Monthly Archives: December 2013

Happy Birthday Anna and Tess!

It’s my little sister’s 26th birthday today! Welcome to your late 20s Anna!

As you do not read my blog (I know, I don’t understand how one could possibly stand to miss out on this opportunity either…) you do not know of my new birthday protocol…trolling my phone for photos of you on your birthday to post for everyone else’s maximum enjoyment. Lucky for you (unlucky for the rest of is) there are a minimum number of photos of you on my cell. There are a few however, and a few more tangentially related to you. Enjoy!


Our way of showing our love to the newly-weds


Dr. Trot's luxurious accomodations en route to Anna's wedding


Getting approval for the bridal shower supplies


The star studded guest list begins ti take form...


...and bouquets of shitloads of little tiny oragami flowers




Happy Birthday Anna!

My family friend Tess is also also celebrates a New Year’s Eve birthday. Unfortunately I have ZERO photos of Tess on my phone so this year we will have to go with only one visual aid — Tess’s delicious granola that got me through the trip back east…


Rest assured/paranoid that this will be made up for in 2014 however 🙂

Happy Birthday and New Year’s Eve!

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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?)


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

    (biking, hiking, swimming…maybe…)

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


  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)


  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
  2. 20131231-134049.jpg

  3. Drink beer Read and knit more…together…

    (~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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Merry Christmas!! xoxo, The Flu


Merry Christmas everyone that is kind enough to have not deleted Dr. Trot from your list of blogs that you follow! (You know, to replace it with something that actually gets updated…I hear this is the thing to do…) So my excuse this time is that I’ve had a freaking nasty case of the flu since December 23rd and have refrained from posting nasty updates over the last 5 days with only you best interests in mind. You’re welcome.

So after one final work week from hell to wrap up 2013 I made my way back to Siberia Minnesota for Christmas. First I went to Philadelphia to visit Dr. Aki (and apparently kick off my bout with the flu). Dr. A took me to The New Deck for some comfort food and therapeutic holiday cocktails the night before I was set to fly out.


In the morning I took the train from Aki’s place in University City to the airport. Now, at this point I was already feeling really crappy. I was feeling badly enough that I figured I also probably looked pretty shitty. The train conductor was kind enough to remove any doubt in my mind about this. After taking our money (this was a very challenging interaction for me) and punching our tickets, the conductor (who’s day job is probably as a lineman for the NE Patriots) came back to where I was sitting, put a fist full of cough drops in my hand from his pocket, and then tucked me in with the oversized collars of the coat I was drowning in! WOW. I tried to say “thank you” (emphasis on “tried”) but he told me to shhhhhh “and keep your face covered when you get off and hustle back in through the first set of doors so you DO NOT breath the cold air.” I just nodded and obeyed 15 min later when we arrived at the airport.

By some act of god I made it though security to the gate and onto the plane without anyone calling a haz-mat team on me. I did my best to pass out immediately after I got on the plane and to not get up again until we landed. Not too hard.

As out of it as I was, it was still hilarious to watch people all but refuse to deplane upon feeling how cold the air was in the jetway once we landed in Minneapolis! They were that cold in the jetway! To be fair, it was -11F outside (without the windchil) and that’s damn cold even when you’ve spent 30 yrs of your life here. But watching adults balk at the jetway was pretty good. 🙂

Drs. Sami and Alex collected my sick ass from the airport and took me to a rather dysfunctional brunch (I’m sorry…at least it was tastey….finally…right…?) and then dropped me off at my borrowed vehicle for the 2 hr drive to Willmar. And we thought I was done traveling!! HA! The drive home really wasn’t all that bad. And then I really was home!

We had Christmas, kind of. I slept a lot and didn’t get out of my pj’s, much less shower, for 3 days or go to church. I still ate and drank a bunch of items that are some how absent from the “What to eat while training for a sub-4-hr marathon” diet, knitted and kicked my mom’s ass at played cards. Not bad, especially while having a bad case of death.

Meanwhile, Dr. M is on his way home to Bangladesh. He left the US on the 26th, my second day home, and should just be arriving in Dhaka now. Hopefully his travels were less infected than mine!

Alrighty, it sounds like it’s time for more embarrassing card games 🙂 and unnecessary consumption of Christmas goodies. I’ll be back with more on the best gifts of Christmas and a running Gin rummey score.

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Antibiotics in Crisis

The point of  my PhD was to develope alternative approaches to effectively treat bacterial infections, relative to our current antibiotics.

The point of my post-doc is to figure out why the __(fill in the blank with your favorite 4-letter word)__ some bacteria aren’t affected by our current antibiotics.


This article gives a fantastic suggestion for how everyone can contribute to solving the global problem of antibiotic inefficiencies (aside from spending 10 years of your life researching the issue). Considering the source, there is really very minimal jargon and it’s short, fact-based and overall very understandable. So, please check out Antibiotics in Crisis.

In the mean time —

stop taking so many damn antibiotics!!

Thank you 🙂



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Strength Training

As you all know I’ve been blabber on about incorporating strength training into my workouts. So far there has been a lot of talk and little action. Well, now that I’m not in the midst of a training season or a nasty work schedule (knock on wood) I’ve run fresh out of excuses. SOOOO, to start things out, here is a pretty nice little article on the importance of strength training from Runner’s World. There are links to useful follow-up articles through out (making all of our lives easier 🙂

Strength Training

Strength Training

Strength training is a supplement to a runner’s roadwork because it strengthens muscles and joints, which can improve race times and decrease injury risk.

If you want to perform at your full potential, you need to take a comprehensive approach to your running. That means targeting areas of fitness you may not normally pay attention to, like flexibility, balance, mobility, and strength. Studies have shown that strength training can improve body composition by helping you maintain or increase your lean body mass and can decrease your percentage of body fat, helping you look leaner and burn additional calories.

Not sure where you stand? Take our tests to find out how fit you are.

This is a very humbling informative self evaluation and gives you a good sense of where you are (or are not) starting from.

Incorporate strength training into your running regimen

So I am personally NOT a fan of the gym. I would much rather use some free weigths at home to supplement body weight and resitance bands for strength training. But, to each their own. If you do fancy the gym, also do avoid these weight-lifting mistakes.

  • Take a class if you’re unsure about how to strength train on your own.

See above comment. The same applies to classes for me. I’d rather read on my own and talk to someone personally than shackle myself to a class.

I have done a bit of yoga and really liked it, but don’t have it as part of my current training regime for logisitcal difficulties of attending a class (and my lack of personal ability to fly yoga-solo). Pilates, no thank you. Gyotonics, WTF? But again, to each their own…

YES!! 🙂

  • Integrate cross-training into your workout routine to build strength and flexibility in muscles that running doesn’t utilize and prevent injury. Try cycling or swimming to improve strength and flexibility.

YES!! While I don’t can’t swim, I love biking. I haven’t done nearly enough of this recently and need to get back on/off (which one is it?) the wagon. I suppose I should also learn how to swim.

Say goodbye to the long run?!?! WHAT? IMHO this is absolute garbage advise!! I’d say keep the long run and ditch another mid-distance run for some high-intensity, low-volume running. Or, alternate week for the long run and H-I, L-V workouts. But to ditch the long run? Put down the crack pipe!


Gain total body strength. Multiple studies show that regular strength training can improve running economy-how efficiently the body uses oxygen-by as much as eight percent, translating into greater speed and more muscle endurance. And it makes sense for runners to focus on their most important body part—their legs.

Try these workouts to strengthen your lower body:

Not the area that I personally need to focus on first, but obviously not a bad area for a runner to spend some time.

But strong legs require a solid foundation. When you run, your abdominal and back muscles fire to stabilize your spine. Strengthening your core will help your legs also grow stronger.

YES!! Well, kind of. Yes = necessary (but painful) for me.

Try these workouts for a stronger core:

I need to rotate all of these into the mix, with an emphasis on the core, back and abs. Ready, set, go!

The best distance athletes don’t just have impressive quads and glutes. They have muscular arms and shoulders that help them maintain speed throughout their races.

Try these workouts for a stronger upper body:


Yes! And this one is going to be fun for me. I’ve natrually had a pretty easy time building and maintaining arm strength. This sounds like a good place to start!

Do a little of everything:

For a workout plan that incorporates all three muscle groups, try our Get-Strong Plan for a total body strengthening regiment.

Not a bad idea at all.

Just don’t forget the importance of rest and recovery. If you occasionally take a break from training while still maintaining fitness, you will come back a stronger runner.

Yes and yes. Rest and recovery are absolutely essential. (In all seriousness….)

Ok, so personally, I will start by focusing on my core, back, abs and arms. My plan is to construct a running schedule that works strengthing all of these areas in with long, H-I L-V and recovery runs.

Stay tuned because there will be more riviting details to follow as finally get my act together!


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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

Thanksgiving 2013

I hope everyone has a wonderful Thanksgiving this year. I had an awesome holiday and an absolute shit-storm of a week to follow (see Week 18 + 1), hence this being just a bit belated. The good news is that rattling on and on about good food never gets old for me, so I’m perfectly happy sharing all of the delicious details re: my Thanksgiving over a week after the fact 🙂

To begin, everything is yummier at a balmy 65 F with the sound of the ocean in the background. (And no, I do not miss the cold and snow during the holidays one damn bit, they do not make it feel more festive and Thanksgiving/Christmasy, they just make it feel cold and snowy.)

Next, everything is yummier when it is prepared for you by a personal chef and his first mate…


To acquire the strength to get through this most strenuous day, we first made a batch of homemade mac-n-cheese for lunch. That’s exactly what one needs for lunch on Thanksgiving day, right?


mmmmmmm 🙂

Then it was on to the more serious tasks of the day…


You can never have too much stuffing!

This is the vegetarian's  assignment?

This is the vegetarian’s assignment?



...and after!

…and after!

Dr.T: Maroof, can you beat two eggs for me please? **five minutes later Dr. M: Maroof 2, eggs zero! Dr. T: sigh

Dr.T: Maroof, can you beat two eggs for me please?
**five minutes later**
Dr. M: Maroof 2, eggs zero!
Dr. T: sigh

Never-the-less, our beautiful tripple berry and pumpkin pies

Never-the-less, our beautiful triple berry and pumpkin pies

Can you guess whose is whose?

Can you guess whose is whose?

And that, ladies and gentlemen, is how you negate 18 weeks of marathon training!

In addition to a most gluttonous Thursday, we took the next 3 days to do nothing but eat and drink our way through Napa Valley. (See above comment.)

We managed to hit 4 wineries on both Friday and Saturday and two on Sunday before heading home in our understated vehicle…


Out of character at all?

1. Laird


That’s a little more like it!

Laird is small, family owned and operated estate vineyard and winery. You get a very nice tasting for $20 and a list of recommendations that should be taken with a grain of salt.

2. Domaine Chandon
Domaine Chandon was an over-commercial, over-plastic, under-authentic, non-appreciated experience. We tasted 4 sparkling wines here for $20, all of which I could have done without. I would not suggest visiting if you are looking for good wine or interesting vineyard/winery experiences. I would however recommend stopping here to survey both employees and clientele for who NOT to trust with your next cosmetic surgery.

3. Turnbull
Turnbull is a medium-sized family owned and operated vineyard and winery. For $20 the tasting was great, one of the best of the weekend, and the self guided vineyard tour was a pleasant way to sober up before getting back behind the wheel.



I kid.


Given the chance to ride a Ditch Witch, you’d be stupid not to!

(Just not now.)

4. Cosentino
Cosentino was a great way to end the first day of tasting. It’s a relative new (1980) but has quickly become regarded as a top winery in the valley. And for good reason. Again, they offer a very nice tasting for $20.

5. Mumm

Mumm Winery was the first stop of day 2. We took the ~1 hr long tour and tasted 3 wines. The tour was very well done with the right amount of info and entertainment. It kept moving without feeling rusehd or lagging. Plus, we got our glasses refilled 3 times en route, which didn’t hurt I’m sure. Regardless, not half bad for $25 each.

6. V. Sattui


V. Sattui

V. Sattui was great. We got to taste just about everything on the menu for our $20 tasting and had fantastic help. This is the one place that we ended up purchasing something, to be cracked open next time I’m in CA. Here’s to hoping it lasts that long!

To complement the fun tasting, there was a retail shop with a bunch of chocolates and cheeses to pair with the wine and a BBQ outside for lunch if you were hungary and around during that part of the day. We were and got a lamb sandwich + a margarita pizza. Both were super good.

7. Prager Port

Prager was maybe my #1 pick of the weekend. It’s a little tiny family owned and operated port winery. Now I love port, so this might be skewing my opinion just a titch, but they had really great Port.



AND, their back tasting room was covered in dollar bills from around the world. (This totally makes the wine that much better…even when you buy it to drink at home…) Of course we signed a dollar and hung it next to the Zimbabwe dollar so we could hang out with Master David and the Fresh Prince of Delaware for eternity in the port cellar. Or until we get stapled over…


Evidence that we were here! (Until we get stappled over by the next port-loving drunk…)

8. Castello di Amorosa

Now the Cstello di Amorosa is very new and a bit over the top for me. It’s an (admittedly beautiful) replica Italian castle. But, it is a replica castle. In California. Maybe this objection makes me a bit of a Italian castle snob, but it just isn’t my deal. (And of course my deal is the right deal….right?) That being said, we took some really nice pictures and had a great time walking around the castle grounds…


Castello di Amorosa


Our new dining room.


Yummy 🙂

The wine tasting was in a cellar tasting room and while the ambiance was great, thea assistance left something to be desired. We split 2 tastings and sampled all of the reds and all of the desert wines…none of which I can complain about.

4x dessert wines

4x dessert wines 🙂

After all of these adventures, we found some feathery and/or furry friends and gathered our strength for the drive back to Napa.


The week’s survivors…


…and their goat and sheep friends.

9. Hess

The Hess Vineyard, Winery and Art collection was a bit off the beaten trail and came to us upon the recommendation of Laird (one of their better suggestions). The grounds were beautiful, the 3 stories of modern art were super fun, the free personal vineyard (with 90 yr old vines!!) and winery tour that we went on was most informative and the wines we tasted (for $20) were delicious. This is another top hit of the weekend for me.


Cold Hess


Pretty Hess


PSA: Every vineyard/winery should also be an art museum.

10. Domaine Carneros

Now for some reason I wasn’t nearly as offended by Domaine Carneros as I was by Domaine Chandon, but it had the same vibe — oversized, plastic and commercial. On the bright side here, we had a table to ourselves on a patio with a beautiful view on a beautiful day. The tasting menu was also sparking wines. The three that we tasted were definitely not my top wines of the weekend, but a hell of a step up from Domaine Chandon.


Domaine Carneros

And with that it was back to Berkeley and then back to the reality of NJ and my F32. Joy.

It was a wonderful 5 days holiday regardless of what was waiting for me. For next time we have learned to scout out the small, less advertised and less traveled options. We will also have to incorporate sections of both Sonoma Valley and the Russian River Valley. There is so much wine tasting yet to be done!! 🙂





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