So Cath really just wanted to brag

So this monday, I'm minding my own business at the lab, studiously working away to try and find out where on my gene of interest a particular insert has been inserted.  The organization that inserted the exon (Fly trap - which makes freaking awesome tool for us!) has the information in one format, but our database (FlyBase - slow, but rocks and is run by volunteers) does not have it. This makes it difficult to compare where the insertion is relative to others IF you're a newbie to reading DNA like me  - leave me alone, I do more cell biology and was not trained as a molecular biologist or anything close as an undergrad.!!!!!

I was struggling to figure out what I needed when I  tweeted a request for FlyTrap and FlyBase to better communicate, which led to a reply from Cath:

I thought, Cath was just sending me an innocent reminder (though she did neglect to wish me a happy birthday, should've been my first clue!).  However, upon checking out the standings, I realize that she just wanted to be able to gloat about how well she did last week. Top point earner of the week AND edged past me for third place.   Not much has changed other than Ricardipus is now tied with Bob for 3rd. Hopefully I will not forget to change my picks again and will actually have a hope of kicking Cath back behind me again.

Lies, lies and more lies

I vaguely remember promising to (1) post more often since I've been saved from hell and (2) to do the hockey pool update this week.  Hahahahahahahahahahahaha!!!!

yeah right. I'm a PhD candidate with a bun in the oven and a 4 yr old running around! What was I thinking! Actually, I'm busy analyzing all that confusing clear data. I've come up with a funky theory to explain what could be going on except for the crucial piece of data that I need to support said theory is not of the clear and convincing variety...URGH science...

Anyways, I'm up for lab meeting this week, and am trying to get a story put together so the hockey update will happen after said meeting, but since I had a crappy week, do we really care if its a bit late? Nope :) 

Data oh Data what are you telling me

Last year I spent a considerable amount of time writing up a mock grant. It had to contain all the thing a real grant would contain, objectives, rationales, specific aims, hypotheses etc. It was a challenge, but won that really helped me to learn more about my subject area and more about what could or could not go wrong. Painful as it was, I did learn something from it. The last few months (since my comps), when I wasn't suffering from nausea, pregnancy induced sleepiness, or crazyness I have been tackling those specific aims. Much to my PI's delight, I have very clear and convincing data. My images are beautiful.  Except the data isn't showing me what I predicted. Yeah, yeah I know cry me river! Hear me out thought

Based on in vitro vertebrate data, I hypothesized I would see a particular phenomenon, in vivo, in my invertebrate model.  (We should all know that I work on the most amazing and wonderful mode organism, the venerable Drosophila melanogaster.) Thing is, I'm clearly not seeing the phenomenon seen in vertebrates.  So WTF is going on!!!

I know I shouldn't complain I should be happy on multiple fronts. The main thing I should be happy about is that  the data is clear and convincing AND more importantly my PI happily accepts clear and convincing data, regardless of whether or not its what she wanted to see.   This is huge, because I have worked for the PI that just had me redesign and redesign the experiment to get the result he wanted. Not. Cool.

Secondly, my treatment is having an effect - I do something to protein X and I get a phenotype. My phenotype is very clear and unique to my protein of interest.  The question is, what is the mechanism of the phenotype? What is the function of X, such that its loss is causing A?  We / I though it was due to a mechanism hypothesized to occur in vertebrates, based on similarity of our proteins and the structures they are involved in. But as I just said that is not happening.  Which means I have to come up with a new theory....which is painful and hard for me. Luckily, I don't have to do it right away. I want to confirm that the phenomenon does not occur by doing some additional controls. These will not take alot of time and will confirm that the phenomenon does not occur vs my assay not being sensitive enough to detect the phenomenon.  No, I'm not beating a dead horse. The mechanism I am looking at is a signalling pathway and I've only looked one step down. There might not be enough of a change to detect, so I'm going to look further down the pathway to be sure that there really is no change.

I shouldn't say I've been in data hell. Since its good, clear data. But something is going on with my Filezilla **such that its downloading files off the server at extremely slow rates (30Kb/s vs its normal >150Kb/s). Considering I have image files near 1G each, its been a frustrating few days. Slow and frustrating because it takes forever for me to get a file, but only about 10 minutes to analyze it. 

But I guess I get lots of time to think about what is going on.....

and PhysioProf, if you're reading this dont freaking tell this is what science is.  Just. don't.

***if anyone knows what could be going on with the Filezilla please let me know.

Importance of Communicating with your PI

I have probably lost a ton of followers and readers over the last few months.  Which saddens me, but eh, what can you do when life gets in the way in of blogging. I still have to write an ode to my little monkey for his fourth birthday, but since I'm over a month late whats a few more days right?

So this post is to shine a light on the good PI's. Yes I know, its hard to believe they exist, with the blogosphere filled with tales of woe (justifiably so).   Heck, I originally started this blog because of the issues that I was having with my original PhD advisor. However, the stars deemed me lucky enough to land me in my current lab, with my current advisor that you are all sick of hearing how wonderful she is. 

Not to say that we haven't had our issues, for which a lack of communication was the core issue.  You would think that would've taught me a lesson but you know, I"m a slow learner :)

My goal for 2011 was to not sink and more importantly to not be feeling like I'm constantly struggling against sinking. I want to swim this year.  Being pregnant and not wanting to spend years getting this PhD, I need not swim. 

I was not swimming this past January. Mostly because the PI for whom I was TAing for was a completely unreasonable douchnozzle. S/he had extremely high expectations for the amount of work I was supposed to be doing, expected me to not only apply course content but to also help create it. I would speak to my PI about it periodically, who would rea-affirm that no SM you only work 12 hrs/week, no you only apply course content, would you like me to say something? Tell PI, you can not do x and y because I, your supervisor, need you to do z. Always supportive.  It didn't matter what my PI said, this person I was TAing for was a controlling bully that refused to understand that my priority is research and helping the students, not being his/her bitch.  At the end of January, I broke down in our lab office, to our Research Associate. I had been up since 3 am trying to figure out how I was going to get all my TA duties done and get enough data for a paper by the time Parasite decides to come out, while actually being a good mom and wife as opposed to the stressed out exhausted person I was. The DemandingPI was not listening to anything I was saying. The students were complaining to me and asking me to do something. It was just a bad situation.  One that I never openly talked to my PI about.

I didn't come in to the lab, the day after I broke down as we were going on a short family trip but I received an unexpected email from my PI. She told me to enjoy my weekend and relax.  WTF, why was she emailing this?  I may not always succeed, but I try my damnest to a mature, independent student. And I try to solve my problems on my own, which is always the smartest thing. Our amazing RA had recognized that I was being bullied by the other PI, that is was neither fair or healthy to be in the situation that I was. S/he also recognized that I wasn't going to ask my PI for help. So she did.

I don't know all the details, other than my PI was not impressed when she found out the details of what was happening. She got on the phone with our departmental advisor and with the PI I was TAing.  Found out what was happening, through various sources and made it clear that the treatment I was receiving was unacceptable.  She stood up for me. She protected me.  To say I feel like a weight as been lifted is an understatement.

I've since had a meeting with our Graduate Advisor to determine what I should've done, where I went wrong etc. It was great to have that meeting as s/he, very diplomatically, assured me that I wasn't crazy, that I did the right thing, and yes I was in the right.  I've been sorta vague on details but through the whole situation I was being made to feel like I was not in the right that I was supposed to be doing these duties etc.

My point is that had I actually openly talked to my PI earlier, I could've saved myself weeks of grieve. If it wasn't for our RA, I would probably still be struggling not to drown. Power differentials can wreak havoc on someones ability to stand up for themselves. The fear of financial are huge to grad students. I did not / do no want to be the "problem TA". I did not want to cause any waves that would make it hard for me to TA in the future. These fears, prevented me from standing up for what was right. Thankfully I have a PI and RA who saw this and stood up for me.  I am also thankful because I don't think my PI is unique in doing what she did. For all their faults, both my MSc and my original PhD supervisor would've gone to bat for their students.

Now that I"m getting closer to a strong swimming stroke in lab and life, hopefully I'll be back posting more regularlys.

Small Acts of Kindness - Thank you

I'm inspired by  Canadian GirlPostdoc to thank the anonymous skiers who were so wonderfully kind to me yesterday.

I've been having a rough time this semester as I'm TAing for the PI from Hell. S/he is very passionate about teaching undergrads, really really wants them to do well and expects me to care and be as excited about the class as s/he is. I've TA'd this course previously, but s/he has changed the content in hopes of it being more relevant. My biggest issue is that she is a control freak who asks for my opinion but then disregards whatever s/he doesn't agree with and gets visibly angry if I express disagreement. And S/he dictates exactly what I must do, to the point of getting angry if I deviate even slightly to help the students. Its frustrating and demeaning.  It is rude and disrespectful to micro manage me and to treat me as if I have no experience or intelligence.


But whatever, I'm away this weekend on yet another ski trip. We're not at are usual 8+ drive away to the amazing family resort we usually go to but to the closer, large touristy mountain. I expected large crowds with people being annoyed at monkey and me for being so slow. I was wrong. I was in the mountaintop food purchasing line up. It was just monkey and my prego self. The poor little guy was tired and hungry from the morning adventures and was basically only capable of holding his gloves and following little instructions like go get the chocolate milk you want to drink.  So I was holding his helmet, jacket, my goggles, toque and wearing all my gear (so I"m HOT!!!), while also holding our tray of food, when I noticed he had dropped one of his gloves in the line up behind us. It was so crowded behind us and I"m no longer able to easily maneuver  that I just said we would have to go look for it after. I tried looking all on the ground to see if I could find it but I couldn't. While this is happening, so random boarder/skier noticed, went back found the glove and gave it to me.  Thank you!

All day, individuals helped me as they saw me struggle to keep monkey engaged, carrying all the gear. Keeping an eye for monkey's gloves, asking if I needed help. I did not expect this at this mountain. It was refreshing.

Shocking but true - lavaland is still kicking everyones ass

are we really that surprised? Ricardipus must be picking the linemates of her her picks, as he's holding perfectly parallel just below.  Bob & GertyZ are slowing down, as am I. I guess we actually have to do things other than follow all the hockey stats, eh? That is a joke.  I shouldn't be too sad, I'm sitting at 10 points for this 2 game week.  Lets see if the player updates next week play havoc with anyones teams. I know they totes nailed me last time.

Hey Pot did you know you're black?

Yep thats me trying to be funny or witty or something.  You know the old saying, its like the pot calling the kettle black? When you tell someone do not something or tell someone they're being unrealistic, even though you are exactly the same? My BFF are kinda like that and when one of us got a bit preachy about the other shouldn't be so hard on themselves, they're expectations are to high blah blah we would look at each and laugh. Or point at ourselves, say "kettle" and then at the other and say "pot".  I'm having that moment.

You see this is where Mxx will laugh at me and say, honey do you not remember you're own advice to me on that post you linked to? Hahahahaha!!!!!

This semester is turning out to be a bit of a bitch. Right now is the first time since probably before christmas where I am sitting down and sorting out thoughts. Its been go go go go. Partly because I'm TAing for the most control freak, incredibly demanding of my time PIs.  S/he wants me to attend every lecture despite the fact its a class I have TA'd before, expects me to meet with s/he at least 1x/week, mark >40 assignment / week and assist with developing the mid-term and homework questions. Since all that would take more than my 12hrs/week I am assigned, I have refused to help develop questions. Plus why the fuck should I? S/he's been teaching for over 2 decades, they shouldn't need my help.  The freaking class sucks up 2.5 days of my 5 day work week. 0.5 day is suck up with lab meeting and whick really leaves me with 1.5 days to get data for the the first aim of my thesis collect before the parasite pops out.

Yeah I'm freaking out just a bit. It doens't help that things at home are busy, only because last year was such a cluster fuck of a year that I'm totally behind on home organizational shit. You know that little things like makings sure all the important papers are filed away in a manner that makes putting out taxes together in a month easy. Getting our personal finances back on track. As in actually tracking where are money is being spent so that I can figure out how to squeeze out another $1000/month for daycare in a year.


Oh and apparently we're supposed to be getting our kitchen renovated so that we aren't paying for heat that is going out the windows that don't shut properly and that we actually have space to put all our dishes etc. 

Did I mention that monkey now has after school and weekend activities? I swear I don't sit down till I got to bed, which is usually by 9:30 because I can't fucking stay awake. It also means I'm waking up at 5am freaking out about the shit I didn't read / prep / clean the night before.

Did you also know that monkey turned 4, over 2 weeks ago and I have yet to write my yearly letter to him???!!!! I should've done that now, but I needed to vent. I'm sure my baby will understand.