Tag Archives: Science

Pre-Prospective Faculty Workshop – Planes, Trains and Automobiles (and breakfast)

Dr. Trot is on her way.

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We took the NJ rail from Pton Junct to (the wretched) EWR. After a complmentary 30-minute delay (of course) we are finally en route to Chi-town. Upon landing it’ll be a mad dash to fetch what is likely be a go-cart posing as an “eco car” for the final leg to West. Lafayette. (At $79.99 for 3 days I really have no justification for being picky…)

Assuming all goes well above, I’ll report back re: the welcome dinner tonight and just how panicked I am about my talk that is still 2 days away. (I’m sorry stomach lining…and I will continue to be until 4:30 pm on Tuesday.) The good news is that I am now down to 10 min and something resembling a coherent discussion for each slide and transition. The bad news is that the majority of my flight’s passengers now think I’m totally nuts.

Alrighty, it’s just about time to sharpen up the elbows and make sure boots, tights and skirt are properly adjusted for optimal mad-dashing. (If the don’t already think I’m nuts…)

Good thing I’m well fueled from this most delicious start to my day…

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Pre-Prospective Faculty Workshop – Secret and Destroy!

Dr. Trot’s best efforts from ~7:30 am until nowish, ~1:30 am, (not to mention the best efforts of a number of my very patient, smart and helpful group mates and friends) have produced what will hopefully be a sufficient 10 min talk on my current and future research for the last minute demand making brilliant faculty of Purdue’s Chemical Engineering Department. Secrete and Destroy! The slides are a little heavy on cartoon bacteria and a little lean on data points. (Never mind the bast background knowledge that’s supposed to be packed away upstairs in the noodle.) But, quite frankly, that’s about as good as you could ever hope to get from this kid in t<20 hrs Purdue.

While I might be just a titch underprepared in terms of my "expertise" that got me invited to the shit storm outstanding professional growth opportunity that I’m sure the next two days will bring, I spent my precious little non-presentation-preparing time ensuring that I was well prepared in the outfit department. 🙂 It’s all about priorities people! Honestly, in the end that is what really matters anyway, right? Right? Anybody? Hello?

Speaking of priorities, Dr. Trot had best call it a night. One needs to build strength for such ventures as going through the living hell masquerading as Newark, NJ, and then driving half way across the one-and=only Hoosier State. (Never mind that Mother Nature is robbing us of an hour of sleep tonight for absolutely no good reason. What a great way to start my adventures in The Crossroads of America!

Please wish me luck!

 

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Pre-Prospective Faculty Worshop SURPRISE!!

By some unlikely alignment of the stars, a generous act of god and/or an erroneous “acceptance” email sent to me by a member of the selection committee, I will be attending a Prospective Faculty Workshop at Purdue University over the next few days. 😀

The rather short back-story (you’re welcome) is that the university will apparently be hiring to fill 107 new tenure track engineering faculty positions over the next 5 years. With this in mind they are holding a 2-day long fishing expedition worshop for 30 “senior graduate students and post-docs” that have the intention of applying for faculty positions over this time frame. Enter an optimistic/delusional Dr. Trot.

God knows how many people applied, but somehow (see above) your’s truly was selected to attend!! 😀

The workshop is two days long, starting with a welcome dinner tonight. The schedule is largely divided into 1-hr segments dedicated to different relevant topic: What is expected of new faculty members? Proposal writing: the art of persuading a sponsor to invest in you! Engineering across cultures. Preparing a personal development plan. Mentoring graduate students. Effective techniques and tips for creating successful learning experiences in the classroom or lab. There will also be a poster session during which all of us present our research, tours of various departments and meetings with a number of current faculty members.

Fortunately I managed to find a direct flight to ORD from (unfortunately) EWR. Please say a prayer. (After a series of irritating logistics email exchanges) I have decided that it then makes the most sense for me to rent a car for the 2.5 hr drive to West Lafayette. I am passing up a 4 hr (each way) shuttle ride (at very inconvenient times) – as difficult as this may be, I’m working hard to get over it.

So this is where things stood 24 hrs ago. A 2.5 day workshop that is super relevant to what I want to do in ~3 years and a direct flight to get there. Good. Great. Grand. Happy Dr. Trot.

And then I received this…

“The Head of the School of Chemical Engineering is requesting that each ChE participant prepare a short 10 minute presentation on their current and future research. This presentation will be in front of Chemical Engineering faculty and a computer will be provided. There are no other guidelines.”

O.M.G!!

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Terrified Dr. Trot.

In addition to this, a schedule was attached to the email stating that I will have “meetings” (read: interrogations) with three department faculty, including the department head! In the blink of an eye my useful and interesting, yet totally benign, next few days have mutated into a most intimidating prospective faculty interview two years too early! And happy Dr. Trot has transformed into a terrified and anxious yet excited, 3-um-of-stomach-lining (max) away-from-an-ulcer Dr. Trot. :-/

Wish me luck in preparing the 10 min talk of my life!

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Check out The Role of Metabolism in Bacterial Persistence!

If you have been particularly insightful, you may have noticed my subtle hinting at the crazy-last-minute-scramble-to-get-things-done approach that I feel is my new reality. You may have notice particular grumbling about the implementation of this SOP while writing a review article in January.

Anyway, given that you had to endure the process, I figure it’s only fair that you also have to endure the finished product! How nice of me, right? 😉 Yesterday morning I woke up to an email announcing that our review is now out and that… “this article is an open access publication, which means that it is freely accessible to any reader anywhere in the world. We encourage you to share the article link with your co-authors and colleagues who may be interested in your work or in this type of research.” TADA!! 

Enjoy The Role of Metabolism in Bacterial Persistence and you’re most welcome 🙂

ABtx

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How went the 13 in 2013?

Happy Annaversary! Can you believe you’ve been reading this high brow literature for a year already?! Crazy, right? Well, time flys when you’re having fun 😉

Those of you who’ve been here from the very beginning, I’m sure you’re itching to know how I did on my 13 goals for 2013. Well, you’re in luck! Here is how they went…

Dr-ing goals:

  1. Become good at learning and remembering peoples’ names 
  2. So I’ll be the first to admit that his is still not exactly my strong suit, but I have become loads better at knowing who the hell I’ve talked to and why. It doesn’t come particularly naturally yet, but the embarrassing situations of clearly not having a damn clue are much fewer and farther between.

  3. Become comfortable making non-painfully-awkward small talk 
  4. Much better. Still not my favorite, but a necessary evil game that I can not only play but also now usually win.

  5. Read one paper a day (NOT the MN Daily)
  6. HA! Fail! Big fail! This will be recycled for 2014. At this stage in my career this really shouldn’t be hard. But it is. It really is. 😦 Why?

  7. Graduate
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    Done! 😀

Trotting goals:

  1. Run 5 days a week (1 mile, 5 miles, 20 miles, whatever, just get my ass outside and do something)
  2. Nope, didn’t happen! In retrospect, this was also not realistic. 4 days a week is reasonable and this happened when it needed to (marathon training season…the second one).

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    ...come hell, high water or 100°F + 100% humidity...

    Unfortunately it didn’t happen during the off season. We will be revisiting this issue for 2014.

  3. Finish the Mt. Kilimanjaro marathon (t < 6 hrs)
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    Done! (By the skin of my teeth and thank god, but never mind…)

  5. Half-marathon PR
  6. So I didn’t have the chance to race any 1/2s this year so officially this was a fail. But, if you’re willing to grasp straws with me, the middle half of my Philadelphia marathon was a 1/2 marathon PR… If you’re not buying this (you shouldn’t be….I’m not…) it’s ok, this will be on the 2014 list with some uncharacteristically high stakes attached. The plan is to pace the first half of a BQ marathon for my faster, more dedicated couisin. God help me.

Me goals:

  1. Be a non-promiscuous, healthy vegetarian again (i.e. eat loads and loads of fresh fruits and veggies, no cheating on tartar, sushi or bone marrow and cheese curds and beer are NOT an acceptable dinner — even during orals season)
  2. I’ve been better… This probably needs to stay on the list.

  3. Drink  enough water
  4. Hmmmmm….unless coffee and tea count in the tally this also needs to stay on the list.

  5. Get a reasonable start on my/our children’s book series TAPP — hopefully this will make sense in a year
  6. 😦

  7. Maximize the use of my electronics: iPad, cell phone, computer(s), mp3 players. All of them.
  8. I’ve definitely been better. This will also continue to be a work in oprogress, but I’m happy to report that my technologically challenged self hasn’t totally failed here.

  9. Be at work during “normal business hours” (+/- 20%)
  10. So this was going reasonably well in MN but is literally impossible in the land of persister assays. Consequently, reestablishing something that loosely resembles a work/life balance has a special place reserved on the 2014 list.

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    Note: it IS important to still look cute when leaving work at 3 am

  11. Start and maintain a blog on the joys, frustrations, enigmas and epiphanies of science and running —  you’re welcome
  12. We’re all still here, aren’t we? A year later you are still most welcome 🙂

This year has been rather eventful actually. I (somehow) managed to graduate with my PhD and move 2000 miles to the armpit of the northeast lovely Garden State for a postdoc (with which I’m still having serious relationship issues), in the opposite direction of all parts of my family. In my “spare time” I got to spend 2 weeks on an adventure in Tanzania (complete with a safari and Mt. Kilimanjaro marathon) and managed a second marathon with my second-to-none Team CEMS and a 10 min PR. Not bad.

Happy end of 2013!

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14 for 2014

So last year I started off 2013 with a list of 13 things I wanted to work on over the year. If I do say so myself, I did a pretty good job of at least making movements in the right direction with most of these line items. (To enjoy an entire blog post of Dr. Trot patting herself on the back, see how went the 13 in 2013.) With this great success in mind, the only reasonable thing to do this year is tackle 14 for 2014… (How clever of an idea will I think this is in 2030?)

Trotting:

  1. Workout 4 days/week
  2. Follow a workout plan that combines running (distance, speed and recovery), strength training (core emphasis) and cross training

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    (biking, hiking, swimming…maybe…)

  3. 1/2 marathon PR
  4. < 4hr marathon

Doctoring:

  1. Postdoc paper #1
  2. Read at least 1 paper a day (+ actually think, take notes, etc… while doing so)
  3. Develop (think, read, write, etc… about and actually have the ability to implement) 2 reasonably competitive junior faculty candidate research ideas
  4. Get a postdoc fellowship (preferably that godforsaken F32 I made a first attempt at in November, but if something else comes falling out of the sky and lands in my lap I’m not going to be super picky)

Me:

  1. Be a non-promiscuous, healthy vegetarian again (i.e. eat loads and loads of fresh fruits and veggies, no (read: exceedingly rare) cheating on tartar, sushi and bone marrow) + drink enough water
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  3. Drink beer Read and knit more…together…

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    (~1 book/month…come on, there’s a lot going on here people, and Dr. Trot is a damn slow reader) and get a reasonable start on our children’s book series (it’s the second day of the year and I’m already behind on this one :-/)

  4. Maximize the use of my electronics: iPad, iPod, cell phone, GPS watch and computer. All of them.
  5. Keep in better communication with my elders, particularly those that I can make fun of for being cheese heads. Although, considering that my pathetic excuse for a football team has stunk up the season and is still getting some very sweet new digs, this might not be in my best interest after all…
  6. Become a reasonably good potter…for a chemical engineer… (be able to reproducibly throw (not on the floor, although I’m sure I could become very good at this as well…with probably a hell of a lot less practice) bowls, cups, vases, etc… and larger items that need to be assembled off of the wheel)
  7. Break even $$ over 2013-2014 (i.e. stop single-handedly keeping the dysfunctional airline industry afloat :-/

Ok, that’s 14 semi-reasonable resolutions/goals (whatever floats your boat) for Dr. Trot’s next year. What are yours?

Good luck to us and Happy New Year!

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How journals like Nature, Cell and Science are damaging science, thank you Randy Shekman

It was (unfortunately) refreshing to come across this article. My guess is that it will also hit (maybe a little too close to) home with most who struggles with the balance of publishing sound research, exciting and impactful research. Personally trying to do all of this while observing what work has been deemed to be all of this by the influential heavy hitters in the field can be extremely frustrating. To be fair, much of the works that do earn press between the luxurious covers of NatureCell and Science are studies that I could only dream of dreaming up, much less having the skill, motivation and resources to do. But, it’s extremely refreshing to hear an extraordinarily accomplished (read: 2013 Medecine Nobel laureate ) scientist’s concern about the clout and exclusivity of these journals and excitement about the new, accessible alternatives and their potential impact on the scientific community and society.

How journals like Nature, Cell and Science are damaging science

The incentives offered by top journals distort science, just as big bonuses distort banking

by Randy Shekman

9 December 2012

Litter in the street

The journal Science has recently retracted a high-profile paper reporting links between littering and violence.

I am a scientist. Mine is a professional world that achieves great things for humanity. But it is disfigured by inappropriate incentives. The prevailing structures of personal reputation and career advancement mean the biggest rewards often follow the flashiest work, not the best. Those of us who follow these incentives are being entirely rational – I have followed them myself – but we do not always best serve our profession’s interests, let alone those of humanity and society.

We all know what distorting incentives have done to finance and banking. The incentives my colleagues face are not huge bonuses, but the professional rewards that accompany publication in prestigious journals – chiefly NatureCell and Science.

These luxury journals are supposed to be the epitome of quality, publishing only the best research. Because funding and appointment panels often use place of publication as a proxy for quality of science, appearing in these titles often leads to grants and professorships. But the big journals’ reputations are only partly warranted. While they publish many outstanding papers, they do not publish only outstanding papers. Neither are they the only publishers of outstanding research.

These journals aggressively curate their brands, in ways more conducive to selling subscriptions than to stimulating the most important research. Like fashion designers who create limited-edition handbags or suits, they know scarcity stokes demand, so they artificially restrict the number of papers they accept. The exclusive brands are then marketed with a gimmick called “impact factor” – a score for each journal, measuring the number of times its papers are cited by subsequent research. Better papers, the theory goes, are cited more often, so better journals boast higher scores. Yet it is a deeply flawed measure, pursuing which has become an end in itself – and is as damaging to science as the bonus culture is to banking.

It is common, and encouraged by many journals, for research to be judged by the impact factor of the journal that publishes it. But as a journal’s score is an average, it says little about the quality of any individual piece of research. What is more, citation is sometimes, but not always, linked to quality. A paper can become highly cited because it is good science – or because it is eye-catching, provocative or wrong. Luxury-journal editors know this, so they accept papers that will make waves because they explore sexy subjects or make challenging claims.

One example of this is this 2007 Science article in which the authors (Asara et al) claim to identify protein sequences from the bones of a 160,000- to 600,000-yr-old mastodon and a 68-million-year-old T. rex. At least 5 follow up articles were published in response/objection to this work, fueling both traffic and citations for Science magazine. While there was a range of tones across the resulting articles (one of which compares the researchers to a small child watching a monkey type on a keyboard), they all raise valid concerns about the technical approach used and conclusions drawn in the article.

This influences the science that scientists do. It builds bubbles in fashionable fields where researchers can make the bold claims these journals want, while discouraging other important work, such as replication studies.

In extreme cases, the lure of the luxury journal can encourage the cutting of corners, and contribute to the escalating number of papers that are retracted as flawed or fraudulent. Science alone has recently retracted high-profile papers reporting cloned human embryos, links between littering and violence, and the genetic profiles of centenarians. Perhaps worse, it has not retracted claims that a microbe is able to use arsenic in its DNA instead of phosphorus, despite overwhelming scientific criticism.

There is a better way, through the new breed of open-access journals that are free for anybody to read, and have no expensive subscriptions to promote. Born on the web, they can accept all papers that meet quality standards, with no artificial caps. Many are edited by working scientists, who can assess the worth of papers without regard for citations. As I know from my editorship of eLife, an open access journal funded by the Welcome Trust, the Howard Hughes Medical Institute and the Max Planck Society, they are publishing world-class science every week.

Funders and universities, too, have a role to play. They must tell the committees that decide on grants and positions not to judge papers by where they are published. It is the quality of the science, not the journal’s brand, that matters. Most importantly of all, we scientists need to take action. Like many successful researchers, I have published in the big brands, including the papers that won me the Nobel prize for medicine, which I will be honoured to collect tomorrow.. But no longer. I have now committed my lab to avoiding luxury journals, and I encourage others to do likewise.

Just as Wall Street needs to break the hold of the bonus culture, which drives risk-taking that is rational for individuals but damaging to the financial system, so science must break the tyranny of the luxury journals. The result will be better research that better serves science and society.

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December 10, 2013 · 11:26 am