How to clean your silver jewelry

Step 1:  Purchase silver polish.

Step 2:  Take silver polish to lab.

Step 3:  Load gel and start it.

Step 4:  Put primary antibody on IF.

Step 5:  Grab a velvet (commonly used for replica plating yeast; the velvet doesn’t have to be sterile, but generally the only clean velvets in our lab are sterile).

Step 6:  Put on gloves (latex or nitrile, your choice) squirt some water onto the velvet using your water bottle to dampen it.

Step 7:  Squirt silver polish onto velvet.  Use velvet to smear polish all over jewelry.  It’s okay to get it on the stone if there is one (well, it’s okay to get it on malachite anyway).

Step 8:  Let silver polish dry

Step 9:  Image gel.  Realize PCR didn’t work.  Cuss a blue streak.

Step  10:  Use water bottle to dampen rest of velvet and wipe off all silver polish.  Wet a cotton swab to use in the nooks and crannies (though I like to leave a little tarnish in embossed areas because it emphasizes the design).

Step 11:  Do a final rinse of jewelry using water bottle.  Dry with paper towel.  Let dry.

Step 12:  Rinse IF and put secondary antibody on.

Step 13:  Put jewelry on.

Squirreling things away

Go read this post over at DrugMonkey (and some of the comments because there are several funny stories in there).  When you are done laughing, come back.*

I confess, I have my own secret stash of things in the lab.  Not expensive reagents like Taq, but a Backup Supply of things that we routinely run out of (the fact that we routinely run out of critical things is a topic of a whole ‘nother post entirely).  In an unlabeled cabinet near my bench I have the following:

  1. Two boxes of medium-sized nitrile gloves
  2. Two packages of paper towels
  3. A box of each kind of tips (this is overly neurotic–we haven’t run out of tips in forever)
  4. A bottle of LB that I made myself
  5. A bottle of YPD (yeast media) that I made myself

In the freezer, I have my own tube of ampicillin, and my own tube of ligase buffer (this is for self-preservation; people leave the buffer out for too long and it starts to go bad and then your ligation doesn’t work and it makes me want to howl in fury, so I keep my own buffer since I know where its been; also they supply so much buffer with the enzyme that everyone in lab could have four tubes for themselves at this point).

I’ve also been known to keep a couple of spare bottle-top filters.

I’m pretty sure I’m not alone in this habit of mine.  I’m guessing everyone in lab has a secret stash of something or other.  What do you guys stash away?

——

*I laughed at those stories until tears came out of my eyes.  Also, if I was the PI, I think the incident would not have happened, because I would have followed PdA back from lab meeting and made damn sure he gave PdB the antibody in question.  However, let’s say it happened exactly as written.  I would send them home for two days, call them both into my office and tell them in no uncertain terms that if anything like that ever happened again they could both find new labs to work in (this might be somewhat complicated if they have their own fellowships, but no way in hell would I want them in my lab).

Doomed Relationships: Why you should not fall in love with your model

Back when I first started in my lab, I started with a continuation of a former grad student’s project.  I hadn’t yet gained the maturity to come up with my own experiments and I was sort of blithely moving along, doing experiments that my advisor suggested.  These experiments were testing a particular model of how we (and by “we” I mean my advisor, really, because I hadn’t put that much thought into it) thought our system functioned.  It was a tough experiment for various reasons and it took a long time before I actually had results (1.5 years), but when I got the results they did not fit the model.  I was crushed.  I thought there might be something wrong with my results.  Then, I desperately tried to make the data fit the model.

My advisor, however, was not too bothered by my results and said we simply needed to revise the model.  I did not want to revise the model.  I liked the model.  The model explained everything I thought to be true but hadn’t proved yet.  And now, I had this bit of data that was fucking it up.

Eventually, I learned to let go of that model and trust my data.  Since that time, we’ve been through two or three revisions of the model and when I’m gone I’m sure the lab will go through many, many more revisions of the model.  My attitude towards models has changed so much that I’m actually excited when I get new data that blows apart the previous model because I know that I’ve made a big leap forward and I’ve really contributed something worthwhile to the field.  It’s also scary, though, because I’m trying to wrap things up and publish and graduate and I can’t do that if I’ve just discovered the way I’ve been approaching your problem is wrong and I’m going to have to do ten more experiments.  Sometimes, when a labmate proposes an experiment to me in lab meeting, and I argue against it, I have to ask myself why I’m so against doing the experiment.  Often, it’s because I’m afraid that the result won’t be what I want it to be and my model will be in big trouble.  And those are the experiments I know that I have to do.

Last week, at lab meeting, I had one of those moments which I later discussed with my advisor.  And he agreed that if a possible result from an experiment scares the crap out of me, then it’s an experiment I should do.  This is maybe the best thing that came out of lab meeting.

At that same lab meeting another student, Problem Child, presented.  She has a model for a different system.  Like any good cell biologist knows, a good way to learn about a system is to try to screw it up.  So, Problem knocked out a gene that she thought should have a significant effect on the system.  It took her a very long time to get this knock-out strain of yeast.  Then, she looked at her cells via immunofluorescence.  If she had significantly screwed up this pathway, it would be obvious by IF.  But, there was nothing obvious there.  She thought maybe, if you squinted, and turned your head so you were looking out of the corner of your eye while jumping up and down on one foot, there was a phenotype.  So, she looked by EM and did some quantitation, but there was nothing there (although she has yet to show us those results in lab meeting, she has told me there is no discernible phenotype).  THEN, she did live cell imaging and took multiple movies of her strain which is what she showed us at lab meeting.

My friends, there was nothing in them worth noticing.

We said as much.  And, at the same meeting, she talked about other ways she could screw up the system.  We thought those were really fine ways and actually much more promising.  But, she wants to continue with this knockout strain.

So, I asked her, “Let’s say, in the best possible scenario, there is a very subtle phenotype in this strain.  What does that tell you?  Aren’t you looking for something much more dramatic?  Wouldn’t it be a better use of your time to pursue these other possibilities?”  Advisor agreed.  Everyone else in lab agreed.  But, she still thought it was worth making more movies and taking more EM images.  “In my spare time,” she said, “while waiting for the other strains to grow up.”  But, she doesn’t spend that many hours in lab and I know that she’s spending a ridiculous amount of time making movies and so on because I have seen her analyzing them.

So, after lab meeting, in a private conversation, I suggested to her that it seemed as though there were two ways she could take her project.  One was a characterization of the protein for the gene she knocked out.  Nobody else has done much work with it.  There are a number of things she could do with it that would be publishable and she could even publish some of the data she has collected.  OR, she could go full force trying to get the phenotype she wants by knocking out her other candidates one by one or in combinations and spend 6 months doing that and if she’s able to get her phenotype, then great.  From what I can tell, this is what Advisor is telling her she should do.

She insists that she really is working toward making those knock-outs but she really believes there is something in this first knock-out strain.  She will not be persuaded–not by her labmates, not by her advisor, and not by her data.  She is in love with her model and she is bound and determined to make her data fit it.  This is dangerous for many reasons.  First, and foremost, I think this sort of blindness to what the data are telling you is how people end up falsifying data.  If I were Advisor, I would demand to always see her raw data and not just her analysis of it (which I believe he does; Advisor loves looking at raw data–it’s what he lives for).  Second, this devotion to a strain with no phenotype is not getting her anywhere.  It’s wasting lab resources and it’s wasting her time.  She is never going to graduate if she doesn’t move forward.

It reminds of talking to a teenager, trying to convince her that the guy she is dating is bad for her.  No matter what you say, she is going to remain with this guy.  Emotion has blinded her to the truth.  Parental guidance holds no sway and she will sneak out in the middle of the night to be with her guy.  Likewise, Problem Child ignores all advice and comes in–literally in the middle of the night–to work on this strain that she insists proves her model.  And there is nothing to do but to sit and watch it happen.

I can’t stand it

I’ve been trying to avoid ranting and bitching and so on lately because I know that some people are seeing my blog for the first time and I don’t want to scare them off (new people:  nothing to see here, please go read these relatively sane posts).

But.

*huge intake of breath*

A HUGE NUMBER OF BOXES OF CONICAL TUBES JUST SHOWED UP IN THE LAB AND THEY ARE NOT THE KIND WE ALWAYS USE AND I LIKE THE KIND WE ALWAYS USE AND I’M TIRED OF PEOPLE* JUST RANDOMLY DECIDING TO CHANGE THINGS WITHOUT ASKING!

AAARRRGGGGGGHHHHHHH!!!!!!

Sorry, I just had to get that off my chest.  I feel much better now.

*By “people” I mean one specific person who is constantly doing this kind of thing in an effort to make things “better.”  Apparently, this person’s motto is, “If it’s not broken, we should fix it.”  For long time readers:  you will know this person as someone with a lot of lab drama surrounding them. 

What Fume Hoods Are For

The last time I was in California, I bought two pairs of leather shoes. Given the wide range of weather I experience in my current locale, I always treat my shoes with some weather-protector spray stuff.

If you’ve ever used this stuff, you will know that it has a nasty, organic chemical smell. Now, the smartest thing to do would have been do would have been so spray the shoes out on the apt. balcony in California and let them dry out there. But, I didn’t have the spray stuff there, and I knew I did have some in Grad School City and I didn’t want to buy another can of the stuff. So, I brought the shoes back to Grad School City unsprayed.

If I had really thought it all through, though, I would have just bought a can of weather-protector in California and called it a day. Because my apt. in Grad School City is small. So the smell of the stuff would be very powerful in the apt. and would probably give me a headache. And it’s pretty cold in Grad School City right now, so I don’t want to leave a window open.

This morning, I was getting ready for lab when I had an epiphany (if this had been a cartoon, a light bulb would have appeared over my head). I’ll bring the shoes to lab and spray them in the fume hood! Which is exactly what I just did. And I left the shoes in there because they always smell a bit for awhile after you spray them.

The funny thing is, a labmate just went into the room with a fume hood and came back out and said nothing.

Me: Are you using the fume hood today?

Her: I just went in there to get some beta-mercaptoethanol [which we keep in the hood].

[Pause while I wait for her to comment on the pair of shoes in there. She continues what she’s doing.]

Me: So, I suppose you’re wondering why there’s a pair of shoes in there?

Her:  Well, one time I had a lot of perfume on my scarf, so I left it in the fume hood for awhile so I guess I thought it was something like that.

Apparently, nothing surprises my labmates anymore.  Not even shoes in the fume hood.

Whoa.

One of the reasons I like WordPress is because it is easy to check the stats on the traffic your blog is getting. You can look at which entries got the most views that day and what links people are clicking on to get to your blog and so forth. Usually, my blog gets around 10 views a day, maybe 20 on the day that Scientiae comes out.

So I was a little surprised (and by surprised, I mean shocked beyond belief) when one day my blog had over 300 views. Several things happened at once. I commented on a post at A Blog Around the Clock over at Scienceblogs which then listed me one day on their daily blogroll (boy was I glad I had the Imposter Syndrome posts up by then and wasn’t stuck on Talk Like a Pirate Day), then I got a link from YoungFemaleScientist and then Scientiae came out and I got a link from Drugmonkey and–Holy traffic Batman! More links, more comments, more everything! I’ve been watching the stats and, I don’t mind telling you, getting a little nervous thinking, Oh shit, now I have to say something intelligent–there are people out there watching!

In thinking about how all of this happened, I realized that a major factor was that what I wrote struck a chord in a lot of people. People are commenting and saying thank you for writing these posts because they felt this way for a long time. This is immensely gratifying. Shouting* that you feel like an imposter is not easy and the only thing that makes it worthwhile is if it helps someone else. An increase in blog traffic is nice and all, but I find helping people to be a lot more satisfying.

A couple of interesting points have come up in the comments and on other blogs. One is that men suffer from imposter syndrome. This was mentioned in one of the papers I read, but the authors also thought that somehow imposter syndrome affected men differently than women. Not being a man, I really can’t speak to that, but it’s clear that there are men out there who are not nearly as confident in their abilities as they project.

Another interesting topic has been what mentors can do to stave off imposter syndrome in their charges. Bikemonkey mentioned it here, and Alethea also talks about it here. Bikemonkey asks, “A related question is what degree of confidence do you project as a PI and mentor?” then adds, “…in some senses the highly confident PI is not good for the imposter syndrome trainee.” Alethea on the other hand suggests, “…I am not sure that an unconfident PI such as myself, who lets the young women in her charge see the bumps and warts of handling it all – family, grants, travel, article submissions, is such a great example and will thereby bring new, liberated scientists into the coterie.” As a graduate student, I appreciate the sentiment. Certainly, as a student you don’t want to have the uneasy feeling that you are on a ship that is barely staying afloat. So, you do want your advisor to project some degree of confidence. On the other hand, having an advisor who is confident to the point of arrogance would definitely get those old imposter feelings bubbling. There’s a difference, though, between allowing your students to see the realities involved in being an academic scientist and telling your students you don’t think a grant will be funded because you are an idiot. Alethea, I’m sure, is talking about the former and I appreciate it when faculty allow me to see the complexities of academic life. It doesn’t make me want to be an academic scientist, but that’s not because I think I can’t handle all of that–it’s because I don’t want to.

Neurolover has this important piece of advice, “One piece of advise I’ve seen offered on how to counteract imposer syndrome is to be specific about praise with your trainees: not “great talk!”, but details about why the talk was good. Then, when the person starts going down the imposter syndrome path, they have factual information to draw on to counteract it.” To which I say, AMEN! This particular example struck a chord with me simply because I know for a fact (because I have done it myself) that people will say, “Good talk,” to a person even when they think it was a horrible talk (not to be two-faced, but to be polite). Generic words of praise are very easy to brush aside.

Not all that long ago, a student in my lab defended his thesis. It is customary for the advisor to introduce the student and often this introduction is full of praise for the student. In this case, my advisor spoke of specific things about this student that made him a good scientist and why exactly he was a joy to have as a student. Looking back at other thesis defenses in my lab, I remember that my advisor did much the same for everyone. And I thought, how sad that we have to wait until we have almost finished our careers as graduate students before we hear something like that. I have gone into my advisor’s office specifically requesting a peptalk because I am down in the dumps about my experiments and the best that I have heard him say is, “You have a good scientific mind.” Um, thanks, but what does that mean??? How do you know I have a good scientific mind? What about me makes you say that? I’m in here because my PCR has failed for the umpteenth time and I need a little bit more than, “You have a good scientific mind.”

When discussing with my labmates our advisor’s introduction to the defense, one of us wondered what Advisor would say at her defense and when we assured her that it would be something good she said (in a classic imposter syndrome moment), “Well, he has to say something nice then, doesn’t he?” Which emphasizes the need for students to hear praise throughout their careers and not just when the advisor, “has to say something nice.” Back when I was a tech, I had a mandatory once-yearly evaluation in which my boss was required to tell me what he thought I was doing well and what he thought I needed to improve upon. I’ve often thought the advisor/student relationship could benefit from the same system.

Ultimately, though, all the praise in the world won’t help if the person with imposter syndrome doesn’t see the reality of her (or his) worth. So, I think it is just as important for advisors (and friends and family) to watch for things like devaluing accomplishments. Don’t let a person get away with saying, “It was nothing.” Do not assume the person is just being modest. Tell them, “It was not nothing, it was very good work and you should be proud of yourself for doing it.” Perhaps they won’t believe you. But at least you have done what you could to counteract their false assumptions.

—————-

*Which is what blogging really is when you think about it. You’re saying something that the whole world can hear.

It was funny, except that it’s not

One of my labmates is interviewing for post-docs.  He just got back from an interview out east and we were asking him where else he was interviewing.  He said he might be interviewing at this one place but the PI just had a baby, so they’re going to do a phone interview first (presumably because she’s on leave or something).  In the lab was me and two other women.  One of us said, in a joking tone of voice, “Babies are gross.”  Then someone else said, “Yeah, you wouldn’t want to work for a woman,” again as a joke.  This kind of joking went on for awhile and culminated in one of my labmates saying, “Don’t go, you’ll come back with no testicles,” at which point, we all busted a gut laughing.  Because, it’s a completely ridiculous notion that the mere fact of working for a woman causes a man’s testicles to disappear.

The not funny part is that there are obviously people out there who actually think that way.  I mean, isn’t that what they mean when they say men feel emasculated when faced with [insert feminist concept here]?  So, some part of me says, “Hey you shouldn’t joke about things like that because there are people out there suffering because of that kind of thinking.”  On the other hand, I’m sorry, but it was funny.  None of us actually meant any of those things and it was more like we were making fun of that kind of thinking.  I hope this doesn’t make me a bad person.

Scene from a local post office

Backstory:  Innocent Junior Lab Member has been asked by Advisor to please send requested plasmids to Australia.  Advisor would do it but he is leaving town to go to the middle of nowhere Michigan where there is no internet so don’t email him.  Innocent Junior Lab Member prepares two plates of bacteria per Advisor’s instructions and prepares Quarantine Documentation the Australian Government now requires for biological samples.  Quarentine Documentation requires Official Departmental Letterhead which will not be relinquished to a mere graduate student without the Department Chairman’s permission.  Innocent Junior Lab Member receives permission from rather confused Department Chairman who says she could use as much letterhead as she liked and why the hell was she asking anyway?  Quarantine Documentation is put in an envelope and attached to a padded envelope (procured from the Advisor’s Office on the instructions of the Advisor and with the help of Jaded Senior Graduate Student who has no qualms about rummaging through Advisor’s cabinets and drawers) as per Australian Government specifications.  Innocent Junior Lab Member set off to the post office next door, fills out the customs declaration and steps up to the counter.

Post-woman 1:  You can’t have two envelopes taped together like that.

Innocent Junior Lab Member:  But, I need to have these documents in a separate envelope attached to the first envelope.

PW1:  But, there are gaps in between the two envelopes.  It’ll get caught up in the machinery.

IJLM:  Well, can’t you hand cancel it?

PW2:  You have to tape all of the edges so that nothing will catch.  You’ll either have to leave or buy some tape here to do it.

IJLM obediently buys the tape and tapes the whole thing except for the top of the envelope containing the Quarantine Documents and goes back to the counter.

PW1:  You’ll have to tape that top part, too.

IJLM:  I can’t tape the top part.  The Australian postal service says I have to leave that open so they can get the documents out.

PW1:  Look, the Australian postal service has their rules and we have ours and you can’t send it without the top of the envelope being taped.  Looks at customs declaration.  What’s in here anyway?  What’s a plasmid?

IJLM:  It’s DNA.

PW1:  DNA?  What?!  You mean like a virus????!!!

PW2 and PW3 look over in horror.

IJLM:  No, it’s not a virus, it’s bacteria.

Mayhem ensues.  PW1, PW2, PW3 are all now shouting.   IJLM starts backing toward the door.

PW1:  We have to call our supervisor!  You can’t just send this through the mail!

IJLM:  Well!  Okay, thank you for your help, I’ll just be going now!

PW2:  No!  You can’t leave!  Come back here!

IJLM makes a break for the door, goes back up to the lab and tells story to Jaded Senior Graduate Student who shakes her head, “Thank God you didn’t tell them it was E. coli.”  JSGS then suggests IJLM just leave it for Advisor to sort out when he gets back from the boonies.

That was yesterday.  Today, IJLM got a secretary from the office to weigh the envelope(s) and put postage on it and the offending package is being dropped in a mailbox (customs form attached) in a different part of town.  What are the odds that it will actually make it to Australia?  I’m thinking they’re not that good.  I seriously doubt you can just put an envelope with a customs declaration attached to it and “Quarantine Documents on the Reverse” written on it in a mailbox and expect it to get delivered.  Hopefully, the post office won’t freak out too badly.  It’ll be really hard for me to graduate if the lab is shut down due to wanton shipment of plates of harmless bacteria through the mail.

Evil SOB

One thing that happens constantly in labs that do molecular cloning is transforming bacteria, that is, making bacteria take up foreign DNA.  The way to do this is to first mix some DNA into a small amount of (transformation) competent bacteria (usually E. coli–a non-infectious lab strain; transformation competent bacteria have been treated with some chemicals beforehand) and let them sit on ice for 20-30 minutes.  Then, you “heat shock” for a little less than a minute by putting them at 42 degrees Celsius (107.6 degrees Fahrenheit) then back on ice.  This essentially freaks out the bacteria and they start taking random stuff inside the cells, including (hopefully) your DNA.  Then, you want to incubate them in a really nice, rich medium for 30 minutes to an hour to let them recover from their ordeal.

Enter the SOB.

The media that we use is called SOC.  Now, we have someone in the lab who makes our media and pours plates for us.  But, she can only do very simple things (take this packet, dissolve it in water, autoclave it) and SOC involves mixing several things and adjusting the pH.  Which means we are on our own for the SOC.  On top of that, SOC contains a large amount of glucose (sugar) which will break down if you autoclave it, so, you have to make it without the glucose, autoclave it, then wait for it to cool, then add glucose.  Before you add the glucose, the solution is known as SOB.  Which always gives me a little giggle.  I’m childish that way.

Wow, that was a long explanation for such a short punchline.

Anyway, I decided the undergrad needed to learn how to make SOC because, well, he’s an undergrad and he needs theis kinds of drudgery learning experience.  Unfortunately, once we put the stuff in the autoclave, he had to leave, so I’m left to finish it off myself.  This is really not how I thought this would end. *sigh*

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.