"I Open at the Close"

When I last updated this blog, I was about to leave for Europe for three weeks. It has now been 2 months since my last posting. I had thought about posting, so many times, but the words weren't coming and I always figured I'd find my words tomorrow. A dangerous habit to get into. "Tomorrow" is a dangerous word and I don't like using it. 

So...no longer tomorrow...Today. Now.

Lets begin with my trip through Europe, and then I'll get to the lab stuff 

I've never traveled those distances before, it was nerve wracking to say the least. My flight wasn't so bad; everywhere I landed, they spoke English, which was calming. I was worried I'd have to translate something or figure out what was happening. I had a wonderful experience when I flew on Lufthansa; I highly recommend flying with them given the opportunity. When I landed in Pisa, I had to wait at the airport for 2 hours, till representatives from the conference arrived with the bus. I arrived at the hotel, which was beautiful; it was off, deep in the countryside, and had a view of the valley below. I didn't have much time, so I took a quick shower and headed off to dinner. The meal was delicious (and not just because I had been living on airline food for the past 17+hrs). Immediately following we had the keynote speaker addressing the group; this would have been wonderful had not everyone there been falling asleep from exhaustion. Though I had no trouble sleeping the first night, I did the subsequent 3, waking up at 3-4 in the morning local time, unable to go back to sleep; this was the only part of the conference I did not enjoy. In the week I was at this conference, I met wonderful scientists. I got to hear some great talks, see some interesting science and go on some beautiful walks through the country. Each meal was just as spectacular as the first and in the end, I fell in love with Italy. The week ended with a wine-tasting at a local vineyard and a banquet back at the hotel. That night, one of the most prominent members in the DNA repair field asked to sit next to me at dinner; him and I had a wonderful conversation. It is astonishing to see the how humble this brilliant mind can be; to know the kind of work he does and to still stay so remarkably grounded is something I could only ever wish to obtain. 

At the end of the conference, I headed back to the Pisa airport where I waited for several hours for my girlfriend to arrive. Once she landed, we hailed a taxi and headed for our hotel, located fairly close by. Our room wasn't quite ready, so we walked around for a bit, found some food and came back. We rested for a bit, called home and looked up the local sites. We kept the evening short because we had booked a tour that would last 13 days and we knew we would be fairly exhausted, so we did our best to get as much rest as we could. Our second day in Pisa, we decided to go for a walk and found our way, quite accidentally I might add, at the leaning tower. We walked around a bit, took some photos (no, none of the touristy ones of us supporting the tower) and found a Hop on - Hop off tour bus that we had booked weeks before. This red double-decker bus was a great idea; we hopped on and took the tour a few times before we had decided we had had enough and would like to have lunch. Luckily for us, our tour bus stopped just outside our hotel (which was situated just across the street from the train station). 

The next day we took the train to Rome (and barring a slight error, which cost us an extra 45 euro) we arrived at our hotel with too much trouble. Here we met our tour director and a few of the others that would be traveling with us. From that night on, we did not stop. The trip was a wonderful blur. We saw amazing things. I won't go heavily into specifics, but I will say that in 13 days we went from Rome, to Pisa, to Florence, to Venice, to Innsbruck- Austria, to Liechtenstein, to Luzern- Switzerland, to Paris- France and then into London- England. We met 8 Aussies (4 groups of 2) that were traveling with us, they made this experience so much fun; we had several dinners with them, the conversations and comradery added to the tour. I know we wouldn't have had as wonderful a time had we not met them.

During this trip, I took a total of 2,300+ pictures and combined a good portion of them into 2 photo albums that adequately summarize my trip. They were rather costly (having them printed through iPhoto, for $125 a book) but they are well worth it. I didn't spend much on souvenirs for myself, so those took the place of what I could have bought. 

Last Days in the Lab 

I returned, after the trip, for about 2 months of lab work. I had signed on, 3 years ago, to do some collaborative work with another, more prestigious, university. The initial proposal of work was modest and certainly accomplishable in a short amount of time; however, after they got the first glimpses of the data, they wanted to change the parameters. This required much more time and so, off and on throughout my Master's degree, I have been working on this side project simultaneously. In these last 2 months I spent 10-14 hour days, 6 days a week in a room just large enough to fit a large microscope and 2 computers. I sat and analyzed microscopy images, in the dark for that time. That process begins to take a toll on a person and can leave you grumpy, disgruntled and disjointed. I also saw my time in the lab winding down and I knew that it was also starting to take its toll.

Several weeks ago, two new undergraduate students joined my lab to finish some of the main work I had done as a masters student. This meant preparing things for them and showing them where everything was. I began to feel myself being separated from the things I had invested so much time in; I even felts a bit of resentment towards these new students. I mean, who could love this projects like I did? Who would dedicate themselves, bleed for this lab like I have? None of them would know the struggles of the project, the frustrations, and the accomplishments. I didn't hold that against them, but I was certainly sad to see my project change hands. 

Last Friday I pulled my last all nighter in the lab. 20 hours in that tiny dark room analysing data. I finished at 5 in the morning and walked out, feeling exhausted and freed. There was something that wasn't quite final though. I still had to clean out my space in the lab and tabulate the data. Yesterday I did just that. I began saying my goodbyes to the professors on campus and all the support staff. They've all said that I would be missed, that I had changed the department and how much of an impact I had had on my PI's life. None of that really hit...none of it...until today, when I had packed up the things in my desk, walked to my PI's office, and handed her my keys. She took them and hugged me...tightly for what seemed like forever. I began to tear up, my heart was and is breaking; I now leave behind a home. It will never be the same and I will forever miss being in that lab. I've grown up a lot in these last 6 years; I've traveled the world, I've loved, I've lost, I've studied, I've partied and I've grown. My PI and I have grown close, she has been more than a mentor, but a friend.

I've now left one "home". In another month, I leave my home for grad school. 

I know that, in a very short amount of time, I will return to both places and things will have changed. Both will always be home, but they will no longer be my home and that thought...it breaks my heart even more. I know moving on is good, and it's necessary, but it is hard and I am falling apart. 

So...I'll do my best to smile, say "thank you for the memories" and get excited about what is to come.

"Let's get down to business to defeat the" thesis... and those standing in the way of my graduating

There is so much to write about, so much has happened in the last few weeks that I've failed to post on here, the question is, where to begin? I suppose that I should start with the obvious. 

My thesis defense date is less than a week away. Next Monday I will be standing in front of friends, family and the entire Chemistry/Biochemistry department presenting the research I've been conducting over the past several years. Where this is nerve wracking, it isn't as terrifying as the Q&A session that immediately follows. Anything and everything is fair game and sometimes there is nothing you can do but say "I don't know" or "I don't have an answer for that." This, to me, is the worst thing a person can say up there; I mean, in all fairness, I would rather someone admit ignorance than try to proffer an explanation that has no reliable material. I, however, am doing my best to circumvent any potential questions by having more back-up slides with didactic and explanations than I have actual presentation slides. 

I gave a practice talk this last Monday with just my professor listening. It well fairly well; minor corrections and suggestions. She suggested my saying a few things differently, displaying things slightly differently and overall said I had made a huge improvement over the last time I presented it (2 weeks ago). My thesis talk is mostly scripted and memorized, leaving very little time for anything extemporaneous. The talk is supposed to be about 40-45 minutes in length, currently mine is about 47. So I am almost at that mark and I have some more modifications to make...but I'll get there.

Additionally on Monday, my professor gave me another round of revisions of my thesis. These corrections are definitely welcome as I would prefer that my final version is devoid of errors, incorrect information or formatting issues. That being said, she also mentioned to a member of my committee that I have a new version that I'm working on. Apparently said committee member has a lot on their plate and didn't appreciate the fact that I've got a new version of my thesis and have yet to hand it to her. This committee member addressed me yesterday (at a point where I had only been give approximately 24 hrs with this new version) asking for the version in a demanding tone and almost in an accusatory fashion; almost as if she had thought I simply was withholding the newest version out of spite. Having explained the little time I've had with it, she still demanded I hand it to her as soon as possible. I don't appreciate the intonation or the manner in which I was addressed...so...now I'm updating my blog. Score 1 for passive aggressive behavior.

I don't believe I've mentioned previously, but my professor, as a means of a thank you of my service, is sending me to a conference in Italy. Having never left the Americas, I am excited to see what Italy has to offer. I was accepted into the conference and immediately began filing all of the necessary paperwork required by the university for international travel. A daunting and overwhelming experience to say the least, however, it was made easier by discussing this with some of the department staff who guided me through everything. They've been wonderfully supportive and I know I wouldn't have been able to sift through it all without them. 

I'm extending my stay in Italy and my girlfriend is meeting me there. Together, her and I are going to travel for about 2 weeks through several different European countries (with a guided tour group). The whole experience looks like it will be an exciting adventure, exhausting but exciting. I'm glad my adventure buddy will be with me for this. 

Lastly, and most recently, in filing for graduation the university reviews your academic history and sends a summary know as a Degree Audit Report (DAR). Last week I received my DAR and did not look closely at it; however last night I began reading it and saw that one category of my degree had not been fulfilled. Immediately I had to reread the statement and began scanning for an explanation. I searched through out the document and found nothing. I had my parents read it, they too found nothing. Checking the online requirements I found that some of my classes may not have counted. My heart sank and I felt sick. I started recalculating everything trying to see where I've fallen short. In one attempt, I figured that I was about 2 units short. I felt even more ill and began to wonder how, between now and this PhD program, I would be able to fulfill this requirement. Questions like "when would I get this done?", "If you don't get your master's, will the PhD program rescind their offer?" and "how could I've let this happen?" began to fill my head. I spent another hour or so trying to identify what may be preventing my graduation. I finally fell asleep, but awoke this morning remembering the terror of the night before. I got myself into the lab and contacted some personel on campus. Much to my surprise, and my pleasure, it was simply that my "thesis units" have not been assigned a grade. My panic was over nothing and I spent the time worrying needlessly. Anticlimactic, I know, but I finally felt like I could breathe this morning and now can focus, once again on my edits for my thesis.

In less than a week from today...I will have defended my thesis, I will be in the final stages of graduation, and I will let nothing...not even my own procrastination attempts, stand in my way!!!

Onward and upward.

Wish me luck

Missed it by THAT much

To quote Steve Carell..."Missed it by THAT much!!!!"

2 days have passed since my deadline and I have not completed my thesis. This was partially my fault and partially not.

As I was entering the final stretch of what would be my first draft, my computer suddenly became glitchy. Without cause or warning, it wouldn't let me save my thesis. Something was drastically wrong and I didn't know what. Having a Mac, I used the "repair disk utility" to see if something was wrong. A few minutes later I discovered that something indeed had gone awry, but it was fixable and fixed. I opened my thesis once again and began working. Unfortunately, a matter of minutes passed and my work was once again compromised. This time, I was highly suspecting something more malicious to be present causing the damage. I installed a malware search program to identify any wrong-doers and dispose of them accordingly. To my surprise, it was clean. Strange to say the least. As I began the disk repair again, it noted several corruptions, though it said that it was unable to repair the damage as it was running on the OS. I had to restart my computer and repair from the Rescue/Repair menue. Easy enough I thought. Before I restarted though, I saved back-up copies of my thesis and relatable files to Google-Drive (an online storage space...I highly recommend using it). I restarted my computer and ran the disk-repair.

Much to my dismay, there was a hard-disk error that was not repairable. My heart sank and I was sick. It suggested my backing everything up and Formatting my hard-drive. Oddly enough, it would not let me re-enter my computer to do so. I was stuck with what I had saved online and saved on my external hard drive (mostly everything... I routinely backup my hard drive every 10 days out of sheer paranoia for such an event as this). I raced to retrieve my thesis and informed my professor of the damage. Having a very understanding and heartfelt talk, she let me know it was okay and that she understood. Calmly I returned home to begin the process of repair.

I initially restored my computer from a previous back-up point. Not a bad solution, taking ~3 hours to do so, I was back in business and began typing away, working at lost figures/legends and all other manner of thesising. Within a half hour, my computer was once again...down. I decided to do a quick format of the hard drive and re-install everything. Luckily for me, I am a minor packrat and hold on to all of my electronics. I have a spare macbook that I was never willing to part ways with and so, I turned to it, my old and trusty friend. As my newest shiny toy was being stripped of all of its files and reinstalled, I began cautiously working on my old one. As I opened my back-up copies, I found that they too, were not functional and so, the corruption was one far reaching beyond my efforts to prevent such a disaster.

A modest amount of work was achieved as I was...disheartened to say the least. Such an event as this takes a lot out of a person...to see my efforts gone, through no fault of my own...no malicious program...no nothing...I felt scared to begin again and the full force of my passion and brain were not behind this. As the night progressed, I watched as the re-installation of my OS occurred (initially saying it would take 12 hours...and then 6) time dragged on. I decided not much would be accomplished at 11pm and so I closed up shop. I was, however, unable to sleep. I finally was greeted by the Sandman at 2am, only to be stirred awake by my Mac, an hour later, letting me know of its completion. A joyous moment, sure, but not one to be having at 3am. I grabbed my external hard drive and had it begin its process of restoration, replacing every file and program from my most recent backup. Hurray for this.

In the midst of everything. I found that the cause of the corruption was the fact that my thesis was "Too Big." To be clear, my thesis was in the 40-50 page range...however, due to figures and charts, the file size was 30+MB. Indeed a large file. Though Microsoft and Mac deny the claims, there are several forums which clearly describe when a file reaches a certain point in Office 2011, there is a problem that arises and this is it. A permanent hard-disk corruption. There is no alternative but to format it and anything new is lost. As I'm not the only one who has experienced this issue, I feel somewhat consoled and somewhat violated. I am angry with both companies...but mostly Microsoft. Having a prejudice against them, I recognize that I must take this into account, but their program cost me time, and energy...though there was no blood, plenty of tears and sweat were poured over this and it only enrages me further. Mac's Pages does not have this problem and I love them for it.

Most of yesterday was reserved for not writing, as it was my birthday and I felt compelled to enjoy it, as much as I could, despite the tragedy. I  removed Microsoft office 2011 from my computer only to find that the version of EndNote I possess would not function with Microsoft 2008. Disgruntled, I removed EndNote and restarted my computer. Alas, components remain and so, today, as I write from my Lab, my newest Mac is once again being Formatted (this time, at the most thorough level...doing a 7-pass sweep to ensure deletion. When I return home, I shall re-install the OS and hopefully continue my work from my newest computer.


Lesson's learned:

1) 1 back up isn't good enough
2) Don't just over-write a old file with a new update. Save Save SAVE
3) Keep old electronics. They may save you
4) Sometimes, you need to sit back, say "FUCK IT" and have some whiskey


Note: I discovered the conflict that caused the corruption to be the cause of an incompatibility between MS 2011 and Time Machine (a program responsible for systematic back-ups on the Mac). This problem normally isn't fatal, however, when a file larger that 30MB is being worked on, it becomes so.

For those who doubt and for those who wish to see for themselves: Microsoft Forum on Autosave/Time Machine


Additionally, I received another "No Thank You" from another school.

New Score:
Yes- 1
Interview - 1
No - 5
Unknown - 4