Dorky present to my dorky self.

I am now going through my dissertation and making the corrections that my examination committee suggested, taking stock of everything that has gone on the last couple of months, and retroactively processing everything that I filed away for later. You know what that is code for? I am now reconsidering every answer I gave during my defense and, in a neurotic frenzy, thinking of how I should have answered differently, what I should have interpreted differently, or presented differently. I am really excited for all this anxiety to leave me already.

I think part of my anxiety and general neuroticism is due to the insecurity I felt in giving some of my answers, not only because of my own self-doubt, but because of frequently conflicting information I pulled out of my literature searches. For example, I was trying to find out if NF-κB can be activated by heat shock. You know what the answer is? Depends on who you ask. Depends on the system used. Depends on the interpretation of the results.

Science is always held up to be as an absolute by society (as evidenced by the evening news), as something that is beyond question and solid as a rock. People who actually do science, however, have a much different view of it. It is fluid, ever-changing, and up for constant debate. I guess half the point of a PhD is learning the skills to wade through the ocean of literature and pick the worthwhile apart from the flawed. Even that is only part of the battle. Many effects/phenotypes are cell type-specific and experimental condition-specific. It is quite possible, and even likely, that two groups testing the same question in two different ways come up with two different answers, both valid within the context of the experimental system.

So what is to be done then? What conclusions can be made? If you are me, in the middle of writing a dissertation and trying to avoid a stress-induced coronary, you pick the paper that says what you need it to say and move on. I hope that something that is relatively, if not absolutely true is good enough.

Although perhaps you shouldn’t.

That’s it. It’s over. I am done with graduate school. Short of a few minor revisions to my dissertation, the event which from now on will be referred to as My Big Fat Russian Defense is complete. Big and fat it was, tell you what (and I am not even talking about the ensuing celebration(s)). My entire family was in attendance: Mom, Dad, grandmother, aunt, uncle, complete with 8 year-old cousin. My people took up the back row during the defense. My advisor flew in from Arizona to give me away, so to speak, for which I will be eternally grateful. Friends from high school, grad school, and beyond were scattered throughout and somehow, the room was packed.

I was panicking, as I am wont to do on many occasions, and had been all morning and night prior. My body had decided that it no longer needed sleep and should instead toss and turn all night, pausing to nap only long enough to entertain bizarre and creepy anxiety dreams. The morning of the defense was fraught with last minute seminar practices and dashes to the department store for stockings. I had just enough time before the defense to worry myself into an ulcer. Please take my advice and schedule your defense for the first thing in the morning, if you can. There is nothing worse than not sleeping all night and having to wait until 3PM to get the show on the road. That hurt everywhere.

The seminar went off without major hitches. I was three clicks past nervous and the nervousness failed to fade after I began speaking, which for me is highly unusual. I was convinced that my voice was shaking in a completely un-doctorly manner the entire talk, but I have since been told it was perfectly steady. Good thing the freaking out was restricted to the inside of my own head. I did not break down in tears as many people do during their acknowledgments. I think I was too loopy and disconnected at that point for crying to be physically possible.

After I was finished speaking, I fielded a few really interesting questions from the audience, shook many hands and was hugged many many times. My examination committee then cleared the room and asked me to step out. The ground rules of the defense were set in my absence. [Oh how I wished for those extendable ears they have in Harry Potter. I was always dying to find out what they were saying about me before committee meetings. I think those closed conversations should be recorded and transcribed, unsealed like court records following graduation.]

I was then invited back into the room – the examiners had arranged themselves around a table to make themselves seem like less of a firing squad (they failed). They then went around the table asking me questions they had prepared having read my thesis. And you know what? They actually read it! all 230 pages of it. I was shocked. I honestly didn’t expect them to read the whole thing. But read it they did, picking up on minor details (apparently, discrete and discreet are not the same thing. Who knew?? Don’t answer that, Richard) and data fluctuations.

I can’t say that the exam really felt like it was a scientific discussion – it was much more controlled than that, with only one examiner engaging me at a time – but it also wasn’t a quizzing session. No one asked questions they already knew the answer to (I think that would have infuriated me. I don’t need to be treated like a peer, but I am not in elementary school). The questions ranged form the nitpicky to the global and occasionally terrifying. I answered most from actual knowledge, some from conjecture, and others prefaced with, “Well, in my own head, I think of it like this…” I only had to cry uncle (without actually crying, thankfully) on one question – I couldn’t remember how it was shown that heat shock factor (HSF) is activated by the denaturation of the heat shock protein (HSP) that sequesters it in the cytoplasm of unstressed cells (whew). In the grand scheme of things, and taking into account the hundreds upon hundreds of papers that I had read in the preceding month, I don’t think that’s so tragic

After about an hour into the exam I heard a quiet click going off inside of me – kind of like that sound the pump makes when your gas tank is full. I was done. My brain was stubbornly refusing to process any more information. Response times lagged, many more umms were inserted into my answers. Luckily, this occurred toward to end of the exam. I was asked to step out again, I suppose so that the committee could come to a decision regarding the outcome of my exam. I like to think this was perfunctory and mainly symbolic, but the fear of failure was still very real for me. I was asked to come back in after only about 3 minutes of sweating (eve more) and shaking in the hallway. Upon coming back into the room, I was greeted by smiling faces and a hand held out toward me with, “Congratulations, Dr. Kushnir!” I know that a lot of people would have shed a tear or a expelled a huge sigh of relief upon hearing those words, but all I could think of were my sweaty palms and how real PhDs don’t have sweaty palms and they will all soon find out I am not doctorly at all.

I would like to blame that particular reaction on the lack of sleep and overall nervous upheaval. I would also like to be able to say that it has all sunk in since then, that I am really done, and I really have received my PhD after 7 years of not always fun work, but I am not quite there yet. It’s not entirely real to me. I have yet to sleep a full night. My stomach is still positioned somewhere between my insides and my outsides at all times. My anxiety level is, however, slowly dropping. I don’t know if I will ever be referred to as Dr. Kushnir again, but maybe one day I will be able to look at my plaque without a wave of disbelief and squeak of panic.

Overall, I have to say that my defense was an overwhelmingly positive experience, one that I have no need to repeat ever again, big, fat and Russian as it may have been.

The plaque in the picture above was a present from my aunt and uncle. Once I make myself stop staring at it, I will find a place for it… perhaps mounted on a wall in a prominent spot in my house.

I have had grad student stomach to the n-th degree this last month while writing my dissertation and getting ready to defend. My stomach has not liked me in a really long time. I ate my way through the week before my dissertation was due and ran for the week before the defense. Turns out my body doesn’t take kindly to either approach. I think I just need to suck it up and wait until after the defense has come and gone and wait for the symptoms to fade away. Hope there is no lasting damage. Guess I will know once my celebratory hangover wears off on May 7th. Or perhaps the 8th.

On a more positive note, my school requires the student to be notified if there is a serious problem with the dissertation 72 hours before the defense. The 72 hour mark passed at 3PM today, Saturday the 3rd. Guess that means the defense is a go! Calm stomach, here I come. Until then, the Pepto is staying close to me at all times.

It’s so surreal. I am done. I finished writing and have handed my completed dissertation (all 230 pages of it) to my examiners. I will defend in less than two weeks and then I am completely done. Done done. It’s just not computing. Seven years of my life are coming to a close. I never expected to get nostalgic at this point. I have been dying to get out of academia and out of labs for at least half of my seven years in school. Now that it’s actually happening, I find the moment to be bittersweet.

I realize now what happened in my graduate career. I went down to the wrong path. It was no one’s fault, it just happened, as it so often does in science. I came to grad school a devout cell biologist with a strong interest in cell signaling (feel free to gag. Most people do) and of course, viruses. I love the stuff. I read signaling papers like candy, like little logic puzzles that fit together into a giant signaling poster from Cell Signaling Technologies. I worked on neurotrophin signaling and NF-κB, until the former failed and the latter was published out from under me.

I was left with gene expression, promoter bashing, and a cloning-based project that I swore would never be my fate in life. Here’s the thing though – I hate gene expression, I am not interested in it in the slightest, I find some of the approaches taken to assay it (especially in the herpes field) to be somewhere left of physiological. Annoyingly (is that a word? Richard?), I had no choice but work on if I wanted to graduate in any sensible amount of time. So here I am, three years and 230 pages deep into a gene expression thesis. I think the process drained me a little, not to sound dramatic. I didn’t like the work, I didn’t like the subject. I am now starting to think that had I been able to work on something I love, I would not have been running for shelter from lab life as I have been the last couple of years. That makes me really sad.

I came upon this grand realization as I was writing the last chapter of my thesis, the out-of-nowhere chapter that summarizes the first three years of my work on a partially-failed neurotrophin/HSV-1 reactivation project. Sick as it may sound, I actually enjoyed writing that chapter. I loved reading the background papers and let my discussion get longer and longer as I rhapsodized about all the possible pathways leading to HSV-1 reactivation. Importantly, I did not feel a single tooth being pulled in the writing process, as I had with the other two chapters and two appendices of my oversized monograph.

So maybe I am not leaving for good. Maybe one day I will pull a Jennifer and return to science. Lord knows I never thought those words would come out of my mouth. Right now though, I need some recovery and recuperation. Maybe now the real world will become my temporary shelter from the scientific one.

As I sit here, frantically preparing for my defense in three weeks on the topic of HSV-1 stress-induced gene expression, I have… Yes, I have a cold sore. It’s almost poetic, really.

On a side note, this defense is messing up not only my body, but also my apartment.

Yes, those are beer bottles on the coffee table. What of it?

I can’t wait to be done!

So wish I could delete posts…

Of all the habits I will have to break once I leave grad school, this one’s not so bad.

A dear friend of mine is a newly minted PI in Texas (the fact that I have friends that are actual PIs is doing absolutely nothing for my firm intention to remain 12 years old on the inside). He has recently applied for his very first big NIH grant, an RO1. Besides the regular gigantic ball of worry, work, and stress that accompanies the writing of a grant, there was also the small issue of compliance with brand new NIH regulations.

Apparently, in order to be considered for funding this year, PIs have to submit a signed affidavit stating that they will refrain from using brain-enhancing drugs, such as Provigil, in the course of their research. Does that not strike y’all as slightly Big Brother-ish? Forgive me for gliding down a slippery slope, but what’s next? Are we only going to be allowed to drink decaf coffee while at lab? Perhaps LASIK will be forbidden so that some researchers don’t have an unfair advantage over others when it comes to microscopy or micro-surgeries?

Provigil, from my limited understanding, is pretty spectacular. Quinn Norton said (sorry, haven’t read the literature myself) that soldiers who were given Provigil performed better on tasks after three nights of staying awake than they did on the first day. Provigil basically eradicates the need for rest, while simultaneously enhancing cognitive abilities and general brain awesomeness. The problem arises when one takes too much of the drug. Rats who were administered Provigil for an extended period of time needed no sleep and performed well on tasks… until they dropped stone cold dead. No explanation and no warning. Just dead. Oy. Looks like you can’t fool Mother Nature for too long.

I am willing to look at the flip-side of the issue, for once. Perhaps the NIH is not simply trying to even the playing field of science (in the process potentially slowing the development of life-saving and world-shattering results), but also to protect a new drug abuse epidemic from taking hold in the scientific community. Drug abuse in other fields is well known and little concealed. The rumors of investment bankers doing lines of coke to stay up and alert for their 20 hour work days has been bouncing around for ages. I, unfortunately, know people who have fallen prey to it. Stock brokers on the market floor, not to mention long distance truck drivers, are no strangers to amphetamines of all colors and flavors. Are scientists next in the wave of “drug” abuse? Is Provigil going to be the scientists’ (or scienticians’, as I like to refer to them) crack cocaine? Are there going to be Provigil Anonymous meetings at every university? Not if the NIH can help it, it would seem.

Needless to say, my friend the PI signed the affidavit and with what I hope was not too heavy a heart, submitted his completed application for NIH funding. I am keeping my fingers crossed that he receives the grant and never ever needs to use Provigil, or enter a 12-step program for anything but his inherent – and endearing – dorkhood.

I have spent an absurd amount of time on PubMed recently and can say in no uncertain terms that it is making my dissertation writing way more painful than it needs to be. I can hold a paper in my hands, search for two authors’ last names and have PubMed come up with nothing. My friend searched for microRNAs and her virus of interest. The search engine (can I even call it an engine? It’s more like a tricycle) came up with papers dating back to 1997. I am pretty sure no one knew about microRNAs in 1997. Yet another friend was only able to find publications about his compound of choice after empirically defining one of its functions in the cell… which is when he found out this information had been available all along. He couldn’t pull up the relevant papers without searching specifically for the compound and that one effect on the cell.

Science cannot proceed at a decent clip if researchers cannot find the most basic necessary information. Has this study already been done? What else has this author published? What papers are related to the one I am reading?

I would now like to mercilessly butcher a quote from John Wilbanks from a talk he gave at the recent Publishing in the New Millennium forum. It went something like “It’s unacceptable that the web is better suited to searching for pizza than it is for furthering scientific research,” or something to that effect. Hopefully, he can correct me. But his point stands. It is way easier to search successfully for restaurants and pizza deliveries than it is for papers relating to neurotrophins and herpes, as thrilling as that topic may be.

Why is PubMed so behind the times? Why? How does it even work? Does it search only the abstract? Does it also search the body of the papers that are available online? Why does it get so massively confused by an author’s initials and last name together, in one search? Why can’t it alert me when papers relevant to my work are published? When is it going to get better? Is there any chance this might happen before my dissertation is due? Because frankly, it’s driving me more bats than the dissertation itself.

There are a lot of things I miss about my old lab – the budget, the giant windows, the equipment, the people. But most often I find myself missing my nap room.

So ok, the room wasn’t exactly intended for my blissful naps. It was a windowless room the size of a small closet that served as an outdated computer cemetery /repository and as the home of our fluorescence microscope. I spent the better part of two years in that dark, airless room, staring at glowing neurons till I saw spots and/or became nauseous (have you ever noticed that gliding through multiple fields under the scope gives you motion sickness? It does me).

For a long time, I was the only person ever to use that scope, ever to sit in that room. Every couple of days or so (especially if I was in lab until midnight the night before), I would sneak off to the scope room, take the batteries out of the wall clock to stop the ticking, shut the door, turn out the light, set a timer for 15 minutes, and embark on the most satisfying nap you could imagine. I woke up feeling refreshed and ready for more bench work… or at least ready to remain vertical for a couple more hours. I knew what I needed to achieve maximum productivity, and that was a power nap.

I feel like labs are divided in two – the nap friendly labs and the nap hostile labs. Some have couches or easily locked rooms, while others have bright overhead lights and no place to hide. That must be at some level, up to the PI. I guess some just don’t see the beauty and benefit of napping. Well, they should. I wonder if there is a study out there correlating researcher mid-day napping to publication output. I hypothesize that if every lab invested in a (clean!) couch, productivity would rise dramatically.

I miss my nap room and I miss my productivity boost. Then again, maybe that’s just my excuse for getting sleepy while slogging through my thesis.

I realized that I was a gonner during a fire alarm in my building today. There was huge beeping, blinding flashing, panic close at hand, and what did I grab in the few seconds I had before fire alarm-induced deafness set in? Not my wallet, not my house keys, not even my warm woolen mittens. Nope, I grabbed my laptop and ran down the stairs clutching it tightly to my chest. While at the moment nothing seemed more important to me than ensuring the well-being and safety of my laptop (and the dissertation within), reflection has revealed to me that perhaps the wallet would have been a good idea.

You’ll be happy to know that the building didn’t burn down (I think some toast met a fiery end in a microwave, setting off the fire detectors), we were let into the building after only a few minutes in the freezing cold – I didn’t even need to hide at a friend’s house until I was allowed access to my house keys (and beloved mittens!) again.

All is well that ends well. And it will end well on May 6. I hope.

The stereotype that a lot of scientists are not well socially adjusted has a lot of supporting evidence. Some of the most awkward people I have ever met have been scientists. People who think that plaid on plaid makes for a well-matched outfit weird. No conversation skills kind of weird.

It’s understandable. Lab work is lonely. There are conversations about science, yes, but those conversations are conducted in a language all their own, one not really related to real life. Spending long hours shut in a lab environment carries a risk of losing some part of one’s social skills.

Nothing supports my hypothesis better than a story I recently heard from a friend. A friend of a friend was sitting between her advisor and her husband (also a research scientist) at a seminar, when her advisor turned to her and asked, “So when will you be having F1s? Can’t wait too long, you know!” Oh. My. Everything. If I had been sitting next to that woman, I could not be counted on to contain my snort. No way. Who says that? It sounds a little forced, doesn’t it? Science has taken over her sense of humor. Eek.

Next in the long list of random lab skills and talents is a finely tuned eye for volumes. I can look at an Eppendorf tube and tell within 5 microliters how much liquid it contains. I can tell 10 mL from 15 at the bottom of a bottle and 1 mL from 1.5 in the well of a 6 well plate. I know if a tube has as much as I need or if I will be short. The task is complicated by frozen liquids, of course, and their completely misleading change in volume, but I have had success even in that tough circumstance.

You wouldn’t think that telling 800uL from 750uL is terribly important, but when every channel on your timer is counting down and a meeting with the advisor is only minutes away, it becomes a matter of life and death.

I don’t know if this volume estimating skill will ever be useful to me down the line (other than judging how many glasses of wine remain in the bottle, of course – I am really good at that too).

Stay tuned for the next installment in the series “My Weird Talents.” Let me know if you have any of your own. We can compare and contrast.

Nature Network is one year old today! And to just think, I remember it when it was yaaaay big (picture very closely apposed hands).

It all started a long time ago, in a land far far away. Ok, it was about a year and a half ago in Cambridge, MA (which for any devout Boston dweller may as well be a land far far away). I found myself attending a launch party for a new Nature initiative, Nature Network, at the Museum of Science (MoS) – I was invited along by a very good friend who is a bigwig in the Harvard Biotech Club. At that time, I had very little knowledge of the wide world of science blogging and absolutely no concept of social networking sites and what services they provide. I was a science blogging NNNeophyte. (I know, it’s a cheap shot, but I couldn’t resist).

The MoS was all ours that night, filled with journalists, bloggers, scientists, and editors milling about, discussing science, blogging, science writing, and of course, Nature Network. We were free to roam about the empty museum with no distractions from pesky tourists. Computer terminals were set up for people to start accounts on the nascent Network and hopefully, to consider starting blogs.

It was a nice evening with wine, pretty finger foods and short talks from sponsors and important people with wonderful London accents. Who those people were, I am ashamed to say, I cannot recall. [There was also short interlude during which I made a profound horse’s behind of myself before a senior editor at New Scientist, but I prefer not to go into those details. I would rather drink them into submission.]

I went home intrigued and impressed, having met some very interesting people (and failing spectacularly to impress others – see above). I met Corie a couple of weeks later to discuss science blogging and the rest is in the blogging history books. Blogging for Nature Network did an awful lot for me and I owe it (and Corie, of course), big time.

Happy BirthdaVersary, Nature Network! Wishing you many more happy years (and parties and cakes and blog posts) to come.

P.S. The cake is from my very favorite source of birthday cakes in Boston – Party Favors.

The verdict is in. The NNCommunity (or at least 26 of its members) has spoken. The new (and technically, the old) nickname for Nature Network Bloggers is….

Nature Network Bloggers!

It may not be the catchiest nickname, but it gets the point across and is, most importantly, our very own – chosen by us, to be used as a badge of the cool NNClub to which we belong. (I will stop with the NNWords soon, I promise, but I am having too much NNFun with it at the moment).

Next step in the NNCommunity – NNBlogger day! Post on Friday, Feb 14 to celebrate Nature Network’s one year anniversary.

I am thoroughly enjoying these exercises in online community building. Hope you are as well.

Nature Network Blogger, signing off. For now.

But then there are Cheetos. I cannot explain my love for Cheetos. I wouldn’t even know where to begin. Maybe it started at the vending machine in high school which provided my daily kick of the neon orange glow sticks. I got hooked. They are so good in such a bad way.

The last time I splurged on the dietary horror that is a bag of Cheetos, I did what I have long since trained myself not to do – I looked at the ingredient list. Oy vey. If I brought Cheetos to inorganic chemistry class in college, maybe I wouldn’t have gotten a C – they would have been a great cheat sheet.

I want to know what all that chemical garbage is doing in my food. Why is it there? What role does it serve? The internet came to the rescue of this miniature chemistry lesson. The following is the (almost) complete ingredient list from a bag of Cheetos, annotated by yours truly:

Enriched corn meal, with all usual vitamin supplements

Vegetable oil

Salt – the third ingredient on the list – no wonder I love Cheetos.

Maltodextrin – polysaccharide produced from starch (rice, corn or potato); easily digestible and absorbed as easily as glucose.

Sugar

Monosodium glutamate – an amino acid that acts as a potent flavor enhancer. MSG triggers the umami taste receptors, making food taste more savory.

Autolyzed yeast extract – often contains free glutamic acids and is, for that reason, used as a supplement to MSG. “…consists of concentrations of yeast cells that are allowed to die and break up, so that the yeasts’ digestive enzymes break their proteins down into simpler compounds.”

Citric acid – Used for tart flavor and as an antioxidant.

Artificial color – apparently, neon orange doesn’t come easily – Cheetos are colored by no fewer than four food dyes

Partially hydrogenated soybean and cottonseed oil

Hydrolyzed soy protein – ”...Soy protein is used for emulsification and texturizing. Specific applications include adhesives, asphalts, resins, cleaning materials, cosmetics, inks, pleather, paints, paper coatings, pesticides/fungicides, plastics, polyesters and textile fibres.” Ok, I am sure that soy protein isn’t as scary as that passage just made it sound, but it sure does give a girl pause.

“Cheddar cheese” – I am sorry, I couldn’t help putting cheese in quotation marks.

Whey – “Whey proteins primarily consist of α-lactalbumin and β-lactoglobulin. Depending on the method of manufacture, whey may also contain glycomacropeptides (GMP).”

Onion powder

Whey protein concentrate – often used in body-building supplements, this is basically pure, milk-derived bioactive protein. Why it is included in my most favorite of bright orange “foods,” I can’t seem to figure out. It doesn’t sound terribly sinister, so I will forgive its inclusion.

Corn syrup solids – sweetener and thickener, dried corn syrup consisting mostly of dextrose. “Corn syrup contains no nutritional value other than calories, promotes tooth decay, and is used mainly in foods with little intrinsic nutritional value.”

Natural flavor – huh?

Buttermilk solids – analogous to dried milk as far as food additives are concerned. “Buttermilk is the liquid remaining from the cream after the butter has been removed from the churn. (This buttermilk should not be confused with the fluid buttermilk sold to consumers, a cultured lowfat milk that resembles buttermilk.)”

Garlic powder

Disodium phosphate – “Disodium phosphate is a sodium salt of orthophosphoric acid and is used as an antioxidant synergist, stabiliser and buffering agent in food. It is also used as an emulsifier in the manufacture of pasteurised processed cheese. Disodium phosphate is added to powdered milk to prevent gelation.” Note: harmful if ingested in quantity. Oooook, limiting Cheeto intake starting…. Now.

Sodium diacetate – basically vinegar in solid form, this additive is used as an antimicrobial/preservative and to add a tangy flavor to foods.

Sodium caseinate – milk protein conjugate used as a binder, emulsifier, or thickener, likely used in the “cheese” in Cheetos.

Lactic acid – ”...fermented from lactose (milk sugar), most commercially used lactic acid is derived by using bacteria such as Bacillus acidilacti, Lactobacillus delbueckii or Lactobacillus bulgaricus to ferment carbohydrates from nondairy sources such as cornstarch, potatoes and molasses. usually either as a pH adjusting ingredient, or as a preservative (either as antioxidant or for control of pathogenic micro-organisms).”

Disodium inosinate – disodium salt of inosinic acid. That clarifies everything, huh? Used in concert with MSG to trigger the umami taste receptors.

Disodium guanylate – “… often added to foods in conjunction with disodium inosinate; the combination is known as disodium 5’-ribonucleotides. Disodium guanylate is produced from dried fish or dried seaweed and is often added to instant noodles, potato chips and snacks, savoury rice, tinned vegetables, cured meats, packet soup. ...The food additives disodium inosinate and disodium guanylate are useful only in synergy with MSG-containing ingredients, and provide a likely indicator of the presence of MSG in a product.”

Nonfat milk solids

Sodium citrate – sodium salt of citric acid, added for tartness and to balance pH.

Carrageenan – obtained from seaweed, indigestible large protein used as a thickening, stabilizing and gelling agent.

Whew.

What I found most interesting in this chemical roster is the amount of MSG and MSG analogs – no fewer than four separate chemicals to trigger that sought-after umami flavor. Cheetos also contain a fair number and preservatives and stabilizers, all chemicals with natural derivations, but chemicals nonetheless.

My conclusion? You probably won’t die from eating a bag (or eight) of Cheetos every once in a while, but perhaps it’s best not to make a habit of it.

What struck me most during the conference was the strong sense of community that I experienced in the company of other science bloggers. We were all there for the same reason, even if our blogs varied greatly in theme and tone. There were science bloggers that write about hard core science and the latest publications, bloggers with a political tint, evolutionists, marine biologists, physicists, and even partly goofy bloggers that write about life in science, but not really science itself (that would be me). Even though the focus of everyone’s blogs was quite different, the entire day was permeated by a sense of common purpose and similar goals.

Once I came home to my beloved wireless connection and comfortable spot for my laptop, I realized that we have the beginnings of the same strong blogger community on Nature Network. Sure, we are facing an unusual challenge being spread all over the world, but we are all online, right? That’s the whole point. We are closely connected through our association with NN. That’s the common thread, along with checking email every 10 seconds and looking for comments on our blog posts, if I may project for a second.

So, in the interest of online community building, Martin and I have set up a little poll for you to take to choose a name that binds us and identifies us. Yes, we already have a name. Nature Network Bloggers. You can either stay with the tried and true original, or vote for something a little more slick. If you are a blogger on NN, join the NNBlogger forum and merge into the blogger community that we have right in front of us, no plane ticket or Visa (of the credit or immigration variety) required. The poll will remain open until this Sunday, Feb 10.

Take the NNBlogger nickname poll

Drum roll please…

I have finally pulled together a defense committee and set a defense date.

May 6. May 6. May 6.

Is it possible to hold one’s breath for close to three months? I am going to give it a try.

I just got back from the North Carolina Science Blogging Conference and let me tell you, it was an absolute blast. It was exciting, fun, and thought provoking (I even got to help chair a session!). One particular provoked thought was the need for Nature Network bloggers to develop the sort of close-knit and clique-y relationship that science bloggers on ScienceBlogs are fortunate to enjoy.

So here’s what we do.

Step 1. We need a name. Bloggers on ScienceBlogs refer to themselves as SciBlings. Siblings. How cool is that? We need that. Ok, maybe I need that. The feeling of belonging and community is what blogging is all about, right?

This is my appeal to all NN bloggers. Think of a name for us! I would help, but clearly I am no good at this: The Naturals? Dumb. NNs? Too close to ninnies.

I am brain-dead and full of LocoPops and shrimp and grits (looove Southern food). Will give our blogger name, and the rest of my awesome weekend some more thought in the morning. Hope you do the same!

Feel free to consider me the most frivolous and ridiculous girl that ever lived, but (almost) more than anything else in my life, THIS makes me want to push to graduate this June. I may die of happiness in her presence.

I knew there was a reason I came to Harvard!

Unfortunately, the walls of my politic-free kingdom (nay, Queendom) are beginning to shake and shudder. I can’t hold out any more. Politics are starting to step on my scientific toes. As I thoroughly ranted before, I am not a fan of mixing science with, well, anything at all other than data. However, lots and lots of people do like to mix. They like to mix and then tell everyone about it. And sometimes, they even run for President of the U.S.

A recent issue of Nature had a handy breakdown of the presidential candidates’ stances on key scientific issues such as stem cells, the environment, space exploration, and of course, one of the hottest topics of current debate on Nature Network and country-wide, evolution. Mike Huckabee’s quote regarding his views on evolution caught my eye… and then my jaw, as it dropped.

“If you want to believe that you and your family came from apes, I’ll accept that.”

I am appalled at the accusatory, condescending, and derisive tone of that statement. There are more problems with it than I care to enumerate here and so will list only the ones I can summarize in a few sentences… and without the use of expletives.

1) His family is obviously not descended from apes, unlike your family. His family is way better than your family.
2) And I know this isn’t what he was getting at. What is so awful about being descended from apes? I would far rather be related to apes than say, crocodiles, or snakes. Apes are fairly inoffensive as far as members of the animal kingdom are concerned.
3) And this is where I risk the aforementioned expletives. I don’t believe that my family and I came from apes. I know that we did. Big diff.

Rant over. I feel better now, and will safely retreat to my politic-free existence. If I can find it again.

More evidence that blogging can help you get a job. Here is how it went, a little long winded perhaps, but then most life stories are.

Two years ago, my friend Melissa and I started a food blog, because all we like to do (and by we, I mean me) when left to our own devices is cook and watch the Food Network. Things progressed, life got in the way of Melissa’s blogging but I persevered.

A few months later I met Corie at the launch of Nature Network Boston at the Science Museum. Corie was recruiting bloggers for the brand new site. I met with her a few days later to discuss blogging, told her about my existing blog and my thorough devotion to the art and business of blogging, and Lab Life was born. I blogged and I blogged and apparently, some people took the time to read the verbal products of my twisted world view.

A few more months passed, a few more NNB posts came into being. Last summer, I was flabbergasted and honored by an invitation to attend SciFoo at the Googleplex. Obviously, I accepted, and flew out to San Jose for a whirlwind weekend. I met more luminaries and progressive thinkers than I could count. Among them were Moshe Pritsker and Nikita Bernstein, founders of the Journal of Visualized Experiments, a start-up in Cambridge, MA. [Remember JoVE, it comes up later].

I got back to Boston all kinds of invigorated and inspired and devoted a fair bit of my time to helping organize a conference on open access publishing here at Harvard. We invited Moshe to sit on one of the panels and offer his view on the direction of science publishing and potential roadblocks in its growth and evolution.

Needless to say, a hefty drinking session followed the conference. I am proud to say that even Bora couldn’t keep up with a bunch of Russians (that would be Moshe, Nikita, and myself. Ok, Nikita doesn’t drink, but still…). Somehow, a joke was made about me looking for a job, haha. I did not laugh at this joke.

The very next day I had a two hour-long meeting at the JoVE office with part of the JoVE crew in attendance and walked out with a part-time job blogging for JoVE! Yep, I am now getting paid to blog, among other things. Please hold your applause until the end of the performance.

The idea was to start a blogging platform or community site on the JoVE webpage to increase traffic and foster conversation around the videos posted on JoVE, life in science and science publishing, and of course, stuff that happens in the outside world (or as I like to refer to it, the real world). Knowing that I am a blogger and have some connections in the online scientific community (yep, I know people who know people) Moshe et al asked me to be their blogger extraordinaire. I recently started a JoVE blog that will soon migrate to the JoVE page, once their platform is up and running (thanks, Nikita!). I will have some input in the design of the blogging platform, which is any blogger’s dream come true, kind of like drawing the plans for your own virtual home.

I will be working for JoVE while I am finishing up my dissertation. Should I ever actually graduate, we will re-evaluate our working relationship to see if they need or want me to come on full time. Right now I am just enjoying being a (very) small part of something new and exciting, and something I really believe in – an open access, online journal that is promoting a novel way of communicating science, a way that not only makes it easier for scientists to learn from each other but also makes it easier for the general public to learn from scientists. Everyone wins. But most of all, I win, because my blogging – much maligned by my friends and relatives for taking too much time away from my lab work – got me a job. Never underestimate the power of the internet. I bow down in awe.

I have freakishly strong hands. Whenever someone can’t open a jar, it’s passed down to me. Whenever a soda bottle is particularly resistant, I step in. Whenever a cork simply won’t come out of a wine bottle, I am there to save the day/evening… although that may have to do more with constant cork-pulling practice than brute physical strength.

Point is, I have developed some serious hand strength from all the things I do in lab on a daily basis. One of those things is opening bottles and tubes with one hand, utilizing what my high school biotechnology teacher referred to as “aseptic technique,” (Thanks, Dr. Toby!).

Here is how it goes. You grasp the tube with your left hand (if right-handed), and twist the top off with your thumb and index finger.

Hold on to the cap to avoid having to place the clean cap on the relatively dirty benchtop. You can then use your right hand to introduce a pipette into the tube/bottle. The tube can be re-covered in an instant, minimizing exposure to the air and the contaminants suspended within it.

With practice, the caps give way easily, but some are more tenacious than others. Occasionally, you have to hold the bottle/tube steady between your knees (that’s what I like to call a “lower body workout”).

Hand muscles aside, I find lab work to be rather physically challenging. I stand practically all day, running back and forth to the cold room, the tissue culture room, the nice gel dock one floor below, or the partially decrepit X-Omat two floors above. Periodic scaling of the chemical bench to get to the teeny tiny bottle invariably buried behind three rows of huge jugs on the tippy top shelf is good for keeping the heart rate up. I am rarely standing still. I will give my inherent cheesiness free reign by saying that sometimes, working in a lab exercises not only my mind, but also my body.

So here’s what happened. Last May, my committee checked my box (wait…. wait… yep, that’s still funny) on the condition that I generate an HSV-1 with a specific promoter mutation and begin testing it. Straightforward, yes? (Play ominous music here). My committee disbanded as I was not required to meet with them again after completing this work. My lab closed, my advisor moved to Arizona, and I moved into the lab of the head of my committee to finish up. Or so I thought.

Eight months later I still didn’t (and don’t) have the stupid virus made. I mentioned some of the reasons for this earlier. I had no committee, my advisor was (and is) far far away, and my adoptive mentor stood behind the committee’s decision. My advisor (she) and my surrogate advisor (he) are on the same grant and she did not feel comfortable pressuring him to let me go for fear of affecting their future working relationship. I realize I should care about their working relationship but at this point I do not. Not at all. Politics are not my thing.

I was getting desperate. Desperate to finish, desperate to stop beating my head against the same virus rock, desperate to get my light back at the end of the tunnel (melodramatic enough? I think so). At the same time, I was afraid of being perceived as a cheater, as someone who was let off easy because of the circumstances, or of being forever gossiped about as the girl who was allowed to graduate with a weak thesis.

After tossing and turning (while both asleep and awake), whining, stressing, and otherwise despairing for a good long while, I gathered up all my courage and asked my committee to reconvene, with my advisor’s blessing. Highly unorthodox, I realize, but what was I supposed to do? I would rather not celebrate my fiftieth birthday in my lab.

My committee and my advisor (in attendance via conference call) heard me out, said “ooh, that’s complicated” at all the appropriate spots in my experimental plan, and made the most perfect decision I could have hoped for.

As I see it, there were three possible outcomes to this meeting. They could have decided that:

1) I can stop now and write up what I have, in which case I would have felt a like a cheater, permitted to graduate with a substandard amount of data.

2) I cannot graduate until I fulfill the original requirements, in which case I would have quit on the spot and never looked back.

3) I should work up until a hard deadline (January 31), at which time I can write and graduate, no matter how much (or how little, in my case) I accomplish.

Happily, they decided on option 3. I will work hard to make this expletive virus until January 31, then quit all lab work, write up my thesis, buy a pretty outfit, defend, walk in a crimson gown, and get on with the rest of my life. This I can live with. Uncertainly and lack of direction, not so much. Besides, Jews don’t believe in purgatory.

All my ranting aside, SITN is a neat organization. It is a student organized, student run group devoted to educating the public about current issues in science, to showing the community how the science blurbs in the news may relate to them. I have been involved (lightly) with SITN for a couple of years. I was too chicken to volunteer to give a talk – something about having to be an authority on a particular subject makes me uneasy. I don’t deal well with authority, you could say. My own authority, that is. Instead, I contributed a couple of review articles that were sent out as an e-newsletter (SITN NewsFlash) to the subscribers to the SITN listserv.

The group presents regular talks at the Mattapan community center and on the Harvard campus. This season’s lectures ranged from global warming to autism and nanotechnology. The seminar on contagious cancers drew 50-70 attendees, most from the local community. They were active and vocal participants in the discussion, asking some really tough, insightful questions. It was nice to be reminded that what we do every day actually matters. Well, maybe not what I do, but what others work on does trickle down to the news, it does affect the community, it does make a difference, little by little.

The PowerPoint slides of all the lectures as well as podcasts of the lectures are available on the SITN site.

I was tagged for this meme by Bora, a blogging powerhouse and all around wonderful person. What follows could be more information than you cared to know about me, but if that were true, you wouldn’t be reading this right now, would you?

Here goes.

Meme of 4.

4 jobs you’ve had:
1. A summer at Blockbuster video when I was 16
2. Do internships count? Many summers at the NIH.
3. That’s all I got.
4. Grad school. Grad school. Grad school.

4 movies you could watch over & over:
1. Out of Sight (J.Lo at her finest)
2. Pride and Prejudice (with Keira Knightley)
3. The Diamond Arm (dumb yet brilliant Russian language musical)
4. Any James Bond movie, the older the better (barring the terrible ones with Timothy Dalton).

4 places you’ve lived:
1. Moscow, Russia
2. Oxford, UK (for a month); Ladispoli, Italy (for a month) – those add up to one of four, right?
3. Charlottesville, VA
4. Oakton, VA

4 TV shows you love to watch (I hardly ever watch TV, but when I do it’s the Food Network):
1. Good Eats (Alton Brown)
2. No Reservations (Anthony Bourdain)
3. Dirty jobs (discovery channel?)
4. Masterpiece Theatre
5. Just kidding. Iron Chef America

4 places you’ve been on holiday:
1. Delhi, India (and all over)
2. Barcelona and Madrid, Spain
3. South Beach, FL
4. Vail, CO (there is no point in skiing anywhere else once you have been there)

4 websites you visit daily:
1. Netvibes, to see which of the million blogs I read have been updated
2. Gmail, to see which of my million of email accounts has new mail
3. Statcounter for my food blog
4. BBC News

4 of your favorite foods:
1. Cheese, in any form
2. Eggs, in any form
3. Lamb, in any form
4. Bread, in any form
5. I am clearly not on a diet

4 places you’d rather be:
1. On a vineyard in Italy
2. On a vineyard in France
3. Jost van Dyke, British Virgin Islands – paradise on this earth. Picture a hammock suspended between palm trees, white sand beach, a bar, and a small harbor full of moored sailboats. Yep, that’s the Soggy Dollar Bar, so named because there is no dock on the island. The only way to get to the bar is in a dinghy, which you at some point have to jump out of to drag it ashore. So your dollars get soggy. Get it?
4. China Bowl, Vail, CO, the day after a major snowfall.

4 lucky people to tag (Nature Network people, help spread the meme bloggy joy):
1. Corie
2. Bronwen
3. Eva
4. Matt Brown

Fair warning: I am prone to ranting, both in person and in silico.

Nothing sets me off more than things that interfere with the progress of science. Religion, personal beliefs, and political views have no place in science, determining science funding or in administering medical treatment. Science and belief are like oil and vinegar. They just don’t mix, nor can one ever benefit from the other.

Creationists and proponents of intelligent design ? What right do they have to dictate which scientific facts (and facts they are) can or cannot be taught in public, secular schools? Don’t even get me started on the whole stem cell debate – there would be no debate if scientific research was truly divorced from the influence of religion.

Likewise, the opposition to the HPV vaccine, Gardasil, boggles my mind. Certain groups argue that administering the HPV vaccine to adolescents will contribute to their promiscuity. I have never heard anything so ridiculous in all my days. I am willing to take the risk of sounding morally superior in saying that parents offloading responsibility for their children’s behavior onto an injection seems absurd. Is the behavior of children not dependent on parents, upbringing and society, as opposed to their medical treatment? Why would any parent make a conscious choice to deny their daughter (or son) protection from a horrible disease?

Belief is the stick in the spokes of the science bicycle wheel. If we could all look at science for science’s sake, analyze the data and abstract ourselves from other undue influence, perhaps progress can be accelerated.

Rant over. Thank you for listening.

P.S. Please do not think that I am speaking as a representative of Nature. I am not. I am perfectly happy incriminating only myself.

The day started off with welcoming comments from Harvard Provost Steven Hyman. He related his experiences with doing research in the pre-digital age, having to go to actual libraries and pull actual, corporeal journals off actual shelves to photocopy articles of interest, praying all along that no one had unceremoniously ripped out that article for their own, exclusive use.

Steven Hyman giving welcome remarks and introducing Harold Varmus.

Harold Varmus gave the keynote address in which he took rather pointed and directed stabs at Elsevier publishers, all the more barb-like considering that Emilie Marcus, the editor of Cell Press (a subsidiary of Elsevier) was sitting in the front row. The sparks continued to fly during the first panel when the pros and cons of open access publishing were debated. A much better summary of the panels than the one I could provide can be found here, here and here. I would rather talk about the behind-the-scenes, the stuff that didn’t get out into the open.

Harold Varmus giving the keynote address.

Harold Varmus answering questions following his talk. Luckily, there was only one crazy lady who yelled things. No one really figured out what those things were.

I had a long conversation with Robert Kiley from the Wellcome Trust before the start of the conference. Through our conversation I got a better idea of just how progressive Wellcome Trust’s policies on science publishing are (all Wellcome funded research has to be published in open access journals. Details on that policy can be found here). I found him to be engaging and thoroughly devoted to the cause of open access. I would have liked to hear more from him on the first panel, but it’s really not his fault – all eyes and ears were on Emilie Marcus.

The most interesting thing I learned (and one I hope I am permitted to disclose) came out of a pre-conference conversation with Mr. Kiley. While Wellcome has not yet released (or collected, not sure which) official data on the percent of labs that keep their promise of publishing in open access journals, the estimates run between just 20 and 40%. I found this to be shocking.

Panel 1. From the left: moderator Kishore Kuchibhotla; Emilie Marcus, Cell Press Stuart Shieber, Harvard University; Isaac Kohane, Countway Library, Harvard University; Robert Kiley, Wellcome Trust

While my initial reaction was to condemn all the cheaters and liars that signed on the dotted line accepting Wellcome’s terms and money but reneged on the agreement, Mr. Kiley was more tolerant in saying that there is simply a lack of understanding in the scientific community of what is being asked of them and what the difference is between open access and traditional models of science publishing. When I asked how Wellcome plans to enforce their rules of open access publishing, Mr. Kiley responded that their current strategy relies more heavily on the “carrot than the stick”. While they have a great deal of weight to throw behind their threats of withdrawing funding, it is in no one’s interest for them to do so.

Panel 2. From the left: moderator Zeba Wunderlich (not pictured); Moshe Pritsker, JoVE John Wilbanks, Science Commons Hilary Spencer; Nature Precedings ; Bora Zivkovic, PLoS ONE

Echoing Harold Varmus’s not-too-cuddly feelings toward Elsevier, Robert talked about how much effort was put into working out an agreement between Wellcome and Elsevier – something like 15 months of continuous negotiations went by before Elsevier agreed to comply with Wellcome Trust’s requirements that publications be made free and available no later than 6 months following the original publication date. Whew. Fifteen months! Wellcome must employ some really patient attorneys.

I will be the one running around the audience with a microphone during Panel 1 and compulsively photographing the rest of the time. And listening, of course. I have found that to be quite useful in the past.

Hope to see many of you there. But don’t despair if you can’t make it out to the Longwood Medical area this afternoon (though I hope you will try really hard) because the conference will be audiotaped and soon posted as a podcast. Stay tuned for the details.

It Just. Won’t. End.

It’s like the villain in a James Bond movie who keeps getting up after being subjected to every evil and force known to man, or those little weighted dolls that pop right back after being pushed to the ground. Yep, that’s grad school.

I had my box checked in May. Why, do you ask, am I still here, five months later? You don’t know? That makes two of us.

That’s not entirely true. I know exactly why I am still here, but I can hardly believe it. I was permitted to write my thesis and defend contingent upon the completion of one seemingly innocent task: introduce a mutation into the HSV-1 genome and begin testing the mutant. I have now been attempting to make this stupid (pardon the emotion) mutant for about 8 months. I have not been successful, to put it mildly.

There are many reasons for why I am having so much trouble, not the least of which is that I am working with the most complicated stretch of HSV-1 sequence in the entire genome (how does about 85% GC sound for a nightmare?), which effectively rules out every PCR-based mutagenesis approach I have tried, half the non PCR-based ones, as well as a handful of magic spells and hexes. I may soon move on to a full-blown curse. I am currently in the middle of the most involved cloning strategy known to man, which has a probability of success only slightly higher than my becoming an astronaut.

My advisor, as well as my surrogate advisor, have been deaf to my pleas for mercy and won’t budge (this is extra irritating considering that I don’t believe that this mutant will add any worthwhile information to my thesis). Needless to say, I am quickly approaching the end of my rope. At this rate, I may be in grad school forever.

I am reluctant to leave graduate school having contributed nothing tangible to the field. I am a little embarrassed to admit that my ego wants to leave a mark, a scientific equivalent of “Anna was here.” I would like to graduate with the knowledge that the many NIH dollars I have spent in the last six years have done some good.

I decided to do something about it. It all started when I went to SciFoo. I was intimidated to within an inch of my life, but I still listened and learned. I found out about open access, self-archiving, the semantic web, and about snags in the current models of peer review and science publishing that are specific to biology. When I got back to Boston, I put my new-found knowledge to use. I became involved.

I am one of a group of HMS graduate students organizing a forum on the current state and future direction of scientific publishing in the biosciences (e.g. open access publishing and web 2.0 applications). We are bringing people together from far and wide to combine their expertise and opinions into a fruitful discussion. This discussion can (and will) educate the audience, myself included, about science publishing, possible issues and potential solutions. Hopefully, it will make people think. Hopefully, it will help bring about change. Hopefully, it will leave a mark.

Please come.

Publishing in the New Millennium: A Forum on Publishing in the Biosciences

Friday, November 9, 1:00 – 6:00 pm
TMEC Walter Amphitheater, Harvard Medical School
260 Longwood Ave, Boston, MA 02115

Make your opinion heard. Join the NNB discussion group on science publishing in the new millennium.

I really don’t understand. Does he think himself superior and impervious to all this new-fangled political correctness (aka, tolerance) or does he simply not understand the impact of his words? Seeing as how he was smart enough to win a Nobel Prize, I vote for the former. But I still don’t get why he routinely chooses to disregard all societal guidelines for behavior, much less why he has such odd (and frankly, nauseating) beliefs in the first place.

My parents came up to Boston for a rare visit about a year ago. Being the compulsive grad student that I am (ok, was), I had to stop by lab to change media on some cells in the middle of their visit and brought them along. I worked quickly, all the while appearing intent, professional, and highly competent, so as to impress my thoroughly unscientific parents. I thought I did pretty well. Nothing spilled, nothing dropped, no cells met their maker (not before their time, in any case). When I asked my parents what they thought of what they saw (angling for an “Oooh, aaah”), they answered, “Eh. It looks like you are pouring the same liquid from one container to another and then back again.” Thunk. So much for my impressing my parents with my mad lab skills.

Thing is, they have a point. That really is all I do. I transfer exceedingly small volumes of liquid from one container to the next, keeping the faith that the clear liquid contains a submicroscopic plasmid which when mixed with yet another clear liquid and placed on top of cells will induce them to express a protein that I will not be able to visualize without the use of another wildly involved technique (Western blot).

This partially explains why scientists are viewed as a little mad, represented in cartoons and movies standing next to beakers bubbling with intensely colored liquid, full of things that we cannot see. We work in blobs on blots, cells on computer screens and lines on gels – all things highly conceptual, abstract, and intangible. No wonder we look off kilter to the outside world.

I do still want to impress my parents, but I am afraid of what I have to do to accomplish that feat… there may have to be some very unhappy mice.

I went to my parents’ house for the holiday this past weekend and saw everyone who has known me since I was little. The meetings with my relatives, old teachers, and family friends went a little something like this :

Question 1 : When are you getting married? (Funny).
Questions 2-18 : When are you graduating? What will you do after you graduate? Do you have a job? When will you start earning your keep? (Not funny. At all).

It was the same story at this year’s Virology retreat (minus Question 1, thankfully), the questions delivered by professors and students alike, with marked vehemence from the former.

Oy.

That’s my answer. That’s the best I can do right now.

Question 1 can just sit in the corner all by itself.
Questions 2 – infinity I am going to have to deal with at some point, whether I like it or not.

The expectations are high, in large part due to the name of my school. I am expected to achieve great things, to knock down the doors of opportunity with the word “HARVARD” as my battering ram.

Well, guess what? It doesn’t work that way. That battering ram is bestowed upon hundreds of people every year. It is not a magic wand that can ensure my financial and emotional security for the rest of my life. I still have to fight for what I want, and I may or may not get it.

The pressure I am now feeling from within and from without to define my future, to draw a schematic of the next 10 years of my life is driving me further and further away from working out the answer. Driving me straight into planning my move to Rome the moment I graduate. I may not come back. Not even for Question 1.

I won’t lie and say that Harvard’s money had nothing to do with my choosing to attend school here. It did. Harvard has the pull and the cash, and can (can) provide the security and freedom that many other institutions lack. We were never gratuitous in our spending in my thesis lab, but we certainly felt few financial constraints. The spend-out at the end of every year was such fun. “Well, I guess we can use an RT PCR machine… .” It went on in this fashion, a bunch of kiddie researchers in a lab supply candy store, until all the ridiculous piles money were spent. I would be lying if I said I didn’t take advantage of it. I didn’t misuse it, mind you, but I certainly didn’t shy away from ordering whatever I needed. It was nice.

And then reality hit. My lab closed down and I was thrust back into the big, scary real science world, back to where I came from. Money, it appears, does not grow on errm, PIs. Labs are losing grants left and right, and at the Neiman Marcus of medical schools no less!! PIs I never thought could struggle for money are having to rethink and reshuffle.

I don’t know or care enough about politics to make any guesses as to why this is happening. All I can comment on is what I see, and I see a squeeze on. I can only hope that the squeeze is temporary because at this rate, it is going to affect the scientific output (if it hasn’t done so already), not to mention give many people very big ulcers.

P.S. It seems Corie and I are thinking about the same things.

…and that’s just half of them

Looking back, it becomes clear that in my first few years in lab I was, how do I put this… an idiot. I missed clues in my data, failed to follow leads, designed my experiments backwards and upside down. It’s a miracle I got as far as I did. At the same time, I can take great comfort in being able to look back and see how far I have come, how much I have learned, and how much confidence I have gained (sadly, confidence won’t make the gaping black holes in my data seal up).

I have made progress, this much I know. I relaxed about some things and became more stringent about others. I can better see the important parts of experiments and how they fit together instead of getting caught up in trivialities. (How much more progress I could have made if I wasn’t quite so slow on the uptake is something I am trying not to think about.) I now have the markedly un-fun task of explaining in my dissertation why I didn’t see the obvious statistically significant difference between two conditions that I tested four years and three projects ago. D’oh.

Is this an on-going process? Do grown-up, mature scientists look back on their data and see things they missed the first time around? Does it get any less frustrating? Are there fewer D’ohs the older and more experienced you get? I sincerely hope so.

P.S. Dissertation update – I am writing! Slowly (very sloooowly) but surely, I am writing. I think the blank page was most intimidating of all. Now that I have started it seems a little less daunting. Only a little less though. I am still pretty daunted.

P.P.S. All apologies to Muse, but I just had to steal their album title – it’s too appropriate.

The one word that strikes fear into the steadiest of scientific hearts. Being scooped is every researcher’s nightmare. It can feel like a bolt of lightning out of the PubMed sky or it can be the long-standing threat of a known competitor. There is the complete and utter “stop and go home” scoop, or the partial “pick up the pieces and run with it” scoop. Either way, while the scoopee celebrates, the scooped is left with some tough choices. Continue with the work and try to fill in the holes left by the scoopee? Try to publish what you have in a lower profile journal? If not too much work had been invested to date, do you walk away from the project altogether? There is not a fun (or easy) choice among them.

No one is safe from being scooped. Even in a relatively calm field such as HSV-1, it happens – and it happens often. I, for instance, was scooped on a project in my 4th year. That project was my baby. It was my very own. I thought it up, planned it out, convinced my reluctant PI that it was worth a shot and I was off. I was so excited about the science, about the implications and future directions, about the certainty (in my own mind) of the hypothesis being correct. As it turned out, it was indeed correct, as confirmed by a JBC paper about 9-12 months into my work.

I did not see it coming – my scooping was of the lightning bolt variety. The paper was not from an HSV-1 group, which explained why I had not seen any abstracts at the meetings or heard mumblings of their work in progress. After the shock, tears (and hangover) wore off, I was left with a pile of conflicting emotions. On the one hand, I felt absolutely vindicated and justified in my choice and pursuit of the topic – I was right! On the other hand, my work was, in a lot of ways, for naught. I was relatively lucky since my pet project was not my main focus. I bid it a bittersweet farewell and embarked on the project that would eventually become my Ph.D. thesis, a little more sure of my ability to come up with valid scientific questions. The rest is (or will soon be, I hope) history.

Anyone that’s ever been scooped, raise your hand. Join my club.

I seem to have reached an impasse. I am stuck. I am staring at my computer screen and nothing is happening.

I am so close to being finished with my degree, yet I can’t seem to make myself simply sit down, shut up, and write. I make the most ridiculous excuses to avoid working – oh yes, I absolutely must shop for an oven thermometer before I can concentrate on writing. Is this a common problem? It seems so awfully mean and unfair to have to face apathy in the very last months of a degree that has taken a fair amount of concentration and persistence.

While grad school has been far from torture, it has not been a dream. We were not the best fit, grad school and I. I should have known I am not cut out for lab work. I should have known it in seventh grade. We had to take a personality test to determine which profession we are most suited for (the very concept, when applied to a seventh-grader, seems slightly absurd to me). I, being the little obsessive that I am, wrote down that I fancy the sciences and lab work most of all. The next page asked what dress code I would most prefer at work. Fully aware even then that lab workers are not generally known for their fashion sense (to put it mildly), I filled in the circle next to “business attire.” That should have served as a sign. I am not cut out for lab life. Science, yes. Lab, not so much.

So why now, now that I am so close to the next step, to moving on and dressing up am I positively mired in inactivity? Is it mental exhaustion? Fear of the future? The furthest extent of masochism? What is it? And when will it pass?

You pulled people into your talk with promises of a Paper Free Home (I turned down Science and Capitalism for you). This concept excited us, opened the potential of a computer to run our home-lives, to keep track of everything from bills to recipes, birthdays, phone numbers… and the best fertilizer for our windowsill basil. You were asked a number of incisive and probing questions about your idea, your magazine, your immense power to subtly introduce basic science to your readership, and how did you respond? You deflected. You mumbled about your 400 varieties of roses, about how you love vacuuming (seriously?), about how your magazine holds answers to all homeowners’ questions.

You missed out. You could have told us what your home manager computer, you paper-free home of the future is like. How is your manager different from the iPhone? Is it a screen on a fridge? Is it portable? Is it on a fridge with a portable satellite? How does one upload data onto the manager, from an insurance policy to the recipe for the very best chocolate chip cookies? You failed to take advantage of the bank of knowledge and expertise that gathered at the Googleplex from all over the world. What a shame.

Sincerely,

Anna Kushnir

P.S. Still love your chocolate chip cookie recipe though. It’s a good thing.

One of the major themes of this free-form gathering has been open access publishing. In a group discussion led by Bora Zivkovic of PLoS ONE, tempers flared (which made it even more fun than staring at science celebrities), and the many complications, pros and cons of open access were raised. Does the term “open access” refer to pre- or post-publication open access? Is it open, non-peer reviewed publication of articles or even complete lab notebooks, or access to reviewed, published articles free of charge? That aside, will open access publishing negatively affect the hiring potential of young faculty looking for tenure track positions or funding from organizations such as Wellcome Trust and the NIH?

What about intellectual property? How does one protect findings aired in a public forum? One attendee replied that you don’t, it doesn’t matter, it should all be free and open. As much as I personally admire this free love, Birkenstock/Woodstock approach to science and research, I do not believe it to be feasible at the moment. Science is run by money. In order to get money or funding, one must publish. The changes and minor revolutions in that need to occur in publishing before the concept of the science paper becomes obsolete are staggering. They are also occurring as we speak.

Back to gaping at people far smarter than me.

Having stepped away from it for a few weeks, I have found it a little difficult to jump back in. I have had to physically force myself to sit down at a tissue culture hood. Once I did, however, I remembered how soothing lab work can be.

So many things we do in a lab are rote repetition, performed more by muscle memory than by conscious direction. They may be boring, tiresome, dry, but they are at the same time hypnotic and relaxing. Filling a 96-well plate for RT-PCR well by well sounds like Chinese water torture, but demands complete concentration. Your thoughts cannot stray from the task at hand, or you will mess up spectacularly. Forgetting which well you are on out of 96? Ouch.

This concentration, this forcing of thought into one narrow lane in preference of the buzzing and whirling that goes on in one’s head on a normal basis has a meditative effect. It displaces the noise, clears the mind, allows it to rest before the next set of cacophonous thought.

Today I have a PCR plate to set up, cells to split, a gel to run. None of this requires thought, but it does require focus. I am not particularly excited about performing these tasks, but I am looking forward to the peace and quiet in my own head.

I spend an inordinate amount of time thinking about food. Eating, cooking, foraging, reading and writing about food are always at the front of my mind. I consider going to restaurants a full-blown hobby (and a most excellent occupation). Since I spend the majority of my waking hours in a laboratory, a lot of my food day dreaming has no choice but take place in a lab. Many may be disturbed by the combination of lab and food. In reality, labs are full of edibles – you just have to look closely to find them.

- The most obvious lab food items are seaweed extracts such as agar and sodium alginate. The former is prized by vegans as an animal product-free Jell-O alternative, while the latter has been elevated to new heights by Ferran Adria, the originator of molecular gastronomy and chef of El Bulli, one of the best-known restaurants in the world. Adria uses sodium alginate to create liquid pea ravioli, in which a thin membrane encloses a sphere of bright green pea soup. The bubble bursts in the mouth, releasing the soup and all of its glorious flavor in one big gush.

- We use 5% milk to block Western blots. It is ordinary, reconstituted non-fat dried milk, whatever brand happens to be sold in bulk at Costco. Milk in itself is not terribly appealing, however, one of the labs I rotated in used autoclaved milk for storing HSV plaque picks (why, I have absolutely no idea). Autoclaving milk turns it a beautiful light caramel color. Does autoclaved milk taste slightly bitter and sweet, like burnt sugar, or is it simply burnt? I had to exhibit considerable self control not to tip some out into my cupped hand and try a sip. I would have done, if it wasn’t for the disgusted and perplexed stares shot my way when I mentioned it.

- Bottles of ultra pure PCR-grade water line a shelf in my lab. Would be the best, cleanest and crispest tasting water of all time, putting Poland Spring and Evian to shame? Likely not since its deionized, but it calls to me nonetheless.

- I, on multiple occasions, have gazed longingly at a giant jug of purified caffeine sitting on the dry chemical shelf. Enough said.

That’s all I can think of at the moment. Have I missed anything? What other food-related items are found in labs? I promise not to tell the radioactivity surveyor.

P.S. On a related note, while in the grip of severe L.O.M. (lack of motivation), my new labmates determined that ocean water is approximately 0.5M sodium chloride. That makes our 5M stock solutions of sodium chloride, 10X ocean.

I have heard switching labs described as switching families. You know what? It really is. You may hate your family at times, yell at them and tell them to go stick their head in the LN2 tank, but at the end of the day they are still your family, comfortable and familiar.

I have switched families. It’s done, it’s over, there is no going back. I have been ceremonially stripped of my ID and lab keys. My old lab has been emptied out and gutted, only dust balls and derelict tubes remain in the corners. The level of my attachment to that space is entirely absurd, I know, but I can’t help it. I spent an obscene number of hours over five long years in that lab – I have slept there, eaten there, watched movies, written blog posts, and had many many beers. Those rooms were home to me and now they are gone.

So what does it take to relocate a large lab? I need to double check this with my PI, but I think what you need is $50K, a very large truck and many many able-bodied men and women. It took four people four full days to pack the lab and offices into innumerable boxes. Another crew of large men then loaded the boxes into the longest truck I have ever seen in my life – one truck housed all the freezers, refrigerators, incubators, boxes, and equipment. A generator on the truck will keep a number of the fridges and freezers at temperature so that the most sensitive reagents (viruses, bacteria…) will remain safely frozen or chilled. The truck is making the drive from Boston to Tucson, AZ in three days without stopping. Let me re-iterate – there will be no stopping between Boston and the Southwest except to refuel. The drivers (two of them, I believe) have everything they need in the huge cab of the huge truck – TV, shower, bed, carpets, kitchen, and copious amounts of caffeine and other stimulants, I imagine.

Happy Driving.

P.S. There is nothing more bizarre than watching a laminar flow hood dismantled, collapsed, and loaded onto a cart. I always considered TC hoods a part of the lab structure, integrated into the walls, a lab limb, if you will. They are not. They are actually rather portable.

I am only now starting to realize how good I had it in my old lab. It turns out that all those things that were done for me by the support staff I now have to do for myself in the new one! Awful. Top off the water baths, make media, pour agar plates, make buffers, restock tissue culture supplies, just to start. All that I can deal with, grudgingly. What gets me is that everyone takes a turn autoclaving and disposing of tissue culture waste. I am not ok with this. I have never used an autoclave. In fact, I am terrified of autoclaves. The ones I have seen (from afar) look like WWII submarines just waiting to explode. I hate being in the same room with autoclaves and had sincerely hoped to graduate with my PhD without ever running an autoclave. I was so close. So close!

Just look at all those plates! I have to make them all by myself from now on. Ick.

I’ll own it, I am a brat. I am used to having many things done for me. If I were to continue in science, in hands on research, this would likely work against me. There are few labs in this world as, ahem, well-endowed as the labs at Harvard (a large number of labs, in any case). Running an autoclave, pouring plates, and making media are part of a required skill set in the majority of labs and I suppose should be learned as part of a PhD program. I am going to learn how to do these things, but I am not happy about it.

When I first started in my thesis lab, I was painfully jealous of the benches and shelves of the older grad students and post docs. They were packed with glistening, smart-looking bottles, in my eyes indicative of the experimenter’s experience and breadth of knowledge. Now, as an almost-seventh-year student (deep breath), I am one of the students I hoped to emulate – I have accumulated tons of bottles. I hardly remember what half of them are for, but there sure are a lot of them. Last week I had to dump most of them out, clean off my bench, move my samples and stocks out of their storage spots at various temperatures and transport them to their new home in my new lab, my temporary shelter.

After:

My old bench looks like I was never there – I scraped all my red tape off, wiped clean all traces of my five year-long stay. I resisted the urge to carve my initials into my benchtop to leave some sign of my occupation. I shouldn’t have held back. Now that I think about it, it would be a really good idea to have a lab-worker scratching post at every bench, so you can mark your name and time of occupancy to leave a record of your existence. Maybe I will sneak back in under the cover of night, and scratch away to my heart’s content.

Now it is here again in my new lab, the envy of those that know what they are doing and seem so comfortable in their surroundings. I am a newbie, as disoriented as a rotating student. I have a question to ask approximately every 20 seconds. I don’t know where the bathroom is, much less where they keep latex gloves (actually, I realized they use nitriles exclusively – how annoying).

It’s a rather odd feeling, to know exactly what you need to do but have no idea how to do it, where to find the components, how to set it up. I have a steep learning curve ahead of me. I hope my samples can get along with their new neighbors in the fridge and freezer. It’s a big change for all of us, my samples and I.