I think I might be an asshole

I think I may have had an epiphany. It seems that many of the Nerd Queen Goddess' (NQG) friends thought I was bad for her, or just straight up didn't like me. I always thought I was a nice guy, who was good to her, and whenever I'd hear about someone telling her we were bad for each other, I never thought too much about why that was, and more likely became angry at said person for crushing on my girlfriend. I've gone through quite the period of emotional turmoil over the last several weeks, in wake of my decision to cut the cord with such a wonderful human being because of my inability to tolerate the distance from Cville to Bmore anymore, and my inability to commit to the extent that would be required to get her to come down here. Fear, sadness, intense random sadness, longing, more sadness... Well, now I think its appropriate for some moments of introspection, and that includes why so many of her friends thought we were bad for each other.

I went to one of our mutual friends, and posed this question to her: If so many of her friends thought the same thing, what is it that I was doing that made them feel that way? The words cold and demeaning were within the first couple lines of the answer. I think insensitive may have been a more appropriate word than demeaning; that was a not exactly heart lifting suggestion from another mutual friend, indicating this was obvious to more than just a few outliers. Something about my interaction with NQG and probably to differing extents, all of my friends, is insensitive enough to create this perception in many observers. This for me is a bit of a nightmare, I'm someone who can be paralyzed by worry over what others think of me, but I think this may be inherent to the problem. I am beginning to think that I probably do not spend enough effort truly trying to consider the feelings of the people I interact with. Many times I worry about how they feel about me, or how my actions will make them feel ABOUT me, but rarely do I purely consider them and their feelings in the absence of my own context.

In any case, I think I may have been a bad boyfriend. And this hurts me because I still care very deeply about her, in fact I still very much love her and it tears me up that I may have been worse to her than I thought. I cannot change that at this point, but I guess what I can change is to try to follow the golden rule a little better, in fact probably try to do one better than the golden rule, since maybe part of my insensitivity may be that I have a fairly thick skin regarding things being done to me, and what may seem to me to be a joke that I wouldn't mind terribly receiving, could be hurtful to someone else with differing sensibilities. I hate my rambling writing. I don't know if I reached any conclusions here other than I continue to dislike myself, perhaps more now, and I have a hard time not worrying about other people's opinions of me, perhaps to the detriment of my consideration of their feelings absent my own desire to be liked. Oy.

Song: Red Hot Chili Peppers, Soul to Squeeze

Goal: Write something useful, stop being an asshole to people you care about.

Goal Succeed! I had a good time in last night's multi-element debauchecrawl. Kidding, there was little to no debauchery per say, but some good old fashioned fun with alcohol, music, and conversationalisms. Started off the night with a primer on programming with perl, which me being a nerd with regrets for not having enough skillz, was actually quite exciting to me, and I think I'll try to continue learning it. Step B was attending a going away liquor tasting for one of the postdocs in the lab, a particularly entertaining if indecipherable and aloof japanese fellow who's managed to do some pretty damn good work with his time in the lab. During this hour, the ol' ticker started going pretty quick, as the next appointment was what my focus was unavoidably resting on: my first date with someone other than the nerd queen goddess in 8 years. And I was never good at dating in the first place.

Needless to say, I started it off well. Being the guy living in Cville for close to 7 years, I remembered there being something weird about the apartment complex I was to pick up blondie the southern bioinformatician belle from, that being the looooong one way street I would inevitably approach from the wrong side, having to make a sizable loop and be late as a result. I don't know if its good when the "how was your week" banter turns so readily into shop talk, but it is kinda nice being able to talk about what you do with someone and not have that blank hazy look come over their face.

In any case, a couple drinks, dinner and some karaoke later, ended up being a nice G rated night that I felt pretty good about. Mental turmoil to follow I bet....

OK, so goal failed again. Wow, not doing good with the goals buddy. Got an interesting evening planned. Drinks with an attractive person waaaaay to early in my mourning period. How did I get here? Still trying to figure that out. But thats all it is right, drinks, a bite, conversation, figure out whether this individual has what it takes to keep up. That last part might sound a little intense, I'm a little jacked up on adrenaline today, haven't been on a date with anyone other than the recently dumped love of my life in over 8 years. Asshole. And she knows about this date, my life has really taken a surreal turn in the last few weeks. Hence this blog. Maybe at some point I'll start sharing things that aren't public domain. In any case, either way it goes, I should have some live band karaoke waiting for me at the end of the evening, which is about as fun as IT gets. For attention whores. Who like classic rock. And have the pipes of an angel. An angel with more ego/enthusiasm than talent. Who's not really an angel, more like a bum with bipolar disorder and a drinking problem.

What does it matter anyway, apparently there was another big earthquake today. Just counting down(up?) till the world ends, and hoping I'm not alone when it does. But then again, if I am, the world just ended, so who cares.

I really need to talk to some old friends, I'm very bad at maintaining contact with people, not much of a phone converser, which is in stark contrast to my lovely(no irony, she's amazing) ex, who absolutely couldn't get enough time on the ringer. I haven't tabulated the data, but I would put money down that greater than 90% of the time I've spent on the phone lifetime has been with her. I would also put money down that she will hold that lead over all others combined permanently, unless I take a job in a phone bank, which would be an unusual turn for an MD/PhD. In any case, I really need to call one fellow fight club enthusiast in particular, might be able to draw some insight from his viewpoint.

Well, off to ride the wave. Or the lightning. One of those two. Hope I don't crash.

Consensus: CAGAC

Scotch: Bowmore 12 year

Drinks: Continental Divide

Goal: Have fun, avoid median

Word: Ortolan (I may wear a napkin on my head at dinner tonight)

Well, goal failed. I went home and watched Parks and Rec rather than run a 10k. To my slight credit, over the course of yesterday I grew progressively sicker with what seems like the common cold that by the time I arrived at home, I could barely breathe through all the phlegm and snot. I think the illness was precipitated by my chronic insomnia, and a more acute bout of unrest due to data analysis of experiment mentioned yesterday.

I don't really have the time or proper mood to be insightful at the moment, I just felt that a lull in my schedule allowed me to force myself to write again. Ding, email.

TTACTGAGCTAGAAACATA

Information requires context to make sense. This is the entire body of an email I've been waiting on, which provides me a discrete and important piece of information I've needed in order to proceed with one of my tasks today. Now, how you might read this information depends on a few factors: 1. Level of education in biology, particularly metazoan molecular genetics. B. How much attention you're paying. And Finally. How much effort you would be willing to invest in order to discover the meaning of this information.

I would make it through probably 1.5 of those factors if I were reading this. So, if you had high school biology, or maybe even middle school, you would recognize the letters this information is composed of to be those representing the 4 DNA nucleotides, implying that this is likely a short DNA sequence. Now if you were paying attention, you would notice this sequence is 19 bases long. If you had upper level undergraduate or graduate level knowledge of molecular biology, you would likely recognize that that is the proper length to be the target sequence for a small interfering RNA molecule, or siRNA as they are referred to. It could also potentially be a target sequence for a microRNA, but it would be hard to differentiate the two based just on seeing that 19 base sequence. Mind you, this will be the target sequence, not the sequence of the RNA molecule because of the presence of the T, rather than U. Now, if you had way too much time on your hands(which this posting implies incorrectly that I do), you could punch in that sequence into the NCBI Blast algorithm and discover that it corresponded to a sequence contained within the 3' untranslated region of SMARCA5, a SWI/SNF type chromatin remodeling factor in humans. Now, if you had Sherlock Holmes level skills of deduction, you would no doubt come to the conclusion that the only reason I would want this information was in order to design a new siRNA to target this gene, because the one I had been using had been resulting in too much off target activity, causing a phenotype in cells that was not reversible by a stable cell line that expresses SMARCA5 minus its 3' UTR, and needed a second oligo to confirm the phenotype I am studying.

Nerd.

Well, this post was pointless, maybe I'll actually write something I care about later.

Mood: Avoidant/Nerdy

Music: Born this Way (lord friggin help me, I never used to listen to Top 40)

Reading: Rap80-directed tuning of BRCA1 homologous recombination function at ionizing radiation-induced nuclear foci

Goal: Survive the day/play squuaaash...?

First post

Hello, world.

So for all you hundreds of thousands of readers, this first post is going to be disappointing. I really should wait to write it until I have some more time to coherently phrase my introduction, but I'm impatient. So there.

I've been feeling for a long time like my thoughts have been evaporating from my hideously porous brain, and recent events have made me decide that it would be fulfilling to not allow them to forever disappear into the ether, but in fact force them to materialize tangibly in cyberspace. These thoughts will neither be profound nor original, but hopefully they will be mine, and if nothing else allow me to look back on my enormous success, or shattered ruins of a life once promising, and see what I did right, or made go FUBAR.

I am in that singular hell called graduate school. This involves getting paid very little to get a piece of paper which allows you to get paid less for doing a more stressful job than your peers. You gotta love the science, or it's not worth it. Then again, the phrase pot committed has been lounging in my head for some time now. It's applied to more than one aspect of my life, and its not a good feeling. Nor a good place to be in a poker hand. I've been pursuing my "higher education" since '95, and some days I feel like a fat man chasing a donut on a treadmill; the goal is always out of reach, but of questionable desirability or benefit to the pursuer. We'll get there though, 12 months or bust.

I had a very successful experiment today. Likely this has begun the endgame for the formation of my very first #1 author publication. An incremental discovery in the regulation of the DNA repair pathway, likely will not lead to more than a brick sized step in an uneven and enormous staircase of knowledge which hopefully leads to understanding and curing cancer(not likely), but mine nonetheless. This has me in a good mood; motivated, a bit hyper, a feeling I've had a good deal lately, I think my lack of sleep has made it easier for me to become hypomanic... but hey, hypomanic folks can accomplish quite a bit while staring down the precipice. Well, more about that later... maybe tomorrow.

I had a dream the other night that there was an intruder in my house, I heard the door slam downstairs(probably the neighbors fighting again), and of course knew this meant there was an intruder in my house, coming to end my miserable existence. I think I dreamt with my eyes open, as I could see my whole room, and felt paralyzed, or at least very sluggish(common theme in my nightmares). In the dream I managed to reach into my nightstand for my pistol and flashlight(another tipoff it was a dream: Loaded + Batteries), and went to confront the intruder, who turned out to be my former roommate, back from climbing in colorado, at 4:00 AM on a sunday morning... I was very confused, and woke up. Then it repeated. I wish the neighbors would stop slamming that door. A week prior, I had a similar dream where my open closet door was in fact a bear coming to eat me and if I did not wake up before it reached my bed I would die in my sleep. This is perhaps the most terrifying nightmare, where you realize you are asleep, but still think with the flawed logic of the dream, and are literally paralyzed from moving. Good thing the house is empty, I think the screaming awakening would have been disconcerting to anyone else there. I've gotta stop dreaming with my eyes open.

I think this was long enough for an incoherent first post. I haven't done much writing lately, aside from technical writing, so this will be a learning process. Hopefully I can expand my vocabulary and communication skills through this process. More importantly, hopefully this leads to me taking a more active role in examining my life, how I got here, and where should I lead it. I feel on the verge of a road to some greater understanding of myself, but if that does not occur, at least I'll have a record of my madness.

Song: Talking Heads: Once in a Lifetime

Movie: Network

Goal: Run a 10K this evening

Word: Kallipygous