Friday, January 30, 2009

Research Crossroads

I know, I know, 5 months in is a little early for any kind of crossroads, but I had a bit of an epiphany yesterday that may shape the next 6 months. The main project I want to pursue has some fairly high up-front cost - at least for my field. Because of that, I have been in a holding pattern of that project until I get grant funding for it. Yesterday I realized that I could do a small-scale test project for considerably less than what the full project would cost and now I am debating what to do.

The reason it might be worth jumping the gun and producing these data before getting a grant is because this project falls under the high risk/high reward category, that is probably unlikely to get funded without some decent evidence that there will be the results that I think there will. When I sent the grant in back in January, we had made progress, but hadn't made the final leap because of the cost. I have no idea, of course, whether the progress we made will be enough to convince the reviewers to suggest funding the project, but if it gets turned down again we won't have much more evidence in hand for the next round. From that perspective, it seems like a huge gamble NOT to spend the money.

The drawback is that it all needs to come from my start-up. Not only that, but if I want to get it done before the July round of grant applications (assuming the grant doesn't get funded this round) I will need to figure out if the Dean will let me borrow against my start-up money for next year, early. When I negotiated my start-up, I got the vast majority in the first year so I could buy equipment and get things running. I have pretty much outfitted the lab at this point and still have about $25K left for this year. Since the fiscal turns over June 30, that should give me plenty to get through this year. BUT, if I were to go for broke and try and pull this off, I will need to pay about $10K to one company and $15K to another. Obviously that would leave me with nothing to use for the other projects going on in the lab and the consumables to keep things running.

I have $75K of start-up available in year 2 (starting July 1), with nearly that much coming in year 3, so time is a bigger factor than money in the grand scheme of things. I have no problem spending the money (that's why it's there), but I don't what to handicap the lab for a few months either. The way I see it, I have three options:

1) Hold tight and see what happens with the grant. I am not a conservative person and this option bothers me. If the grant doesn't get funded, I will have very little to add in the next round, which is only treading water.

2) Spend the $10K to complete the first step of the project and have at least made that progress in the even that the grant does not get funded in this round. Even if it does, I would have to spend this money anyway, but from the grant rather than start-up. I could live with this option because it shows that we can do what we claim, but it will not provide any evidence of the eventual outcome.

3) Squeeze the Dean for some of next year's money and produce the data. This option is the scariest in the short term, because the lab finances will be dodgy until summer, but it would provide enough data to push the grant over the top, for sure. These data could also be folded into the larger data set once we had the funding for the whole project. Of course, this is predicated on squeezing blood from a stone in this financial climate because the Dean may not even be able to provide any money for me to move forward.

Thursday, January 29, 2009

Motivational metric

There have been a number of metrics being devised since Drug Monkey revived the establish your own scientific eponym meme. I bounced a few around in my head, but was embroiled in grant-related issues at the time and never got around to putting any down. In the past couple of days I have spent a lot of time tinkering with the structure of my course and putting some lectures together. As I am putting the finishing touches on some of them, it's been pretty clear that I have created a motivation metric, without having to think about it. It's simple and direct. The motivation I have to get parts of a lecture done are inversely proportional to the amount of challenge I find in the subject. Therefore, when I am teaching something a little out of my comfort zone, I focus on getting the slides together in a very organized way to get my point across clearly. If the topic is something I am very comfortable with, I leave the slides blank while I do things like blog about why I'm not actually doing the work I need to finish.

For the love of salt

Our entire area has been turned into a giant skating rink by Mother Nature's latest hijinx and in its infinite wisdom, Employment University decided to plow everything in such a way so as to leave a half inch of ice on everything. Well, since they did not plow the sidewalks at all, there are 2 inches of ice on those, but who's counting? When I drove in this morning, students were walking in all the roads around campus because the probability of being crushed by a sliding car was apparently less than that of cracking one's skull on the skate-walks. With ice and students everywhere, navigating to my parking lot had to be done with surgical precision. Luckily, I have been conditioned to walking on ice because both PhD City and Postdoc City were frozen wonderlands for much of the year. In addition, due to the construction on the new building next door, the university plows have decided that they should not get within 200m of anything that resembles a construction fence, so icy walkways have been the norm around the current building all winter.

Figure 1. PLS's walk from parking lot to building.

On might think that salt and sand might be a simple way to combat the problems associated with an ice coating, but Employment University believes in green energy and prefers to let the sun do that job, no matter how long it takes and how many shattered pelvises must be endured. While I have to admit that the jerk in me found comedic value in watching three students dramatically yard-sale on my short walk in (with no apparent injury, save for their egos), I do wonder who makes cost-saving decisions like not using salt and how they factor in the injuries of their clients (students) and employees into how much money they are saving.

Wednesday, January 28, 2009

Defying Big Blue

I have a confession. I am a Mac guy. From the very early days of home computers I have pretty much always had a Mac, either at school/work, home or both. My lab is entirely Mac and I was never forced into using a PC throughout grad school or in my postdoc, since those labs ran Macs as well. I can use a PC with no problem, but the times I have owned them make me pine for my Mac. There really is no comparison, especially when you consider the rate of performance decline as the machines get older. You can run a Mac for years on end, but a PC is basically a doorstop in 5 years or less.

Despite my personal bias, I have always used Microsoft products because there was no real alternative. Remember in the early 90s cursing because someone sent you a WordPerfect document that couldn't be opened in any other software? I do and I didn't want to be that guy. The good people at Apple also realized this and when they made their Office equivalent, they went to great lengths to ensure that people could import ppt documents with ease and export presentations in ppt format. Despite this, I hesitated making the switch because of the "unreadable file" prospect that looms over any potential speaker at a conference. I wasn't going to make two presentations (one in PowerPoint and one in Keynote) just to avoid this, so I continued using PowerPoint.

The difference now is that I have a class to put together and I am using my own laptop. There is virtually no way that I might face any compatibility issues here, so I think I am going to create my lectures for class this semester in Keynote. But before I do, I thought I would solicit any advice on potential drawbacks of moving to Keynote. I don't that Mac has the answer for everything, so if I am about to run into a massive pitfall by switching (for class, not international presentations), better to know that now.

Tuesday, January 27, 2009

NFtOS 2. Alveolates: Nature's genomic mind-fuck

Today I thought I would get into a bit about the bizarre beasts in the alveolate group (Fig. 1). Chances are, the term "alveolates" means nothing to you unless you care about the classification of eukaryotes on a broad scale. However, you will certainly be familiar with some of the organisms that are within this group, which includes ciliates (e.g. Tetrahymena), apicomplexan parasites (e.g. Plasmodium, Toxoplasm), dinoflagellates (responsible for red tides) and a couple of other odds and ends that are not important for today's topic but have features heavily in recent debates over the evolutionary history of the lineages.

Figure 1. The major groups of organisms that make up the Alveolata and their evolutionary relationships to one another. The branch leading to Chromera is dashed, indicating uncertainty of its exact affinity.

What is really interesting about this group of organisms is that the all seem to have something really strange going on with their genomic structure. Ciliates contain two nuclei within their single-celled selves, one of which functions as the germline nucleus (called the micronucleus - MIC) whereas the other is the somatic nucleus (macronucleus - MAC). The MAC is the transcriptionally active nucleus and is a highly-processed version of the "silent" MIC and can range between ~120 chromosomes large chromosomes to over 25 million, gene-sized chromosomes, depending on the ciliate. In all known cases, the MAC of daughter cells is produced in a complicated RNA interference-based process of comparison between the parental MAC and the MIC. The processing of genetic information in ciliates is a fascinating subject that science is only beginning to figure out.

Apicomplexans are another unusual group, but I've already discussed them a bit in the past. The moral of the story is that you shouldn't tease little algal cells because you never know when they'll evolve into parasites and cause millions of human deaths annually.

Finally, you have the dinoflagellates. Even though the Amoeba nucleus is the Godzilla of genomes (~670,000 Mb), some dinoflagellates could make a case that their nuclei are at least the Mothra of genomes. Gonyaulax, for instance, has an estimated nuclear size of 98,000 Mb - a mere 34x the size of the human genome. While this alone puts dinos in an unusual genomic category and pretty much ensures that it will be a while before we see a dino nuclear genome completed, it is their plastid (chloroplast) genomes that are truly messed up. Rather than having a single circular plastid genome containing all of the plastid-encoded genes, dinos have fractured their highly reduced plastid genomes into hundreds of plasmids, called minicircles. Only a few genes are individually encoded in multiple copies on these circles and a large proportion of the minicircles are non-coding, containing only the screwed up results of recombinations between different copies of genes. Each minicircle has a a core region, which presumably functions as the site of transcription. Clearly the system has evolved in response to some genomic pressure, but what the possible advantage is of having hundreds of divergent copies of a few genes and a large amount of junk being transcribed in your plastid is, remains a mystery.

European ref letters

As much as I bitched about not getting any decent candidates with a week to go in my search for a PhD student, I did get a couple good applications in the end. I have asked for reference letters from the list provided by my top candidate and have been surprised by what I got back. I have two out of three in hand and the first was sent to me less than an hour after I inquired. What I received was a three sentence email paragraph basically stating that the candidate was highly recommended, but little else. I got the second letter last night as an attachment, but the first and last paragraph used the wrong pronoun to refer to the candidate, whereas the middle two used the correct one. Ummmm, okay... How am I supposed to take that? The two middle paragraphs are a total of four sentences and indicate a high regard for the candidate, but how highly can you think of someone if you don't even take the time to read over you letter for them? Can I trust that someone really puts their "full and unreserved support" behind someone when they use the wrong pronoun to refer to them in the same sentence?

The mitigating factor here is that the candidate is from Europe and I don't know much about what would be expected as a reference there and whether it would be different from what North Americans might write. An additional complication is the language barrier, so the reference writers may truncate their comments if they have to write them in a non-native language. Is there something I am missing or did the candidate just pick lazy reference writers?

Monday, January 26, 2009

Less Neurotic than most

Because today was an absolute wash in terms of getting anything done, I took the blogger personality test that a few others have posted about. Basically I am the polar opposite of both River Tam and PiT, more along the lines of Arlenna, but less neurotic and less open to new ideas. What does it all mean? I have no sweet clue.
You scored 14 out of 50. This score is higher than 4.1% of people who have taken this test.

You scored 42 out of 50. This score is higher than 86.7% of people who have taken this test.

Openness to experience
You scored 42 out of 50. This score is higher than 52.9% of people who have taken this test.

You scored 43 out of 50. This score is higher than 90.3% of people who have taken this test.

You scored 44 out of 50. This score is higher than 89.7% of people who have taken this test.

Friday, January 23, 2009

NFtOS 1:Are you a heterokaryon?

Today's question is whether all your genes are yours. It's a more complex question than it looks, but we have some history to deal with.

I think we can pretty much all agree that prokaryotic cells (bacteria and things without those pesky organelles) are more ancestral in the grand scheme of life than eukaryotic cells (with a nucleus, mitochondria and sometimes plastids). Based on that, we can probably agree that prokaryotes evolved earlier and were the earliest form of life as we know it on our planet. There's lots of data to back this up that I won't get into here, but you can search it out if you think I'm making shit up. The two big questions in the biology of organisms way back when, are 1) how did the first cells evolve, and 2) how did we get from prokaryotic cells roaming the Earth to the first eukaryotic cell? At the moment, we just don't know. There are lots of hypotheses out there, but in the current state of science the question of how the nucleus came to be and the origin of the genetic material that now inhabits this organelle are merely questions we can argue over. I happen to think we will someday be able to explain the phenomenon, but we're stuck at the moment.

An aside here. If you are reading this and thinking that the solution has anything to do with a divine being of any kind, it's time for us to part ways. Seriously. I'm sure there are blogs out there on fairies and imaginary friends you can talk to at night, but we're not having that conversation.

Though theories on the origin of the nucleus abound, we know considerably more about the origin of the other organelles in eukaryotic cells. It turns out the plastid (aka, chloroplast) evolution is a complex mess involving (probably) one instance where a cyanobacterium (photosynthetic bacterium) was engulfed by a eukaryotic cell, but never digested. Over time, the cyanobacterium and host cell learned to live together to their mutual benefit and, as often happens in these situations, the cyanobacterial symbiont became reduced over generations and time to the point where it became obligately bound to the host cell. Once this was established, eukaryotes spent the time between then and now swapping plastids around like lice in a daycare.

The case of mitochondria is very different. The mitochondrion became part of the eukaryotic cell in the same way the plastid did, but much earlier on. In the late 1980's it was thought that there were organisms that did not contain mitochondria and that they were the most primitive eukaryotes. Since then, it has been shown that the position of those organisms in the tree of life was an artifact and that eukaryotes don't entirely lose mitochondria. Ever. Mitochondria got in once and they got in early. So early that there is no evidence of any eukaryote that lived prior to mitochondria.

But here's the kicker folks. We think that the ancestor of mitochondria belonged to the group we know know as the alpha-proteobacteria. Current day alpha-proteobacteria have good sized genomes with a couple thousand genes to make the proteins they need and we have no reason to believe that the ancestral proto-mitochondrion needed fewer genes than current day ones. However, modern mitochondria have anywhere from 0 to less than 100. In fact, almost all animal mitochondrial genomes have only 13 protein coding genes, which is another reason my animals are really damn boring, but that's for another day. So, what happened to all those bacterial-turned-mitochondrial genes? If the genome came in with a few thousand and now has, in the case of animals, 13, where are the rest?

That question brings us back to the topic of the day. It turns out that while many of the "missing" genes have been ditched because they were no longer needed in the cell's new role as a mitochondrion, 13 proteins are not nearly enough to run the mitochondrion. Rather than make the proteins in the mitochondrion from it's own genes, it has out-sourced that job to the nucleus. The vast majority of genes that make mitochondrial proteins are encoded on the nuclear genome and the proteins find their way through a complex targeting pathway. But, what should be the interesting thing here is that these genes have all been transferred from a prokaryotic cell and incorporated into the eukaryotic nuclear genome. Many of these genes are identifiable in phylogenies based on the sequence affinity to prokaryotes that they have retained, but some have been part of the eukaryote for so long that they just blend in. Therefore, the typical eukaryotic genome is home to thousands of genes that have bacterial origins and many of which perform cellular functions unrelated to the mitochondrion because they have replaced the canonical copy or they have assumed a novel function in the cell. So, in addition to the recent estimate that humans carry more bacterial cells than human cells, we also carry a decent number of bacterial genes in our genomes.

Thursday, January 22, 2009

Easy screening

The college did what appeared a few weeks ago to be impossible. Our new building actually opened on schedule and classes have been held in there this week when the semester began. Since all of the classes that were formerly taught in our building have be moved to the new building, the halls here a very quiet. Large signs have been posted at the entrance to our building that scream in big red type "All classes for old building are now being held in new building. The one right behind you. Yes, turn around and walk" - or at least something like that.

Despite the big signs, the deserted halls and the fact that the classrooms are dark, locked AND have different numbers than the ones in the new building, there are still students walking the corridors with the vacant, lost look in their eyes. I have no idea how many times I have answered the question "Do you know where room xx is?" in the last couple of days. It's hard for me to answer these kids with a straight face, because they are essentially admitting that they ignored the building name and number on their schedule, the big red signs and are oblivious to the fact that there are no other students in this building. I should get every one of their names so I can screen them from anything I do in the future.

I teach my first class tomorrow (hence no sciencey post today) in the new building and the lab moves in less than two weeks! I would walk my equipment over there barefoot if it would get me in any sooner.

Wednesday, January 21, 2009

New series: Notes From the Other Side

Considering I just started this blog in October, I would say that there might still be a whiff of that new blog smell around here. As a newcomer to this community I have learned a lot and gotten a good amount of useful feedback from those with more experience in matters of blogging, teaching, being a PI and everything that comes along with that. I appreciate the comments and they have actually changed the way I approach what I post here. My initial intention was to chronicle my experiences with the hope that they would inform those who are now in the position I was a year ago. While I still try and do that, I also now use this forum to draw on the experiences of those who are further along in this process than myself.

With the new semester upon us, I think it's a good time to add another aspect to the blog and that is to talk a bit more about actual science. As I have begun to explore some (I wish I had the time to read further than I do) of the other sciencey blogs out there I've realized that the research programs of bloggers roughly reflects research biases in the US - that is to say that a large sector of the community works in biomed-type fields and of those who do not, many still use model organisms (human, mouse, fruit fly, yeast, Arabidopsis, etc.) in their experiments. Though a lot of people don't reveal their field, I get the impression that nearly all of the bio-bloggers are working on organisms that would be household names (alright, maybe in a geeky house, but still). That puts me in a niche market, I suppose.

Over the next couple of weeks I'm going to try and put a few coherent posts together on some of the interesting things going on outside model organism world. My motivation for doing this actually came from a manuscript I recently reviewed for a high-impact journal. The authors actually wrote the line "We have shown that xx holds true for the entire spectrum of eukaryotic diversity, from humans to yeast". This kind of shit drives me crazy and is the equivalent of saying "Last summer I drove all across the US, from Maine to New Jersey", but I have seen similar statements in a grant and two seminars. I have no idea if the posts in this series will actually attract any readers, but if I can get just one person to realize that eukaryotic diversity hasn't been neatly classified as Animal, Plant or Fungus since the 1950s (or earlier) or that the organisms we can see out our window represent the minority of eukaryotes, then I will be happy. At the very least, it will save my grad students from having to listen to my crazed rants when I come across statements like the one above.

Tuesday, January 20, 2009

Applicant Hell

Recently I have had to advertise for a PhD student and did so using a few listservs that have fairly substantial followings in the fields I am interested in. My deadline is not until this Friday, but the applicants I have so far are making me very nervous.

I was somewhat specific with what I am looking for. I would prefer someone with an MSc in a related field (even tangentially), some lab experience related to the tasks we are undertaking (which covers a wide range of basic techniques) and some ability to perform, or interest in learning, rudimentary XX. These requirements should not unreasonably narrow the field.

Nevertheless, I have only 7 applicants at this point (still four days prior to the deadline), and only one of these even partially meets my preferred skill set. The majority of the applicants have sent their CVs because I am working in an emerging field and they would like to learn some of the techniques and apply them to their own field of interest. While that is a reasonable goal for them, I am not looking to train a PhD student who is more interested in how they can use our methods to answer questions in their (completely unrelated) system, than they are in working on the project I need people for. It is one thing to have this goal and at least feign interest in the advertised project, but when your letter specifically discusses how you want to learn techniques Y and Z so that you can use them to improve your worm breeding project, then go on to describe the worm breeding project for a page, I'm just not gonna call you up to get you in here.

Granted, I could be worrying for no reason at this stage, with the deadline still ahead. When I applied for positions I never sent in my package substantially before the deadline, so I wouldn't expect others to. But with each new application that comes in from a Pakistani bee-keeper or Romanian goat herder I am becoming increasingly concerned that I may not find anyone suitable. If that is the case, I will essentially lose out on a departmental TAship to support the student and having one more person in the lab who can advance my projects. I don't plan to bring in a seat warmer just to keep the TAship this year, because I know that a bad student in the lab can cripple progress, but it makes me very uncomfortable giving up a lab position at this early point. Therefore, I may be faced with the unappealing options of either taking on a student who I will have to train from scratch and hope for the best, or declining the TAship for a year.

What makes the latter option even less palatable is that the process for assigning TAships to labs is one of the major policies being changed in our college-level reorganization. I was hoping to grab one before the changes happen so that my lab would go into the new system with two TAships, which might bolster my future claims on two or more TAships in the future. If I go into the "merge" (everything has taken on a "Survivor-like" flair around here lately) with only one TAship, I may need to battle to get a second in the future and it will likely take me longer to secure a third. Therefore, obtaining the second TAship or not has longer-lasting consequences than just the next year. We need a metric like the PiT Theorem for the cost/benefit of taking on inexperienced students and securing TAships for the future.

Monday, January 19, 2009

Long hair: Not just a lab hazard

When you have a child who is under a year old, you spend more time than you ever thought possible around poop. It's a common topic of conversation and you are constantly cleaning it up or evaluating it's consistency. There is no conscious decision one day to make poop a bigger part of your life than ever before, it just happens when you have a small child like getting used to the cold happens when you move to Winnipeg (aka: Winterpeg). Despite our newfound comfort with the topic, I don't seek out poop-related experiences. I guess they just find me.

I took both Saturday and Sunday to stay home this weekend and not do work. It was great to have two consecutive days off and to do family activities. Sunday was snowy here and a perfect day to hang out in the house, play with the wee one and watch some football, which was conveniently on. With the Wee one asleep, I settled into the couch with beer in hand, ready for some mindless entertainment. From behind me I heard our cat scrambling up the basement (where we keep the litter boxes) stairs at breakneck speed until he hit the kitchen laminate floor and lost all traction despite churning his legs at a blurring pace. I couldn't figure out what had spooked him until he bolted into the living room and I could see that he had a ball of poop whipping around behind him like a tether ball in a hurricane and attached by a strand of hair to apparently yet-to-be-excreted poop. Upon reaching the living room floor he instantly pushed his ass to the floor, legs splayed, and performed the front-legged ass-drag, commonly associated with dogs. He made it about 5 feet before I could reach him and pin him down long enough to pull a paper towel out of my pocket (I am now often armed with a cleaning device of some kind), grab the poop-caboose and pull on it like turning on a lamp. Luckily the hair snapped rather than pull the internal turd free from the cat and I was able to set the beast free while I disposed of the shit-on-a-rope and got some soap to clean the violated stretch of floor.

Ah, the joys of relaxing at home.

Friday, January 16, 2009

Humor me, politically

I try to avoid politics here because there are plenty of sources out there for political views. But allow me an indulgence, because it bears on what many of the female bloggers in this realm are often faced with. We'll get there in a sec.

Last night I was curious to see how the US president over the last 8 years was going to sum up his terms in office. How would he put a positive spin on 8 years that have been characterized by bad decisions, lack of accountability and deep divisions within the country? I put up with that smarmy smirk for 15 minutes (a personal best) to find out. The answer was trusty old 9/11. The best thing Bush could come up with was "sure, thousands and thousands of civilian lives have been taken since 9/11, but none of them were American!" Well, I feel better.

But what really struck me about the farewell I've been waiting 8 years for was the middle of the speech, when Bush highlighted his “random honorable people of note”. Other than the fallen 9/11 officer who Bush mentioned, four people had been invited to the speech for Bush to pat them on the back for honorable service to the country. There was a charter school principal, the religious owner of a half-way house, a military hero, and the father of a fallen soldier who had petitioned the armed serviced to be allowed to join the army at the age of 64 in order to be a battle medic and up-hold the memory of his son. Fair enough, I can hardly argue whether or not these individuals are worthy of Presidential praise. But the thing that stood out was the fact that not a single woman made the list of presidential honorees. Not one of four.

As a confession, I will readily admit that I might not have thought this was a big deal not so long ago. Is this outward sexism as featured in an after-school special? No. But it may be every bit as important because these types of “oversights” subtly reinforce the idea that men should be recognized for achievements, whereas woman should operate in the background. I have heard (read) similar types of complaints regarding scientific awards, teaching awards and seminar invites in the last couple of months and it all adds up over time. Who are the role models being paraded before us? Who are the people winning the awards? Can anyone really argue that the four men Bush chose to invite to his final speech as President better represent the good in our country than any women candidates out there? My only explanation other than Republican arrogance is that many women were invited, but none wanted to be associated with Bush. Now there’s an honorable stance.

Thursday, January 15, 2009

I swear, I'm gonna face it

Between grants, preparing to move the lab* and having a new student start it has been very easy to ignore the elephant in the room. Now that I have weekend plans (including a date night with my wife, who has been very tolerant of my long hours) and only a few days before classes start up again, the elephant is starting to get gassy and is becoming impossible to ignore. In my case, that elephant is the course I have to teach this semester.

As courses go, it should be incredibly straight-forward. It's a grad class with only about 6 students and it's on a topic that I find fascinating. I think this class is going to be something I really enjoy doing, but for an unknown reason I am completely paralyzed when it comes to planning for the class, now that it is right around the corner. I have a general idea of how I want to teach it, but I can't bring myself to lay out the schedule or deal with the syllabus. There is no real reason of my complete avoidance, but it is a bit daunting to have an entire course to plan from scratch. Like most people in my position, I don't have any formal teacher training and have never had to plan a course. Since I have been here I have only concentrated on research, which is entirely familiar and not the least bit scary. It's what gets me up in the morning (well, technically I get up to the screaming of our hungry alarm clock that needs a new diaper) and why I put in long hours. Teaching is the thing I always knew I would have to do, but haven't looked forward to. I am confident I will enjoy teaching, but for now it represents the great unknown. Today, however, I brought my elephant gun and it's huntin' time... after lunch.

*I got to go over to the new building again today and tour my new space. I didn't want to leave. Like yearning for a distant lover, it's constantly in my thoughts. I can't wait until I can see it again, move in with it and start a new life together. Alright, maybe that's creepy, but the space rocks.

Wednesday, January 14, 2009

Officer, what seems to be the problem?

For various reasons, I'm relatively new to applying for NSF grants. One thing that I have been told from a number of people was to write to my potential program officers and ensure that the proposal I am submitting fits their program. I did not do this with the grant I submitted before moving from Postdoc City and it ended up getting bounced to a different program from the one I had sent it to. In this funding round the second grant I am submitting (with Senior Collaborator) doesn't fit neatly into any of the program descriptions, so I figured it was time to get in touch with some of the POs and figure out the best home for it.

I contacted two POs from different divisions under BIO. The first got back to me with interest and the second wrote back with questions that suggested that they had not really read what I had written. I sent an email back to both, taking time to carefully explain the project in greater detail to PO2. PO1 got back to me and said that our proposal could likely fit under their program, but that I should also look into the program of PO2. I never heard from PO2. Three weeks go by and with the deadline less than two weeks away, I recontacted PO2 about the proposal. After a couple of days I got a response, suggesting that I should send it to their program and how PO2 appreciated me doing my homework ahead of time. Fair enough.

Then we ran into some problems and SC decided that the program deadline just wasn't going to happen. I wanted to let PO2 know that we might be a couple of days late so that I might get some assurances that they would still take the proposal, so I wrote 3 days before the deadline. Nothing. The day of the deadline, I wrote again. Nothing. Now we're two days past and I still haven't heard anything. It may all be moot because SC called me last night to let me know that it might be better to hold off until March for a different program and after seeing the draft of the proposal for the first time last night, I can see why SC feels this way. Can I get a "This is why I wanted to spread the writing between us!" from the congregation?

But I'm left with two issues. 1) I know that POs are busy and have a lot going on, but PO2 is one of 4 POs for this particular program, which receives fewer than 75 proposals according to NSF stats. Is it unreasonable to expect that a PO will get back to you in a timely manner, particular about specific requests having to do with the deadline? A simple "we won't take proposals after xx date" would be fine, but no answer is a bit shitty. 2) Now that SC has run up the white flag on this round, do I bother to contact PO2 and say "Uh, we're more incompetent than even we thought, so you don't have to worry about our late proposal anymore."? I probably should out of courtesy because I may send something to this program in the future, but if PO2 is too busy or doesn't care enough to get back to me, it's possible yet another email will just elicit an exasperated sigh.

Tuesday, January 13, 2009

Faculty Fiasco

What is it about academics that so many of us feel the need to wax poetic about the problems associated with any process that is bringing about change? Our college is in the process of dramatically re-organizing it's structure at all levels. These changes will be harder for some of the small departments than the large ones, but the Dean has suggested a plan, which is being tinkered with by a committee of the department chairs with feedback from their departments. No one is being left out of the process and there have been many opportunities to weigh in.

One of those opportunities was yesterday, in a full meeting of the college faculty. The chairs and the dean presided over the meeting and discussion. Because there has been so much turmoil over the different re-organization models, the meeting started off with a very simple premise. A motion was introduced that essentially stated that the faculty would empower the committee of Chairs to create a small number of sub-committees, each of which will have the task of investigating a specific aspect of the re-organization (eg. Graduate education, undergraduate education, administration of the new organizational bodies, etc.). So, already we have a committee of departmental representatives begetting a new generation of committees. Great.

But here's the kicker. We don't even have a proposed structure of the college that anyone can agree on yet! Several have been proposed, but people felt that it was impossible to evaluate them without filling in the details of the models. But how are we supposed to fill in details when we don't have a defined structure? Are we supposed to waste time filling in the details of five different models? The whole thing is a giant steaming turd as far as I'm concerned, and all people wanted to do was complain about change rather than doing anything. We spent an hour and a half letting people vent about why and how they were opposed to the idea of change. One guy even started out with "I feel adrift, with no idea where I'm floating and no land in sight." This prompted me to turn to my neighbor and friend to say "I had no idea the drama department was in our college!" Maybe having two junior faculty trying not to make it obvious that they were mocking others in the college was not the best idea, but for fuck's sake.

I don't envy the dean. He is trying hard to have the final plan come from the ground up rather than forcing us into a scheme. I think that is a good idea, but it's like herding cats. Trying to get almost 100 faculty members to agree on anything is a monumental challenge, but on a completely new organization for the entire college? Epic.

Figure 1. The Dean's new job.

Monday, January 12, 2009

A big day

There's a lot going on today in the land of PLS. The first and most obvious is that it's grant due day. My solo grant is ready to go after one last once-over. I didn't get all the data I wanted to put in, but I think I got enough. Combined with strengthening the methodology and the Broader Impacts section, I'm pretty happy with it. My only fear is the dreaded "too ambitious" tag. Obviously I don't think it is too ambitious, but it could be read that way by someone who doesn't do the type of stuff we do. I guess I will have to wait.

Grant #2 is an unknown. Still no draft from Senior Collaborator after promises to have it to me on Friday. Still nothing back from the program officer to allay me fears that it is going in late and that she won't accept it. Nevertheless, my part is done (without being able to comment on the proposal) and I will have my grants people sign off on it today.

I also have a New Grad Student starting today. I don't know that NGS will get the chance to do much today but figure things out around the dept./university, but it'll be good to have another person in the lab.

Finally, as though this wasn't enough, the college is having an all faculty meeting today to battle it out of the new structure going forward. I'm not sure if it's going to be a giant cage match or a civil presentation, but it could be anything along that spectrum. Will there be blood? I don't know, but I think I'm hiding a smock under me seat in case it gets as messy as the front row at The Blue Man Group.

UPDATE: Grant #1 submitted. Still no draft from SC and no answering their phone either. College-level faculty meeting = epic fail.

Friday, January 9, 2009

Mandated Post-doc Mentoring

For anyone who is not writing an NSF grant for this round, you might be surprised to note that, as of January 5th, there are new rules regarding post-docs. The text reads as follows:

One of the most significant changes to the PAPPG is implementation of the mentoring provisions of the America COMPETES Act. Each proposal that requests funding to support postdoctoral researchers must include, as a separate section within the 15-page project description, a description of the mentoring activities that will be provided for such individuals. Proposals that do not include a separate section on mentoring activities within the Project Description will be returned without review.

I am all for the proper mentoring of post-docs, but this seems to me like just another thing to put words around in a grant. It's not going to change how I run the lab or how I plan to metor my post-docs. Is this just in here for old-timers who ignore post-docs?

It's actually a challenging little piece to write because my first version came across as though I was heaping a ton of responsibility for the lab onto the post-docs and sitting in my office with my feet up. Now I'm strugling with making it sound like a mentoring relationship without sounding like I'm going to be stalking my post-docs and smothering them. Ugh.

The Kübler-Ross grief grant cycle

I have a confession to make. I actually kinda like writing grants.

Before you immediately think "Dude, you should seek treatment", let me explain. I don't like the deadlines, the number of grants we have to write (each with their own format) or moving target of satisfying the panel. I do, however, like taking an idea and "selling" it in a way that makes someone who has never thought about what you are doing say "I want to see how this ends up." I think it's what we all like about what we do - the ability to excite people about our ideas and projects. If you can't explain what you are doing to someone and get them excited or interested, you're in the wrong business. Seriously, you're wasting your time.

Grants are the written embodiment of this pursuit. When you are writing a manuscript you have the results and you are reporting what you find in the best way you can. With a grant, you are selling the potential of something, which requires you to convince others of your ideas in the relative absence of data (even though you now have to have half a project done in order to get it funded, but that's a topic for another day). It requires a different way of writing and it's something I take a bit of perverse pleasure in.

That's not to say that the process isn't arduous. It is. But I have come to see it in terms of the The Kübler-Ross steps of grief:

Shock: Holy shit, that deadline is coming up fast! Is it that time of year already?

Denial: I still have plenty of time though, I can get a few things done before I really get into the writing.

Anger: How did I let myself wait so long?

Bargaining: This is the part where you figure out how to structure the grant. Which part do I emphasize for this particular grant opportunity? How ambitious do I make it? What can I fit into the budget without looking greedy? What personnel do I need to complete the project?

Depression: There is a point when writing every grant (at least for me) where I lose the forest for the trees and it seems like the grant is a scattered mush of directionless words, associated only by being in the same document. I usually have to put the whole thing down for a couple of days and come back and read the whole through, from start to finish. Only then do I regain some perspective and start making the connections.

Testing: I try and send it out to a couple of colleagues who are in different sub-fields. If they get it and understand why the project is exciting I know I'm on the right track. If not, it tells me where I need to strength my description or make connections more obvious.

Acceptance: When everything falls into place and I can read it and feel like I got all my points across. The only left to do at this point is submit the thing and hope for a second stage of acceptance.


I knew there would be a name for it, there is for every fear. Tropophobia: the fear of moving. I would impress you with the derivation of the word if I haven't spent so much time in grade school Latin class giggling at words that sounded dirty.

In any case, there is a lot of Tropophobia going on around the building these days. As I mentioned earlier, I'm ready to walk out the front door of this building and toss a grenade over my shoulder, but others don't feel that way. I can understand that moving after being in the same place for 20+ years would be intimidating. Some of the labs around here are crammed full of shit from the Nixon era and I can hardly imagine what will be unearthed when we really do make the move. To me, the move would be a great opportunity for a fresh start, unencumbered by years of built up garbage equipment. But what the hell do I know? Many of the older faculty are looking at the move like it is going to cause an enormous loss of productivity while the lab packs and unpacks, but those who are complaining about this most vocally have time to do so, because they haven't published in ten years and I'm not sure what productivity they are worrying about.

What has not helped is the fact that we don't know when we will actually be moving, but we know it will be "soon". Basically, as soon as we CAN move in, they will want us out of here running, but no one knows when that will be. Rumors swirl around and we get updates like the Bush administration used to update the Terror Alert, post 9-11. I think the current move alert status in yellow, but it could go orange next week.

Thursday, January 8, 2009

Good grant/Bad grant

Monday is the target date for these two grants and it can't come soon enough. I will be very excited to have these done and out of my life for now.

Grant #1 is my baby and the main project I want to pursue in my lab. I'm really excited to pursue the questions in this grant and it will be the first step of my lab's long term goals. I am the sole PI on the grant and it is getting to my favorite stage of grant writing, where everything is coming together - the budget is all set, the text is in decent shape, with only a few little sections to fill out, and the higher-ups have mostly signed off on it, meaning I won't have to run around on Monday tackling people in the halls for their signature. It's organized, together and I won't be stressing about it in the final minutes.

Grant #2 is a totally different story. #2 is a collaborative project with a Senior Colleague. It's also a really exciting project and will lead to some kick-ass data at the end of the day. The physical grant, however, is a bit of a mess. SC has been doing most of the writing, but I still have yet to see even a decent draft. The budget is a skeleton and we are scrambling to get our broader impacts section project set up. To top it off, SC isn't exactly reading all my emails very well.

Actual conversation yesterday
PLS - I have a meeting with my grant people tomorrow, so if I could get the budget on your end and a draft I can have them sign off on it here.
SC - I'll see what I can do, but I hadn't planed on meeting with the people here until Tuesday.
PLS - Um, you do realize that the deadline is the 12th, right?
SC - I thought you told me the 15th.
PLS - It was the 9th, until I decided to send it to a different program after talking with the Program Officer.
SC - Not the 15th?
PLS - No, never the 15th.
SC - Hmmm, I'm not sure I can catch everyone here to get it signed off by the end of Monday.
PLS - (Long pause)
SC - Let me see what I can do, but can you talk to the PO and find out how "hard" the deadline is?
PLS - Suuuure, no problem. (thinking - Great, I get to go to the PO and tell her we're incompetent. Excellent.)
SC - Alright, talk to you tomorrow. Oh, I'm busy until 2:00.
PLS - Right then.

Thank goodness the NSF dates are "target dates" with a little flexibility, but for eff's sake.

No animals were injured in the making of this reinactment.

Wednesday, January 7, 2009

Budgetary Bulimia

Why is it that every time I finish putting my budget together I look at the final number and feel sick. I'm going to ask them for how much? Where's the nearest bathroom?

Should I worry?

When I took this job there were three features that made it very attractive. 1) Location. Both my and my wife's families are within a 2 hour drive from where we live. After spending nearly a decade in a distant place and with a child under a year old, it was very appealing to finally be near family again. 2) Collaborations. The university is investing heavily in my subfield and has made several hires in that area recently, with another planned (assuming they lift the hiring freeze one day). 3) Work/Life balance. Though Employment U is not a superpower R1 research juggernaut, research is a major focus and well supported. Our class load is not overwhelming 1:1.5 (with the .5 being a journal club-type "class") and the deans are generous about accommodating active research. At the same time, one could putter along with a small research group and limited funding and still get tenure.

I have no plans to putter, but unlike Isis, I am too tall to sleep on my desk. I aim to build a decent sized lab (not a small corporation) and juggle between 2 and 4 grants at any one time. That's what I think it will take for me to feel happy with the progress my group is making and still be able to spend time with my family. There are people in the department who pull this off, but they are the minority.

Obviously, I have been pushing hard in the last month with the two grants I am about to submit, but I would say that I am generally here longer hours than most (maybe all) of the other PIs. I have been told several times in the last couple of weeks something to the effect of "people here just don't work as hard as you are", and if my experiences being the only person in the building over the holiday are any indication, they're right. This situation might change entirely when I move to the new building, in which only active labs are going, but maybe not.

Now, I may not get any of the grants I have submitted and might find myself nursing a single grant along for several years, I have no idea. I don't think that will be the case, but at this early stage I can only speak to my ambitions and nothing more. Nevertheless, am I going to be motivated to churn out grant proposals at this rate in five years if I am one of a few who are pushing that hard? The culture of your environment can have conscience and sub-conscience effects that influence your actions. I am (perhaps naively) relying on my internal drive and the pace of others in my field to keep me motivated to keep running, but will that be enough to keep from starting to jog?

Of course, the running metaphors are also serving to remind me that even jogging would be an improvement to sitting behind my desk or standing in the lab all day. Must. Get. Exercise. Fat ass.

Tuesday, January 6, 2009

Granting conundrum

In the midst of writing the grants I have been furiously working on, I have been approached about another opportunity by someone who was a post-doc in the lab I did my PhD. The grant combines part of the focus of my current lab with some of the work I did as a PhD student, so it is well within my wheelhouse. The problem is that I have an exceedingly low opinion of Former Post-Doc and don't trust FPD to tie their shoes, let alone write a million dollar grant that is fundable. But, before I dismissed the opportunity outright, I got some details and it turns out the FPD has recruited a Major Player in the field to be another co-PI.

So, the situation has changed, at least on the surface. MP would not likely get involved with something that stands no chance of being funded and MP is young enough where they are not just lending their name to the grant, but they would be involved in the writing and data analysis. MP also has the downstream resources to make this all work, whereas FPD most certainly does not and I am not ready to commit the resources required to a side project. With MP on board, there is a serious chance this could all work.

Normally I would throw my hat in the ring, but I can't escape the memories of FPD's incompetence in all things research related, and particularly in matters of data organization, which this project would require a lot of. After thinking about it, I see three possible outcomes if the project gets funded.

1) FPD makes my life hell with constant bungling of data and resources to the point where the student I would have dedicated to the project would be in a state of constant frustration and not get the most out of their degree.

2) MP exerts enough influence to keep FPD's insanity to tolerable levels and the project moves forward without too much trouble.

3) I carve out part of the project to focus on and exist on that island, while contributing to the whole in a minor way.

I could deal with either #2 or #3, but I would feel very good about option 3. No one wants to work with someone who flies with their parachute packed and one eye on the door, ready to jump at the first sign of trouble. That's also not how I like to operate. At the same time, if I get involved I absolutely have to safe-guard my interests from the natural disaster that is FPD.

Perhaps if I insist on a clearly defined list of responsibilities well before any writing gets done, I can adequately assess FPD's potential to sink the ship. I am loathe to get involved with a potential crippling collaboration so early on, but the possible data have me weighing the pros and cons.

Monday, January 5, 2009

Technically, you're an ass.

I understand that technicians are often under-appreciated for the work they do and that they regularly have to field demanding requests from lots of people. I also get that some of those requests might be beyond the scope of their job and that this can lead to a somewhat jaded and protectionist persona, but I don't think these factors excuse someone from being a miserable human being.

This morning I contacted the facility whose ultracentrifuge I used over the weekend to tell them about the drive malfunction and find out if they had experienced the problem before. They had not, but the junior technician in the lab asserted that the reason for the malfunction was because I had selected the "hold" option, rather than program in a time. I've worked with these centrifuges for 5 years and know that his argument holds no water. When I told him that I had never run into that problem, he became more defensive and confident in his diagnosis, which I just let slide (even after he admitted that his boss had much more experience with the machine - the same boss who set the run up with me) because maybe their particular machine is quirky. Plus, I was only looking to tell them in case the machine needs service, I was not suggesting that the failure of the run was anyone's fault.

After that "discussion" stalled out, I inquired whether he could suggest another lab that might have the tube caps, which would prevent my tubes from collapsing again. I prefaced this with the fact that I would be ordering my own set for the future, but that borrowing a set in the interim would be helpful so that I could complete my experiment. The response I got shocked me so much I didn't know what to say. "Well, that's really your problem and not something you should depend on us for." My simple request for the names of people to contact was really too much heavy lifting for him? He eventually suggested two labs who use the rotor frequently, but WTF? So, Junior Technician in Core Facility Across Campus, I raise a glass of F.U. in your general direction and hope that you don't live your life like you work your job.

That experience, combine with me going tits-up in the icy parking lot and landing on my computer bag, not two steps after leaving my car this morning, has made for an enjoyable day. Now I get to go home for dinner and bed time for the wee one before coming back and watching more experiments go as well as the Titanic's maiden voyage. Next Tuesday can't come soon enough.

Novelty in Science

Last week, Comrade PhysioProf asked how people go about generating novel scientific concepts in their field. I've been bogged down in the lab and didn't get a chance to sit down to respond until now. Most people responded suggesting that they either apply new methodology to an old problem or follow up on the most unusual or demanding data. While I think that is a key element, I would like to introduce another possibility: capitalizing on the diversity of nature.

I don't work on model organisms. In fact, one might argue that I do the exact opposite. My work thrives on finding the odd balls and misfits and trying to understand why they are the way they are and how they got to be that way. I don't mean chasing down spiny echidnas or duck-billed platipi, more like collecting and working with groups of organisms that you likely don't even know exist. It can be a painful way to proceed when so many major techniques can only be used when you have a basic knowledge of the organism. When you are starting from square one with a bug (generically speaking, not an insect) that has never been described before, or from which only basic descriptive details are known, there is a steep hill to climb before there is a big pay off.

Of course the flip side of that is the possibility (probability) that you stumble across something totally novel. As an example, take the case of the malaria pathogen, Plasmodium. The actual pathogen has been know for a long time and, as one might expect, been the subject of intense research since it was first isolated. TEM studies had shown an unusual organelle in Plasmodium of unknown function, which was termed the apicoplast (because this organelle is shared in other members of Apicomplexa, such as Toxoplasma, as well). It was unclear what the organelle did, but people hypothesized that it was involved in infection.

Combining established methodology and contemporary evolutionary hypotheses regarding the evolution of the group that includes apicomplexans, an international group showed conclusively (McFadden et al. 1996. Nature 381:482 - no link because of age of the paper) that the apicoplast is a relic plastid (chloroplast). Not only did this indicate that the apicomplexans evolved from photosynthetic algae into some of the nastiest pathogenic bugs out there, but it also provided a novel way to attack malaria without human side effects. If you can target drugs to plastid genes, there is no concern that human genes will get caught in the crossfire.

Now, if you have traveled to a country where malaria is a problem and taken the drugs, you are probably thinking "Bullshit, I took Chloroquine and there were certainly side-effects." That's true, mainly because of the difficulty in specific drug targeting into the apicoplast, but this avenue remains one of the most promising opportunities to prevent and even eliminate malaria at some point in the future.

So, novelty in science, for me, comes from exploring the strange and unusual things that have evolved all around us. There is no shortage, I can assure you, and there are probably fewer people studing 90% of eukaryotic diversity than there are studying a single human cell line. In fact, of this I am sure. If what got you into biology was not how blood flows through the body or that you wanted to hug dolphins one day, it's time to realize that animals are boring and plants are just dry algae. Get into to the literature a bit and see what else is out there.

Sunday, January 4, 2009

What's the worst that can happen?

Was what I was thinking when I left the lab across campus after starting the centrifuge. I had gone to a facility to use their ultracentrifuge for a project I am working on and was shocked to find that they did not have the caps that sit on top of the plastic tubes and keep them from distorting. Who has this rotor without the caps? It didn't make any sense. On the other hand, people had been using it for months at even higher speeds than I was, so I figured the tubes wouldn't be too badly affected. If they were, other people wouldn't be using it, right?

Figure 1. The worst that could happen.

Well, as you can see, they must be using something else. It's a fuzzy picture, but let me fill in the details you may not be able to see. That's a tube that previously contained material that I do not have much of. In fact, that was about 3/4 of the sample that I had spent a week in North Carolina getting. The tube utterly collapsed and crushed most of the sample out, which apparently then evaporated, because there is no sign of it anymore. The sample is likely useless now, though there is a slim chance I can recover a bit.

Deadlines will make you do stupid things without thinking them through. Dude. Fuck. Sigh.

Thursday, January 1, 2009

Why I shouldn't be trusted...

At least with kid's toys.

For Christmas this year, my sister-in-law bought our daughter a toy that basically shoots small plastic balls into the air with random amounts of force and, to a lesser degree, direction. While I appreciate the gift, it might be a bit early for the wee one because the balls go everywhere and it would take her forever to go collect them all and put them back into the ball-firing-mechanism. Nevertheless, it did amaze her to watch her older cousins play with the new toy and the noise of the music and fan added to an already overwhelming day for her.

Figure 1. Random ball-firing mechanism that can assult your child. Notice the green ball about to attack. Subsequent pictures have been confiscated for evidence.

So, what happens when you leave Daddy to entertain the wee one for several hours? He finds ways to get the wee one involved with her new toys. Knowing that the wee one likes fans and air blowing in her face, I thought it might be fun for her if I tipped the toy over and just had it blow air at her. Solid plan, it seemed, because wee one though this was very funny, with her limited hair blowing in the breeze. That was of course, until the one fatal flaw in the plan was revealed when the ball chamber, thought to be empty of contents, was hiding one surprise. I watched a two inch plastic ball launch out of an item I was aim at my daughter's head and plunk her squarely in the face and the wee one's transition from laughing to crying was seamless. The good news was that I did this directly in front of my mother-in-law. Oh, wait, that's not good news.

The interesting thing is that up until recently, the wee one has had a goldfish memory and would have been playing with that same toy 10 minutes later. That stage has apparently passed, because anytime we turn it on now she looks terrified and tries to scootch up any part of the nearest adult. This might be a toy that goes away for a while and comes out in a couple of months for a retry.

This is the last non-science post for a while, I promise. Happy New Year.