Tag Archives: science

Let there be pie

It’s 10:45 pm, Monday night. Monday 03-14, Pi(e) day. I breeze into my kitchen after a long day of work and couldn’t NOT make pie on Pi(e) day. I’d been going back and forth on whether to go to the hassle most of the afternoon and evening. When I was still at work at 8:00 pm, I almost convinced myself that I didn’t really need to do it. After all, I have two manuscripts to finish editing, graduate student qualifying exams to review, undergraduate letters of recommendation to write and who knows what else. Pie could wait until another time.

But a thought struck my mind.

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It’s the start of spring – I might actually be able to grab some rhubarb from the store and wouldn’t that pair wonderfully with the ginger ice cream I had made a few day ago? Ahhh, the allure of rhubarb is simply too tempting for me to ignore. Store number one – out of luck, I live in Georgia now and wasn’t entirely sure that I would spot it at all. However, store number two (I love residing within walking distance to not one, or two but three grocery stores!) revealed a few vibrant pink stalks. I quickly grabbed the few remaining pieces and silently cursed (or not-so-silently, but hey, I was at the Murder Kroger). Not nearly enough for a full pie. Now what? Another stroll through the produce section had me stopping at the peaches. And the third pass through at the blackberries. Alright, I may be a little off script, but I think, just maybe, not only will it not be a complete disaster, but it may actually be quite good.

I’m quickly and assuredly making decisions as my pie idea forms in my mind – it borderlines on manic. I choose a buttermilk crust since I have some leftover buttermilk from a batch of biscuits I made over the weekend. Yes, I think that should do the trick. Given extra wet nature of the rhubarb, peaches and berries – I think I’ll not only par-bake the bottom crust, but seal it with an egg wash as well. Because the difference between an okay pie and a transformative one is often in the details of the crust. Oh! I’ll do a lattice top – won’t that be pretty! So, perhaps I’ll do 1.5x the recipe for the crust. No big deal.

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I toss together my coveted rhubarb, a few bordering on underripe peaches and the handful of blackberries along with some sugar, flour, a dash of cinnamon and a couple of teaspoons of grated ginger and give it all a good toss and let it meld while the pie dough chills. A couple of cocktails, a load of dishes and the beginnings of a long and rambling blog post happen.

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Pie, no matter how well done, is impressive and needs to be shared, if only to glory in the accolades it will undoubtedly receive. Perhaps because of the underlying assumption that it is a brave soul who attempts to put together such a concoction of pastry and fruit. The dough could be too tough or crack when rolled, the fruit too watery or worse, sickly sweet from adding too much sugar, the ratios of the two could be completely unbalanced. The sheer thought of baking a pie is overwhelming enough to scare people away. Consequently, offering pie alà mode the day after Pi(e) Day was met with an absurdly high level of enthusiasm from members and friends of my lab.

For the inexperienced, pie seems impossible – and rhubarb-peach-blackberry pie made up on the fly, particularly when paired with homemade fresh ginger ice cream (a stroke of genius) even more so. A number of students expressed awe and wonderment at the ability to tackle such a task, followed by a sad statement regarding their lack of confidence in this arena.

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My actions Monday night are reminiscent of the recent days that I’ve spent in my lab. We finally arrived at spring break during my first semester of teaching undergraduates (the semester prior was dedicated to graduate teaching) and it was a busy, and sometimes impossible to maintain semester. I desperately craved a break and contemplated renting a cabin in the north Georgia mountains to escape from it all. Yet, in the end, I spent most of that time in the lab after a seemingly endless hiatus. Regardless of the time spent away, I storm into the lab and begin tying up a number of experimental loose ends.

I’d forgotten how much at home I feel in the lab. I certainly had forgotten the sense of accomplishment one has at the end of the day spent on your feet, running around from the warm room (our yeast like to grow at 30º C) to the bench, to the autoclave, to the glassware cabinet, to the PCR machine, to the centrifuge, to the gel electrophoresis rig, etc. There is an underlying ease and confidence to my actions. It feels good. And if the gel of my PCR is any indication, I haven’t lost my lab hands. Not only is it comforting to spend time back in the lab – it’s genuinely fun.

It’s difficult, after nearly a decade of time spent in the lab, to remember that it wasn’t always second nature. That the very reason that I can waltz into the lab after six months away and nearly immediately encounter experimental success is precisely because I’ve had a decade to slowly, but surely, hone my skills, encountering a turning point that remains imperceivable to me as to when exactly it occurred. One of the more challenging aspects of my job is to to teach people how to think scientifically and importantly, to not judge too quickly when they are not immediately successful. Or to judge too harshly when a young scientist can’t immediately pick up on the nuances of an experiment or how to optimize a protocol or manage their time.

{Note: there are MANY new aspects of my position that I attempt with complete uncertainty – and am learning to forgive myself for not knowing how to do all of them with expertise. But life in the lab? That I know something about.}

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What’s it like to be unsure? To not know, or to carry the confidence that what you’ll do will end well? Intellectually, I know I that I did not arrive in the lab (or the kitchen for that matter) fully formed. But now it seems foreign to me, the notion that I didn’t always have such a deep intimacy of my study subject or, when in the kitchen, flavor profiles and techniques or to have a repertoire of resources and accumulated knowledge to draw upon. In hindsight, there are a few things that must have contributed to my development. 1) The sheer repetition of action and consistency in results contributed significantly to my confidence. 2) Learning who to trust with protocols/recipes – just because something is available online does not it will yield reliable outcomes Who are the scientists/chefs that I respect and want to build my own work off of? 3) Appropriately testing a technique and establishing a baseline before making educated modifications – but not to be afraid to try something a little different and outside of my comfort zone. 4) And finally, embracing the notion that sometimes I will fail. And possibly fail spectacularly, knowing that the failure is worthwhile because I will have learned something critical.

I struggle to find ways to extend my patience with naïve scientists, to remember to acknowledge the small victories and to cultivate an environment in which failing is a beautiful learning opportunity. To be able to remind them that the very process of doing something is as important as the result. That we may not know the outcome as we embark on a new project, but, that we can hopefully navigate logically and with our collective knowledge through the murkiness to a breathtaking destination.

And when that fails, sweeten them up with pie.

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Rhubarb-Peach-Blackberry Pie with Buttermilk Crust

Buttermilk Crust:

  • 1 7/8 (aka 2 cups – 1 T) cups all purpose flour
  • 3 teaspoons sugar
  • 3/8 teaspoon kosher salt
  • 12 tablespoons butter, cubed
  • ½ cup plus 1 tablespoon buttermilk
  • 1 egg, beaten with a little water for egg wash

Filling:

  • 2 ½ cups rhubarb, chopped in ½ inch pieces
  • 3 peaches, peeled and chopped in ½ inch pieces
  • 2 cups blackberries
  • 1 cup sugar
  • ¼ cup flour
  • 1 tablespoon arrowroot starch
  • 2 teaspoons grated ginger
  • ½ teaspoon ground cinnamon

In a food processor, pulse the flour with the sugar and salt. Add the butter and pulse until the mixture resembles coarse meal with some pea-size pieces remaining. Drizzle the buttermilk on top and pulse until the dough just comes together. Turn the dough out onto a work surface, gather up any crumbs and divide into two disks – one a little larger than the other. Wrap in plastic and refrigerate until well chilled, about 1 hour.

Preheat the oven to 400 degrees. On a lightly floured work surface, roll out the larger disk of dough to a 12-inch round, a scant 1/4 inch thick. Ease the dough into a 9-inch glass pie plate. Trim the overhanging dough to 1 inch, fold it under itself and crimp the dough decoratively. Line the crust with parchment paper and fill with pie weights or dried beans. Bake the crust in the lower third of the oven for about 20 minutes, until barely set. Remove the parchment paper and pie weights. Brush with egg wash, reserving remaining wash. Bake for 15  minutes longer, until the crust is lightly browned. Let cool on a rack. Leave the foil strips on the crust rim. Reduce the oven temperature to 350°.

Toss together all ingredients for the filling. Pour filling into par-baked crust. On a lightly floured work surface, roll out the smaller disk of dough to a ~12-inch round, a scant 1/4 inch thick. Using a pizza cutter or knife, cut into ten, 1-inch strips. Place strips in a lattice pattern (5 in one direction and 5 perpendicular). Brush with remaining egg wash. Cover the edge of the crust with strips of foil and bake for 45-60 minutes until top lattice is browned and filling is bubbling. Let cool.

Serve with homemade fresh ginger ice cream spiked with some Au Thym Sauvage from Farigoule de Haute Provence (and why it has a place in my liquor cabinet is a story for another time). Although, to be fair, most any type of ice cream will suffice.

 

Scientific Style

I’ve fallen out of the practice of writing. It’s gotten to the point where I actually fear having to do it. There’s a manuscript hanging over my head, a paper that I desperately need to publish so that I’m known for something other than finding Candida albicans haploids (although, to be fair, this study also regards ploidy variation). More importantly, to wrap up the loose ends of my postdoctoral research and develop my own independent program.IMG_4027

If only I could wish that the words would write themselves. Except the paper is already written, had even been submitted and subject to review. At first glance, the rejection was hardly a blow – all reviewers agreed it was technically sound, however there were mixed feelings to the degree in which it advanced our knowledge and thus, wasn’t impactful enough for that journal. The solution seemed simple: a few quick edits and submit to a lower-tier journal.

That was five months ago. It shames me to admit that, I don’t usually operate at snail speed. Granted, that first semester as a faculty member, combined with the cross-country relocation was a substantial transition. Unbelievably, in that time, I set up a functioning lab, hired a technician and now have experiments in progress (!!!). But the manuscript continues to sit stagnant on my desktop. I usually circumvent writers block by finding an existing document and revising, editing and re-writing the whole damn thing to transform it into something distinct from the original. Not so with this paper.

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The brick wall my head keeps pounding into? I took the reviews personally. Strike that: I took the slightly less-than-glowing review personally. The positive review didn’t resonate in the least. As a naïve graduate student, some time ago now, I remember being told to not take these things personally. And most times, I think do a pretty good job of it. I’ve internalized that perspective to the point that I find myself frequently qualifying the comments I provide with the ubiquitous “it’s not you, it’s the science” statement. But is that the truth? I enthusiastically stand on my soapbox, advocating that scientists are individuals with interests and lives beyond just their science. Yet, that sentiment does not diminish the degree in which the work that we do; the research we perform and the context in which we convey the results and their significance reflects who we are.

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Scientific style has been on the forefront of my mind as I’ve been making decisions after decision on establishing the lab and the direction to move towards. So the “it’s not the science, it’s the lack of impact” comment struck an overworked and exposed nerve, disabling me in a way that I am not proud of. It wasn’t that I received that particular review, I support the rigor of peer-review, it’s that I knew it wasn’t an unfair statement. The paper, as previously submitted, DID lack meaningful insight and failed to emphasize the novelty of the results. I take full responsibility for its lackluster appearance. Ultimately, I appreciate the rejection – it has given me the opportunity to give the paper a desperately needed makeover.

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Why shouldn’t my scientific writing and research have a signature style? As with so many other elements of my life – I like being distinctive and striking to the beholder. I’m currently obsessed with residing at the intersection of form and function. Too ‘functional’ and you end up with boring ideas and dry writing. Too much form and flair and you run the risk of losing substance and credibility. I’ve spent hours crafting a single paragraph and months upon months playing with data visualization. Finding the balance between form and function not takes time, but an enormous amount of work, all in the hopes that it looks effortless.

In this day and age of ‘publish or perish’ in academics, my proclivity towards staying true to my style (not to mention my idealism towards mentoring) will certainly prevent me from being my most productive. I know that. But for me, external metrics (like number of papers published) are rarely sufficient for my sense of satisfaction. Up to this point, my own high expectations have guided me in my career, with measurable success. We’ll see if this holds true in the future.

Expectations

(Woosh)

That was January, flying out the window. I won’t lie, January 2013 was a pretty complex month me. I spent most of it hibernating in my apartment (and the numerous days of sub-freezing temperatures only reinforcing my behavior).

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I tackled ghosts from last year and it was more difficult and took a larger part of me than I anticipated. 2012 was a hard year and it was only okay because I had allowed myself the year to heal. Heartbreak takes time, I had learned the hard way previously in my life and as such, I had no expectation that I would bounce back quickly. But when the one-year mark passed and despite a significant career achievement, I was disappointed in myself, an emotion that digs deep into my mind and settles in for while (and let’s face it: it’s the middle of winter – who doesn’t want to settle in for a while?). And once that happens, it’s nearly impossible to get yourself out of that downward spiral.

Why wasn’t I happy yet?

I’ve all but abandoned this blog – it’s primarily been about food, yet I don’t want this to be a perky, isn’t-life-grand!!! and OMG are you as obsessed with quinoa as I am? sort of space. Those sorts of blogs are increasingly irritating to me, resonating as shallow and superficial and isn’t something that I want to participate in or even be associated with. I have no interest in food styling and having a whole cupboard full of food props. Instead, I strive to have similar tones of emotional honesty that I read here and here. (I’m not entirely sure if its a coincidence that both authors live in the Pacific Northwest). Don’t worry – I still love food.

It’s just that I’m moody.

And that mood has had undertones and, in most cases, overtones of sadness. There’s been a rain cloud that’s been hovering over my head for longer than a year now – and in January I got fed up with it. I tried to actively push it away. Turns out, it’s pretty challenging – pushing a cloud. I even went to a pretty terrible social dating event that completely freaked me out and made me realize that perhaps telling myself that I was ready isn’t actually the same as really being ready. Did I mention that I am currently writing a big career development grant? No? Well that’s happening also and wrecking all sorts of havoc on my mental state.

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And then suddenly, my perspective shifted. I read two articles (one I can’t recall where I found and this other one). The first referenced a book I distinctly remember reading as a 10th grader for Honor English, Man’s Search for Meaning. Now, while I remember reading it, I can hardly recall any of the details aside from it was written by a psychologist and Holocaust survivor. But, this article, the one I can’t seem to place, made the point that you don’t need to be happy to having meaning in your life. It’s a somber thought, I know, but it made me realize that perhaps I shouldn’t have happiness be the state I aim for. There is oodles of meaning to my life and it turns out that this emotion is much more important to me.

The second article centers around the idea of joy. That it is not only distinct from the idea of pleasure (my first cup of coffee in the morning is a moment of pure pleasure); but that joy is intense, complex, simultaneously surreal and yet fully rooted and at times exceedingly uncomfortable. As I’ve been holed-up, writing my grant, I’ve come to realize that’s how I feel about science. Being a scientist is hard (and not because you have be super-duper nerdy smart, but for a whole host of other reasons). I’ve even at times considered leaving it – but something, something that has always seemed beyond definition, stops me.

I’m pretty sure that something is joy.

Then a funny thing happened. Once I let go of the idea of happiness, accepted the meaning in my life and realized my joy, I’ve been able to see things clearly. It feels different. It feels good.

Oh, and that rain cloud? It seems to have lifted.

My Break-up Nature Paper

I have an article in Nature that is going to be published at the end of the month. As a biologist, it’s kind of a big deal. Academics are horrible elitist snobs and the truth is, where you publish your work matters and Nature is at the top of the food chain. So this is a notable accomplishment.

I got the final acceptance letter of the manuscript exactly one year after a significant relationship ended. That break-up was instrumental in fueling the progress of the project. I was left homeless for several weeks, relying on the hospitality of friends, and spent long hours working in the lab on nights and weekends so not to take advantage or disrupt my hosts’ everyday lives. I spent my summer holed up, digging deep into the ancient literature (for my field that means the 1950s and 60s) and writing the manuscript, the perfect excuse to not go out and enjoy the weather or have a life. This fall was a whirlwind of travel, revisions, rebuttal letters and calls to the editor and finally acceptance.

It’s normal for me to hate a paper by the time it gets published. You spend inordinate amounts of time fussing with the explanation of the details of an experiment, the formatting of the figures, finding the balance of conveying the meaning and relevance of your results without overstating. It’s exhausting and by the end of it you can no longer see the story through the words. This particular paper has been more painful than most for a whole variety of reasons.

I know that I should be proud of this accomplishment, that it’s worth celebrating, but I find it impossible to do so because my thoughts almost immediately turn to the driving force of this paper. I vowed that I would try and get back ‘out there‘ once this paper was finished. Now that I received the pre-prints and we have a tentative publication date, that time is nearer than I’d like or am ready for. I’ve held on to this heartache longer than I should have. Tying it tightly to this paper was an excuse to not let go or possibly allowed me to avoid dealing with my feelings. I don’t discuss it, my horror story of a break-up but I carry it around with me; my own personal rain cloud. I’m not angry, but rather, severely disappointed in what happened and, at least for me, disappointment is a more difficult emotion to resolve than anger.

I’ve been hibernating lately (which the weather in Minneapolis facilitates nicely this time of year), acting the recluse, mostly because I’m terrified of the idea of letting somebody into my life, and becoming a part of somebody else’s. The problem is, that I miss it terribly and readily admit that I am lonely, but I haven’t gathered quite enough courage to make it happen.

Looking at the pre-prints of the Nature paper (meaning that it’s typeset and actually looks like what will be printed and is no longer a drab Word document) allowed me to read the article with a new perspective – as reader and not as an author. It turns out, it’s pretty cool stuff. I had forgotten that. Yet, woven within the text are the discussions over authorship order, the last minute hobbled-together experiments, the frenemy-like correspondance with reviewers and the agonizingly slow response from the editor. Ultimately, the paper is stronger and better written because of it all. But those challenges are not easily forgotten.

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 This is a self-portrait from a few days ago. I like it because this girl (although I don’t know if you can call somebody approaching 32 a girl) looks interesting. She has bright purple hair and likes to wear jewelry, but not makeup, and has a style that garners compliments from strangers. She has a nice smile and intelligent eyes, and although you might not see it in this photo, has a highly expressive face. She’s even been called charming and people like to be around her. Yet, without a doubt, there is more than meets the eye, as life experiences shape and change who you are. I just hope that it’s for the better.

I don’t have a good conclusion for this post, or my life for that matter. It’s only fitting, I suppose, just because you’ve published the paper doesn’t mean that you are finished with the story…

Defining Moments

There are moments in your life that are game changers. Sometimes they sneak up on you, quiet and stealthy and alter the course of your life subtly but significantly. Others walk right up and hit you over the head, leaving you dizzy and seeing stars.

If you are lucky, you can see the latter coming. (Other times, perhaps not). In these cases I believe you actually have the ability to  wield some control over the situation. Last week I found myself staring straight into just such an opportunity.

A few months back I wrote about the thrill of discovery. What’s just as satisfying as making a discovery is sharing it with your colleagues. I was at a fungal biology conference last week and had the opportunity to stand on stage and present the work I’ve been busy with over the past six months. It was a strategic move – my mentor and I  are currently writing up the manuscript and we wanted to break the news and gather feedback before we submitted.

I have very strong thoughts about how science should be presented. Which meant I put a tremendous amount of pressure on myself to meet my exceedingly high standards. Not to mention the mind-blowing nature* of my current work, and the pressure builds. And let’s not forget, I am a post-doc entering the job market and need to be unforgettable. This was perhaps the most important 15 minutes of my career to date. Maybe I’m being melodramatic, as I tend towards the theatrical, but this was a big deal and the reason I’ve had so many late nights.

For a while, I thought I was going to crack under all that pressure. I’m not sure if it was psycho-somatic or an actual illness, but I was sick to my stomach the entire 24-hours before my talk (and even several hours afterwards). I am embarrassed to even admit it, as I usually relish any opportunity to be in the spotlight. But I knew this was one of the defining moments. In fact, the last time I felt this type of pressure was when I was interviewing for graduate school. I was a naive 23-year old who had gone to hippie college and didn’t have a clue as to the academic architecture. I only had gotten an interview at Duke, as the other graduate schools I applied to flat-out rejected me, and I knew that it was my only chance to get into a Ph.D. program. I was sick to my stomach then as well. I even had to leave in the middle of my interview with the director of the program in order to run to the restroom to empty the contents of my stomach. But I must have done something right, as I made it into the program, and the rest is, well, history.

And I made it through this talk also. Adrenaline is a powerful anti-nausea drug. In fact, I am proud to say that I nailed it. It’s a moment in my life that I will never ever forget. I could feel the buzz of energy in the air as I was on stage – people really got it (one person told me later they could feel the hairs on the back of their neck rising as I was speaking). As I opened the floor to questions, the first response that I received was a marriage proposal (from an already married woman, but a proposal nevertheless). I couldn’t have asked for much more, except for perhaps a job offer.

It’s been a boost to my scientific self-confidence, which as been on a roller coaster ride for the past couple of years. And it feels damn good. Success is a mix of hard work and luck and I got extremely lucky to fall into a such a compelling project.

*For my nerdy science friends interested in what I am working on:

I’ve been working on a yeast species that is a human commensal and occasionally, if the opportunity arises can become pathogenic. For decades, its been thought to be an obligate diploid with no known sexual cycle (which makes genetics and molecular biology in this organism challenging). Recently a parasexual cycle has been described in which diploid cells mate to form tetraploid cells and subsequently undergo a non-meiotic process to return to a near diploid state. We’ve found that there is also a haploid state in the lifecycle of this organism. Not only will this greatly facilitate future genetic and molecular biology studies, it suggests that a haploid phase may be important for revealing recessive alleles, and thus exposing genetic variation for selection to act upon. Furthermore, mating between haploids cells can restore heterozygosity, a trait we observe readily in clinical isolates, that as been paradoxical given the propensity of this organism to undergo loss of heterozygosity events in response to stress.