Living the dream...

...and it's a not a good one.

Yesterday I shared with you my horrific nightmare, in which I accidentally purchased a Dell computer instead of a Mac PowerBook.

Computer Karma got the best of me today, however, as I spent two futile hours attempting to perform what was supposed to be the straightforward task of converting my dissertation from a Microsoft Word document to a PDF file (without losing any of the formatting, bookmarks, or links). My department's Mac Information Technology professional and I attempted to use three different Mac computers and countless combinations of older and newer Microsoft Word and Adobe Acrobat versions to effect the .doc-to-.pdf transition.

After over two hours of fruitless labor (and a discouraging email from the Electronic Theses and Dissertations help desk), we threw our arms up in surrender. I conceded defeat, swallowed my pride, and took my dissertation to the computer lab-- where I used a brand new (and yet still strikingly sluggish and decidedly non-multitasking) Dell Computer to successfully complete the task.

Dude, I am still a Mac snob.

(Mostly) civil defense

His first question was funny.

My advisor had slipped my father (a marketing consultant, not a biochemist) a piece of paper with a query that he should pose during the question period of my dissertation defense.

"Have you considered a possible role for the yeast 14-3-3 proteins as regulators of the phosphorylation event you've discussed today?" he asked, having no comprehension of the words that were coming out of his mouth.

"That's a very interesting question, Dad," I responded. "In fact, I have considered such a role for these proteins, as you might have known this had you been paying attention during the conclusion of my presentation." He had of course been paying attention--he'd videotaped my every word and gesture for posterity. The language barrier, however, for the uninitiated can be intense, as every other word in such a presentation tends unavoidably toward the jargonish. Phrases like "altered sensitivity to an adenine analog", "half-time of dephosphorylation in the absence of de novo phosphate addition" and "multimerization of heterotrimers into higher-order structures" can be overwhelming even to a scientist working in a different subfield.

The audience laughed at our little exchange, certainly not a typical Ph.D. defense Q & A. I prepared to take other (legitimate) questions, but he continued with a new line of interrogation, this time of his own invention, asking about the naming conventions of yeast genes: "Why are your words sometimes in capitals and other times in lower case?"

I laughed politely and asked, "Are there any other questions?" I asked, attempting to restore some semblance of post-presentation normalcy.

"And, sometimes, you have them in italics!" he added, enthusiastically, to scattered chuckles in the audience. It was clear from his exuberance that my dad was in fact proud of me. It was also clear that he'd never been to a biochemistry dissertation defense before (most haven't).

Fortunately, my dissertation committee was (nearly) as supportive as my father. In the closed-door portion of the exam (no proud fathers allowed), the committee members asked a few obligatory questions to ensure that I was capable of sustaining scientific conversation. Four of the five members were willing to accept my dissertation without revision. The fifth member I had run into at a Pittsburgh Pirates baseball game two nights prior.

"Shouldn't you be studying?" she had asked me at the home plate entrance to PNC Park in front of the Honus Wagner statue.

"Shouldn't you be reading my dissertation?" I retorted, feigning confidence. Touché.

"It's on my things-to-do list--I'll read it by Monday," she promised.

She lived up to her word--and then some. In fact, she read the document more thoroughly than the other committee members and was equipped with a list of questions and concerns. "Why didn't you include a discussion of the connection between XYZ enzyme and the subject of your work?" she asked.

"Well," I began, attempting to craft a careful response, "There was one paper written that connects these two in the manner to which you elude. It was written by a research group in Wisconsin, but as far as I know, there hasn't been any additional significant work corroborating this linkage."

"There is one other paper," she responded.

"I'm not aware of it," I replied.

"I wrote it."

My advisor and I responded, simultaneously: "You did?!"

She did.

Fortunately, despite my oversight, she and the other committee members were willing to sign off on my magnum opus, asking for minimal adjustments (two to three additional paragraphs). Forms were signed and handshakes exchanged, and the deed was done: I had passed my final exam.




Bonus feature for today's blog entry:

Pictured at left is one artist's rendering (mine) of the heterotrimeric enzyme that is the subject of my dissertation research. For the sake of the pseudoanonymity I manage to maintain on the blog, I have replaced the protein names with their generic designations: alpha, beta, and gamma.

Watson and Cricket

 

I defend my dissertation tomorrow.

I took Friday off to prepare. I re-read my dissertation in the morning, brushed up on the details, and attempted to practice the PowerPoint presentation I'll be delivering to a crowd of students, professors, friends, and family in a mere two days. This turned out to be a fool's errand. I never quite made it through the entire talk without an interruption.

I set my timer and attempted to deliver my talk. Five minutes into my presentation, Watson needed something to drink and his bowl was empty. I filled his water bowl and began again. I made it through the introduction slides when Watson decided it was time to play. I took him for a walk in an effort to tire him out.

Watson did indeed become fatigued, and he crashed at the foot of the bed, so I felt it was safe to try once more.

It wasn't.

"Beep beep beep," the Instant Messenger chimed, announcing incoming messages. Time for a chat break.

Chat chat chat.

Finally, I mustered the willpower to terminate the texting. "gtg," I concluded.

I closed my chat window and recommenced the rehearsal.

"Beep beep beep," repeated the Instant Messenger not many minutes later. A few more lines of chatting were required for closure before I could in good conscience terminate the application.

Time was slipping through my fingers. The wife would be home in three hours and I had not made it through the entire PowerPoint one time. My anxiety intensified. Convinced, though, that I had seen the last of the interruptions, I took it one more time from the top. I would surely be able to complete the 45-minute presentation at least once, if not twice, before the little lady returned home from work. Soon after that, her parents would arrive, and the weekend festivities would begin.

I made it through the first several slides without a hitch. I had been talking for 25 minutes and was on slide 29 of 47 when my cell phone rang. My wife's name flashed on the screen. I was a little surprised, because I thought she was in a meeting and wouldn't be leaving for home for at least another hour. I paused my presentation to answer the phone.

"Hello," I greeted her.

"Um, yajeev, I did something really bad," she replied. I could hear that she was in her car already. I wondered what thing she could have possibly done that she would have categorized as really bad. The wife is practically incapable of doing really bad things. Did she say something to accidentally offend someone at her meeting? Could she have made a parent of one of her students angry? Might she have gotten a traffic violation?

"What is it?" I asked, emoting preemptive supportiveness.

"I'm bringing home a puppy."

I laughed aloud. She was joking. "You're joking."

"I'm not joking." She wasn't joking.

I paused. For a long time. I opened my mouth to speak, but only silence escaped. It was if my vocal cords had been snipped. The pause continued.

"Are you mad?" she asked.

"You're bringing a puppy home?"

"Yes."

"Really?"

"Yes."

"Tonight?"

"Yes."

"You really are joking."

"No."

She really wasn't joking. She arrived at home about thirty minutes later with a 5-week old black lab/beagle mix. Apparently one teacher had given this puppy to another teacher, but the recipient's husband had informed her that he would not allow that puppy in their house. By the time the conversation between the recipient and her husband had transpired, the puppy donor had already left for the weekend. And somewhere in the time between the husband's refusal to welcome the puppy into their home and the phone call I had just received from my wife, the puppy recipient had talked my wife into taking the puppy for the weekend. The coercion, I understand, took the form of the puppy recipient placing the puppy in my wife's lap, where the puppy quickly fell asleep.

That was all it took. And now, we had a five-week-old puppy in our home for the next few days.  A puppy was exactly the last thing I thought we needed at this particular junction in our lives.  I knew that a puppy would mean being awakened every few hours during the nights that we had it (which is what happened).  I knew that a puppy would mean strong emotional attachment and delusional fantasies of keeping the puppy far into the future even though finding a reasonably priced apartment which would accommodate two dogs in the city we were moving to would be next to impossible (which is what happened). I knew a puppy would mean a distraction from preparing for my dissertation defense (which is what happened).

"I'm so sorry. It was really stupid. I should have asked you."

I was truly speechless. Shortly after we hung up the phone, the wife and little canine arrived at our front door.

"See, look how cute she is."

She was really cute. "Huh," I grunted.

"Don't you just love how soft she is."

I pet her head. She was really soft. "Huh," I grunted again.

Watson, on the other hand, could not hide his enthusiasm for the potential of a strange, new, wonderful little playmate. The two were fast friends. Watson led the puppy to our backyard, where he showed her all the cool places to go potty and good spots for eating grass. He was enamored by his new pint-sized pal, and they began to size each other up, jumping on top of each other. Watson, for the most part, and to his credit, was careful not to crush the tiny, tipsy pooch. He stood up on his hind legs, extended his front legs as if to pounce hard on the little girl, but descended ever so gently.

"What's her name?" I asked my wife as the two played.

"She doesn't have one yet."

"What do we call her?"

"I don't know."

Just call her dog. Just call her dog. Just call her dog, I kept telling myself. To give her a name would be to create a point of attachment, and I most certainly did not want to become in any way attached to this thing. "How about Cricket?" I volunteered, involuntarily. "Cricket is a great dog name," I added, not believing the words that were coming out of my mouth. I said their names aloud: "Watson and Cricket."

"That's a great name," my wife replied.

Throughout most of the evening, the dogs alternated between incessant (borderline annoying) playfulness and sudden bouts of sleep. The narcolepticness was almost endearing. Almost. Watching that teeny tiny little puppy curl into a little ball on a velvety blue blanket on the living room floor. The only major scuffle occurred when we attempted to feed Cricket some special gourmet puppy food (provided to us by the original puppy recipient). Watson has never had to share food before, and this wet dog food smelled much, much better than his daily dry doggy kibble. Watson bared his teeth and growled at Cricket, attempting to create a barrier between Cricket and her puppy food. Ultimately, Cricket, with a little help from the wife and me, was victorious: I carted Watson up to the bedroom, where he pouted and sulked, while the wife served Cricket her fancy dinner.

I deliberately made no effort to initiate contact with Cricket. Which apparently made me pretty attractive to her. My wife had picked her up to sleep in her lap, but Cricket would not settle until she had wriggled into my arms. I pushed her away, but she kept returning. Later, as we lay in bed (and as I attempted to blog), my wife pulled Cricket to her chest to snuggle, but Cricket would lift her little head, point it in the direction of mine, and forage her way around pillows, over sheets, until her head was resting on mine. Her head on my head. That was how she wanted it. The cycle repeated several times: I brushed her off of me, she returned with greater resolve, each time more determined to burrow herself into some nook or cranny on or around my body. It seems that the less interested in an animal I am, the more they want to be near me.

(I have a way with animals I have no desire to have anything to do with. When we house sat for a favorite professor (one of edutainment's finest) several years ago, he assured us that we would never even see his cat, Smokey. That was good news to me, because I didn't particularly care for cats. And, I was allergic. As you can probably guess, then, Smokey did not leave my side for the duration of our house sitting.)

Cricket struggled to be close to me, as, the wife looked on in pleased satisfaction. Her eyes sparkled with the ecstasy of having a puppy, if even just for a weekend, even as it clamored to snuggle with me.

 

"I figured you out," I told the wife.

"What do you mean?"

"You want me to decide to give this puppy to you as a congratulations present for bearing with me until I graduate."

Silence. She began, "I had no ulterior motive-- I just thought having a puppy for a few days would be nice." There was a long pause. "That would be a nice present." Another pause. "but, no, that's not what I'm trying to do." Not consciously, anyway.

Yesterday afternoon, the wife returned Cricket to the teacher who had yesterday given Cricket to the wife.  Parting was such sweet sorrow.

Just Dissert(ation)s

 

This post is an expanded version of a comment I left at Unbalanced Reaction’s blog this afternoon. She’s preparing her doctoral dissertation and hoping to turn it in on Monday.

I have just finished writing my dissertation. It’s been five months of dedicated reading, studying, writing, editing, wrestling with EndNote citation software, and coping with Microsoft Word crashes. That’s five months I would have rather been blogging, but, unfortunately, I still have not accumulated enough sponsors to turn the Land of Yajeev into a full-time gig. Until then, I’ll have to keep on keeping on with the science stuff.

So the way this works is essentially as follows. I spent the first two years of my graduate program completing my coursework requirements. For the next two and a half years, I engaged in full-time research in a biochemistry laboratory working on my dissertation project. I came up with a few hypotheses and set out to testing them. Funny, when I write it like that, it sounds so easy. Then came the write-up: my Ph.D. dissertation. Basically a 150-page lab (uber)report to be read and graded by my dissertation committee, a panel of professors with expertise in my field of study.

I have spent the past several weeks editing, revising, tweaking my dissertation. Printing, proofreading, re-printing, re-proofreading, re-re-printing, etc. Printing the final draft, making photocopies, collating, and, finally, preparing for distribution to the members of my committee.

My advisor has told me that there are some professors (perhaps, say, like my advisor?) who, as long as they have a “pretty good feeling” about the doctoral student, won't even read the stinking thing. I'm not sure which would be worse: to have put all this time (and caffeine) into my dissertation only to have the doctoral committee merely flip through the pages (even though some might argue that just turning every page would actually constitute a complete reading)... or having them scrupulously read every page, parsing each sentence, demanding that I re-think, re-edit, or re-write.

Yesterday, I visited the professors on my committee to personally hand each of them their very own copy of my opus. Two professors humored me and greeted me great enthusiasm. The other two were nowhere to be found, so I left their copies on their desks. Which is sort of anticlimactic. I mean, you exhaust so much blood, sweat, and tears on this thing, and you at least want the satisfaction of handing it to the committee members. Maybe a handshake. Or a high five.

I did receive the following email message, though, from a professor on whose desk I deposited my dissertation:

Your dissertation’s here; I just finished it. Couldn't put it down, better than a Grisham. Just kidding; looks impressive and I will read it eventually.

By "impressive", I'm assuming he means "bulky", and I hypothesize that "eventually" just may be a “maybe” euphemism. (though, I do appreciate his humor and recognition of the appearance of impressiveness, if only in heft.)

If my first round of critics (ie, the committee) appreciate it, I think I’ll adapt the dissertation into a screenplay: a science-fiction tragicomedy about an enzyme that finds her purpose in protecting the cell in which she lives from the stressful conditions that threaten its very existence, the proteins which provoke her to action, and the evil villain who would dampen her life-preserving impact on her cellular environs.