What if?

What would doing research be like if I didn’t have to worry about whether or not I was ever going to graduate?

What would it be like to be in a lab and know, if it all went pear-shaped, I could quit without losing everything I had worked for the last 8 years?

Would a string of experimental failures be as crushing as it once was if I was actually sane and had a good support system?


Hello?  Anyone out there?  It’s been so long since I’ve posted anything at all here, that I’m not sure anyone is paying attention.  Actually, it’s been so long since I had anything to do with this blog and the email address that is associated with it that I had trouble logging into both accounts and had to prove to Google and WordPress that, yes, indeed, I am the owner of these accounts that have been dormant for so long.

It would be difficult to tell you everything that has happened in the past couple of years in one post and I’m not sure it would be particularly helpful or interesting.  The short answer is that I’ve been staying home with my daughter, Monkey, volunteering in certain places, teaching some at home science classes, and trying to figure out what to do with my life when/if Monkey starts preschool.  I will want/need to re-enter the workforce at that point but the question is, what sort of work will I do?  What do I want to do?

Among other things, I’ve been considering looking for a lab job.  Not a post-doc, some sort of senior technician/lab manager sort of job.  Something 9-5 with benefits.  Does such a thing even exist for people with a PhD?  I dunno.  Do I really want to go back to that life?  I dunno.  Although, I’m starting to realize that, in fact, it wouldn’t be going back to the kind of life I experienced in grad school.  The stakes are different and not nearly as high.  And, frankly, I care less about what people think of me and my intelligence.  I’m not sure when that happened or why.  I suppose graduating helped me with that, in a way.  It’s not like top tier schools hand out PhDs like candy, I must possess a fair amount of intelligence and tenacity or I wouldn’t have graduated.  What I forgot while I was there was that I always had that intelligence and tenacity or I never would have gotten in the program in the first place.

So, what would research be like without the constant pressure to prove myself, the overwhelming loneliness and desire to just finish already so I can get on with my life?  Maybe it would still suck.  But, maybe, it might be interesting or even fun.  It might be worth trying to find out.

Equipment failure

I have been writing my thesis on my old imac desktop (the kind with the dome base, a stem, and a flat screen). I never turn it off, but the power went out in the apt. very briefly yesterday and so the computer was abruptly turned off.  In protest, it now will not turn back on.  This happened once before a few months ago when I accidentally turned off the switch that went to the outlet that the power strip was plugged into.  What worked in that instance was plugging the computer into a different spot on the power strip.  No such luck this time.  I even tried plugging it directly into the wall, sans power strip, but it stubbornly remains off.

In case you were wondering, I did back up my thesis onto a usb drive.  But, I hadn’t backed up my most recent, very detailed outline of the lit review chapter.  I’ve got an old version of it on a portable hard drive, but I will have to reconstruct some of it.  For awhile, I thought I was going to have to do more than that because I couldn’t get my laptop to recognize my usb drive or the portable hard drive causing me to panic and dig through my sent email folder to get an email to my advisor that had an old draft attached to it (also, I have an old hard copy in a file drawer and was contemplating retyping Chapter 2 which is the only thing that I have written out at this point).  But, then I reset the PRAM on my computer (a trick I learned at the Apple Genius bar when I had this problem in the past) and, considering how this day was going, it miraculously worked.  Now I have a recent draft of Chapter 2 and an old version of my outline and I’m happy I didn’t have to break out the ativan to deal with this little crisis.

I’m worried, though.  The fact that my laptop frequently forgets it has usb ports does not fill me with confidence.  I’m taking the imac to the Genius bar tonight to see if the problem is the power cable.  If that’s the problem then, fine, we get a new cable and I go on using the imac.  If it isn’t, then we have to decide if it’s worth it to send the computer in to get fixed, whatever that would entail.  It’s an old computer, I’m not sure it would be worth it.


The bottom line is I might be looking at getting a new laptop.  That’s not an expense that we are really looking forward to, especially since it turns out that I will have to pay my tuition for the quarter I graduate in (right now, I’m on leave, so no tuition is being paid).  Tuition is $3800/qtr so it’s a significant expense.  And, I had wanted to go to the blogging conference but given all of these other expenses, it might not be feasible financially speaking.

So, it’s kind of been a bummer of a day so far.  Cross your fingers for me that the imac just needs a new power cord.

Also, thank God for backups!

Letting go

In the last couple of days, I have noticed that I’ve been a little in denial about the fact that I’m leaving the lab for good.  The first moment of realization came when I started cleaning out my shelf in the -20 freezer.  I had kept every cut plasmid and purified insert that I had used for cloning over my entire graduate career (because, yes, I did sometimes reuse them in other cloning projects).  I had also kept a large number of genomic DNA preps, diluted primers, vectors that had been linearized for integration into the genome and PCR products.  In all, I had around 12 boxes of this stuff.  And it was hard–really, really hard–to just throw it in the garbage can.  I kept thinking, “But, what if I need this?”

See, I’m a packrat.  A major packrat.  I have a very difficult time getting rid of things so it’s a good thing I’ve moved every 4 years or so because that forces me to purge my belongings.  Usually, all I have to do is consider the likelihood that I’ll use an item again and compare that to how much I really want to have to pack it in a box.  When my husband moved to California, it was even easier because I had to look at an item and decide if I really wanted to pay to ship it clear across the country.

In the case of lab, it should be even more cut and dried.  I’m leaving.  I’m not just leaving this lab, I’m leaving benchwork.  I am not ever planning on working in a lab again.  Therefore, I absolutely do not need any of this stuff.  Not a bit of it.  I had to keep telling myself that, though, while I threw out old plates and precultures from the cold room and cloning intermediates from the freezer and files in my desk.  I’d say, “But what if I need it?” and then wonder under what circumstances in my post-lab life I could possibly need the manual from a Qiagen miniprep kit.  I still can’t force myself to throw out my NEB catalog, though.  That thing has been my companion and reference book for so long, it would be like throwing away a part of myself.  And who knows, maybe one day I’ll be making dinner and I will suddenly really want to know if you can do a double digest with BamHI and HindIII.  Granted, this seems highly unlikely, but you never know.  I just can’t part with it.  Maybe after a year or so of being out of the lab I will be able to throw it out.

The thing of it is that, including the years I spent as a tech, I’ve spent about the last 12 years of my life working at a lab bench.  And, while I’m still certain I do not want to do a post-doc, leaving the lab bench has me feeling a little scared and a lot sad.  Don’t get me wrong.  I am overjoyed at the fact that when I go on vacation I will no longer have to ask someone to look after my yeast plates as well as my pet.  I am thrilled beyond measure that I will never again need to do a ritual dance around the PCR machine or have such bad lab karma that I get my grandmother to send me a bottle of holy water which I then proceed to wipe down my bench with because it’s either that or sit in a corner and cry.  I will never again stomp into lab and shout, “For the love of Qiagen, why can’t people clean up after themselves when they spill a culture in the shaking incubator?  Why???”

But there are plenty of things that I will miss, too.  I’ll miss going to see a really good seminar and then coming back to the lab to discuss it.  I’ll miss being in the lab when someone finally, finally gets the result she’s been waiting for and she runs through the lab screaming, “I did it!  I did it!” while waving a picture of a western blot.  I’ll miss being the person waving a picture of a western blot.

And so, I imagine that when I wipe down my lab bench for the very last time, there will be a few tears shed.

And as one the lab cried from the very depths of their souls: OH NOES!!!!!!1!!!!!!11!!!!!!

A new edict has come down from On High (that is, the Advisor).  From now on, complete sequences of every plasmid that is in our papers will be submitted as supplemental material.  Which means we need to have complete, annotated sequence files for every plasmid.

Advisor told me this little tidbit of news when I went in to see him with a few sample paragraphs of my Materials and Methods section which describes plasmid and strain construction.  Advisor had previously told me that he likes a very detailed M and M section.  So, I wanted to know if I had achieved the right amount of detail.  He told me that what I had would be fine because of this new rule had had just devised.  He further went on to tell me that this should not be much of an issue for me since he knows I have been making these sequence files all along, so I’ll just gather them up and if I email them to him he will convert them into genbank format.  He was not being sarcastic, the man honestly believes that I have annotated sequence files for every plasmid I have ever created (there are 62 of them, not that all of them will be in the paper only maybe a quarter of them).  I do have sequence files for most if not all.  But they are not annotated.  And if they are it’s in an obscure shorthand only understandable by me.

I casually mentioned this to a couple people in the lab and there were immediate cries of dismay.  And then I politely suggested to Advisor that he send an email detailing this exceptionally brilliant new planof his so people could start planning ahead.  Also, that I wasn’t going to spread the news because I didn’t want people to shoot the messenger.

Dedication or Stupidity?

It is the week of Christmas.

The weather has turned seven shades of ridiculous.

The boss is out of town for the week.

My entire lab is here working (except for, you know, the boss).

And, just on a personal level, my husband is in town and I still don’t have all of my Christmas shopping done.

What the hell are we doing here?



So, my advisor already made CPP’s suggestion of doing all of the figures and figure legends first.  However, after spending hours of time moving images miniscule distances to the right or left and changing the font on the figures several times, I had to accept that I was procrastinating.  So, I thought I should start writing the text of the Results.  I still have a couple of figure legends I could write, though.  Maybe I should do that.  Especially since all I’ve really done is change forms of procrastination.

I’m not even thinking about the introduction.  There is no introduction in my fantasy world.  Panic does not even come close to describing how I feel about the introduction.  I’m just going to get through the results first.



I’ve got the sleeping pills.  They helped me get to sleep, but I didn’t stay asleep for the first couple of nights I took it.   Then, I started sleeping through the night and needing to sleep through half of the day, too.


No sleeping pills = no sleep, tired all the time

+ sleeping pills = lots of sleep, sleepy all the time

Not sure this is an improvement.  I think I’m going to try a different sleeping pill and see if that’s any better.



If someone could make my super simple subcloning work right, I’d appreciate it.  I really don’t understand what the problem is.   Cut fragment out of vector 1, ligate into vector 2, transform, miniprep.  But, then I do a digest to check if it’s right and the digest comes out all wrong.  On all of them.  This is the second time I done this damn cloning.  If I have to do it a third time, I’m going to be wicked pissed.

Drip guilt trip

I think I’ve said before that I don’t want to do a post-doc, don’t want to do research at all once I finish my PhD.

I guess this makes me a drip (from the leaky pipeline of women in science).

Thing is, sometimes I get the feeling that research isn’t so bad and things are bound to get better after grad school. Everyone says that the end of grad school is a miserable experience. So, then I start thinking that maybe I could handle a job at a small liberal arts place with a small research program. But part of what makes me think I should try this is guilt.

I feel guilty for being a drip.

This is ridiculous, I know, but I feel like I’m letting down womankind by leaving research. How are we supposed to get more women in the upper echelons of science if we all just keep leaving? It makes me feel like I’m part of the problem. I should suck it up and stay.

But, I get the feeling that I would be miserable.

First, because I hate the failure associated with research. A large portion of what I do fails on a daily basis with no real explanation for why. That used to depress the hell out of me, but I think I’ve developed a thicker skin over the years and now it’s just frustrating.

Second, because I want to have children. Now. I just don’t think that being pregnant and giving birth would be conducive to getting a lot of research done as a post-doc. And, I’m 34 years old; I can’t afford to wait until I finish my post-doc, get a faculty position, and get tenure in order to have children. I know that doing all of those things is hard work, requiring long hours, and I don’t want to miss half of my children’s childhoods because I am always at work. And then, there’s childcare to think of. It’s damn expensive. Could we afford it? I mean, being a post-doc doesn’t pay all that much.

Third, because I see how hard it is to get a faculty position in the first place. Do I really want to go through a post-doc or two only to become a drip out of the pipeline because I can’t find a faculty position? And, let’s say I do find a faculty position. Would it be at a place where my husband could get a job? He’s an astrophysicist and has no interest in becoming faculty. That means he needs to be at a place with a large enough program that they hire staff scientists or at a NASA research facility. Those are few and far between.

Fourth, because I have lots of interests outside of science and I want time to pursue them. These days, I get up in the morning, eat breakfast and go to lab, come home late at night, eat a small supper and go to bed. I’ve been trying to leave weekends partially free so I can do things like laundry. This leaves little time to do simple things like read a book or knit a sweater or, well, just about anything (including spending time with my future children). I want free time, I guess I’m saying. I want a couple hours in the evening that I can do whatever the hell I want. I grew up seeing my parents work ridiculous hours just so we could survive and I thought if I got an education I would not have to do that. But, I guess I overshot on the education front because it seems that now I have so much education I’m expected to work a ridiculous number of hours, not so that I can make enough money to feed and clothe my family but for the fun of it.

So, when I look at all of those reasons, logically I know that I am making the right choice for me.

But, I still feel guilty.

Moving forward

So, my experiment has gotten to a place where, while not ideal, is manageable and I can get some data from it so I’m moving forward.  I should be ecstatic about it, but instead, I feel as if I failed somehow.  I cannot get the thing working at its former glory and I’m not sure I’d ever be able to no matter how long I worked at it.  So, there really isn’t any option except to move forward with what I have.

I guess, I feel like I’m putting something out there that is subpar.  Logically, I know that’s not the case.  The data is good and the conclusions are sound.  But, the pictures are not pretty because the staining is not pretty.  I may never publish another paper again, depending on my ultimate career path, and I want it to be the best that it can be.  I don’t want to show crappy pictures, I want to show beautiful ones.  But, crappy pictures is all I’ve got and all I’m ever going to get and frankly if I can’t make this experiment look more beautiful then nobody can.

But I just can’t be happy about it.

Impostor Syndrome sighting

The most popular posts on this blog have been the ones I did on impostor syndrome. When I wrote them, I never thought they would be so popular, would be linked to by so many different sources or that they would lead to an interview. I wrote them because impostor syndrome was something that I was dealing with at that time and I thought I might not be alone in that.

Impostor syndrome, for those who might not know, is the feeling that you are a fraud, that, despite any evidence to the contrary, you feel as though you have somehow fooled everyone into thinking that you are smart and competent when in fact you are anything but. I bring it up today because I recently had a meeting with a tenured professor here at my school and she said something that reminded me of those posts.

When I first came to grad school, I was funded on a training grant. The meeting I mentioned above was with the co-director of the training grant (something they do in an effort to keep track of all former trainees). At the meeting, Professor X asked me if I had any ideas on improving the training grant program. I suggested that the students could benefit from more peer-to-peer mentoring because most students (at least in my program) don’t believe that the faculty remember what it was like to be a student and therefore don’t take advice from them about how to be a good student as seriously as they take advice from other students. Professor X’s response was that faculty remember that it was miserable (!) and then she said that it doesn’t necessarily get better as faculty. It really sucks when a grant is rejected, she said, and then, “you start thinking ‘Am I phony? Have I been fooling everyone into thinking I’m a good scientist when I’m not?'” It was classic impostor syndrome-speak.

And as I sat there across from this obviously intelligent, successful woman, I was reminded that everyone has self-doubt. That it is possible to be successful and still doubt whether you are good enough. It made me feel a little bit better about where I am in dealing with my own impostor syndrome issues.

A plea

Dear yeasties,

We’ve had a pretty good relationship over the years.  So, why are you being so stubborn these days?  In particular, why have you decided to build a cell wall that cannot be permeablized with lyticase and beta-mercaptoethanol (but only when you are in a particular growth media)?  This behavior is really unacceptable and it is actually going to get me into trouble with my committee.  I was supposed to have my penultimate committee meeting this month and because I can’t get the IF pictures and subsequent quantitation (because of your little cell wall issues), I’m not going to be able to have it.

I am especially puzzled because everything was fine between us before and only in recent weeks have you had these cell wall issues.  Perhaps you are angry about the whole killing you for science thing.  Perhaps you think I will stop killing yeast if I can’t get you to behave.  I assure you that is not the case.  I will keep trouble-shooting this experiment, killing millions of yeast in the process, until it works.  This is not a threat, dear yeast, just reality.  But, if you cooperate with me, then your death will not be in vain.  I will be able to get information that will be useful to scientists all over the world and I will put your picture in a nice journal, maybe JCB or even better.  Won’t that be better than dying a silent, unnoticed-by-everyone-except-me-and-my-advisor  death?

Perhaps you are foiling this experiment because you realize that I will not be able to leave if I don’t have it and you don’t want me to go.  I appreciate the sentiment, dear yeast, and we’ve had some good times over the years, but I really need to finish and graduate.  And it is not like you will be lonely–far from it!  There are many people in the lab who will still be doing experiments with you long after I leave.  And they will all being trying to make you famous, just like I am.  I promise.

So please, please, please, dear yeast, let me go.  Lower your wall and let the antibodies inside so that I can take beautiful pictures of you and write the paper and my thesis and go to California and live with my husband and make babies.


Mrs Whatsit

Search terms

Sometimes, a search engine term shows up in my stats that I feel I should address.  Today, it’s this:

ypd media does it ever go bad

No.  Well, it does get contaminated (if it’s cloudy, it looks contaminated).  Then, you need to get rid of it.  But, in general, I have used media that is a few years old and the cells grew fine (I was desperate and I found some that belonged to some former student).  Beyond that, I suppose I couldn’t say, but usually people use their media within a year or so of making it.  If you don’t, then you are likely making too much at once which I wouldn’t recommend because of the risk of it becoming contaminated before you get around to using it.

At least, that’s what I assume you mean when you ask if it goes bad.  If you are talking about how it gets darker after autoclaving, then I would say that is normal–it’s just the sugar carmelizing.  If you leave it in the autoclave longer than a typical 20 minute cycle, it can get quite dark–almost black.  It’s still okay to use, though.

There, that’s my public service for today.