In which I torture a poor, defenseless undergrad

An undergrad just joined our lab.  He’s been here for a couple of weeks, now.  In general, we seem to get two kinds of undergrads 1) giddy and clueless and a disaster to work with or 2) thoughtful and kind and you wish they weren’t going to med school.  This guy is one of the latter.

This morning, the post-doc Undergrad is working with wasn’t here, so he was hanging out surfing the net and I don’t remember how it came up but he said, “So, what is all of this cloning you’re doing?”  At which point, I–in my enthusiasm to talk about my project to a new person who had some background knowledge of biology–proceeded to drag him lengthwise through my entire project, including all of the data that came before my project that led me to start this project.

I know, I know, but he wanted to know!  About my project!  Few people actually want to know, they just ask to be polite.

To his credit, he actually paid attention, never sighed, didn’t run screaming from the room shouting, “Enough!  Enough!” and even went to lunch with me after that.  And he asked questions.   I feel kind of bad about it, though.  He only wanted to know what cloning I was doing and I could’ve answered that without all of the background information.  But, I am pathologically unable to answer a question without giving some background information.  I mean, what’s the point in answering a question if you don’t put it into context?  The thing was, at times it seemed to resemble a class lecture because I was trying to tell him about something and I would say something like, “Do you know about small GTPases?”  And he’d say no and so I’d have to explain what a small GTPase is so he could understand the background.  Then, we got to a point where I was going to talk about a biochemical experiment I did and suddenly I realized this guy had no idea what GST or glutathione were.  So, then I had to explain that in order for him to understand the experiment and the results.

You know, there are times that I think about how much stuff I don’t know.  My advisor appears to have a photographic memory.  I swear he remembers every article he ever read, every bit of data anyone in the lab has ever told him about, every seminar he’s been to.  He has this vast wealth of knowledge and can bring up the most obscure thing from some other cell biology field that I had either completely forgotten, or never knew to begin with.  And I know I don’t keep up with the literature like I should.


Talking to this undergrad, I was reminded of all the things I do know.  And that’s a lot.  I forgot how much I have learned since I started college, since I started grad school, since I started my current project.  And, because I’m always interacting with people who are at the same level or higher, I forget that the knowledge that we possess on what seems like the most trivial things is far beyond the basic knowledge of cell biology.  I’m not sure where I’m going with this except to say that so often the emphasis seems to be on the negative–what you don’t know: what experiments didn’t work, what you’re having problems with, what data is missing from your planned paper/thesis/proposal.  It’s equally important to remember the positive:  what you do know, what experiments did work, what data you do have.  It makes life in lab a lot more enjoyable if you can keep those things in mind.

Things that make you go hmmmm

Two of your labmates going down the hall, heading toward your lab, sliding along with Kimwipes under their feet holding a geiger counter inches from the floor, carrying a box of Kimwipes and a spray bottle of radiac wash.

Um, should we be using a different door in and out of the lab????

This just in!

Scientist Enters Incorrect Incorrect Info on Own Plasmid, Screws Self

Mrswhatsit, a senior graduate student at WantstobeHarvard University, discovered this afternoon that her cloning project will not work because the information in the database about a particular vector was incorrect.  Sadly, this information was entered by Mrswhatsit herself.  Mrswhatsit freely admits her responsibility in this mix-up.  “It’s my own  fault,” she said, “I fucked it up.”

Mrswhatsit has been plagued with difficulties throughout this cloning project.  Up until today, these difficulties have centered around other people’s fuck-ups (one vector not only had the wrong gene, the gene was from the wrong species).  These problems have caused the cloning project to drag on and on, wasting precious time.  After spending a month trying to sort out the various misinformation surrounding the starting plasmids (including good old-fashioned sequencing of the plasmids), Mrswhatsit was looking forward to finally getting the damn cloning finished.  But it was not to be.

The cloning project is an ambitious one, involving the insertion of multiple genes, done in a sequential fashion.  While the first step of the cloning procedure seemed to go okay, the second step tanked.  “Essentially, I was getting an insert cut out when I was just trying to linearize this construct which was the product of the first cloning step.  Since I thought I knew what the sequence was, I couldn’t figure out why this was happening.  Finally, I looked over the sequence files for the insert from the first step and lo and behold, there are restriction sites I didn’t think were there.”  Mrswhatsit had tried to be clever and PCR amplify her insert from a construct she made several years ago.  “The extra sites hadn’t mattered when I first made this construct, but now that I was trying PCR amplify something from it, it mattered a great deal.  I went back to my lab notebook and found that the way I made the vector was not the way I reported it in the database entry which was what I was basing my cloning strategy on.  I have corrected the database entry, but that doesn’t give me back the weekend I spent in the lab trying to do this damn cloning.”

Mrswhatsit credits her organized lab notebook for helping her get to the root of the problem.  “If I hadn’t had a table of contents, it would’ve taken me hours to find that details of making that old construct.  As it was, it took me about 10 minutes.  Too bad I didn’t look it up earlier.”

When asked for advice for future lab generations, Mrswhatsit had this to say, “Trust no one–and that includes yourself.”


What does it say about me and my labmate that, as we struggled to find a way to get him some clean flasks that it never occured to either one of us that he should wash them himself? That it actually took another member of the lab to say, “Wash them by hand”? And then, once Labmate #1 accepted this strategy he asked, “But what about sterilizing them?”

Puzzle: How many PhDs does it take to figure out how to get clean, sterile glassware?

2.8 (One full-fledged PhD plus two grad students who are 90% done)


I have a confession to make.

I believe in God.

There, now you know.  If you started reading this blog unaware of this fact, you can now leave if it bothers you.

Growing up as a Catholic in a small town in Iowa, I was a minority (there were no Muslims and the only Jewish person I knew of was the mother of  the only other Italian family in town and the father and all of the kids were Catholic).  I experienced a minor amount of religious persecution (I had a baby-sitter tell me she didn’t like my church because we worship idols), but apparently things used to be a lot worse for Catholics long ago (cross burnings in their yards) so really, it wasn’t too bad.  Still, I grew up knowing that there were a lot of people who thought my church was “bad” (evil, even) and that there were some people who liked me “in spite of” my religious affiliation.

Then I went to college in Boston and I swear, everyone there was Jewish, Catholic, or atheist.  Seriously, I met very few Protestants.  The ones I did meet, however, had even stronger opinions about the Catholic church (apparently, there are secret warehouses full of gold and jewels in the Vatican, also, the Pope is the Whore of Babylon–who knew?).  As you might imagine, this did not endear them to me.  However, for the first time, it seemed that I was in a place where Catholicism was mainstream.  Lots of people were Catholic!  They talked about the Cardinal on the news!  For the most part people were not telling me that the church I belonged to was a cult just like Satanism (this was way before all of the priest pedophile scandals came to light; I imagine the atmosphere was quite different after that).

Now, I live in another large city with lots of Catholics, so it’s been awhile since I’ve had to justify being Catholic to anyone.  However, it seems I am a glutton for religious persecution because of all of the careers I could have chosen, I decided to be a scientist.  However, instead of being looked down upon because I am Catholic, I have run into a more fundamental problem.  Now, it’s my faith in God that is considered questionable.

I gotta admit, I never thought this would be a problem.  And, really, it’s not so much.  That is to say, most people don’t care or if they do they don’t say anything.  And I would say that half of my labmates also believe in God, so it’s not like I’m being persecuted at work.  But, recently, I have started reading a lot of science blogs and it’s pretty clear that many of the blog authors think that anyone who believes in God is, well, stupid.  I mean, they use a lot of much fancier words (even made up words, like “faithtardation”), but it really all boils down to the fact that if you believe in God, you are an idiot.

See, it never actually occured to me that there could be a conflict between being a scientist and believing in God.  Science and religion are two very different things, after all.  Now, I know that many people perceive science and religion to be in conflict.  The fact that many people can’t keep them separate is what is causing the controversy over teaching evolution in schools.  However.  I always thought that it was the religious side that couldn’t quite grasp that science has nothing to do with religion and vice versa.  But, it seems like there are scientists out there who really don’t get that concept at all, either.

People on both sides of the fence seem to think that you can’t be a scientist and believe in God.  And it’s true, there is no scientific proof that there is a God.

But, there’s no scientific proof there is not a God, either.

At best, it seems like science can only really make a case for agnosticism.  I mean, until someone comes up with an experiment that tests for the existence of God that has an interpretable null result.

Still Alive!

Most of the chemicals we work with in my lab are pretty harmless. They fall into the “may cause cancer sometime later in life” variety. And even those are relatively benign. One, Ethidium Bromide, which we use routinely, purportedly was once used as a food dye (I’ve heard it said that it was what made red M&Ms bad for you years ago but I can’t find any data to support this).

However, for one of the experiments I am doing, I have to work with a particularly nasty chemical. The Material Safety Data Sheet (MSDS) for this particular chemical states, “Fatal if ingested! Fatal if inhaled! Fatal if absorbed through the skin!” Further down on the page it lists an “antidote” and this precaution, “DO NOT USE MORPHINE!” Exciting!

I’m always a little nervous when working with it and actually wear a lab coat (!) as well as gloves and a mask AND I work with it in the fume hood (in theory working in the hood should mean I don’t need the mask, but I’m just being extra cautious). I say cheery things to my labmates like, “I’m going to work with X now, so if I fall down in a seizure, bring the MSDS sheets when you take me over to the hospital–and for God’s sake, don’t let them use morphine!” (Fortunately, the hospital is just across the street.)

So, when I finish working with X and still no seizures or respiratory distress or severe eye burns, I feel pretty good. Woo hoo! Dodged that bullet! Let’s go get some tea to celebrate!

I imagine this is how rock climbers feel when they get to the top of whatever large rock they are climbing and they haven’t fallen to their death on the canyon floor. High five!

I acknowledge this may be an indication of how incredibly and pathetically boring my life is that working with a toxic chemical can make me feel daring and grateful to be alive (I also ride my bike to work without a helmet–the danger, the audacity!). But, you know, you gotta work with what you’ve got.

Science is awesome #1

While I don’t feel like I’ve done any real hard core bitching per se, I feel like I should go ahead and do a science is awesome post, anyway. I was thinking about what I should write about and it hit me yesterday afternoon after leaving lab. Only, it’s not really a post about why science is awesome, but more about why working in science is awesome, or at least why it has been for me. Working in science has allowed me to interact with a huge variety of people from different ethnic backgrounds.

Let me explain why this is such a big deal to me.

I grew up in a small town in the middle of Iowa. It was not what you would call a very exciting place for many reasons. One of the things that made me want to leave it was the fact that I seemed to think about things in a way that nobody else did. Everybody thought the same. Everybody was the same. Ethnic diversity was whether you were German or Norwegian. Religious diversity was whether you were Methodist or Lutheran. For the most part. There were a few exceptions.

I went to college in Boston. There, I met a more divisified group of people. There were a few embarassing moments (“Why are all of those guys wearing beanies? What’s up with that?”) but mostly it was a positive experience. I met people with different religious backgrounds, people with different socioeconomic backgrounds (I had a roommate whose parents wrote a check for the tuition and room and board at my private university every semester; I was maxxed out on student loans, grants, scholarships, you name it), but in the end, I mostly hung out with people who were pretty much the same as me.

As a technician and then as a graduate student, I have worked with people from Chile, India, Poland, Lebanon, Greece, Italy, China, Japan, the Ukraine, and Switzerland as well as people from all parts of the US and first generation Americans. I have worked with people who were Christian (Protestant, Catholic, Mormon), Muslim, Jewish, Hindu, Buddhist, atheist. And because of our close proximity, we talk about our lives and those conversations include tidbits about culture, traditions, values. We talk about religion. We talk about politics. We talk about families. And at the same time that I’m learning about other people’s beliefs, traditions, cultures, I am learning more about my own. Because people ask me questions. Sometimes, I can answer the questions, sometimes I can’t.  When I can’t, I look it up.

I suppose, you might get the same exposures to different cultures just by living in a large city (which I do).  But, I’m not so sure.  The people that I work with wouldn’t even be in this country except that they are going to school here or doing a post-doc here.  Most of them have every intention to go back to their country of origin.  So this seems like a very unique environment.  And, due to the nature of our experiments, we have some downtime and it’s during that time that we talk about these things (or we discuss things while doing experiments).  I’m not sure we’d get that kind of opportunity working in an office (though maybe we could, I’ve never worked in an office, so I couldn’t say for sure).

So, working in the lab has been an educational experience in many varied ways.  Working with such a diverse group of people is one of the things I’ll miss when I leave benchwork for good.


I am lucky enough that my advisor is not a stickler for working on weekends.  Nevertheless, I feel a certain amount of pressure (mostly self-inflicted) to go to lab on Saturday and Sunday.  But, I rarely actually go.

At this stage in their careers (the “trying to finish my thesis work and get the hell of here” stage),  most people spend the vast majority of their time in lab.  This includes nights and weekends.  And I think it helps them with their push to graduate.  At least, it seems to from the outside, I can’t really say for certain.  However, if I work that much, I start to become non-functional.  I can continue to go to work, but I make a helluva lot more mistakes than if I only work 9-10 hours per day and don’t go in on the weekends.  I don’t know if this is just the limit of my capabilities or directly due to burnout; it’s hard to say at this point.

This weekend, I spent a lot of time sitting in front of the TV watching episodes of Stargate (SG-1 and Atlantis) that my husband had taped for me (I don’t get the Sci-Fi Channel, but he does).  I essentially became a hermit.  I did some laundry, I left the apt. a couple of times to go to the store, but mostly, I stayed home with the shades down (it’s really hot out and I want to keep it as cool as possible inside).  I didn’t even knit while I watched TV–I just vegged.  And it felt great!

The last few weeks, I’ve had numerous personal things happening on the weekends so that even though I wasn’t in lab working, I was still on the go the whole time.  I didn’t get a chance to relax at all.  And I think my labwork suffered for it.  Looking back, I see a bunch of mistakes I made that I don’t think would’ve happened if I had gotten the rest I needed.  From this, I conclude:

There’s no way I can ever be a research scientist.

My PI spends a ton of time in his office.  He’s there during the day, he’s there at night, he’s there during the weekend.  So are most other professors.  I don’t think this is simply because they are workaholics, I think it’s because this is what the field demands from you in order to be successful.  Well, I just can’t do it.  It’s not even that I won’t do it, or I don’t feel like doing it, or that I think it’s unreasonable (it is, though).  I am simply incapable of spending that much time in lab.

It was a difficult realization to make, but the more I thought about it, the more I saw that such a life would kill me.  And I wouldn’t be very good at it besides.  At a certain point, my brain would just shut down and I’d make more mistakes and nothing would work right and I’d be frustrated and never publish and never get tenure.  It’s too bad, too, because I think I am a good scientist.

I just lack the stamina for it.

How much is too much?

And how little is too little?

It is an unofficial requirement of my program that I need to publish a first author paper before graduating.  Some of my data has been published in another person’s paper (by that I mean I was not the first author, I was the third or fourth author).  Some of my data is unpublishable (Journal of Negative Results, anyone?).  But, I do have actual, honest-to-goodness publishable data.  Not enough for a paper, but I’m working on getting more.

Here’s the problem–when is enough enough?  My advisor and I have been “discussing” this in terms of my paper.  Because until I have “enough” for a paper, I ain’t leaving here.  And there are all sorts of reasons why I need to leave here as soon as possible (not just my reasons, but my advisor’s reasons and the department’s reasons).  We agree on what my paper should be about, but we only sort of agree on the scope.  That is, I put forth what I think is reasonable and will make a nice story and my advisor half-heartedly agrees.

Today, it was my turn to present for lab meeting.  I showed the lab my outline and asked them what they thought.  And one of the things we talked about was whether or not the data I am calling Figure 3 really needs to be or fits in my paper.  But, since this is only a four figure paper, leaving out Figure 3 means I will only have enough data for three figures and is that enough?  On the other hand, if I leave it in, do I need to add more experiments and if so, how many do I add and when can I stop?  And the very wise conclusion we came to was: it’s not clear.


Yes, I do want to have a good paper and a good thesis and so on, but I am weary and frankly, I think I’ve learned as much as I can learn about doing science as a graduate student.  This is not to say I know everything there is about being a scientist.  But there is a limit to what one can achieve as a graduate student.  To really progress, I’d have to move on, go to a new lab, be a post-doc, be semi-autonomous and work and think in a whole new way.  The one thing I haven’t done is write a paper.  And I suppose you could argue that writing a paper is an important lesson.  So, maybe it’s appropriate that I am stuck here trying to get enough data to write a paper.

I also know that writing a good paper is necessary to get a good post-doc.  However, I don’t want to do a post-doc.  As soon as I’m done defending I’m running as fast and as far away from benchwork as my little legs can take me.  I have had it up to here with the benchwork.  That may change after I’ve been able to take a break from it (a real break, not a “I’m going home for the holidays” kind of break), but for now my plan is to high-tail it out of lab and focus on classroom education.

So, I don’t need a Nature paper, or a Science paper, or a Cell paper (and I’d be kidding myself if I thought the data I have are important enough for that kind of journal).  I just need a paper.  A nice, tight little paper that contributes to my field in some meaningful way.

Right now, the point is moot, because I don’t have enough data for a paper anyway.  I suppose when the time comes and I think I have enough data, I’ll call my thesis committee together and see what they think.  Hopefully, they’ll see it my way.