Last (paid) day in my doctorate laboratory tomorrow. Still churning out experiments up until the end. Shit. I may be in Saturday to do yet one more. We’ll see.

I still haven’t gotten the chance to go up to Toronto to find an apartment yet. That’s going to be on the docket for early next week.

I’m trying to wrap my head around the fact I need to be packed and ready to move in about two weeks. I am clearly going to lose sleep over this.

Apparently this week was not the week to start following YourAnonNews on Twitter. Fascinating amounts of information that I don’t usually catch through social media (aka Twitter and the once-a-month visit to Google News), but between the Boston Marathon bombing, the Ricin-laced letter threats, and now the West plant explosion, I think I’m getting overloaded on news.

My immediate family is flying out to watch me get cowled during commencement this spring at UB. This will be the first time my parents have ever come out to visit (second time for my brother) since I moved to Buffalo. Considering I haven’t been back home to visit in almost two years, this is going to seem a little weird and surreal.

So much random stuff flying around in my head, and so little time & motivation to get it all out. I hope things will slow down to allow me a breather once I get to Toronto and get settled in. If not, I’m probably going to end up very hermit–like for the first few months of my time there (due likely in large part to having to write a review for my postdoc mentor once I get there).

The phrase, “save me from myself,” comes vividly to mind right now. The next month is going to be all kinds of high–strung Jamie, through and through.

Wrapping up 2012 was a bit exhausting. I got a copy of the first four (hopefully complete) chapters of my thesis to my mentor just before Christmas out of town at Cori’s parents’ place. Coming back from that, we had to promptly pack and I drove the crew out to Long Island for Cori’s college friend Kenny‘s wedding. As she was in the wedding party, it wasn’t exactly a tame weekend. We were basically busy every day. Without having a lot of downtime, it at least provided me some time to decompress from the thesis writing, and play around with the replacement Nikon I picked up (as my D80 was finally on its death throes). I got a few lovely shots out of the weekend, but I learned the hard way just which focus mode I should be using (I knew I should have stuck to my old guns!). We spent all weekend hopping from domicile to domicile to hotel. The first two nights were rough and short in sleep, and the stay at the coastal hotel was far too short, especially considering the lovely view!

Coming back from Long Island, I was pretty much a zombie last Sunday. With ten hour drives back to back over that busy weekend, I needed just some raw sleep. Using that down time to recover, finally got to thinking about how I need to setup this year.


This lack of activity is killing me. I’m no longer power-walking around the lab, lifting 50–lb centrifuge rotors, or squatting down regularly to get into low cabinets and floor–sitting incubators. Writing my thesis has killed my muscles and my ass. My quadriceps and hamstrings are tighter than they’ve ever been, and I’m so tired of sitting in a less than adequate computer chair all the time. I need some steady exercise, and it needs to be doable. I have been taking roughly three mile walks to break the monotony of writing. Considering they only take about 50 minutes, I figure I can eek out at least four of these a week. Ten miles of walking a week. Hopefully more, weather permitting, but I got to get this body moving again. I’m learning the hard way what happens when you neglect to regularly use your day–to–day muscles, let alone put them through full ranges of motion.

In addition to that, I will really need to get back into a gym again at some point. I’m worried my torn calf (from November of 2011) is weakening and getting tighter. My patellofemoral pain in my right knee has flared up a bit more than usual. I still do okay lifting heavy objects, but my back needs more work supporting my upper body and arms in those endeavors. I need to do some resistance training. Free weights. Legit squats. Calf raises. Good mornings. Good ol’ bench press and cleans. Get my core back to somewhere I’m comfortable with. With that in place, shucking the pounds to get me back down to 200 (or less) should be substantially easier.


Writing needs to be more frequent. More organized. More coherent. I’m going to need to write a lot more in my post-doctoral work. I’m going to need to put it together faster and better than I am now. Anything and everything I can do to improve that, I should be. A good start would be regular blogging, much to the desensitizing chagrin of others. Doing this in the early days of Toronto should be easy. The trick will just be to keep it up! Keep it something novel. Not just day–to–day humdrum or trivial stuff. Congeal some coherent, novel writing!


That pretty much sums up what’s on my mind right now. There is more floating around in there, but those thoughts will have to be coalesced later. For now, I need to give the laptop a break, revel in the Bison having won the NCAA FCS Championship Game, and root on Green Bay to a win on this wildcard weekend of playoffs!

Time and time again, I’m terrible at keeping up with this thing. But also as in the past, time to update with some big news.

Thesis is pretty close to done. In the necessity of this stage of my dissertation, I’ve also secured a postdoctoral position in order to continue my work in academic research. Hurrah! Once I have successfully defended my thesis and finished up my residuals in the my current lab, I’ll be moving on to the Department of Molecular Genetics at the University of Toronto, in Ontario, Canada. I’m extremely pumped about this! I’m going to get some legit, useful, and beautiful biochemistry in my tool-belt in the lab up there. It’s borderline biological chemistry, it’s that great!

Not only am I getting to delve into new research, I’m delving into a new home, and even a new country at that. Canada is not exactly new, but Toronto is a relatively undiscovered gem for me. Migrating from Minot, ND to Fargo, ND, and subsequently Fargo to Buffalo, NY, I have progressively moved to larger and larger cities. I really thought that would go the other direction after Buffalo, but I apparently predicted that one wrong!

Until recently, I have really felt like I’ve been stuck on an island, trying to finish this degree with no idea when or where I was going next. Now, I have the destination in sight, and although I know what I should expect, I similarly feel like I have no idea what to expect. I can prepare a laundry list of what I expect to have to deal with, but I feel like there is so much uncertainty ahead.

This is the plan for at least the next two to three years. I have three years secured, with the expectation and hope that I can procure a postdoctoral fellowship to boost my CV and establish my own support. This could potentially go beyond three years, especially if I can further diversify and publish work. Granted, this time frame should not be nearly as long as my graduate school career, it will likely be another significant piece of my life before reaching permanence.

I feel like a sailor, getting ready to set sail. I have the destination set, and I have no idea how long I will be there, nor what to expect. I just need to try and put it all out of my mind for the next month or two to finish up this whole PhD thing first!

15. August 2012 · Write a comment · Categories: Grad Life · Tags:

My mind has been anywhere but one place lately. Being amidst the throes of finally finishing this PhD, I did not realize just how much extra crap came along with that. Instead of just finishing experiments, I’m doing that in addition to searching for post-doc opportunities and writing my thesis. Mark highly encouraged me to get as much (if not all) of the introduction done while I’m finishing up experiments. However, the frustration over just trying to get normal cDNA synthesis off of some RNA preps is driving me crazy right now, in addition to staving off the last few of my experiments (qPCR analysis of ~8 strains over 4 different genes).

Unfortunately, I could only wish that that was the extent of my mental spread. Here at home, I’m trying to deal with the craziness of Cori’s dog, who can be a real hellion when he wants to be. That is of an off-and-on nature, and more than anything just sours the mood I’m in if anything, because he seems to bipolarly swing between a sedated, relatively tolerable dog, and an insane brat with no regard for listening to anyone. Add that in with his tendency to overreact to any aggressive-like activity/motion/action, and I’m spending far more time concerning myself with what actions that I’m about to take than I probably should. However, he’s the sideshow to the disastrous ruin to my primary electronics at the moment.

At some point after moving into the new apartment, my Mac Pro started to have issues. It would spontaneously shutdown as if it was experiencing a thermal event (read: overheating), and the indicator lights on the mainboard indicated as much. The machine was far from being overheated, and other troubleshooting guides also dictated that this error can also be indicative of a failing power supply. Considering the power has been less than stellar in both this apartment and my last apartment, I figured it was finally time to get a line-conditioning UPS to help deal with power fluctuations. This appeared to have resolved the issue for a few weeks, but the problem has since returned. This evening, taking apart my Mac Pro once more to compressed air-blast out the heatsinks and power supply, I revisited booting it up again and watching the stability.

The system seemed stable enough. I was able to successfully rip another movie DVD to transcode it onto my file server, but I was watching the power supply temperatures in a paranoid fashion in the process. I typically keep an eye on this through the iStat Pro widget, but after reading some other forums on cooling issues in the pre-2009 Mac Pros, I fired up the full-blown iStat Menus to see the current draw in my system at the time. Upon closer inspection, I happened to notice a disturbing set of sensors: the CPU cores and the CPU heatsinks. The two CPU cores (this is a dual-processor system) were idling at approximately 65˚C, while their respective heatsinks were essentially at ambient (25˚C) temperature. Now, I know there is to be expected at least some difference between the two devices due to thermal transfer rates, but a difference of 40˚C (72˚F)?!? That’s just ridiculous! So, alas, it appears it is time for me to really gut my Mac Pro down to the motherboard, strip the heatsinks out, and reapply some thermal paste there. This won’t be an easy endeavor: I’m missing a tool necessary to unmount the heatsinks, and while I’m gutting everything open, it would apparently be in my best interests to reapply the thermal paste on the Northbridge chipset as well.

Oh. Did I mention I’m writing a thesis right now? Oh, yes, I did! And I need this machine for some of the structural renderings that I do, not to mention for designing figures in Adobe Illustrator. *facepalm*

To further complicate my electronics issues, I purchased upgrade components for my file server around 3-4 months ago and finally got to installing them about a week ago. Much to my dismay, I neglected to remember there was no PATA port on the motherboard. My entire FreeNAS operating system was on a CompactFlash card with an adapter running directly into the PATA port on the old motherboard. I no longer could use this after the upgrade, nor could I get it to boot from a CF->USB adapter. Apparently, the FreeNAS 7 project has since been renamed and updated to the NAS4Free project, with a full recoding of the OS off of FreeBSD 9.0, lending lots of new support to the project! Unfortunately, upgrading from FreeNAS 7 to NAS4Free was less than easily straightforward. But now that I had trashed being able boot my old FreeNAS 7 system, it seemed ironically convenient to make the upgrade now. So, for the past week, I’ve been trying to tweak that system into working again, so I can get back to backing up my lab documents on it and supplanting my evenings with the movies and television shows that I’ve transcoded from my discs to watch over the TV2 I have hooked up to the television. I’ll follow up with those issues a little more in the near future, as there is apparently little coverage of fixes for the bugs present in the NAS operating system so far.


So. To recap.

  • Busy trying to finish experiments.
  • Busy trying to troubleshoot early steps of final experiments.
  • Busy trying to write my introduction to my thesis.
  • Busy trying to figure out what the hell I’m interested in doing research on so I can properly scout for post-docs.
  • Need to start writing letters/emails to prospective post-doc mentors and get the interviews going.
  • Trying to keep my Mac Pro running, so I can use it to finish some of this lab experimentation/figure generation without incapacitating my poor little MacBook Pro.
  • Trying to get my file server going again so I can have some stress relief via some good ol’ cartoons when I get those moments of downtime.
  • Trying to learn more FreeBSD than I should have to in order to get NAS4Free running the way I need it to.
  • Trying to avoid getting chomped/bitten/otherwise maligned by the resident Eskimo doggie of the house when he’s well hydrated on Haterade.
  • Trying to lose some weight by biking to work, getting out and walking/running, and watching my diet.
  • Deciding what the fuck I still have to unpack, and what I should still leave packed, because I’ll likely have to move (again) for whatever post-doc position I take.

Honestly, I’d go bang my head on a wall somewhere if I knew I wouldn’t be wasting valuable time in doing so. I so so so SO can’t wait for this all to be over. And I do mean ALL of it…

58 pages…

28 double-spaced pages of Introduction, Results, and Discussion.
4 more double-spaced pages of Materials & Methods.
5 single-spaced pages of references for a bibliography.
7 tables, of which at least two will likely be full (or very near full) pages.
Two more pages of single-spaced figure legends.
8 figures.

This beast of a paper was officially submitted to Molecular Microbiology on Friday afternoon. This paper has been a morphing work-in-progress since late last summer. You have no idea how relieved I am to finally have it finished and submitted!

Hopefully I will be even more ecstatic if/when the paper is officially accepted! #CrossingFingers

Dear lord, I keep trying to sneak in here to blog away, and something is always sneaking up to keep me occupied.

Camping was amazing up in Wellesley Island State Park. I stopped in Rochester to pick up Cori, and grab some lunch with Greg and Kelly at The Distillery. After some delicious eats, we were off to northern New York state!

It may not suffice as a legit vacation1, but a 3-4 day weekend kicking back with an awesome young lady is a very good substitute. We setup camp Friday afternoon and just took it easy for the rest of the day. Once I figured out how to put the tent back up again, that is. It’s been a few years!

Cori rocked it on the food front. I had brought bacon, eggs, pork chops, chicken breasts (to marinate with sesame & ginger dressing), and some sausages and a couple chicken burgers of varying styles (cheddar/broccoli/bacon, polish, feta/spinach, respectively). I had asked Cori to take charge of bringing some marinated veggie concoctions, and boy did she. Gallon bags of eggplant and onion, mushrooms and peppers, green and yellow sliced squashes, and balsamic-marinated portabellas. And that wasn’t including snacks! Dear lord…apples, peanut butter and caramel dip for said apples, gallon bag of mixed berries (*drool*), ingredients for caprese (*drooling even worse*), and I’m sure I’m missing something else there. Regardless, I was thoroughly shocked at the additional smorgasbord that was coming along.

Saturday, we checked out the Autumn Festival that goes on in the park every fall apparently. It isn’t anywhere near the size of the Ellicottville Fall Festival that I’ve already been to, but it was a quaint little festival nonetheless. Not much to see (besides some alpacas and calves), but the $5 boat tour of the nearby islands was worth the fare!

Sunday ended up as a ~5-mile hike in the park and an afternoon trip for delicious alma mater foodies from Cori’s college years. And some lawn chairs. The wooden bench was wearing at our asses in the evening. Anyhoo, late lunch/early dinner ended up being at The Bagelry, which is essentially as the name implies: a bagel deli of sorts. Delicious, open-faced bagel sandwiches at an expectable price range. We dined on those while enjoying the riverfront nearby, followed by a short tour around the hotspots of her college years in the area. Half-dozing, we got back to the campsite well after sunset.

Monday we spent gobbling up the rest of the eggs, berries, and another helping of our daily bacon before closing camp. We hit up Alexandria Bay to take a boat shuttle out to Boldt Castle, in the middle of the St. Lawrence River. Wandering around for a few hours on a self-guided tour of the castle undergoing restoration was pretty amazing. Still awesome to see what kind of structures have been and are still being built in the last century!

Heading back out, we splurged on a lunch with apples & Nutella (not sure how Cori missed me mentioning that the first afternoon), caprese, and some salad with the leftover marinated chicken. We ate like royalty that weekend, I swear! And to top it all off, her parents’ invited me to stay over for dinner upon returning to Rochester: chicken parmigiana with homemade sauce, homemade spaghetti, salad, garlic bread, and baked marinated squash (that we didn’t even touch all weekend). Omilord was I spoiled! After trying to relax and digest all that food, it was indeed difficult to muster the willpower and energy to drive all the way back to Buffalo after that weekend.

I didn’t even stay in Buffalo that long. Cori procured us tickets to go see Andrew Bird over at Harro East in Rochester, so off I went immediately after work on Wednesday for that show! Following up a modestly long performance by Dosh and Bird, some food was necessary. An unexpected drop in at Jay’s Diner hit the spot! Some awesome clam chowder2 set the meal off right. I can’t even remember what else I got; the chowder was the best part!

A necessary crash at the Bed & Breakfast was necessary before hitting the road and driving right back to Buffalo. So much back and forth in just a week! Thankfully, it’s only an hour drive; anything over two hours would quickly become a bit miserable to deal with, uffda.

So here I am, finally trying to finish out this week. I’ve got a Chinese dinner night in planned for Friday3, followed by documentation of Rachel’s lopping off of her hair for Roswell Park on Saturday morning, some linguine alla carbonara with fixings for dinner, and then off to the Buffalo Philharmonic to see the ‘Dead Russians concert’, as Cori likes to describe it. Sunday is supposed to involve a trip out to the Great Pumpkin Farm’s Fall Festival over in Clarence with Nicole, Kate, and likely some other social media-ites, before finally sending Cori back off to Rochester. It’ll be a modestly busy but enjoyable weekend!

I’m not even going to bother with dumping my photos to my blog from the camping excursion. I’m still trying to play catchup with the pictures I took from Nicole’s birthday wine tour as well, so just go check my flickr stream if you really want to see what turned out.

In the interim, I think it’s very much time for some sleep…the clock just passed midnight…


1I still haven’t taken my two weeks off this year yet. It’s starting to wear on me…uffda.
2Not just a modest cup of it either, a whole bowl was necessary after the deluge we ran through after the concert!
3Presuming that it doesn’t get sidetracked or derailed by anything else immediately upon arrival…*raises a brow*

Last week was a mess of playing catchup so I could enjoy my crazy-assembled weekend, and now this week is playing the intermediary before another big weekend.

I’m pretty sure I wasted too much of Monday evening cranking out that enormous, relatively incomplete and/or rushed blog post, only to have to rush off for some birthday drinks. In reality, I should have been finishing writing my paper, which I ended up having to crank like crazy on Tuesday and Wednesday evenings. Between the fact that I was going to be out of town over the weekend, and I had dinner plans both Thursday and Friday evening, I really had no choice but to finish just about all the writing by Wednesday evening so I could stay a tisch distraction free. It’s been tricky lately to stay terribly focused; I’ve been trying to juggle a lot lately mentally. It may be time to start working on a written list of tasks again.

Thursday’s dinner at The Viking Lobster Company was delicious! Splitting out a Viking Seafood Feast for two resulted in a pair of lobsters, broiled haddock, enormous scallops, some jumbo shrimp, and some large crab leg slices. Mind you, this all followed a Portuguese clam chowder1 and a house salad with a clam & peppercorn creamy dressing2. Friggin’ delicious! Combine that with an amazing (and mildly amusing, despite bruising conveyed in a recent update) night in afterwards, I was very ready to decompress after all that writing from earlier in the week. Friday night supplemented that very nicely with a dinner at O’Connell’s American Bistro for Restaurant Week with most of the social media crew. A delicious four-course sampling with about a half bottle of some (rather mild and smooth) Malbec left me about drained of energy for the week. ‘Twas difficult to let Cori go for the evening after the past 28 hours, but she had a deadline to make back at home, and I had to start prepping for my trip to Cincinnati over the weekend.

Last year, myself, Doc Hohle, and Doc G all took a trip down to Cincinnati for the Bills/Bengals game, being that Hohle is a Bengals fan, and Gerrish is a Bills fan. I was offered an invite on the trip, it sounded fun, so off I went with! We also made an informal pact to attend the next Bills/Bengals game if we were all still in the general area of the country at that point. Little did we realize that both teams’ dismal standings put them into a matchup again the following season, this year. So off we drove, early Saturday morning, to another Bills at the Bengals game, down in Cincinnati. Adding to this trip, we picked up a friend of Doc G’s in Pittsburgh along the way, making the drive marginally longer.

Nearly ten hours on the road after leaving Buffalo, we finally made it into Cincinnati. A quick check-in to the Hotel Motel Holiday Inn, and we were off to get some dinner at Buckhead Mountain Grill. They have a pretty amazing chicken pot pie, that is complemented by a pair of a veritable slew of sides. I was terribly disappointed by the enormous Shiner Bock that I had ordered, so it was a doubly dumb decision to order such a large bock without having tasted it first.

Not much to say about the Bills/Bengals game. If you watched it, you saw the lovely attempt at control the Bills had, before the Bengals took over. If you didn’t? Well, Cincinnati lost, finally putting the Bills out of their undefeated streak to open the season with. I always get weird looks wearing my Packers jersey at non-Packers games, but I do enjoy me a little football, and I’m clean about enjoying it, regardless of where I’m watching it! Surprisingly at the gate, the guard that patted me down mentioned how she has often seen people wearing non-game jerseys (like mine own) just to cover offensive clothing, so she asked to see my clothing underneath. I was kind of shocked by this, but apparently it has happened before. It rather saddens me that fans have resorted to such a thing at a sporting event. I mean seriously people: it’s just a game! If you’re so upset that you take any criticism of a game personally, then you need to really re-evaluate your stance on the sport!

Leaving the game is only a step towards the weekend I’m craving. Nine hours of driving only left me daydreaming of camping all weekend long. Surveying the week, I’ve actually got a bunch of stuff to finish.

  • Tonight was my (weak-ass) attempt to catch up on all the TV season premieres that I follow. Yes. Premieres. I’m already two weeks behind on my television. I have a very valid excuse, no worries!
  • Tuesday night is dedicated to checking the tent gear and making sure everything is there. Also, any last minute shopping for gear in case I’m missing something. Pretty positive that I have everything, however. Oh, right, and comedy night down at Nietzsche’s to see Mr. Rizzo at work!
  • Wednesday night is jelly night. Time to crank through the rest of my hot and sweet peppers and get some jelly done!
  • Thursday is grocery shopping and prep night. Getting all the roaster veggies chopped up and marinating for campfire cooking! Also, packing my gear would be good to do, as well.

Then, once Friday gets here, it’s time to pack up the car and hit the road3!

Now, if you’ll please excuse me, I have an almond cake to dig into for the third time tonight…*Homer drool*


1Supposedly a brothy, sweet chowder, but I can’t seem to find any recipes online that are adequately describing it. Onions, potatoes, carrots, clam, and a little bit of lobster. It was quite tasty, despite the cooked carrot taste messing me up a little.
2The restaurant makes all of their own dressings for their salads, so this sounded terribly appetizing!
3I may have to make another check into the County Clerk’s office. The final processing on this divorce is taking foreeeeeeeeeever. Ugh!

Waking in the morning has become a less dreadful experience for me in these later years of my life. I use to loathe seeing the sunshine in the morning. Now my body attempts to welcome it willingly. Although the mind isn’t as willing; it still likes to enjoy the sluggish time in the morning. However, restlessness always takes over, no matter how long I linger. My body itches to do something with the day!

More »

With yesterday’s partially unmitigated disasters still around to deal with this morning, I was thankful I didn’t find anything new to wreck the day. At least nothing major.

The tire with the flat was nearly empty in the morning, but it was enough air to delicately get me to the nearest gas station with an air machine. Filling the tire back up, I made it back over to Dunn where they conveniently had an opening to deal with the tire. I asked them to re-examine one of my tires that they missed a bulge on during my last rotation, and just even with a cursory inspection they determined that it would need to be replaced. Additionally, they discovered the leak in the flat tire was a sidewall puncture, so that one had to be replaced as well. I’m now sitting at 25% of my original new tires still on the car in less than a year since purchasing them. Two bulges, one debris-less sidewall puncture. I’m starting to think I’m jinxed! Thank goodness Dunn has been so good about replacing them so far.

Over on the work front, unfortunately I still do not have my appointment established yet. I’m going to be antsy like my pants are on fire until that gets resolved. Having a lapse in my payments is totally going to fuck up my plans to try and get back to North Dakota near the end of this month. I still need to get back there for a vacation of sorts, and moreso to help out my parents with the house. It’s gutted down to the frame, awaiting an electrician’s repairs and inspection, before it can be sealed back up. Once that goes through, then it’s walls, insulation, and new sheetrock up ASAP before the cold weather moves in as long as the HVAC systems pass muster as well.

I was sent confirmation last night that my order from BioRad was supposed to show up today. Unfortunately, even despite my late arrival at work, no delivery showed up from them. Purchasing told me it should be delivered by today but then the forwarded email that said that was ambiguous as all hell. It claims expected delivery to have been today, but since the order was a single item, the whole “following items on back order” blanks being present have me uneasy.
Biorad
It worries me even moreso that those important remarks are blank.

Ugh. I’m starting to worry that I’m either (a) being a drama queen about all of this, or (b) that I’m freaking out way too much about this. Also, the fact that I’m stuck waiting on this BioRad order even further puts off finishing this paper. I’m rock-solid on finishing this paper and having it submitted to the journal’s editor before leaving for Minot. I can’t put it off any longer, and would leave a convenient period to insert my belated vacation time that never came this summer.

Oye. As if I didn’t have enough on my platter already. Some days, I really do swear I need drugs to keep my brain straight and try to manage all this crap going on at once. May be time to just man up and start taking them out with a bat, one by one. Messy, unnecessarily excessive and exhausting, but damn well effective.