Abba on finding a rotation

Y'ALL.

Did you know that Abba wrote a song about finding a rotation?

Here, I changed it a little bit:

If you change your mind, I'm the first in line
Honey I'm still free
Take a chance on me
If you need me, let me know, gonna be around
If you've got no students left, if you're feeling down
If you're all alone when all the rotons have flown
Honey I'm still free
Take a chance on me
Gonna do my very best and it ain't no lie
If you put me to the test, if you let me try

Take a chance on me
Take a chance on me

I can do PCR, troubleshoot some westerns, as long as I'm working
Reading some papers, maybe just talking, get to know you better
'Cos you know I've got
So much that I wanna get done, when I dream about your R01
It's magic
You want to take your time, tell me to get in line
But I think you know
That I can't let go

If you change your mind, I'm the first in line
Honey I'm still free
Take a chance on me
If you need me, let me know, gonna be around
If you've got no students left, if you're feeling down
If you're all alone when all the rotons have flown
Honey I'm still free
Take a chance on me
Gonna do my very best and it ain't no lie
If you put me to the test, if you let me try

resolutions revisited

I finished my first rotation, I'm about to start my second, holy-crap-grad-school-is-everything-i-ever-imagined-and-a-million-times-better-and-a-million-times-harder, and it's only day two.

The least I can do is go back to see how I did on those resolutions. (At least the ones that are applicable.)


So here we go:
_Keep a paper notebook, but transcribe everything electronically at the end of each day.

Fail. I did not do this. I kept a paper notebook, but I didn't transcribe anything, and this predictably bit me in the ass about 500 times. New resolution: keep an electronic lab notebook. I am never underestimating the ability to ctrl+F anything ever again. I've been flirting with google sites right now, trying to figure out the best interface. Basically this also fuels my procrastination but hey, productive procrastination is my middle name.

_Apply for NSF GFRP my first year (and second, if applicable.)
_Apply for travel awards for conferences
_Write the methods as I do the experiment
_Outline the paper I 'want' to write, and do the experiments simultaneously
_Attend the Physiology course (or any other MBL course!) at Woods Hole
_Attend any course, really

N/A

_NO GCHAT 9-5 (ok 10-4)

Fail, but baby steps. It's hard to break habits. Still working on this one, and this is definitely carrying over. New resolution: Still no gchat.

_One (1) blog post a month on a paper I've read. (resurrecting journal club!)

Fail, and this one is getting dropped. Between class, studying for class, reading papers on random things, reading papers in my rotation, something has to give. This would be nice? But I'm not kidding myself. I would like to tend this blog more though. New resolution: One blog post a month, period. 

_Go to as many relevant/semi-relevant seminars as I can and no iphone! notes only!

I tried to do this over the summer, and I sort of did ok. This will be easy this year because two of my classes are seminars. Same resolution: NO IPHONE.

_No shit talking. about anyone or anything. No exceptions.

I'll give myself a C on this. Same resolution: Everything has a positive aspect that we can discuss with our peers! Except maybe over beers. Hey that rhymed!

_Be writing my thesis by the time I'm 30.
_Polite, prompt and short emails from now on. (Following the rule that if it can't be answered/explained in 3 sentences, pick up the damn phone.)

I'm not sure I did this, but this is a good one to keep.

_Work hard in rotations, so at least two labs want me to join.

Duh.

_ASK QUESTIONS IN SEMINARS.

WIN I did this one! and then felt absolutely terrible afterwards. So that was really fun. Same resolution: be a rockstar.


_And for gosh's sake rachael, PLEASE STUDY FOR EXAMS.

Yeah, I need to be doing homework on tetrad analysis. See you later, blog.

**

Hindsight is always 20/20, and I have this problem where I tend to have really lofty goals and then shitty follow through. I was thinking this morning how I really want to be a role model, for like, women in science or something similarly vague. And then I was thinking, jeez, self, you haven't even done anything yet.

New, final resolution: work really really hard, and be awesome. 

That should be easy to quantify.

i don't think anyone warned me about this...

At some point* when I mentioned that I wanted to go to graduate school someone may have casually said to me, "You need to have really thick skin."

*This of course is the joke, because one of the first things everyone said to me when I said, 'I'm thinking about grad school', was 'BETTER TOUGHEN UP.'

So, it's been two or so months of being in grad school, and man, my confidence is through the ROOF. 

Here's what happened first. About a month ago I went to a seminar of this guy that I was really excited about. I really liked his research, he was young-ish, small lab, etc. I asked a question in the seminar, which, go me. and then I went up to him afterwards to introduce myself. I did this, and I said that I would love to talk with him about a possible rotation in his lab. And he says, within five minutes of meeting me, "I'll have to check, but I'm not sure I have room for any graduate students." And then some other faculty came up to talk with him and I jetted out. 

It's funny to think about and admit this now, but I was devastated after that interaction. In no particular order, the thoughts that were going through my head were, "I shouldn't have asked a question, it was a stupid question," "How does he already know that I faked my way into grad school in the first place," "Seriously, I duped everyone to be here!" "Why doesn't he like meeeeeee?"

This is hilarious right? Because like, the answer is, he probably literally did not have room in his lab, and really just had to check to see if he could financially/project-ily handle another grad student in his lab. There's no way he could possibly know that I duped everyone to get into graduate school. Yet. 

I took this so personally for about four hours, because it's hard not to, no matter what people who are really secure of themselves say. I put a lot of thought and effort into my actions. It would almost be loathe if I didn't feel anything. Luckily logic wins out in the end (usually), and I can pick myself up, dust myself off, and try again. I also am so, so thankful for the scientific community. After moping around lab for a little bit, I quietly, sheepishly told one of the post docs what had happened, and she said that happened to her all the time. She said when she was looking for post doc positions, she would just get these outright rejections and finally one day went to her graduate adviser and said, 'Why do these people already hate me?" (Or some version of that.) And the answer of course, is they don't. It's the funding situation, it's the lab situation, it's a myriad of things, very little that have to do with you. 

Which is inexplicably how I am probably the most confident I have ever been in my life. Something just clunked into place (probably when I was crying alone in the dark) and I've realized that now, 25 years old, starting graduate school. Right now? I have nothing to lose, and everything to gain. 

**

The other weird thing that I'm encountering is that I never know how to address these people. I've been following this bizarre rule in my head that after three corrections/emails exchanged with them signing with a first name, I'll switch from "Dr. so and so" to the more casual "Hey you."

Unless if the first time it's very clear I've made them feel wildly uncomfortable while addressing them so formally. In that case thank goodness for recognizing social cues, and I switch right away. 

in the thick of it

In the middle of my first rotation, and here are some random things I'm thinking about. 

Good Candidates for GWAS studies: attractiveness to mosquitoes, lovers of exercise, people that are chronically late for things, neat vs. messy. Random common things that must have some reliance on random common variation. I think every time researchers enroll people into a GWAS study, they should have some questionnaire that they fill out with questions like, "Do you prefer sweet or salty things?" and "People that do CrossFit are crazy: Agree/Disagree"

Genetics in general: (This goes a little along with a book i'm reading.) How much faith should/do/would/will we put into our genomes? I had a PI that was a chronic runner/biker, ate healthy, and had incredibly high cholesterol. He always said the only sure way to lower it was to take drugs for it. The "can't fight city hall" approach to genetics I guess. 

Rotation things: How do you pick a project, a lab, and a mentor that's perfect for you? I am constantly marveling that I came into grad school with a very clear idea of what I wanted to do, and after one month that idea has completely changed. More on that later, I guess? Thank goodness for open minds. 

Here are a few things I'm reading:

--- Here is a Human Being: At the Dawn of Personal Genomics by Misha Angrist. --- It's a great honest, smart account of what the questions that we'll have to ask, and the issues that we'll have to face at (to borrow the phrase) the dawn of personal genomics. I love all the personalities of the people involved. Every field has it's egos. I'm barely halfway through, but it's fun to start thinking about where I fall on the spectrum of conservative to cavalier about my own genetic material. (I would currently classify myself as---naive to a fault on the subject of open access.)

--- Garfield, D., Haygood, R., Nielsen, W. J. and Wray, G. A. (2012), Population genetics of cis-regulatory sequences that operate during embryonic development in the sea urchin Strongylocentrotus purpuratus. Evolution & Development, 14: 152–167. doi: 10.1111/j.1525-142X.2012.00532.x  --- Well, number one, sea urchins. And okay I will secretly admit population genetics doesn't really get me going, usually. But it is a reminder of the amount you can do with 'big data', and what secrets that the genome reveals about itself. I'm really interested in new ways of analyzing and interpreting data we already have, and I think papers like this are great reminders of that. 

resolved

It's my last day of funemployment before I start my summer rotation, and I'm sitting at this amazing coffee shop at the edge of Durham, and I'm thinking now would be the perfect time to write my grad school resolutions.

So here it goes, in no particular order, and some are tangible, achievable goals, and others are more lofty, amorphous, general whims.

_Keep a paper notebook, but transcribe everything electronically at the end of each day.
_Apply for NSF GFRP my first year (and second, if applicable.)
_Apply for travel awards for conferences
_Write the methods as I do the experiment
_Outline the paper I 'want' to write, and do the experiments simultaneously
_Attend the Physiology course (or any other MBL course!) at Woods Hole
_Attend any course, really
_NO GCHAT 9-5 (ok 10-4)
_One (1) blog post a month on a paper I've read. (resurrecting journal club!)
_Go to as many relevant/semi-relevant seminars as I can and no iphone! notes only!
_No shit talking. about anyone or anything. No exceptions.
_Be writing my thesis by the time I'm 30.
_Polite, prompt and short emails from now on. (Following the rule that if it can't be answered/explained in 3 sentences, pick up the damn phone.)
_Work hard in rotations, so at least two labs want me to join.
_ASK QUESTIONS IN SEMINARS.
_And for gosh's sake rachael, PLEASE STUDY FOR EXAMS.

My biggest character flaw, (if I had to choose just one! I know, hard) is that I am sometimes (ok most of the time) slightly over-confident and can sometimes (ok most of the time) think that I know a little more than I actually do. I am working on that.

So if I had to pick one phrase to sum up my goals for grad school, it would be this:

Stay humble, stay curious, work hard, there is always an alternative hypothesis, and no goofing off on the internet.

I look forward to revisiting these goals in 5.7 +/- .7 years.

Should be fun.

grad school jitters

aka FREAK OUT.

I sent this email to my pops yesterday.

i'm starting to get nervous about starting my rotation. 

like, how do rotations work?? do they just give you a project? when am i supposed to start thinking for myself? how much am i supposed to talk with the PI? how much do i have to do on my own? am i going to have a harder time over the summer with L because it will be harder to work on weekends and things? 

POPS am I making the biggest mistake of my life?!?!?!?!??!?!?!?!

Apparently, I am starting a summer rotation and also having a panic attack. Luckily, I've got my pops.

He sent me back the most rocking awesome of all emails. 

Remember stay calm, there is absolutely no question that you can do this. Don’t forget that. What you’re really asking is whether you’re going to be a “famous” scientist, trust me, you can get a Ph.D. 

This is so on point. Because I think I am worried about not being good enough to be a PI, or writing a nature paper, or some other bullshit like that. But that's not what I'm here for, right now, at 25 years old. I'm here to learn to do good science and get a PhD. And I can do that. I'm good enough for that, right now. I got into the grad school I wanted, they wanted me. This is the right thing.

Pithy answers:
like, how do rotations work??
Random, they work how you want them to.

do they just give you a project?
Yes, typically they give you a grad student or postdoc to shadow

Oh, big help, pops.

when am i supposed to start thinking for myself?
Day 1, but the hardest part is to not be too annoying. I wouldn’t say be demure, but don’t be ashamed to ask questions, and get over whether they are stupid or not.

The word I think he's looking for is "modest". Got it.

how much am i supposed to talk with the PI?
Depends totally on whether you even see them. See how s/he interacts with the other students and use that as a gauge  Don’t be shy, it’s your relation with the PI that will dictate your degree. If you are comfortable I think that trumps everything else.

am i going to have a harder time over the summer with L because it will be harder to work on weekends and things? 

Nope, the best scientist I know, John Carbon was an 9-5 guy. It’s called efficiency. What you will miss are the endless hours of wasting time and schmoozing. You  might have to develop tricks to make yourself the most efficient. [Redacted] in my lab was master of that. She would get her reading done, when most people (today) would be texting and social mediating. Literally, she’d be living on the scope and have a little reading light to read papers while she was babysitting the scope.
Don’t worry about weekends and things- focus on being efficient-
[Redacted] works about 10-4 on average and she’s a great student, it’s really called working well and efficient and not to fall into the grad student trap of being there all the time. That is one of the biggest myths that is still perpetuated. That said, you do need to be thinking all the time and really probing deeply into the problem

Can I just pause for a second and point out that my dad calls it "social mediating"?  Gotta love that guy.

I'm starting my first rotation June 3rd. I won't go too detailed into why I chose to do a summer rotation, suffice it to say, it's getting my feet wet, and I am really excited about starting grad school. I'm really nervous. I've never been a grad student. I've been a technician for 4 years, and while I started out thinking very highly of myself and that this was a great preparation for grad school, I'm not that confident anymore. (A good thing, probably.) I'm nervous about getting to know new people, seeing how a new lab works, learning new techniques. (What if I have suddenly forgotten how to pipet!) I'm nervous, but it's the good kind of nervous. The kind of nervous that means you're really excited, that means you're on the right track. It's like learning to swim for the first time. Or riding a bike without training wheels. You're wobbly at first, you can put your feet down at any time to stop, but you can tell it's going to be a thrilling ride.


Any other PIs or grad students or post docs have good tips or tricks for first rotations? Is anyone else as freaked out as I am? So far I have decided that I am going to be modest, hardworking, inquisitive, and efficient. Oh and not annoying.

Controversy in science

Had this email exchange with my pops yesterday:

From: Pops
To: me
Subject: another controversy
You don’t want to be part of:

Indeed, he declared war on molecular biology, seeing it as evolutionary
biology’s Scylla. The Charybdis was the Modern Synthesis, which hedescribed as “the private domain of a quasi-scientific movement, whosecreted it away in a morass of petty scholasticism” [3].

From: me
To: Pops
Subject: Re: another controversy
'liberating biology from the Procrustean bed of dogma on which it has been cast for so long,'
I'm not sure what a 'Procrustean bed of dogma' is, but I'm pretty sure I don't want to be there.
me

 This was regarding this article: 

How the Microbial World Saved Evolution from the Scylla of Molecular Biology and the Charybdis of the Modern Synthesis

doi: 10.1128/​MMBR.00002-09

Microbiol. Mol. Biol. Rev. March 2009 vol. 73 no. 1 14-21

I'm really not sure if this type of article is the zenith or nadir of a scientific career, but I'm pretty sure I don't want to be on the receiving end of this article. 

**

Scientific controversies are really interesting to me. At one level, I think it's exciting to be at the cutting edge of a field where there is the chance to be controversial. At another level, it's probably really hard to fight against dogma. And then, everyone says "oh science isn't personal", yadda yadda yadda, but you know what? Sometimes I think that's a bunch of bull. Yeah it's not personal, but if you've put all your time and energy into developing an idea and someone publishes something against your idea, then of course it's personal. (Except it's not.. I dunno. It's a fine line. Work-life balance, and all that.)

My dad is in a cool controversy (from his perspective, because he thinks he's right) about...oh gosh I'll butcher it...number of proteins at the kinetochore? *ducks*. My PI has forever been defending GWAS in the GWAS vs candidate gene/sequencing camp. Somewhat recently there's been some controversy regarding the claims made by the ENCODE project. It's interesting because some of these are more or less just matters of semantics. Some are less about the real science, and more about competition for funding and publishing in high profile journals. Some are actually about the science. 

**

I really think my dad is one of my personal heroes, despite the fact that we didn't get along all throughout my middle and high school years. He said that his graduate adviser told him something along the lines of this:

You can disagree with a conclusion, with a method, with a whatever, but you can't argue with the data. Because it's all about the data. And nature doesn't lie.

Nature doesn't really do us that many favors though either, so, there's that. 

(I double-checked what pops's grad adviser actually said about the data vs conclusion thing, and got this email back:)

From: Pops
To: me
Subject: Re: hey what's that thing 

Yep, exactly. So if you’re writing a paper, you should cite the author’s data positively, rather than citing their conclusion in a negative way

It's a pretty good way to go about life too, if you think about it.