay in bed.

I question myself about this almost every day and usually select option 1, although on bad days, I’ve gone with option 3.  Sometimes, I manage a combination of 1 and 3 where I’m capable of getting myself out  of my apartment for the afternoon at least.

This is really not the way to get a PhD finished.

But, I’m not prepared to select option 2.