An incredible transformation.

Exactly one year ago today, I had brain surgery.

I was reminded of this fact when I woke up this morning with this achy feeling all over - it's like when a morphine drip runs out and you've just had surgery. I remember the morphine drip. The crazy thing is I still have morphine in my medicine cabinet. Now that I think of it, I have a cornucopia of pharmaceuticals that I was given after I left the hospital. But frankly, the morphine is no good because it was accidently doused in grapefruit juice and is now mostly stuck to a kleenex. Last year when I was still taking morphine, I woke up one morning - I had the grapefruit juice in one hand and the morphine container in the other. Before I knew it, there was morphine in the juice, juice in the morphine container, juice and morphine mixed up and on the bathroom counter. At the time, I thought kleenex was a good option.

It's weird to think of it because so much has changed in a year. I mean, it's unbelievable. I think for me this summer was really good for my career. At least that's what everyone tells me. Who knows, right? It's an up and down ride.

Right now, I feel pretty good about me and the possibility of an academic career. Dr.PureEnergy is really making an effort to mentor me into a t-t position. After we get some really cool next gen data, we'll write a grant together for NSF on which I'll be a coPI. Lately my scientific work is getting some recognition, and best of all I'm incredibly focused and have managed to get manuscripts out the door. Sweet damn.

For HippieHusband, things are definitely better, but he's still in a bit of a holding pattern. It's been about a month since we've arrived in YummyLargeCity and he's had 3 in-person interviews: 2 postdocs and 1 biotech company. His hippieness has been replaced by the millionaire playboy look (not Hefner style). And let me tell you he looks hot in a suit and tie - so I'm hoping for the biotech company. Hot damn.
I recognize that things are impermanent - so I don't plan on getting too comfortable.

But at the same time, I plan on enjoying a few things. Did I mention how incredibly hot HippieHusband looks in a suit and tie?

Moving forward to someplace different

I've been invited by the folks at LabSpaces to join their social scientific blogging community. The new digs are here.

The old house will stay standing for those who want to peruse the archives. I hope you will join me in my new home.

Schadenfreude

Not all buddhist, but then today I feel like a bitch. But I love it when poetic justice happens in real life. HAAAHAA!!

Good news

Back at the end of Feb, I applied for a small grant to fund some collaborative research on the biochemistry of food production by the MightyGreenMonster. I thought was a long shot, but I got it!!!

Second bit of good news: The Harper government has finally fallen in a non confidence vote!

I wish I had US citizenship.

For those minority postdocs and early career tt who are US citizens or permanent residents, apply for this award.

If I could I totally would apply.

I have faced this problem over and over again. As a scientist from an underrepresented minority, I would love to apply for the different postdoctoral fellowships and awards aimed at me. But because I am not a US citizen or a permanent resident, I'm not eligible. Unfortunately there is nothing like the Ford Fellowship, or FASEB (Federal American Societies of Experimental Biology) awards in Canada. As far as I'm aware no federal Canadian organizations offer this kind of support to its minority scientists. And with Stephen Harper I'm not holding my breath that NSERC or CIHR will have the money to do this. NSERC canned the University Faculty Awards designed to increase the representation and retention of women in academic tt positions. The last awards were given in 2008. I know someone who was lucky enough to get one of these. Timing is everything.

So those of you who can, take advantage of this support while it still exists! Here's the description of the award.

Advanced postdocs or new assistant professors who belong to underrepresented minorities and have "demonstrated research productivity" are invited to apply for one of the 6 Postdoctoral Professional Development and Enrichment Awards presented annually by the Federation of American Societies for Experimental Biology (FASEB). Each winner receives $3000 in unrestricted career development funds plus $2500 in travel funds.

Applicants must be US citizens or permanent residents and members of one of the FASEB constituent societies. The deadline is May 31. Application information is here.

Women in Biology - is it worth it?

Just yesterday, I had a friend send me an email about a three-day symposia for women, in the biological sciences. It's for those who are at a critical transition period, ie PhD to postdoc and postdoc to tenure-track. This is considered a critical period because it's where the pipeline of women from graduate training into leadership positions in academia springs a leak.

Recently, Ceci and Williams (2011 PNAS), suggested that the evidence for discrimination against women in hiring and peer review (Wenneras and Wold 1997) was weak and is not the reason why in math-intensive fields only 8.8 to 15.8% of tenure-track positions at the top 100 US universities are held by women. Instead, they argue that the primary factor in the under-representation of women in STEM fields is preference and choice - freely made and/or constrained by societal influences. It's a well written article and worth the read. And there are some interesting and debatable points. But that's a different post. I bring it up here because if "self-selection" out of the academic track is the issue, then providing a support system might be the answer.

Funded by NSF's ADVANCE program, the conference, called WEBS (Women Evolving Biological Science) is "aimed at addressing the retention of female scientists and issues related to the transition of women from early career stages to tenure track positions and leadership roles in academic and research settings."

For 30 lucky women in ecology and evolution, the symposia provide the following :

Concrete skills and take-home tips for addressing a range of issues from navigating the tenure track, designing a research program and managing time to establishing and maintaining successful mentoring relationships and balancing career progression and life responsibility.

Opportunities to build a peer network and potential mentoring relationships with senior scientists.

Exposure to the range of potential paths and success stories of women in the biological sciences.

The application process approximates an application process for a tenure-track position, requiring a one-page statement from the applicant describing how attending will help her achieve any long and short term goals, a one page statement explaining research and teaching interests, online questionnaire, CV, and two letters of recommendation. The deadline is April 15 2011.

All of this would take an incredible amount of time. So my questions to you folks are: Do you think its worth the time and effort? And if so, what would I really get out of this event?

I'd appreciate the weigh in.

how not to get pubs

When I first started thinking about my long-term goals, I realized that I needed some advice. So I emailed a friend and assistant prof, SeriouslyProductive at TheDarndestUniversity. Here is the original advice she gave me about writing. This advice helped me get Postdoc manuscript #1 (Killmenow) to a place where it could be submitted to Dr.Add'EmUp and one senior collaborator.

What is the status of this fully written manuscript? This saga is not worth going over again. Suffice to say, I think that this may be of the reasons why this lab has had trouble getting external funding. The manuscript is on hold until Dr.Add'EmUp sorts out things on his end. I can't tell you how frustrated I am about what seems like an indefinite holding pattern. How did I find myself here? I finished the manuscript back in January but now I have to sit on it! For a postdoc this is death.

When I think about it, I should have known better and listened to my gut about SmallUniversity. The lab I went to do Postdoc#1 was not super productive. In fact, when I got there I found out that it took Dr.Add'EmUp two years to get his first empirical paper out. That should have been a red flag.

Okay, stop crying over stupid spilled milk chiquita. If I want a fighting chance at a tenure track position, I need pubs. Early in January, I joined a postdoc writing group in YummyLargeCity and it has been super helpful. First thing we did, is write out all the "open loops" or projects/manuscripts that were still lurking in the deep recesses of our computers. Open loops are any project that lead to a manuscript. This included collaborations where you weren't the first author as well as any grant applications that would eventually lead to manuscripts.

I had 8 open loops but I'm only presenting a few here:


Scale represents my interest in the project, where 10=totally juiced and 0=can't stand it get me far far away. From this table, we picked the projects closest to being done and each week set small goals that could facilitate the completion of the manuscript.

Although KillMeNow looks like the one I should be pushing given the pain and saga surrounding it, I've written it off for the moment. What emerged as the project to work on was StillHangingOn and the surprise for me, SmallButAvailable. StillHangingOn is the third of four manuscripts from my PhD. So its an obvious priority. SmallButAvailable is this little experiment I ran in my first postdoc at SmallUniversity that got some cool results. All the data is collected so really, I just need to chip away at it.

Each week, we meet and set small tasks and then we're accountable to the group for the previous weeks' tasks. If there is a series of weeks where the same tasks don't get done, then there is an intervention. The intervention is to help the individual figure out why the tasks aren't getting done. For some, it's a matter of interest in the project. For others, it's simply just stuckage in terms of what to do. And that's where the group dynamic really helps. Because we come from various backgrounds we can prod each other with questions, excite, and inspire the lifeless and difficult projects.

Plus, don't knock the need to be a "disgruntled postdoc" in a group of seriously "disgruntled postdocs", who bitch about the full throttle stupidity of our supervisors and the system.

Is this a scam?

Today I received this email:

Dear GirlPostdoc,

Sometimes ago you were contacted by my colleague, who offer you the possibility to publish your thesis/dissertation in the form of a printed book.

He asked for your permission to send you further information about our services and the publication process.

Unfortunately, he has not received a feedback from you after sending out an e-mail with the detailed information.

I was just wondering whether his email got lost or if you took it as an unsolicited email and deleted it. LAP takes pride in publishing academic books in a wide variety of topics. Specialist books are usually no best-sellers, but our business concept allows us to publish academic works (or any other works) in a variety of niche topics, that is why we contacted you as well.

Perhaps more importantly, having a book published is a major professional asset to the author. More often than not, it can open up career opportunities and lead to new contacts and/or invitations to lectures or conferences.

It would be highly appreciated if you could confirm or disclaim your further interest in publishing your book project with us.

Looking forward to hearing back from you at your earliest convenience.
Thank you very much!

Best regards,
Kevin Woodmann
Acquisition Editor
LAP LAMBERT Academic Publishing GmbH & Co. KG

I don't believe it for a second. But then I read this. What do you people think? Anyone else had this weird email? Suggestions as to what I should do?

The "training" in postdoc

Well I've been mainly absent from this blog site because I was trying to prepare a grant, deal with manuscript revisions, complete the analysis for another manuscript, get my samples ready to submit for next gen transcriptomics, and deal with all the shit that life loves to throw at us.

The grant was really taking up major chunks of time. It was a relatively small one (not an NIH or NSF) but still I couldn't believe how frickin' hard it was to write. Luckily my supervisor, Dr.PhotonEnergy (new name still haven't found the right one) is really good at grant writing. Thank god, cuz frankly right now, I suck.

I'm learning and now I realize that for me this is the training in postdoc that all the blogger PIs rant about. Some of the most interesting lessons from this first small bout of grant writing include:

1. Know your audience. Who are the most likely peeps on the committee?

2. Know the grant program and its focus. Really establish how what you want to do fits into the guidelines of the grant. You need to make it interesting to

3. What's the big picture?

4. How does the work you want to do fit into this big picture.

5. Understand realistic short term goals given the amount of the grant. Define the specific objectives and then describe how you will test this question or objective. Think about time, funding and what is available in the lab!

6. Narrow the focus of the question.

7. The first paragraph is the most important one - it's the selling point. If you convince them that you are truly a good fit - they will read the grant more carefully.

8. Start early. Have a first draft at least 1 week before the deadline.

9. Avoid words like "understand" and "discover" - apparently this implies you don't really know what you are testing. And the passive voice is the voice of death.

10. Trust your own ideas and voice. I realized that I spent a lot of time trying to assimilate what others thought (ie leaning on what others wrote) and not enough time, exploring the logic of my own ideas.


Drugmonkey over at Scientopia has a wealth of information on grantwriting for NIH. But frankly reading about how to write a grant is nothing like having to do it yourself.

It's going to be time to put on the 'big kid meatpants' soon - Dr.PE wants me to submit an NSF next year as a co-PI. Let's just say, I have a long road to get there and I'm sure it will be filled with big and small potholes.

Swampage

Sorry folks, I've been swamped. No time to write posts - spending my time on manuscripts. I have been working away on the analysis for my third PhD manuscript and writing a review paper. At some point I'll finish that post on this really cool plant genetics paper. But for now, it will sporadic.

Is everyone this busy?

Small acts of kindness.

I'm feeling much better today - you could even say more hopeful. In part because of everyone's suggestions. And because I had the courage to stand up for myself and have a frank discussion with my PI, who I still believe, is awesome. She was totally on board with my request.

And in part because this morning at 7am, I was standing at the register of a coffee shop near where I live, waiting and wating for the barista to give me change for the bus. But clearly it was too early for him because he was moving so slow. And of course, what happens? I watch as my bus drives right by. I expressed my frustration out loud to the barista and told him not to worry about the change but to just give me a coffee. A young woman standing in line witnessed the whole thing. As I'm adding cream to my coffee, the next thing I hear is this:

"Hey, I saw that you missed your bus," she said.

"Yeah. Sucks." I'm so darn eloquent at 7am in the morning.

"Where are you headed?"

"Up to the university."

"Oh I can take you in my car," she replied.

"What? Oh my god, how kind of you," I said incredibly shocked.

It's amazing what a little generosity can do. It didn't hurt that she thought I was an undergrad.

Yeah, there is fuckage, but there are also many small acts of kindness.

When chocolate doesn't work.

I have been feeling like shit over the last week. All work-related. I'm feeling continually screwed by academia and acdemics. I'm hoping this will pass.


What do you do to make yourself feel better? Chocolate normally works, but it didn't this time.

Famous sayings...

It takes an asshole to scare you out of your stupid ass head space.

Riding the bus

Riding the bus has made me lose hope that an equitable American society is possible.

I think it must be the slow accumulation of "I can't believe what I'm hearing."

I recently attended a conference where I had this same feeling. Three people were having a conversation (two female faculty and 1 male), but a second male faculty came up and joined the conversation. As soon as he joined the conversation, both males turned their bodies away from the two female scientists and proceeded to ignore the women. They made no eye contact. In fact, the conversation itself was subtly nuanced with language that was sexist. One might brush it off as just shooting the shit at a conference, but if you listened to how and what was being said, it became imminently clear that their words devalued the presence and contribution of the women standing near them. The surprising (or maybe not so surprising) part of this was that these two men were young faculty - probably in their 30s.

So yesterday, when I got back home, I sank into the couch, poured myself a glass of wine and came to the realization I just needed to accept it. It's not like I didn't intellectually understand this, but I don't think I emotionally understood the consequences to my long-term career. I guess naively, I still believed at some level things would change by the time I got there.

Intrinsic biases just aren't going away. They just aren't. And frankly they just aren't going to change fast enough to make a difference in my lifetime, my daughter's lifetime and perhaps even my granddaughter's lifetime.

I am, needless to say, quite depressed about this.

What it takes to be a scientist.

Web of Stories • EO Wilson • What it takes to be a scientist

The one.

Okay peeps, I know that many of you are lurkers at this website (according to the visits from the sitemeter stats). But I want you to come out of your closet and tell me what scientific classical text do you think that every young academic should read? It can be a book, an article, essay, book chapter etc. And I don't want to limit this to biology. Just include the discipline of science when you name the text! You don't have to give your name, just comment anonymously if you're too shy.

Idiotic pissants.

So I'm working on a manuscript from my postdoc at SmallUniversity in SmallTown. And to do the analysis I used a specific kind of sequence analysis software, which is not free and comes with a very expensive license that can only be used on the computer it was installed on. Dr.Add'EmUp told me to take the laptop he had bought for me and return it when I was done. Great! And I submitted a draft version of the manuscript to him a week ago. Great again.

Once he gives me feedback (which I'm waiting for) I should be able to get revisions done and resubmit the paper to him, right?

Well, that would be the sane universe. The logical and rational one.

But SmallUniversity in SmallTown isn't a rational or sane place, instead, it's a place run by shortsighted bully goats. And that's being generous.

It turns out that the administrative morons (read TheGodfather or TheBully) via his lapdog have decided that I need to return the computer ASAP, like Monday.

I get that it is university property but isn't it bought with the intention to produce manuscripts. And my plan was to send the computer back, once the manuscript is in press.

Inevitably, there will be revisions (both from Dr.Add'EmUp and reviewers) and some of it might entail redoing or doing alternative analyses using this software. You tell me, how does one do revisions on a manuscript without the appropriate software?

I understand that it is university property and under normal circumstances, it would probably be fine if there was someone else in his lab who could use the software. But there isn't. He has an undergrad who has never performed a PCR and a lab technician, who is just learning. Neither have a biology degree. (Let's not go to that happy place of mine.)

Although Dr.Add'EmUp clearly said in his email he thought it was entirely counterproductive, he also said he didn't think we'd get any sympathy. So clearly he's not going to argue the case.

Right now I'm fuming mad. It's simply stupid to have to learn and completely redo all of the analyses on a different set of software when we're this close to having a manuscript submitted. Fuck it. If Dr.Add'EmUp or a reviewer asks about additional analyses, Dr.Add'EmUp is going to get a nasty hand drawn sequence alignment, with a cartoon bubble, saying, "You have the tools, good luck."

Frankly, I thank my lucky stars, for my current supervisor and lab. It's so nice to be in a place where intelligence, competency, and sanity reign supreme.

To share or not to share?

Over at Academic Jungle, GMP has a controversial post on sharing code. A scientist requested some code that was used in a published manuscript. She says this in her post,

"I actually replied politely, thanking him/her for the interest and stating that regrettably I cannot share the code. My group develops detailed microscopic simulations of certain physical phenomena. These codes can have wonderful predictive power and take years to develop. Sharing the codes is absolutely not the norm in my field, and there is no way in hell I would share any of my research codes with anyone other than close collaborators and colleagues.

Now most of the responses from commenters are in complete disagreement with GMP and I want to add I believe that it is utterly wrong to deny any request of published data to anyone, if the science is publicly funded.

But before jumping on GMP and calling this "despicable behavior," I think it's important to delve a little more into this issue.

GMP would not be first researcher who has refused to share. According to Heather Piwowar at Research Remix, almost 40% of scientists are not willing to release data. Why? It could be as in the case of GMP, an outright refusal, or because researchers are "not able to retrieve the data."

How many of you who are now well past your graduate work could provide data from a paper in your postdoc or PhD?

I have experienced this problem when I wrote to request data from someone who completed their PhD in the early 90s . The person responded by saying they didn't have a copy of it anymore, but that they could send summary tables from their dissertation. I wanted the original data because I felt that the analysis used at the time was incorrect and sending me the summary tables simply recapitulates the analysis.

GMP's post indirectly raises the issue of do we share data?

First, I define data to include but not limited to cell lines, evolved critters, genetic data, morphological measurements, images, maps, character matrices, seeds, and maybe (with some qualifications), computer code.

I am firmly in the camp of yes, we share data. If it's published, its not yours anymore. (Not that I really think it ever was...but that's another blogpost.)

In an editorial written in the journal Evolution, Rausher et al. (2010) outline the reasons for data sharing. As they highlight, much of our progress in understanding the natural world depends on building upon previously collected data. But too often that original data (not summary stats) is lost because the researcher just moved too many times or technology advances such that the data irretrievable. Who remembers floppy discs or zip discs? I have stuff that I can't access on a floppy and not that it matters, but in 10-20 years when whatever we're using now, becomes useless, how will anyone be able to access that data? An online database would preserve our scientific history.

Researchers typically refuse to share data for many reasons, probably top among these reasons is that they want to publish more papers and/or they want exclusive use of the data. But let's say decades later, after the faculty member retires, a young upstart researcher wants to conduct a meta-analyses on original data. A common data repository would make this young person's life a lot easier. And as Piwowar states in her slideshow called Research into Open Research Data, not sharing data is hurting mainly the young. She cites a survey of doctoral students and postdocs, saying that 28-50% report a negative impact from data withholding on progress, discovery and the quality of education.

Rausher et al. (2010) also suggest that data that is archived and available is more likely to be useful and to be cited more by other scientists. We only have to look to GenBank to see that this repository has afforded many different researchers a chance to use data collected by others to ask very different questions.

A final reason that we should share our scientific data is accountability. Data that is made accessible means that it can be checked for errors. Good data means good science and progress. According to Piwowar, more than half of all papers contain errors, but only 5-10% contain errors that change conclusions. Sigh of relief.

Recently, several journal editors within the ecology and evolution subdiscipline of biology came together to form DRYAD.

"Dryad is an international online repository of data underlying peer-reviewed articles in the basic and applied biosciences. Dryad enables scientists to validate published findings, explore new analysis methodologies, repurpose data for research questions unanticipated by the original authors, and perform synthetic studies. Dryad is governed by a consortium of journals that collaboratively promote data archiving and ensure the sustainability of the repository."

Already journals like The American Naturalist (American Society of Naturalists), Evolution (Society for the Study of Evolution), Molecular Ecology, Journal of Evolutionary Biology (European Society for Evolutionary Biology) have become interim partners with Dryad. These journals will be introducing a new data-archiving policy which will state that as a condition for publication, data used in the paper should be archived into an appropriate public database. The policy does, however, allow for an embargo period after publication and for longer periods of restriction at the discretion of the editor.

So what about computer code?

Unfortunately, Dryad is not set up to accept computer code. My programming friends tell me that the main reason coding geeks are reluctant to share code is the licensing problem. Freely available code means that anyone can take your code and use it to make a commercial program that they could then sell for cash. A second reason, I'm told is that computer code is dynamic and changing unlike data that is collected. For computer nerds, it's important that code change and evolve because that makes it better. And really in my field when I think about it, this is true. But, some of that evolution comes because the code is made public. Feedback from the user is essential to finding the bugs or problems with a given code.

In a recent article to Nature, Nick Barnes, a software computer engineer suggests that turning raw data into published papers requires a little programming, meaning that scientists write software. And he argues that yes, it isn't very good because of poor commenting, weird variable names and a lack of indentation. But it works. And if it works it should be made accessible.

But I would ask, all of it? Some of my R code is just a one-off and it isn't really necessary that I archive it. I do, however, have code that is associated with a particular dataset and could be useful to future users. And I would like to deposit my code somewhere and ensure that it was associated with that particular dataset.

Luckily for us in biology, things are improving, we have places where we can access shared code. Often the code is located in websites run by researchers but this means that it is essentially anywhere in the web. What is needed is a single resource where users can find and share code. Well, a new place called The Molecular Ecologist, associated with the journal Molecular Ecology Resources will provide a blog that highlights important papers in the field; list computer programs and other code (e.g. R packages) useful for analyzing genetic data; and a site to discuss methods.

I know it's a lot of work getting your "data" ready for submission - there's the formatting, the organizing, and the worry about mistakes being found or the data being misinterpreted.

But in the end, I feel better for having submitted data to a public repository. After all that blood, sweat and tears, I don't really want my hard work to end up in a black hole.



Photo taken from Website: Astronomy Picture of the Day

Other Sources: Rausher MD, McPeek MA, Moore AJ, Rieseberg L, Whitlock MC. 2010. Data archiving. Evolution. 64-3: 603-604.

What is the purpose of a university?

Okay, thanks to those of you for your words of encouragement.

It's in the making. In the meantime, I suggest that you follow Nat Blair's lead and refresh your memories by reading these posts.

Or you could just chew on this quote from Alfred North Whitehead,

"The tragedy of the world is that those who are imaginative have but slight experience, and those who are experienced have feeble imaginations. Fools act on imagination without knowledge; pendants act on knowledge without imagination. The task of the university is to weld together imagination and experience."

Maladroit?

Went to a party this past week - had lots of different sorts: profs, postdocs, biotech folks, artists, etc. It was tons of fun.

The most amusing conversation was with a prof that I met, who knew Asperger's, my co-supervisor during my PhD. Like so many academics, although brilliant at his work, this faculty member was more than deficient when it came to social etiquette and just plain social interaction. It made me wonder if there was some form of antagonistic pleiotropy at work on these two traits. Selection for academic brilliance, reduces the ability to understand and follow social etiquette.

Dr.Bobblehead never looked directly at me or HippieHusband when he was talking with us. Even when he was talking with his wife. Instead, he would look at the wall or up at the ceiling or side to side, like he's scared or freaked out that he's engaged in a a non-scientific conversation. And when you ask him questions, the best he can muster is either "Yes" or "No" even if they're not yes or no questions. Unless of course he's talking about his science.

When I mentioned where I did my PhD and with whom (because they always ask), he said,
"Asperger's is a nut. He's so maladroit at social interaction."

I had a really hard time containing myself.

Kettle meet pot. Pot meet kettle.