Well thank God

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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.

BUT

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.”

Spoiled?

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)

Confession

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.