(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.

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.

Land of Yajeev Announcement, 4/1/08

My subscribers and friends of the blog have just received the following disturbing email. The postscript was not included in the original text, but has been appended below for clarification.

Dear Friends of the Land of Yajeev,

It is with bittersweet sentiment that I announce to you that I have posted the final entry to the Land of Yajeev. I'm throwing in the towel. As I've long feared, I have finally exhausted my life's supply of bloggable material. I want to thank you for visiting the site, for leaving your comments, for providing blogworthy inspiration, and for sharing this experience with me. I am hanging up my blogging boots and will be focusing on other writing ventures: my dissertation and the great American novel.

Please visit the Land of Yajeev to read my final post--I think you'll find it quite meaningful. Even though I'll be retiring yajeev's pen, my posts will remain online for you to enjoy in reruns. Consider the Land of Yajeev to be Nick-at-Nite of the blogosphere. Good times, great oldies.

Sincerely,
your humble blogger,
yajeev

P.S. APRIL FOOLS! You didn't actually think my dissertation would take priority over the blog, now did you? It'll take a lot more than a doctoral dissertation committee to keep this voice down.





Speaking of foolery, this morning, my advisor made me the victim of a horrific April Fools Day prank. We recently published an article in the Journal of Biological Chemistry. The paper was the fruit of two years of hard labor/ indentured servitude and is, thus far, the crowning achievement of my scientific career. This morning I received this email from my advisor:

Yajeev,

I just got this intense letter from NIH [our funding source] saying that our last paper had been cited in a fraud investigation and we will have to produce all primary data. Lets talk when I get in.

- Advisor

When I read that, my heart just about stopped beating. My mind, already spread thin across about twelve different things, began to melt. That's it, I thought, my career is over. Even if we were cleared (which we eventually would have been, mind you), I didn't know how long this would take or how far a " fraud investigation" would follow me. I began compiling a mental checklist of where all of our "primary data" could be found. The sweat balls I encountered during last summer's job interview returned, beading at my forehead before gliding down my cheeks.

A few minutes after I read his note, my advisor entered the lab, holding a folded sheet of paper, bearing a grim expression on his face. He handed the paper to me, saying, "Here's the original message."

I unfolded the page. It took several seconds of staring at the words "APRIL FOOLS!!" typed in large print across the middle of the paper before I comprehended the hoax my advisor had perpetrated. Before I could experience a full measure of relief, a wave of anger overcame me, and I heard myself uttering some very unkind, unfiltered words to my advisor-- words of which, once the relief finally set in, I was very much ashamed. Fortunately, my advisor was quite amused with his prank. My response only confirmed to him the greatness of his deception.

Practice makes perfect

Two anecdotes about two beginners in two different fields.

1. A medical doctor recently joined our laboratory. He is a skilled physician but is still cutting his teeth at the lab bench. He recently learned how to perform a western blot, a basic biochemical technique used to detect specific proteins within a cellular extract.

This is an artist's rendition of what a good western blot looks like.


This is what the good doctor's first western blot looked like.



We had gotten off-topic during our most recent lab meeting, somehow discussing the myriad complications and maladies that can arise with human health and during childbirth. My ever-wise advisor (click here or here) commented, "It's a miracle a baby ever comes out normal."

The young doctor replied, "That's how I feel about western blotting. Childbirth is nothing."




2. We had lunch today at CiCi's pizza buffet where a new pizza chef was being trained.

I watched as the novice removed a pizza from the conveyor oven and attempted to divide it into eight proportional slices. He failed at this task, and this is roughly what his pie looked like.

The manager, displeased with his protege's poor sense of symmetry, took a deep breath and explained (as though this wasn't the first time he'd said it), "You need to visualize the center of the pizza." He paused to demonstrate, carefully cutting eight pieces in a sample pizza. Proud of his perfectly divided circle, the manager added, "This is an art form."

The neophyte retorted, under his breath, "Mine is an abstract pizza."

Another Advisorism

I attended a seminar with my advisor, where he ran into an old friend.

Old Friend: I saw you yesterday, but you ignored me.

Advisor (offended): I didn't ignore you. (Pause) I just didn't say hi.