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.

Science goals: Hold on to this feeling.

I’ve been thinking a lot about what I want to get out of my scientific career, and what I want to bring to it. This can be summed up, I think into my “scientific goals”. And who doesn’t love a list?

I’m starting to keep a running list--and I’ll fill it with no-brainer things like “keep up with the literature”, and “write some awesome papers”, but also maybe more intangible/sound bite type things like, STAY CURIOUS!

Here’s my first goal as I embark on my graduate school (!!!!!!!!!!) career.

Hold on to this feeling.

Y’all, I cannot contain myself. I am so immensely excited for graduate school. I’ve picked my school, which I’m still keeping a little quiet about until they send me my official letter and I officially accept, and I’ll write more about choosing the school later, but suffice it to say, it was one of the easiest decisions I have ever made, and I am so confident that it is the write place scientifically for me, and I am so ready and excited, and am reading papers for people’s who’s lab’s I’m interested in working with...etc...

So, dear lab-girl, what should you be doing right now? Holding on to this feeling.

I’m reading more papers than I ever have before, which is great. I’m getting excited about people’s science, but I’m also learning how and why we read papers. (I wrote a blog post a while back on “how” to read a scientific paper, and while yeah, It is how I read them, I think you have to read a ton to really get it.)

While I was reading papers as preparation for grad interviews, I realized that there were a variety of reasons people read papers. A flavor for every mood, if you will. Sure, some of it is reading for the science but if you’re reading out of your field, it can be more about the types of experiments, the logic and the progression of the story. Gosh, while I was reading all these papers it really became about the story. Somewhere along the line, something just clicked into place, and I thought to myself, wow, this is why we read. I mean, it’s why we read books too--it’s the story, it’s the writing, it’s the craft, it’s the plot. It’s exactly the same for scientific papers. It’s the plot, the experiments, but it’s also the craft of writing. I’ve gotten to this really weird place in my life where I’m actually enjoying reading papers. (Thank goodness this happened right before I decide to go to grad school.)

And I just want to hold on to this feeling. I want to hold on to being really exciting about attending the university I’ve chosen to attend. I want to remember being excited about going to seminars from future colleagues and faculty members. I want to remember that this amazing feeling.

I want to hold on to this feeling when my experiments don’t work, when I’m trying to learn something new and it’s hard, when I’m frustrated with something I cannot control, when I do something lazy and I have to make up for it 10-fold later, I want to remember this feeling. This excitement, this zeal. Knowing that going to grad school was the easiest decision I’ve ever had to make. That I have never been happier in my life because of this.

This was a choice I made, and I did everything to get myself to this place. I worked really hard, so don’t lose this feeling.

One of my biggest fears is that I’ll get burned out. I’ve been a technician for three years, and I’ve seen a lot of disgruntled post-docs and frustrated grad students. I don’t want to be these people.

Eric Lander (famous scientist) did Reddit’s Ask Me Anything the other day, and someone asked him this:

As an advisor to the President, what is being done or do you think will be done to increase the attractiveness of students finishing PhD programs in science?

He gave the most badass reply ever:

We need to shorten the time for getting a PhD and for a first faculty job. Young people should get out into the scientific world early, when they have lots of fresh ideas. We should encourage grants to young scientists and should encourage them to take big risks. When you're taking big risks, science is amazingly fun.

So, goal numero uno in entering grad school. Hold on to this feeling. I want to forever be excited by what I’m doing. I want to love my projects, and to be excited about what other people in my field are doing. I’m excited to work hard as a grad student. I want to keep being excited about that well into my graduate career.

Pre-interview prep. And fashion!

My first interview is this coming week. It's a Thursday-Friday-Saturday one, where Thursday is like, dinner or something, Friday are all the interviews and stuff, and Saturday is something else. I don't know the exact details because I haven't received my itinerary yet.

I'm not an overly anxious person in general, but I am starting to get nervous.

I had this crazy dream last night that I received my itinerary, but it was blank. I wasn't interviewing with anyone. Then I realized that it wasn't blank, but all the names had been whited out, so I had to hold it against a window in order to see through the white out. So I do that, and I read the names, and none of them are people that I've requested or prepared for...and they're all MDs.

This is funny because I didn't *think* that I had anything against MDs, but apparently my subconscious dream self is really worried about them?

What am I doing to prep for my interviews you might ask? Here's what I'm doing.

1. Reading papers

My schools all asked me for a list of 10+ people that I'd be interested in talking with. I spent a fairly long time generating these lists, so I had a pretty good idea of the people whose research I was interested in and about a one line description of what they do.

I'm reading one paper (and preparing questions!) for about...five of the ten faculty that I chose. To be honest, this is about all I could manage. Nothing like slogging through a paper to figure out whether you're really interested in a topic or not...

It's sort of a hedging-your-bets kind of scenario. Reading papers takes a fair amount of time. I'm hoping I get the people I've prepared for, but when my final list comes, I'll focus on those people's research, and hopeful I'll have a small headstart with the papers that I've already read.

I had to push myself to read primary papers. For me, reviews are way easier to read and understand, but the more time I spent with them I found out that primary papers are easier (for me!) to find things to ask specific questions about. For one field and a PI that I'm really excited about, I read both. (I hope I get her.)

2. ...not mock interviewing

Other people are doing mock interviews, which is totally a good idea if want to do them. I chose not to...mostly because I've been a tech in a university for the past four years. I can talk about my science and my contributions to my projects at the drop of a hat. I've presented posters at international meetings. I've successfully ridden the elevator with faculty members of my department and not said anything too asinine. I spent a long time making the decision to go to grad school, so I can defend and articulate my motivations. I'm totally just going to wing it.

Clearly most of my preparing is reading papers, thinking up questions and...

3. ...agonizing about what to wear. 

Okay! I know! I hate that this is like almost as troubling to me as the science, but it is, okay? Let's not fight it. Let's deal with it.

Me and my labbies have been in a constant debate that goes something like this.

me: No one in lab/grad school dresses up.

everyone else: It doesn't matter, it's an interview. 

me: But I would feel like a complete moron pipetting in 'slacks' or 'business casual' whatever.

everyone else: It doesn't matter, it's an interview.

me: But that's not how it is in real life!

everyone else: ...

The point is, as much as I want to fight against it, everyone else interviewing is going to be in business casual, and if I'm the only one not, even if labs are casual and I know this, I'm going to be the one that looks bad.

The anxiety part is this: I've been a tech for the past four years and my clothes/personal style ranges pretty much on the 'slightly disheveled' end of casual so...there's that.

One of my favorite quotes ever is "Beware of any endeavor that requires new clothes," and I hear H.D. Thoreau on that because this is definitely an endeavor that requires new clothes and you best beware.

So I did it. I went to the mall and bought myself an outfit. A whole outfit. Everything fits, everything looks good. It's new, so I don't have to iron anything. And let me tell you, having a whole outfit ready to go for Friday has alleviated so much stress.

Because I don't need to be worrying about what I'm wearing. I want to be worrying about getting myself into grad school.

And looking really good doing that can't hurt.

Bad lab blogger!

Sorry for the web silence lately. I've been applying to grad schools and waiting to hear back from grad schools and I've been so wanting to write about the process but also I was kind of freaked out that if I didn't get in anywhere then why the heck would anyone want to read about what I thought about applying to grad schools...but I also realize that maybe that's not the point of this blog, or why I like writing, or science, or whatever, so web silence will end...soon.

I'll write about the whole process and my experiences with applying, and finding letter writers, and deciding what to focus on in my personal statement, but I'll start out right now saying this.

I got my first rejection yesterday. Berkeley. Which was not entirely unexpected for reasons I will go into later (I promise!), but here's the best thing to come out of it.

I was making coffee in the break room when my PI came in, and he asked me how I was doing, so I told him, "I got my first rejection yesterday."

His reaction?

"Get over it."

Which...was awesome. And exactly what I needed to hear. And exactly why I love academia, and why I know I'm so ready for grad school. I feigned surprise at his response, of course, and he replied, "What did you want me to say, go home and feel sorry for yourself? You know you're wanted other places, get over it."

He actually added one more expletive in there, but it seems slightly unnecessary here.

Because yeah, what am I going to do, wallow? Nope, gonna get over it.

(I received some less than nice responses, one from another tech on my floor, "Oh you probably just weren't good enough to get in." That's cool. I'm cool.)

But that's just, the way of the world, you know?

Emily Dickinson

My dad sent me this poem in an email today:

"Faith" is a fine invention
When Gentlemen can see
But Microscopes are prudent
In an Emergency

--Emily Dickinson




This needs so little commentary, but speaks so perfectly (and succinctly!) to how universal the themes of discovery and science are. And Emily Dickinson, how awesome is she?

Deciphering ENCODE

Phew, the internet is abuzz with the newest publication of Nature by the ENCODE Project Consortium.

I'm just starting to chew on it, but if you're interested at all in human genetics, a great place to start would be Ed Yong's post on it. It's about as comprehensive as the paper's themselves (there's a few). I'm getting into both of them right now, but Nature.com also has a super cool graphical interface to get you started.

I'm starting here.

(Ed Yong's post is a great place to start, because he's doing an awesome job keeping up with what other scientists are saying quite publicly about this work. Fun times--It helps that the authors make a pretty audacious statement that over 80% of the human genome, you know, does stuff. And that's ruffling a lot of feathers. Because other scientists maybe are taking it personally? I love science.)

Anatomy of asking a question

image credit

I started my first grad school class this week, and it looks to be a good one. Two lectures a week, a ton of reading, and an hour recitation where we discuss the papers we've read. We're graded on participation, which is pretty much my only incentive not to sit anonymously in the back of the room and doodle. The easiest way to participate in class, besides coming up with amazing insights into the material is to simply ask questions. (Or a question. Let's not get too carried away.)

All of us have had some form of the phrase "There's no such thing as a stupid question" drilled into our heads from a very young age. (Alt: "The only stupid question is the one not asked.") The problem is, in the circle of our peers, there in fact is such thing as a stupid question. But there also isn't. Ok, let's back up for a second. Is there such thing as a stupid question?

Answer: To the people that matter, no. 

If you have just heard something that you don't understand, and you need clarification to understand it, and you ask for clarification, clarification is given, then that was a perfectly acceptable use of a question. 

Caveat: To other people, (hereby known as jerks) yes, there is such thing as a stupid question.

I hesitate to even mention this here, because other people's opinions don't matter, yadda yadda yadda, except in what realm of the universe is this true? (Rhetorical question--and obviously not mine.)

I think we can all pull up some anecdotal evidence of being in a class where someone asks a question the most everyone else in the class already knows, and there's some form of eye-rolling (if you're lucky) or snickering (if you're not) from the back of the class. (My eye roll this week came from someone asking the definition of "-ploidy" in an upper level genetics class. But again, the person that asked the question got their answer, therefore, not a stupid question.) And like most unfortunate things, they are almost always hilarious except when they happen to us. 

Here's what happened to me yesterday.

I asked a question about primer binding specificity and the introduction of bias in the 4C technique of chromosome conformation capture. Follow up question how are they relating sequence read depth to frequency of what's actually happening in the cell. (If you're really interested, we were discussing this paper by Zuan et al.)

Two things went wrong. 

1) I tend to garble my words sometimes when I ask questions in public places like classes or seminar. I just get nervous or something, so instead of saying something calm and relatively straight forward, what came out of my mouth was more like, "Ermmm sequencing bias primers...." And then I sort of trail off expecting someone to finish my thought because right? You know? 

2) This know it all in the row behind me really nice girl sitting behind me because I don't arbitrarily judge people based on whether or not they are very rude immediately interrupts me (to be fair I had sort of trailed off, see above) to say that my question is just wrong because of the restriction digest sites and something else completely unrelated to my question. 

And then the conversation ended. 

Which brings me to the anatomy of asking a question. 

There are two parts to asking a question.

The first is actually asking your question.

Coming up with a question

This may seem kind of silly, but the first thing you need to do is to pay attention enough to know what's going on, so you can ask a question. 

If you've been doing that, congratulations! You're caffeinated! The next step is coming up with a question. This could be something as "simple" as you don't understand an axis label on a figure, or if you don't understand the way someone is using a word, or a technique, or why they chose those controls, etc. If you can do that, congratulations, you've been really paying attention. 

Finally, and this is where I always  get stuck. You have to actually ask your question. You can't just think about your question, you can't just second guess your question (also known as "questioning your question"--this is a very deep and unprofitable wormhole that can only lead to paralyzing insecurity--let's try to avoid this), you have to actually ask your question. If you're me, you will give yourself a pep talk that sounds like this: Okay rachael, deep breaths, slow your roll, enunciate, and make sure your words come out in the right order.

(Also if you are a normal person and have no problems asking questions, feel free to ignore all of this advice, and haha--I don't really need it either I'm just kidding around because who me? I'm not neurotic at all.)

If you get your question out, and for goodness sakes, don't tail off at the end like I do, and don't assume that other people know what you're talking about--also be clear and concise and there are no stupid questions but 90% of the time no one likes extraneous information in questions--it's not over yet.

I think this is what a lot of people forget, and this is definitely what I forgot in my class yesterday, the second part of asking a question is making sure that your question gets answered. 

I wish I could bold this and stress this so much, because I think while this isn't a problem for seasoned professor that Knows What They Are Talking About, I think it can be a problem for a student that Isn't So Sure About What They Are Asking Thus The Whole Reason For Why They Are Asking it. 

Making sure your question is answered!

The thing that you have to remember is that it's no ones job but your own to make sure your question gets answered. Your question is your baby. No one is going to advocate for it for you. There probably isn't anyone else in your class (unless you're lucky!--more on that later) looking out for you. So here's what you have to do.

You have to listen to the answer. Duh, but this is basic Respect 101 for the person you're asking. But it also can help you. If they misunderstood your question, now is the time to gently put them back on the right direction. In my opinion, you usually get one chance to do this, and you're allowed to do this out loud--it's for everyone's benefit, your own, as well as the audience and the person answering. 

If they still don't answer your question, (and even if they do, but not satisfactorily, or if they do and you have more exciting questions), form follow up questions! But write them down so you don't forget, and I would suggest waiting until after the talk/class in order to ask them. Unless no one else is asking questions, and yours seem like good ones. In which case, go for it. 

Yesterday I pretty much forgot the whole second part of asking a question. I didn't feel confident enough in my question to rephrase, or verbalize why the girl behind me's answer was insufficient and also not related to my question at all, and the TAs weren't about to defend my question either. That was all on me. And this I think is a flaw of classroom discussions. You have to remember that not everyone that sounds like they know what they're talking about actually knows what they're talking about.

Which begs the question (ha!) in the classroom/grad school setting, which is better, misplaced over-confidence, or paralyzing insecurity?

It's a trick question--you really shouldn't ever choose one or the other. The answer is both, and I think the point is to try to live (and ask questions) with an open a mind as possible. 

Last part of my story:

I actually went back to lab feeling kind of shitty about myself after this girl responded to my question so rudely. And I spend the next few hours feeling like maybe I can't hack grad school and why is everyone smarter than meeeeee? But then I (luckily!) saw a guy from class later that evening, and he said that they thought that girl totally missed my point in class, and he had some of the same questions too, and he had wanted to rudely respond to her in class, but then didn't want to be the dude that starts some crazy loud discussion in class. 

Moral of the story--Ask your questions. Advocate for your questions. There are jerks in life. Don't let the jerks keep you from asking questions. And stop calling people jerks. It's not nice. 

You know when...

...you figure something out, then you don't use it for a while, and then you have to completely relearn it?

This is me and Endnote. Every six months or so.

So after I figure out Endnote one more time, I'm totally posting a tutorial on here. Purely for my own use.

Abstract clouds

Hey--

So I'm sure you've all seen word clouds ala wordle, where it takes all the text from a word document or webpage and then uses word frequencies to generate a kind of infographic where you can see the most used words, the big ideas if you will. 

Check it--someone made an app that you can input an author, it pulls all their pubmed abstracts, and then you can input that into wordle. It's called pubmed2wordle.

I decided to look up some of the PIs on my floor, in case I'm ever in the elevator with one of them, I can have some talking points. 

For example, 

I will know to talk about microRNAs with this dude, or

microRNAs but specifically let-7 with this woman, and also, oh look she works on C. elegans and development.

I think can be a great resource if there's a visiting faculty giving a seminar, or you're trying to pick a lab to rotate in, or you just want to know a little bit more about someone's research without spending hours poring over papers, this might be the first place I go from now on for all those things.

And just to mix it up a little big, because contrary to popular belief I'm not only interested in microRNAs...

That's my dad. He works on yeast and kinetochores and chromatin and microtubules!

It also makes for an interesting discussion of how much information do we actually need to understand something. And is relying on a tool like this, is that being lazy or being efficient? Obviously, it will never become a substitute for reading papers, but it's a pretty neat tool regardless. 

Do you think you could find yourself using something like this? Could you see yourself directing a student to it?  

Revolution

I predict that within the next 10 years there is going to be a scientific revolution. And it's going to happen online.

Hear me out--(This is sort of like the time that I told my the dean of the med school that I thought that social media and online presence is going to start becoming an issue for faculty seeking tenure and grants. He may or may not now think I am a teenage moron, but I still go out of my way to say hi when I see him on campus.)

But here's the thing. Me, early-20's, bright-eyed and bushy-tailed, and all of my peers are online all the time.

And, as much as anyone would hate to admit, we're the future of science. Logic would follow then, that you would want to reach out to us. Grab our attention. Mold us into images of yourself.

I'm starting to look at grad schools and while that whole subject is deserving of a post of itself, here's what's really frustrating.

A lot of PIs don't update their websites regularly, and that's a problem. Sure I can find someone's most recent publications through PubMed, but what if I can't get to them because of access issues? (I know--this can also be turned into more of an open access discussion too.) One of the nicest lab's I've looked at, the PI had a list of publications and some of them had an asterisk at the beginning of certain citations, indicating that this paper had come from a graduate student in the lab. This is something that I think people need to, if they don't already, take note of. There are probably few better indicators of a productive and plentiful learning environment than if a lab is producing paper. Notice I said a lab. I've started to become wary of PIs that tend towards review papers, or ones where they're part of a larger collaboration and it's only them, and no one else from their lab. (Gosh I want to say something really mean here OHOKAY I'll just say it, those who can't do, review!!) (I'm also acutely aware of the fact that I know absolutely nothing about anything and may all instances of snark and judgment act karmicly against me in later life--there, I said it for you.)

It's all about the internet.

I'm painfully aware that I'm part of this generation-can't-I-just-look-it-up-on-wikipedia, and if I hear one more disgruntled post-doc telling me that when they were in grad school they had to walk to the library and request a journal, I'll write a blog entry about it, but this is the way it is. Let's not fight it, embrace it. It's so hard to grasp for people that didn't grow up with the internet that you can build substantial relationships and communities online. Yeah, the usual arguments of "impersonal" still exist, but more and more those arguments are vastly outweighed by the enormity of good things that come from the internet.

Take my most recent example of photobleaching. I photobleached my cells. I had one meaningful face to face conversation with someone about the fact that I was probably photobleaching my cells, and then I was depressed and went home and went on facebook, and this happened:

Edited for brevity, and in short, I got tons of comments from real live people, all with real live experiences, with their own labs or microscopy facilities. I learned about 'pseudo-live view' and about different types of fluorophores, all on facebook. facebook!. 

And here's the thing. I do know Wendy and Omar from real life, and hey uncle Ray!, and if I saw them at the grocery store I would definitely stop and say hello (if of course we weren't in different states), but my itty-bitty-in-the-grand-scheme-of-things-although-seemed-like-a-very-huge-deal-at-the-time photobleaching problem was not big enough that I would have thought to pick up the phone and call any one of these vastly-overqualified-to-be-answering-my-questions people. But facebook allowed them to do just that, on their own time. 

The internet is this amazingly powerful beast that I honestly predict is going to allow a lot more people's voices to be heard, scientifically and otherwise. Of course, we're going to have to learn to filter, but you know, you have to filter in real life too, it's not like the crazies only exist on the internet. 

But the advantages: an open access revolution, more transparency about authors on publications, PIs interacting with peers and students online and in real time? Scientific discourse over twitter? Tenure-seeking faculty might poo-poo this now, and half the people in my lab think I'm crazy for even having a blog, but these are really powerful things that the people in academia are going to start to realize are really important to my generation of budding scientists. 

We're young, we're excited. We like to think we're cool, but that's only because we think that being nerdy is cool. If academia can start having real online conversations outside of an ivory tower that I can watch, learn, and maybe even be a part of, well, you'll have my endorsement. Even if that endorsement is in the form of a tweet. And then a grad school application. 

Oh, and update your damn lab webpages more often. 

ETA: in retrospect, everyone in my lab thinks I'm crazy for having blog.

Monday problems

Check on cells or make coffee.
Check on cells or make coffee.

Sit paralyzed at desk wondering whether to check cells or make coffee?

Yep, it's Monday.

That awkward line between tech and student

The day has come. You're all set up to do an experiment. You've spent days preparing. All of your pipets have been lined up the night before. Tip boxes are full, waiting. Media is warm, gloves are out...and your PI walks by your bench and demands that you attend a seminar with him (or her.)

(Alternate universe: Your PI emails you the week before alerting you of the talk and you're really thankful because you didn't have that much to do that day anyway.)

EITHER WAY--you attend dutifully.

On the way to the seminar (in which you lead the way because Techs Know Everything including all the shortcuts between buildings), your PI reveals to you that the seminar speaker is a moron, has submitted a moronic paper to a moronic high profile journal, in which your PI is in the middle of reviewing. But of course he doesn't want to affect your view (yeah right) but instead wants your thoughts on the talk afterwards. (No pressure!)

Tech-PI relationships are a funny beast. It's a fine line between employer-employee (which it is at face value) and mentor-mentee (which it may evolve into). Each has it's own unique sets of issues. I'm in the lucky situation where my PI knows that this job is just a step in the direction of a career for me. He knows that I'm probably going to be leaving soon to go off to grad school in...something, or try to move up and out into a new position...sometime. When your PI knows that, and better yet, respects that--that's when you can start pushing the boundaries of employer-employee into mentor-mentee territory.

However, a big thing to keep in mind is: Cave Canem...ma.

source

Or, for those not well versed in Latin/English (Lat-glish?), beware of dogma.

I think a lot of scientific disagreements, the higher up you get on the ladder, tend to be fueled by competition and ego more than anything, while the differences are more or less just differences in dogma. But vastly different ways to look at problems are more or less what fuels scientific discoveries. I mean, someone has to be thinking outside of the box. I guess if you're the tech you just hope it's your PI.

It's a funny thing...and I'm having trouble writing it now because I'm trying to say it as delicately as possible, but keeping an open mind is the most important thing you can do in this situation. (Apart from staying awake during the actual seminar. Obviously that is priority numero uno.) At this very very very early stage in my career, the most important thing I can be doing is looking for places to think critically. Both of my PI and of his competitors. It's not always easy, and it's obviously very important to keep in mind who's grant you're being paid off of, but it's also really important to remember that thinking critically about something is not synonymous with criticizing it. And dogma and broad generalizations and effective public speakers get funded, because sometimes making things seem black and white is the best way to make sure your research gets noticed...but that's not I as a tech or a student, or whatever weird limbo position I'm in now as I'm starting to have my own ideas and taking ownership over my own research...that's not necessarily the position I want to be stuck in.

I wonder how other people in my position deal with this kind of thing. Thoughts?

Adventures in photobleaching

There are a couple of ways to act when you make a Really Big Mistake in lab.

1) Correct it, tell no one, and pretend it didn't happen. This method is preferable when you do something small and stupid. Like one time some sequencing results didn't look very good. And I realized that I had completely diluted my primers to the wrong concentration. Like, mMols off. This would be an okay mistake not to tell anyone else around you in lab, just as long as you fix it and make sure never to make that mistake again. (And also that no one else will be using your primer stocks.) (This also isn't exactly how it went for me because it took someone else pointing out that I had made a blaring error in my primer dilutions, so everyone knew about it in the end.)

2) Admit you made a mistake, ask for help, correct it, and then pretend it didn't happen (but never make that mistake again.) This method is especially useful when something big is going wrong, and you can't figure it out on your own. This is when you just have to suck it up that you'll look like an idiot for about 5 minutes while someone is explaining what you did wrong (or as I prefer to see it, what you weren't doing right!) but in the end it's all for the best because a) hopefully you learned something, and b) you won't make that mistake ever again. And it's a win-win! Because when you come across another poor soul who's made the same mistake as you, after you help them figure out what they weren't doing right, you can choose whether or not to admit to them that you too made the same mistake.

3) Ask for help, figure out that you were a complete idiot about something, and laugh uproariously about it. This might include just yelling PHOTOBLEACHING every 20 minutes or so for the rest of the evening after you figured your problem out. 


So this may or may not have happened to me today.


I will start off by saying that my lab does not do fluorescent microscopy. No one in my lab has fluorescent microscopy experience, and so we're looking at some fluorescence in our cells (just to check transfection levels) and using a scope in a lab downstairs that we've never really been formally trained on. The one caveat is that I come from a family of fluorescent microscopists--so this what follows is sort of unforgivable.

Here is what happened.

We walked downstairs with our little flasks of cells, and we put them under the microscope. We turned on the light, turned on the laser, made sure we were on the right filter, opened the shutter, and looked at our cells.

"Ooh!" My post doc says, "Pretty glowing cells!"

"Awesome," I say, "Let's put it on the screen!"

(I am clearly paraphrasing here.)

So, with the fluorescence still on, we manually switch the scope from eye to camera, we press "Live", and we wait for the picture to come up on the screen.

(If you're keeping tally of time blasting cells with fluorescence, we're now clocking in at 2 minutes.)

It takes another few seconds for the image to come up, then of course we have to refocus slightly for the image to be in focus for the camera.

Then we take a picture.

(Fluorescence still open, in case you were wondering.)

Then we hmmm and hawww and write down the settings we used so we use the same settings for all the other flasks.

Then we go get another flask.

I will skip the rest of the nitty gritty details, because the short of it is, we kept looking from eye to camera and back again, and since apparently neither my post doc nor I were feeling incredibly competent today, we kept forgetting to manually change the scope from eye to camera, all with the fluorescence on. 


And then we wondered aloud to each other, "Why are all of these flasks getting progressively dimmer?" And of course, being scientists, we say, let's get that first flask out that was really bright!

So we get the first flask out and everything is really dim.

In retrospect:

It didn't even occur to me that this was the problem until later I was talking about what I was doing to someone who actually knows how to do microscopy, and they were just like, You focused with the fluorescence ON?? My post doc still isn't quite convinced that this is the problem, but I think she just doesn't want to admit that it's the problem because it makes us look like complete idiots.

And me?

I am perfectly ok with looking like a complete idiot. Because, you know, how else would you learn? (By actually listening carefully to what people tell you to do so you never make mistakes? Where's the fun in that?)

And for the rest of the evening, yes, I have yelled PHOTOBLEACHING aloud at odd intervals. Because, arrrghhh.....PHOTOBLEACHING!

Incomplete

I love doing homework, reading a problem, knowing exactly where and what in your notes you need to look up, (in this case multiple hypothesis testing) and then seeing this:

Dear god what was I thinking! I clearly was there, I remember the lecture, I obviously knew that multiple hypothesis testing was important, I even underlined it. But what! What about multiple hypothesis testing?

With each question, so many more questions. (<--which ironically is sort of what multiple hypothesis testing is. Or so I would imagine.)

Thank goodness my prof posts his lectures online.