I Really Should Be Working...

...but this was just too funny not to share. A friend emailed me the following "conversation" which apparently took place between a Catholic church and a Presbyterian one via their church signs. LMAO!!!












Update: ScienceGirl clued me in to the fact that this was not real, but created using a church sign generator (thanks, ScienceGirl!). Kinda sad, because I found it much funnier when I thought it was real. :-(

Of Clocks And Decisions

One of the funniest incidents I remember from grad school was during my final thesis committee meeting, when my committee members and I were discussing when I should schedule my defense. We had already agreed on the remaining experiments I would do and I had told them how long I thought these experiments would take, when my committee chair (a.k.a. Bigshot PI) turned to me and asked, "Do you have any other clocks ticking?"

For the life of me, I couldn't think of any "clock" other than the proverbial biological clock, and I was stunned speechless that my chair would actually ask me something like that. I must've spent several seconds trying desperately to think of something to say before my PI helpfully piped up, "What he means is do you already have a postdoc with a specific start date set up?"

Oh...that clock.

Bigshot PI only looked a little confused by the long silence before I managed to choke out that I hadn't found a postdoc position yet. My PI, on the other hand, was by now turning red from the effort not to laugh out loud. Bastard!

Anyway, I remembered this incident because I've been thinking about clocks lately. Specifically, biological clocks. See, March Hare and I decided a long time ago that we weren't going to have kids. We love our niece and nephew and playing with our friends' kids, but that has never translated for us into a yearning to have our own. At the end of the day, we've always been perfectly content to hand the kids back over to their parents and return to our kid-free life.

Neither March Hare nor I have changed our minds about this in the 15 years we've been together. But strangely, when I tell other people I don't want to have kids, very often their response is to tell me about some friend or cousin who spent her entire life not wanting kids until the day she woke up with a completely different opinion on the matter. Interestingly, it's always other women, not men, who come up with these "someday you'll change your mind just like my friend did" stories.

I gotta tell ya, I'm extremely skeptical that these stories can be true. Yes, people do change their minds about important life decisions, but I have a really hard time believing that one's interest in having children can unexpectedly go from 0% to 100%. More to the point, I don't generally vacillate from one opinion to another, and I can't imagine any likely circumstance under which I would have so profound a change of opinion. Then again, some female PhDs and MDs whom I know personally to be rational and decisive people have sworn up and down that they felt no maternal stirrings for years before mysteriously changing their minds.

So what is up with that? Does this actually happen and if it does, how and why does it happen? And if it doesn't, why the hell are all these other women trying to convince me it'll happen to me?

Biologists Don't Know Shit About Computer Programs

I am watching ESPN, chatting with March Hare, petting Dormouse, blogging, and running a program to analyze sets of data all at the same time. How's that for multi-tasking?!

As has happened often recently, I am amazed tonight by what computers and software can do for biologists. Seriously, how else would I be able to align two DNA sequences, each of which is over 120,000 bases long, with each other without going completely blind?

Given the trend toward doing experiments that generate ginormous datasets--microarrays, mass sequencing, etc.--it seems a shame to me that so many biologists (including myself) don't really know much about the programs we use to analyze these data. We know just enough to get the programs to do what we need them to do, but not enough to understand how the algorithms work or how to tweak the parameters to generate better analyses. In this age of increasing reliance on computational biology, perhaps biology graduate programs ought to require some kind of remedial bioinformatics course, no?

This point was driven home earlier today by a paragraph in a paper I was reading. The paper was about a comparison of the efficacy and sensitivity of several different computer programs for detecting repeat elements either in sequencing reads or in assembled contigs. In the discussion section, the authors addressed the fact that they had compared the various programs using the default parameters instead of trying to optimize the settings:

Of note, each tool was evaluated using its default parameters. We chose not to conduct tool optimization because, in our experience, it is very common for biologists to operate bioinformatics tools using default parameters. Some likely reasons why optimization is often avoided are as follows:

1. Many biologists have little or no understanding of the algorithms and programming behind computational tools and thus do not feel comfortable changing program parameters.


2. Public domain tools rarely come with documentation that can be easily understood by those lacking experience in computational biology.


3. Because software developers cannot anticipate every dataset and/or application on which their tool may be used, they often provide only vague suggestions as to how optimization might be conducted.


4. The act of optimizing a tool for a particular dataset or application can be very difficult and time consuming.


5. Program default settings often become ‘standards’ to which researchers adhere so that they can directly compare their results with those of researchers who have used the same program in default mode in the past.


6. What constitutes an ‘optimal result’ differs from user to user prompting some scientists to use the default parameters as a way to limit introduction of their own biases into results/conclusions.

So...numbers 1, 2, 5 and 6 basically translate to (1) biologists don't know shit about computer programs and have absolutely no clue how changing various parameters will alter the result, (2) we could try reading the manual but we wouldn't understand it anyway, (3) um...we'll just do what that other guy did cuz we don't know any better, and (4) if we knew how to tweak the program, we could make it give us any result we wanted...just like with PhotoShop!

I might consider being offended on behalf of biologists if all of these points weren't so true. I mean, I did just spend almost an entire afternoon annotating a genome by copying and pasting each ORF one-by-one into the query box at Blast, right? Sigh.

So instead, I laughed my ass off at seeing our shortcomings in this area so...um...tactfully described in an actual journal paper! Kudos to the authors for having the guts to be so candid. And the program they recommended for finding repeats had better damn well be idiot-proof and work like a charm or I'm going to need some serious help.

A Hatter In Sin City

March Hare and I just got back from a week-long trip to Las Vegas. We had an absolutely fantastic time! But unfortunately, I am now up to my eyeballs in all the work that piled up while I was gone. So, blogging will be light for a while, and in lieu of real science-related content, I will leave you with some vacation photos.

I have to say that I was very pleasantly surprised by my Vegas experience. I had expected a crazy, over-the-top kind of place with a seedy undertone. I had also expected that someone who wasn't into gambling or shopping wouldn't have much to do. Crazy and over-the-top it was, but in an entertaining and strangely endearing way.

We stayed here:



The hotel was beautiful, the staff were really nice, and the bed was to die for. Seriously...we're trying to figure out what kind of mattress they use so we can go buy one!

March Hare was actually there on business, so I got to play tourist by myself during the day. Turns out there was plenty to do. For one thing, just walking from one end of the Strip to the other takes up a good chunk of time. Not to mention the fact that the people-watching there is unparalleled.

I rode this:



and watched this:



...and got a good laugh out of this:



And the food...oh, the food! We had the two best meals of our lives there, one of which was at this restaurant:



I think I'd be willing to go back to Vegas just for the food. That is, after I manage to save a year's worth of my salary to pay for it!

I had planned on trying my luck at the slot machines or the blackjack tables. But I actually found more than enough ways to amuse myself and just never got around to it until we were at the airport waiting to board our flight. I figured I had to at least gamble once, right? So I put a dollar in a slot machine...and promptly lost it.

Oh, well...at least I still have an unbelievably gaudy refrigerator magnet of the Strip to remember this trip by.

Two Pieces Of Good News

There's been a fair bit of moping around in my lab lately. These days, with tenured faculty downsizing their labs, junior faculty closing up shop or barely keeping their heads above water, and senior postdocs finding hiring freezes everywhere, the anxiety in the department is palpable.

But there are two pieces of good news that have, at least temporarily, dispelled the gloom-and-doom mentality.

1. A postdoc in my lab just got a tenure-track job offer. A female postdoc who is married, has a young child and is pregnant with her second child. Nothing like a success story and a celebratory lab lunch to cheer people up.



2. My hijacked manuscript has finally (and unexpectedly) been liberated. I can't say why or how, but now it's full steam ahead to get it submitted. I might even get to be on a patent resulting from this work.

By next week, I'm sure we'll be back to trading stories in lab about junior faculty we know who have no grants and are rapidly running out of start-up funds. But for right now, things are looking a hell of a lot sunnier in my little corner of academic research!

Too Smart To Talk To?

I was flying home from a trip to Austin, TX to attend an old friend's wedding several months ago, and ended up chatting with the guy who was sitting next to me on the plane. After the usual introductory chitchat--where are you from, why were you in Austin, etc.--we started talking about our respective jobs.

We were having a pretty decent conversation...that is, until I mentioned that I was faculty at Wonderland U. and had a PhD. There was an uncomfortable pause, and then he said awkwardly, "You have a PhD? Wow...I don't know why someone like you would even want to talk to someone like me."

He wasn't joking.

Now, I realize I don't get out of the lab much. And my department is so chock-full of MD/PhDs that I spend a good deal of my time explaining, "No, no...I'm just a PhD." But this seemed like a really bizarre reaction to me. I mean, we were getting along just fine before he knew I had a PhD, so it wasn't that I had been acting like an arrogant, elitist jerk all along, right?

Are those three little letters really so intimidating? Because my feeling is that getting my PhD had more to do with perserverance and determination than my immeasurable genius. Has this happened to any of you?

As an aside, this wasn't the first time I'd been told I was "too smart" to hang out with. A guy on whom I had a crush in high school told me at the end of our senior year that he had considered asking me out, but decided I was too smart for him.

And yeah, I'm still a bit pissed off about that!

How To Use Your Foreignness To Get Ahead In Science

[rant]

I was just reading a post by YoungFemaleScientist about the ratio of foreign-born to US-born scientists in this country.

Personally, I was much more surprised to note how few US-born scientists there are in the US. At all levels. We're not just less than half, we're on average only a quarter of the total scientists at the post-PhD levels.... In other words, most of our science faculty in the US are not from the US.

YFS goes on to discuss possible reasons for the success of foreign-born scientists:

• "I can't help feeling like it's somehow perceived as more okay to be smart and professional if you have a cool accent...."--we use our accents to charm our way to the top


• "...or that it's somehow more permissible to occasionally make a mistake and blame it on English not being your first language?"--we use the language barrier as an excuse when we screw up and that gets us a free pass


• "Is this just a cultural perception that they work harder?"--we take advantage of the perception of immigrants as hard workers when we're really just slacking off all the time


• "Is this the 'my visa is running out' phenomenon I've blogged about before, where PIs prioritize which postdocs they promote based on who is most likely to be deported?"--we use our immigration sob stories to get sympathy promotions and jobs

Now some of you may be thinking that this is reminiscent of the kind of xenophobic rhetoric spewed by the far-right wing, but by golly, I think YFS has hit the nail on the head! I mean, I totally got to where I am in science today because of all the advantages I had as a foreigner.

The professors who interviewed me for grad school were so enthralled by my exotic accent they didn't even notice my 2.0 GPA and pathetic GRE scores. And what about the time I destroyed the ultracentrifuge in grad school and told my advisor I just didn't understand what the postdoc had said about balancing my samples? Not only did I not get in trouble, that postdoc got yelled at for not taking a poor foreign student under her wing.

Then when I was a postdoc, my PI was so predisposed to think of immigrants as hard workers that I had him completely convinced I was working 24/7 just by making sure he saw me in lab when he arrived in the morning and again when he left at the end of the day. And my promotion to faculty? Man, you should've seen the unshed tears gleaming in my PI's eyes when I told him about the sacrifices my parents had made so I could come to the US and build a new and better life for myself here.

So all of you foreign-born scientists out there, learn from my example and use your foreign status to climb your way to the top. Because the day we foreign-born scientists are right up there with THE MAN on YFS's list of those who have kept her from her rightful position atop academic research is the day we'll know we foreigners have made it in the good ol' U. S. of A.

Oh, and the title of YFS's post? "As an American, I'm a minority in my profession." Cuz only people who were born in America are real Americans.

[/rant]

Scientist, Gagged

One of the things I've always taken for granted in my academic career is the ability to discuss my work with colleagues and to present and publish my data. So I'm a bit dumbfounded to find my freedom of scientific expression, so to speak, curtailed on not one, but two of my projects.

For the first project, this situation was expected and is, unfortunately, unbloggable. Suffice it to say that I had to sign a confidentiality agreement whose length would've made Tolstoy green with envy.

The second project was a collaboration between several labs including one in Faraway Land. Everything had gone swimmingly--we got cool data, we wrote up a manuscript, there was no authorship drama, and everyone liked the draft.

Then out of the blue, we discover that a Faraway Land government official is refusing to let us publish the data unless he is first author. Why do we need Government Official's permission to publish? I haven't a clue. But I do know that Government Official has not done any of the work, provided any funding or reagents, or contributed intellectually to the project in any way. So I'm thinking that Government Official doesn't deserve any authorship, let alone first authorship. Hell, that level of non-contribution doesn't even deserve mention in the acknowledgements!

So now I can be sued for discussing one of my projects, and the manuscript for the second project is being held hostage by a foreign government. Seriously, how bizarre is that?

If You're Writing A Challenge Grant, Clap Your Hands

Clap Clap

If you're writing a challenge grant, cla....

Okay, okay. I'll stop.

So, how many of you spent part of the afternoon reading the behemoth of an RFA? I think I received the email announcement from at least 4 different sources, and it got forwarded to me at least another 3 times.

This comes at a rather inopportune time for my lab. Our PI is away at the moment and will not be back probably till the end of the month. I have been left in charge as substitute PI, and there are 4 members of the lab including me who are eligible by our institution's rules to submit NIH grant proposals. We know we're expected to help write these grants, but it's not clear whether we are going to be PIs, co-PIs or ghost-writers.

It's also not clear how many we are expected to submit. I mean, let's face it--every PI in this country is going to submit as many as possible, and any PI with faculty-level lab members is going to ask them to submit additional ones. How the hell are all these grants going to be peer-reviewed in two months??? Will all PIs be dragged away from their labs this summer and sequestered until they've scored all gazillion challenge grants?

And speaking of inopportune times, March Hare and I are going to Las Vegas for a week later this month. We planned this trip last November...before we knew about Dormouse's condition, before I knew my PI was going to be MIA this month, and definitely before I knew I was going to be writing X grants for an April deadline.

So I guess I'll be keeping tabs on the lab by email and working on challenge grants in Las Vegas.

Sigh....

At least I won't be gambling away what remains of our investment portfolio playing blackjack, right?

To My Awesome Blog-Friends

I logged into my blogging email account today for the first time in a while and was really touched by all the messages you've sent. I'm so sorry for having vanished from the blogosphere for so long and am absolutely amazed and flattered that you guys are still coming here. You're a fantastic bunch of blog buddies, I gotta say.

I honestly only intended to be away during the "crazy deadlines" period, but then one thing happened after another and before I knew it, it had been months. And the longer I was away, the harder it was to write the new post.

Some of what's been keeping me away has been work-related, and some of it has been personal. One big thing is that Dormouse was diagnosed with transitional cell carcinoma in January. She's been on chemo since, with the goal of giving her the best possible quality of life for as long as we can. The vet thinks maybe 6-9 months....

We got Dormouse as an adult from a shelter 13 years ago. She's old and we knew she wasn't going to be healthy forever, but it was still devastating news. We're trying not to think too much about the end, and to focus on making her happy for as long as we have her.

I definitely want to start blogging regularly again, but I'm not sure when I'll be able to do that. March Hare and I have had to adjust our work schedules a bit to minimize the amount of time Dormouse is home by herself, and March Hare switched jobs in the midst of all this, so things are a bit unsettled at the moment. Every few days, though, I do find myself composing blog posts in my head, so it'll be nice to have an outlet for that again.

Thanks again for all your messages. I really do appreciate it. Hope all is well with you and I'll try to post again soon...I promise.

MH