I guess five months is a long time to not update a blog. Most people have probably deemed this blog dead by now, and I wouldn't necessarily disagree with that just yet. I can't quite say if this is just a quiet pop from the fire before the embers cool beyond having the capability of setting alight a new log or if this is a spark of rejuvenation that signals an old engine returning from its year long slumber. In any case, like times before, here I am.
Certainly many things have happened in the last year that are at least of some note. I've officially joined the Comeron Lab and am slowly climbing hand-over-hand toward the next rung of my professional career. I now live in an apartment where I don't want to run outside and scream at the blabbering drunks who think that pulsating low frequencies somehow bring them closer to undergrad Nirvana every weekend. Which also means that I now have my cat living with me--which, is more of a highlight than I'd like to admit, truthfully. I've also been in a relationship with a cultured human being for the entire year too. I hope I've not scared her off after bringing her down to Alabama this holiday season.
Bama is always curious. I returned to my hometown after a year to see that absolutely nothing has changed, save for a new exit off the highway that was designed as a sort of heart bypass,but now is a frivolous plastic surgery since most of the hosiery mills have moved away. Everyone's a little bit fatter, including me, and going on with their lives with a pace that you'd think was predetermined at the point of conception. They're buying houses, getting married, and having children. Now the pattern is so clear. Everyone is doing the same thing that the generation before them did with only minor alterations to the plan. How change comes about in any form is remarkable.
So I suppose I'm trudging on in my own way. Towards some fantastic goal that is sure to impress my friends and family. Some days I yearn to be a cabinet maker or fisherman, producing immediate results with my own hands, cracked and dry after years of work.
I've been so cut off from reality. My work is all about thinking: How can we do this? How does this fit our model of X? What is the purpose of Y? Can we demonstrate that Y affects X? How can I spin this in a way that the government will give me money? Science is not for the impatient. That's what I learned in 2011. That, and sometimes you've got to stop and appreciate where you've been and where you are. Graduate school has taught me that it's okay to feel stupid and that each person is here for their own specific reason--not just for the same reason I'm here.
It's taken me too long to realize the importance of family and friends. Before, I was so focused on the end that the journey was irrelevant. Anyhow, welcome to 2012. Lets see this as a spark that returns the engine to life.
Thursday, January 5, 2012
Wednesday, June 8, 2011
History Lesson of the Day:
When Germany invaded Denmark in World War II, the Hungarian chemist George de Hevesy dissolved the gold Nobel Prizes of the German physicists Max von Laue (1914) andJames Franck (1925) in aqua regia to prevent the Nazis from confiscating them. The German government had prohibited Germans from accepting or keeping any Nobel Prize after the jailed peace activist Carl von Ossietzky had received the Nobel Peace Prize in 1935. De Hevesy placed the resulting solution on a shelf in his laboratory at the Niels Bohr Institute. It was subsequently ignored by the Nazis who thought the jar—one of perhaps hundreds on the shelving—contained common chemicals. After the war, de Hevesy returned to find the solution undisturbed and precipitated the gold out of the acid. The gold was returned to the Royal Swedish Academy of Sciences and the Nobel Foundation who recast the medals and again presented them to Laue and Franck.[5][6]
--Taken from Wikipedia. Confirmed on the Nobel Prize webpage.
--Taken from Wikipedia. Confirmed on the Nobel Prize webpage.
Tuesday, May 24, 2011
Cooking in the Laboratory Part I: Spicy Denatured & Disrupted Ova de Gallus gallus
An Oppressed Graduate Student’s Guide to
Cooking In the Laboratory
The following protocols are intended only as a joke though would likely produce palatable food with only a minimal risk of hazardous contamination leading to injury or death. As always, use proper personal protective equipment (PPE) when dealing with any potentially dangerous chemicals or equipment.
Spicy Denatured & Disrupted Ova de Gallus gallus
Protocol:
1.) Manually lyse two unfertilized, mature Gallus gallus ova (appx 110g) via forceful disruption of medial cuticula into a ~500mL Erlenmeyer flask. Discard outer calcareous shell as hazardous biological waste.
2.) Add 1900uL 5M NaCL, 5mg Capsaicin (dissolve in 5mL 100% EtOH), and gently swirl to equilibrate.
3.) Add 100mL Fresh Bovine Mammary Secretion (pH 6.8). If unavailable, substitute an appropriate amount of dried Casein in deionized water.
4.) Vortex mixture vigorously (>1500RPM) until complete disruption of vitelline membrane. 3uL 5mg/ml Trypsin may be added to accelerate this process.
5.) Grease a 1L beaker with 10mL 3:1 Oleic Acid:Palmitic Acid solution. Heat to 150°C on a magnetic hotplate with a large magnetic stirbar.
6.) Add disrupted ova mixture and denature for 3 minutes until mixture solidified.
7.) Remove from heat, consume. Make undergraduates clean up your mess.
Sunday, May 22, 2011
Six Months Later...
And so it continues...
It's been quite a while since I last had a blog post, despite the occasional words of encouragement from Claire. Things in graduate school are pretty much always busy. It's hard to justify wasting time writing a blog. It's far easier to waste time on Reddit or elsewhere in the cesspool of the internet where no remnant of the lost moment will remain.
Alas, things are pretty good here. I have a deeper understanding of my expectations now and have learned to grow as a scientist and be sane simultaneously. Our year lost a couple more students, I can't help but wonder if they're better off. It seems like every week I read another article about how the university system is the next unsustaniable bubble that's going to burst, or how the Ph.D. is useless these days. There's lots of Ph.D.s and simply not enough jobs I fear. Academics don't retire and open up the gates for new academics. I guess that's an artifact of not actually enjoying your life until you're 40 when things settle down and you're actually running a lab. I've said time and again that I wouldn't be doing this if I felt like there was something else better to do. I guess I have this pipe dream of being a bona fide scientist with his own lab doing what he wants and letting his interests guide his work. It seems like quite the journey from here.
So what have I been doing in the last six months? The short story is, well, a lot. I rotated through Josep Comeron's lab early this year and sequenced 24 complete genomes to address the question of how recombination varies within a species at different conditions. It was a really great rotation project, and added to the labs over 4000 genomes they've compiled in the last year. It was a lot of work but I really enjoyed the people, pace, questions, and approach.
The rotation ended and then I got to go to Sarit Smolikove's lab. Sarit is perhaps the best adviser that one could wish for. She's dedicated, interested, and very involved. I have to reject the null hypothesis that Ph.D.s don't actually do benchwork when I'm around her (P<.01). She teaches and spends at least 10 hours a day actively doing research, and that gives me a lot of hope for my future career. My project in her lab was to determine what proteins interacted with one that they had implicated in synaptonemal complex dissassembly (the protein scaffolding that holds together homologous chromosomes during meiosis)--the first protein discovered to be involved in this process. I produced a lot of hits, and knocked a few of them out in vivo to see how they affected meiosis. A really cool project. I feel like I'd be in her lab right now if she had a grant. It's sad, but she already has two graduate students and no grants to keep them going. I think she'll eventually pick up a solid grant, but I just can't risk having to teach every semester and watch my productivity take a nose dive.
So, that left me to join Josep's lab. I started last week and will be there for the next four to five years working on recombination variation. Our first task is to get a review paper out the door. As such, I've been reading articles pretty much every day. Basically this way I can get my first paper in the lab, the first quarter of my comprehensive exam written, part of a grant application, and a piece of my thesis written within the first semester of my work in the lab. I think Josep is really thinking ahead on this one, which is a very good thing if I'm to get out of here in a reasonable amount of time.
I suppose the next obstacle in my way is our Qualifying Exam. We've been given the topics for the exam and are expected to know them well enough to answer specific questions within the topics on July 10th. I've started the studying process and should be ready by that time. Some topics are specific and doable, like "The biology of small interfering RNAs", while others are extremely broad, "The origins and maintenance of diversity in natural populations." Oh well, just another hoop to jump through.
I suppose that's all I've got. Haley will be passing through Iowa City in early June and staying the night at my place with Ari--I still haven't told her that I don't actually have a couch for her to sleep on, but I'll drag out the small mattress for her. It should be a fun time.
Cheers,
Andrew
It's been quite a while since I last had a blog post, despite the occasional words of encouragement from Claire. Things in graduate school are pretty much always busy. It's hard to justify wasting time writing a blog. It's far easier to waste time on Reddit or elsewhere in the cesspool of the internet where no remnant of the lost moment will remain.
Alas, things are pretty good here. I have a deeper understanding of my expectations now and have learned to grow as a scientist and be sane simultaneously. Our year lost a couple more students, I can't help but wonder if they're better off. It seems like every week I read another article about how the university system is the next unsustaniable bubble that's going to burst, or how the Ph.D. is useless these days. There's lots of Ph.D.s and simply not enough jobs I fear. Academics don't retire and open up the gates for new academics. I guess that's an artifact of not actually enjoying your life until you're 40 when things settle down and you're actually running a lab. I've said time and again that I wouldn't be doing this if I felt like there was something else better to do. I guess I have this pipe dream of being a bona fide scientist with his own lab doing what he wants and letting his interests guide his work. It seems like quite the journey from here.
So what have I been doing in the last six months? The short story is, well, a lot. I rotated through Josep Comeron's lab early this year and sequenced 24 complete genomes to address the question of how recombination varies within a species at different conditions. It was a really great rotation project, and added to the labs over 4000 genomes they've compiled in the last year. It was a lot of work but I really enjoyed the people, pace, questions, and approach.
The rotation ended and then I got to go to Sarit Smolikove's lab. Sarit is perhaps the best adviser that one could wish for. She's dedicated, interested, and very involved. I have to reject the null hypothesis that Ph.D.s don't actually do benchwork when I'm around her (P<.01). She teaches and spends at least 10 hours a day actively doing research, and that gives me a lot of hope for my future career. My project in her lab was to determine what proteins interacted with one that they had implicated in synaptonemal complex dissassembly (the protein scaffolding that holds together homologous chromosomes during meiosis)--the first protein discovered to be involved in this process. I produced a lot of hits, and knocked a few of them out in vivo to see how they affected meiosis. A really cool project. I feel like I'd be in her lab right now if she had a grant. It's sad, but she already has two graduate students and no grants to keep them going. I think she'll eventually pick up a solid grant, but I just can't risk having to teach every semester and watch my productivity take a nose dive.
So, that left me to join Josep's lab. I started last week and will be there for the next four to five years working on recombination variation. Our first task is to get a review paper out the door. As such, I've been reading articles pretty much every day. Basically this way I can get my first paper in the lab, the first quarter of my comprehensive exam written, part of a grant application, and a piece of my thesis written within the first semester of my work in the lab. I think Josep is really thinking ahead on this one, which is a very good thing if I'm to get out of here in a reasonable amount of time.
I suppose the next obstacle in my way is our Qualifying Exam. We've been given the topics for the exam and are expected to know them well enough to answer specific questions within the topics on July 10th. I've started the studying process and should be ready by that time. Some topics are specific and doable, like "The biology of small interfering RNAs", while others are extremely broad, "The origins and maintenance of diversity in natural populations." Oh well, just another hoop to jump through.
I suppose that's all I've got. Haley will be passing through Iowa City in early June and staying the night at my place with Ari--I still haven't told her that I don't actually have a couch for her to sleep on, but I'll drag out the small mattress for her. It should be a fun time.
Cheers,
Andrew
Friday, November 5, 2010
1,3,7-trimethyl-1H-purine-2,6(3H,7H)-dione
It's been a couple weeks since I've last posted, but rest assured that I am managing to stay sane!
The NSF proposal is coming due soon, and it's starting to shape up in one form or another. I've not begun on the personal statement portion of it yet--It frightens me what I'm going to write.
Which reminds me of something really creepy and mildly disturbing: I keep seeing Amy Bishop in this town. I know it's not her; there's someone who works nearby that I always see from afar and my heart skips a beat. From behind, she has the same exact stature, same cream colored skirts, same poor posture, same black hair cut to the same length. I suppose I'll have to live with these types of creepy reminders for a while.
Anyhow. Three of us in the lab have Bruegger's bottomless cups now. For $139 you too can have all of the coffee you want for the next 14 months. Now I'm really living on the sinusoidal wave of caffeine addiction.
I'll try and post something sciencey in the near future.
The NSF proposal is coming due soon, and it's starting to shape up in one form or another. I've not begun on the personal statement portion of it yet--It frightens me what I'm going to write.
Which reminds me of something really creepy and mildly disturbing: I keep seeing Amy Bishop in this town. I know it's not her; there's someone who works nearby that I always see from afar and my heart skips a beat. From behind, she has the same exact stature, same cream colored skirts, same poor posture, same black hair cut to the same length. I suppose I'll have to live with these types of creepy reminders for a while.
Anyhow. Three of us in the lab have Bruegger's bottomless cups now. For $139 you too can have all of the coffee you want for the next 14 months. Now I'm really living on the sinusoidal wave of caffeine addiction.
Saturday, October 16, 2010
Thinking about changing the world...
As of now, I'm sitting in the library trying to think of a good way to change the world with my Ph.D. dissertation. It's an NSF exercise, basically,...that if I got lucky enough would fund me at $30,000 + tuition and $8000 for research for the next three years. The money isn't the big goal though, receiving one of these NSF GRFP fellowships basically means that you can do postdoctoral work wherever you want and, more, ensures that you're likely to get more NSF money in the future. The National Science Foundation really likes keeping their money for people they like, so they support people throughout their scientific career. This would be nice, while they don't dish out quite as much dough as the National Institutes of Health, they do provide researchers with hefty grants nonetheless. Money like this is essential to doing really big projects and getting tenure at a major research university.
So that leads me to my project proposal....
I have no idea what I'm going to suggest. The problem is, they want to see transformative ideas that will go a ways toward revolutionizing a field. NSF loves this kind of stuff, and wants to see this along with what they call "Broader Impacts". Essentially, this means that my work has to be distributed to the public in some form of outreach. They want to see that I'm going to go out and disseminate all of the knowledge I gain through their money.
Unfortunately, most of the people that I'm competing with have spent the last five years in Kenya teaching science to crippled children while rebuilding medical facilities and searching for an AIDS cure. Competition is steep...and if you don't have a transformative idea, you're dead in the water. Since I didn't quite get to the grad schools I pitched my transformative ideas to, I need to start again. And in a hurry.
At present, I'm twiddling with a few things that could be done. Most of them, however, hinge on having more genomic data about our snails in the Neiman lab. I've got to say...that just sucks. I'd also like to test our assumptions about Polyploidy or Asexuality, but there are way too many variables in this system to pin down just one! At this moment, I'm thinking about looking at how snails become triploid or tetraploid. I've got an interesting idea to look at the process...I just need to spend a few more hours on PubMed to see if it's even feasible. But then, I've got to relate it to the bigger picture and suggest how it will change the world. I think it might, I just have to solidify the connection!
Maurine returns from her European journeys this week. I've not gotten as much lab work done while she has been gone as I expected to. That's okay, though, since I really feel like I've spent a lot of time thinking and learning lately. Alas, back to work!
Sunday, October 3, 2010
Spherical Assumptions
Well, I've completed my second month as a for-real graduate student.
I've finally figured out why I've been uneasy with this whole shebang: I finally am beginning to understand just how stupid I really am. I'm surrounded by really smart people, doing smart things, talking about smart stuff. All the while being defeated during my own projects. There's a vast, vast, wealth of knowledge out there and I can't hope but to chip away at a tiny fraction of it. This, combined with the fact that in undergrad you could actually know everything you needed to know. Sure, biochem was a lot of material, but by the exam you could know all the answers and get an A. Now, (to take a phrase from Derek) It's like trying to drink from a firehose. Simply put, Graduate school makes be feel very dumb.
These last two months have been awfully humbling for me. Biology has gone from something that I do because I'm good at it, back to the thing that I loved as a small kid--discovering new things, rich and intricate that unite all beings on this planet. That's probably a good transition, though I can only wonder how people that were only 'just good at it' are faring.
Part of what is keeping me in it is seeing people that got through it that probably shouldn't have. I mean, if they can do it---so can I!
Another awkward thing is that we, as grad students, don't really fit in with a crowd except our own. The undergrads are well, undergrads...and drinking with those that you teach and look up to you is quite a bit awkward. And then you don't exactly fit in with the professors either...they're either married and have kids or involved in their own mid 30's life.
So that leaves us grad students together... Except we're all busy as hell. The only real form of camaraderie that we exercise is drinking; let me tell you: grad students can drink. This point has been made to me every Friday thus far. What's worse is the fact that Iowa is a Mecca for beer when compared to a place like Alabama. I've already imbibed more booze during the last two months than I did in all four years of undergrad combined. I don't guess that's saying much...but the liver has taken a pounding since I've been here.
Anyhow.. I'm finally experiencing some level of success! With the help of a collaborator, I've managed to prepare decent nuclear smears to quantify. I've already made 8 slides and counted + measured over 400 nuclei. I was hoping to have some images and flow cytometry data to show off for you, but I'm not in the lab (for once). I'll try to snag a few screenshots on Monday. At this rate, I'll have some sort of conclusion in a few weeks. Past that, I'm going to try and play around with karyotyping some of our snails so that we can confirm their ploidy levels...though that's a whole 'nother beastie.
Well, Maurine is off to Europe and won't be back for two weeks...meaning I'll have a couple less meetings now. It'll be interesting to see the lab dynamics while she's away. It'll also enable me to see Emily when she comes up from 'Bama this Thursday. If only this NSF grant would write itself. And now my Bioinformatics class is starting up. Can't get a break, can I?
Till next time,
Cheers!
I've finally figured out why I've been uneasy with this whole shebang: I finally am beginning to understand just how stupid I really am. I'm surrounded by really smart people, doing smart things, talking about smart stuff. All the while being defeated during my own projects. There's a vast, vast, wealth of knowledge out there and I can't hope but to chip away at a tiny fraction of it. This, combined with the fact that in undergrad you could actually know everything you needed to know. Sure, biochem was a lot of material, but by the exam you could know all the answers and get an A. Now, (to take a phrase from Derek) It's like trying to drink from a firehose. Simply put, Graduate school makes be feel very dumb.
These last two months have been awfully humbling for me. Biology has gone from something that I do because I'm good at it, back to the thing that I loved as a small kid--discovering new things, rich and intricate that unite all beings on this planet. That's probably a good transition, though I can only wonder how people that were only 'just good at it' are faring.
Part of what is keeping me in it is seeing people that got through it that probably shouldn't have. I mean, if they can do it---so can I!
Another awkward thing is that we, as grad students, don't really fit in with a crowd except our own. The undergrads are well, undergrads...and drinking with those that you teach and look up to you is quite a bit awkward. And then you don't exactly fit in with the professors either...they're either married and have kids or involved in their own mid 30's life.
So that leaves us grad students together... Except we're all busy as hell. The only real form of camaraderie that we exercise is drinking; let me tell you: grad students can drink. This point has been made to me every Friday thus far. What's worse is the fact that Iowa is a Mecca for beer when compared to a place like Alabama. I've already imbibed more booze during the last two months than I did in all four years of undergrad combined. I don't guess that's saying much...but the liver has taken a pounding since I've been here.
Anyhow.. I'm finally experiencing some level of success! With the help of a collaborator, I've managed to prepare decent nuclear smears to quantify. I've already made 8 slides and counted + measured over 400 nuclei. I was hoping to have some images and flow cytometry data to show off for you, but I'm not in the lab (for once). I'll try to snag a few screenshots on Monday. At this rate, I'll have some sort of conclusion in a few weeks. Past that, I'm going to try and play around with karyotyping some of our snails so that we can confirm their ploidy levels...though that's a whole 'nother beastie.
Well, Maurine is off to Europe and won't be back for two weeks...meaning I'll have a couple less meetings now. It'll be interesting to see the lab dynamics while she's away. It'll also enable me to see Emily when she comes up from 'Bama this Thursday. If only this NSF grant would write itself. And now my Bioinformatics class is starting up. Can't get a break, can I?
Till next time,
Cheers!
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