Post-Vacation Grad School Blues

Having recently returned from my vacation (as in, yesterday), I am confronted with the typical post-vacation work-related feet-dragging. There is certain prevalence of the idea that vacation is supposed to "recharge" you for work, that you will return ready to kick science-butt with renewed energy. Instead of being recharged, however, I find myself wondering: who are these people that are recharged after vacation? Does this really exist?

I think for the majority of graduate students, this vacation recharge is a myth.

Case in point.

However, maybe there are people that are truly rearing to go after they get back from vacation. I think that my PI is probably one of them. He let us in on this little secret of his when he told us that he spent a lot of time thinking about the philosophy of graduate school while on his most recent vacation in Mexico. Sitting on a beach, thinking about how best to mold these young minds into great hypothesis-driven, problem-crushing, publication-writing machines. This is a man who obviously enjoys his job.

...

Of course, it is probably unfair to say that most graduate students fall into the "I'm on vacation, so we're NOT talking about lab" category. I have known some fantastic grad students who remain truly curious about all things science, even while Science slowly erodes their hopes and dreams on a daily basis. They stay upbeat, read journal articles for fun at night, etc. I believe these are the people that are going to make great professors someday.

For the rest of us, it's not to say that maybe we won't be useful scientists or even great professors. I think the issue is more about the work mindset that is necessary to succeed in graduate school. For instance, I now cook as soon as I come home from school, in part because it allows me to achieve something on a shorter timescale. Many of graduate school's successes (for me anyway) are few and far between. It is difficult to celebrate an attractive gel when you have yet to get your first paper published.

For students like me, graduate school is a long and tiresome process. It is a journey. When I was a first-year, I was told by a senior grad student that graduate school is a marathon, not a sprint, and that many of his classmates were no longer there because they didn't have this particular brand of perseverance. This same student also told me that you stay in graduate school either because you love your project, or your professor. If you love both, obviously that is the ideal situation. Of course, I didn't take him very seriously at the time, but it's true that when your project is giving you grief, the only thing that really pushes you to continue with any fervor is your professor. And when your professor is a true pain to work with, genuine interest in the project is the only thing that keeps you there.

So, while I know I don't quite have the right blend of working style and personal attributes to really soar in graduate school, I know it is temporary. And I know the journey will teach me the skills and knowledge to land a career where I may experience that recharged, go-get-em attitude... when I come back from vacation :)

An Open Letter to Senator Michael Bennet

Hi Michael,
I am very pleased to learn that you are on the Senate Committee for Health, Education, Labor and Pensions, and are currently considering the Preservation of Antibiotics for Medical Treatment Act (PATMA S1211). I hope you consider passing this bill for numerous reasons, as a scientist, a consumer, and a citizen.

First, I am a graduate student at the University of Colorado in Boulder in the field of Biochemistry. In fact, in particular, I study the molecular components of pathogenic bacteria, like E. coli and Salmonella, that make us sick, in hopes that in learning more about them, we can create new drugs against them. One of the major reasons for this work is the growing anti-biotic resistance in the civilized world, and it is also a fact that this low-level use of antibiotics in factory farming is greatly contributing to this growing problem. The levels of antibiotic are not enough to kill all the bacteria present, and the constant exposure to the antibiotics causes resistance genes to arise. Any bacterium that comes in contact with these drugs can develop resistance genes, which can then be picked up by pathogenic bacteria. This is a particularly insidious problem. By restricting the use of antibiotics for only medical use, you can use a more potent dose for a limited amount of time, wiping out all bacteria that come in contact with the drug, and preventing resistance from arising. It is exactly like getting antibiotics for strep throat from your doctor, and why it is especially important that you complete the full course of antibiotics. Any bacterium that is left will have been exposed and has a higher chance of developing resistance.

As a consumer, I am concerned about the misuse of antibiotics in factory farming because it contributes to the mistreatment of animals. This low level of antibiotics allow farmers to keep the animals in close confines with each other, maximizing space use, but at the expense of what? These animals are treated as mere commodities in these situations and all respect between the farmer and his herd is destroyed. By halting the widespread use of antibiotics as a preventative application, farmers will not be able to crowd the animals as much, keeping them in more humane numbers in order to maintain health. Healthy animals create a better consumer product for consumption, as well, being of higher quality and nutritional value. Finally, the situation these animals are kept in can be likened to the confines of slave ships that brought Africans over to the New World, a deplorable circumstance that we now view as incredibly inhumane.

As a citizen, the threat of growing antibiotic resistance to the health of my loved ones and myself is very real. Pharmaceutical companies are not spending as much money creating new antibiotics. Pursing new antibiotics is not as lucrative because resistance is growing so rapidly. As a nation, we should be appalled by this misuse of antibiotics and should all be made aware of the ramifications. The profit that these factory farmers are making is not worth the health of our nations people.

If this practice is allowed to continue, perhaps Big Ag's profit should be put to developing new antibiotics instead of lining their own pockets. Even though the funding of my current research is somewhat dependent on the growing antibiotic resistance problem, it would be a great miracle if we could slow the pace of the problem. There are many other avenues in science to pursue, after all. I believe that this bill can and will help slow the rate of antibiotic resistance development and help create a better, more humane nation for our livestock and our people.

Thanks,
Michelle Turco

PS. This is the sister bill to HR 965. If any of your representatives are on the committees that are looking at these bills, please write them! You can check S1211 here and HR 965 here.

Fish / Cat / Lab problems

I have been having many problems lately. Things are not going according to plan in lab. They never do. No surprise there. I had a slight success today, though, so that is good.

I am going to Europe on vacation, so of course, some of my pets get sick/ injured. They love this kind of timing. Georgie has somehow injured her achilles tendon and is now walking around with one flat foot. Pretty weird. If she's not better by Monday, going to take her back to the vet and get her a cool splint to immobilize it. She should be fine with a gimp leg splint while I"m on vacation, right?

My biggest headache has been my fish. Estefan/Fifi has developed fin rot to a small extent. He previously had a cloudy eye and septicema in his fins, but that had been ongoing for months with no alteration of behavior. His life is not in danger, so I set about cycling the hospital tank before putting him in. It was taking longer than planned with gravel from the established tank and a sponge, added fish food and poop so the bac would have something to eat. Ammonia was 0 and nitrites were like 5 and wouldnt go down. Got a MIRACLE PRODUCT from the fish store (Safe Start). Tank was cycled overnight. I love that stuff. Put Estefan in last night, dosed with Ampicillin, he is already looking a little better I think, the edges of his fins are not "fuzzy" anymore. BUT there was a slight amount of ammonia build up in the night.

My main problem is now trying to get rid of this ammonia so it won't stress Estefan out further. I am unsure whether the ammonia detoxifying products would react with amp. Amp has amino groups, so... maybe? Also, there is this nitra-zorb matrix which absorbs and detoxifies ammonia and the NOs. It says not to use it with medication, but ALL medication? Also, I am trying to decide whether to listen to the fish store guy and dose Amp every other day, or every day like it says on the box... Amp doesnt last very long at higher temps in solution, but maybe a full dose is not necessary since the fin rot is quite minor.

Kanye and Jay and Elsevier

OBSESSED with this song! Gonna be in Paris in less than a month. "I'm in France, I'm just sayin"

Reading this article about the future of academic journals. Knowledge should be freely accessible. How do we move forward as a society otherwise? I get miffed when I run into an article I can't read in entirety because the University's subscriptions don't cover it. Just try and stop progress, b**ches! That sh*t cray. Elsevier, show me why you deserve it all!

BTW that panther at the end with the statue in the background, that imagery is EPIC. Like, wolf t-shirt epic.

I'm Baaaaaack!!!

Back from Europe, jet lagged, not really so bad though, just have an old person's sleep schedule, early to bed early to rise.

Miss the grocery stores all over the place and every one of them had fresh cheap bread. Nice to not be living out of a bag though. Probably miss Prague the most. There's just a feeling about the city that gets to you, or maybe it was just appealing because it was cheaper. There is an honesty about the city and the people, maybe.

Current thoughts about grad school involve QUITTING. I feel more serious about it this time. We'll see.

Nothing interesting to say...

Except that science sucks.

I'm going to Germany in 7 days.

I'm not done with my Christmas presents yet, one involves a resin that you're supposed to have lots of ventilation for because of fumes, and I think I inhaled too much of it because my lungs feel sort of weird, but maybe thats just all in my head.

I figured out that I shouldnt drink coffee when under stress, it just makes things worse.

We are having a Christmas party tonight, I made a jingle horse costume that is pretty sweet. I hotglued on the bells instead of sewing them and it saved tons of time and they still jingle, so who cares?! I'm supposed to bring egg nog and brandy. Just realized that I don't know if anyone's bringing Christmas cookies!!

Having someone on the instrument I need isnt really that upsetting because I have no time to hang around here in lab anyway, and this purification I'm working on has probably already failed, so it would just be a waste. I managed to run my samples all off the gel I was running yesterday; either that, or they leaked out a crack in the glass somehow...? In any case, if I were a good scientist, I would probably be running another gel right now, but that takes up too much time.

I need to figure out which train pass to get in Germany, I'm going to the Czech Republic and Austria also, at least thats the plan... It seems that getting a two country pass and then a separate country pass costs the same as a three country pass, except that you get more days. I don't even know how much train travel I will be doing in any of these countries!!! Or say, I have a pass in Czech Republic, but not in Germany, and I'm going from Munich to Prague... Would the Czech pass count?!?!!? Probably not...

And that, my friends, is a small sampling of the mental noise in my head on this Sunday morning.

Pictures of Atomic Bonds Using Atomic Force Microscopy

Awesome. I'm depressed and I still think its awesome.

Science article for those who have access.

Gizmodo article.

As a side note: Grad school is depressing.

Less is More?

MANY of you may have seen the opinion piece in NYTimes recently, "The Joy of Less." I had wanted to comment on it when I first read it, and was reminded of it today when I was on this other site Three At Sea. (They actually call it Three@Sea, but I refuse to support that because the @ is WAY too tacky, and the people used to be in computers and stuff and well... Not hip, guys.) Anyway, its about a family who used to live in Boulder, but sold their house and most of their stuff and bought a boat and are planning on traveling around the world during their daughter's middle school years. THE POINT BEING: That these people have bucked the status quo and are living their own way somehow, with the lack of many material possessions (although they remain entirely wired to the rest of the world).

All of this sort of jives with the whole grad student lifestyle. I am poor, live in a small apt, no longer watch tv, and because of my whole environmentalist leanings, am also disdainful of the consumerist society we live in. That said... I have a lot of stuff. But I figure I may need some of it some day, so I have to keep it, because otherwise I would be feeding the consumerist beast, right? My life is less about the pursuit of things and more about the nurturing of the BRAIN. This is true with what I actually do for money, and for what I do in my spare time. Also, the pursuit of the body is in there somewhere, cuz I live in Boulder, and we are all fit and beautiful here. You could say this is also a mind-pursuit of sorts, as theres all sorts of thinking and refreshing you can do while youre working out, if youre not plugged in, which I rarely am.

Anyway, I am not so sure about the pursuit of happiness part being entrenched in these drastic lifestyle changes. It is true that hectic lives make people crazy. And that a more moment-to-moment life, like that achieved on a boat (OR being a forager/hunter/gatherer, my personal favorite escapist fantasy), where you have to be paying attention to your surroundings in order to live, seems more fulfilling than doing some drivel that you find meaningless. However, I am unsure about the necessity to buck the yolk of society in order to obtain happiness. I agree it is probably not found in things. Maybe too often people associate the obtainment of things with a typical American life, but maybe you can do the normal things like have a regular job and not be obsessed with the pursuit of things, and whatever happiness can be obtained that way. There are just a lot of people who seem to think something drastic needs to be done with their actual life situation in order to be happy, but maybe it is just the internal adjustment, which often accompanies that outward change, that is truly the key.

Or...

Is this how people talk themselves into settling down for a common life?

Eh heh.

Sorry I am so lazy. :-/

I read "Into the Wild." If I ever get the ambition, I will write about it. Talk about escapist fantasies, man.

In the sciencey bits, I am reading about CML, which is some sort of leukemia, and I can't remember what the other letters stand for, but it results from a chromosomal translocation that fuses two genes together (called the Philadelphia Chromosome, I remember that much). This sort of thing usually happens from RADIATION EXPOSURE. Anyway, this particular fusion results in a constitutively active kinase, which basically means that the gene has been truncated by the fusion, and it used to be self-inhibited, and now it is active all the time, turning all sorts of shit on, like a naughty toddler or something.

And suddenly, I am distracted by The Beatles "Something" that is playing right now, because I am all sentimental lately. Something of an honest confusing love song. (I do not suggest watching the video, it takes away from the lyrics, I think)

ANYWAYS. Um, so theres this kinase running amuck, that is normally involved in regulating the cell cycle and inhibiting the apoptotic pathway (which leads to CELL DEATH) upon DNA damage (that might occur upon radiation exposure). So you see, the kinase normally is involved in killing off sick cells that have DNA damage and may turn cancerous. When it is doing things wrongly, the cells don't die, and they proliferate uncontrollably, and in this case, you get all sorts of crazy unnecessary blood cells being made in the bone marrow, and I'm not really sure of the mechanism, but it eventually leads to death.

SOOOOOO, this is a success story, because someone figured, Dude, let's just inhibit the kinase. And they were able to develop/find a specific enough inhibitor that you are just inhibiting this particular kinase and not all the other ones that have to do other normal things. BTW, kinases are responsible for putting a phosphate group on particular amino acids on proteins. (I really am so out of touch with what terms laymen know, so this probably makes no sense to anyone outside the field. But oh well, thats what Wikipedia is for.) So, they actually have a super awesome, specific drug for this form of cancer. Honestly, if you were to get a cancer, I would choose this one. Cancers are a**-scary, but its nice that this one makes so much sense.

IN ANY CASE, one of the people involved in this whole saga, Jean Wang, is coming to give a talk next week and that is why I'm learning about sh*t, because I have to, because I'm on a training grant and this is what is expected of me. But it's pretty cool.

In other news, my car developed a nasty brake fluid leak and I think I am getting ripped off by the car mechanic man, but there is not much I can do about that now.

In some even more remote news, that is related to escapist fantasies, I am daydreaming about flying away to Munich, because it is less than $400 to get there, see. But this whole paying for expensive car repairs thing is not very conducive to that sort of thing. Ah well.

I might also mention that citing so many wikipedia articles is bad form for a scientist, but honestly, we all look at wikipedia. YOU MUST TRUST IN YOUR FELLOW MAN.

And Now... You are Reading the Blog of a Shiny PhD Candidate! BAM!

That's right. I have been out of commission for the past several weeks because I was studying for my oral comprehensive exam, which is something that all second year grad students have to do. Basically, you write a proposal for your research, and then you get locked in a room with three professors and you tell them about your research. And they proceed to ask you WHATEVER THEY WANT about your project or about biochemistry or chemistry in general (in my case... Presumably not if you were an English major, har har). So NOWWWW I am all fancy and am feeling pretty smart because the whole thing really went very well and I was done in an hour, which is pretty fricking quick if you ask me. ANYWAY. It was awesome. I kicked its ass. And it is such a huge relief and I am so happy that it is finally over. The morning after, I woke up in the middle of the night thinking about kinetics, dP/dt = ... and I realized, I don't have to care about kinetics anymore. HA! Take that Kinetics! And now I can go back to doing things I used to like to do, there is such a feeling of freedom, and I am excited about my research as well, so Everything is all Really quite great right now!!!! HOORAY!!

I will say that the entire orals experience was really quite horrible, weeks and weeks of dread and counting down, and I got sick and had a headache for like 5 days, and THEN I got strep throat, and then Phillippe got sick and died (thats for another post), and everything was all sucky in the world and I wasn't sure if I was going to make it, I couldn't even consider how I was going to do, and I was SOOO sick of studying, but I had to, just because I don't even know what I would do if I failed. But now I did it and it is GREAT.

Graduate School

There are a surprising number of comics created by graduate students (or recent grads), who are probably supposed to be doing real work instead of creating comics. Oh well, it makes for a great time waster. Other comics by graduate students, off the top of my head:

xkcd.com
PhD comics

Ok... I know there are other ones, but I forget.

8-Bit Theater is also a classic, but more for dorks. Those other two I listed are also by science dorks, but the pictures for sad children I have been posting is by a lit grad student, from what I can gather.