Before....

Chicago street art.... What do you want to do with your life?

Block

I've been writing. I'm doing relatively well with the writing more often goal with the exception of a few 13 hour days in the lab last week. I just don't like anything that I've written enough to subject the two or three readers of my blog with the accumulated drivel. The writing is saved and hopefully will lead to real, longer posts that I'm proud of.  

In the mean time, a bit of academic humor pertaining to writer's block...

http://scienceblogs.com/omnibrain/2010/12/unsuccessful_treatment_of_writ.php

My Paper: Part 1

Anyone who has watched a TV crime drama has a basic idea of DNA. Your DNA is your genetic fingerprint; it distinguishes you from your neighbor and links you to your parents. Although true, the CSI description of DNA is only a part of the story. DNA is more like an instruction manual, the longest, largest, most detailed instruction manual EVER.

Each cell in our body acts like a large international company with a couple thousand employees and DNA as the corporate handbook. In every large company there is a subset of employees that are responsible for market research; the 'receptors' of information get an idea of the current environment and reports back through the cellular hierarchy to the corporate center, ie, the nucleus. While information is working it way up the ladder, proteins within the communication route become excited, recruit others and sometime even provide feedback. Finally at the end of the communication network is a transcription factor (TF).  TFs are the urgent memo that gets handed directly to the CEO. The TF is special in that it acts as a key to the DNA and only unlocks specific chapters of the manual thus giving the cellular CEO the exact information and instructions to make the necessary changes to the business practices; make the company grow, make more products, expand to a new location, shut down completely.

If you want to get a global picture of what is going on in a company, looking at all the memos that cross a CEO’s desk is a good place to start. Paralleled in the cell, looking at the ‘active’ TFs in the nucleus (how well it can bind to and ‘unlock’ the DNA) gives a good measure of cellular status and of the upstream signaling network. In a company, you can potentially find failures in communication or in the structure of the company by studying the corporate memos; did some information get pass on too quickly? did something important get left out? were duplicate memos received? We can use the same basic ideas to identify markers in disease in a cell. By comparing the TF activity profiles of cancer cells verses healthy cells we can more precisely pinpoint where things went wrong and therefore develop more directed therapy.  

External signals work their way to the nucleus to effect gene regulation. http://en.wikipedia.org/wiki/File:Signal_transduction_pathways.png

And now for something completely different...

Mainstream science reporting drives me nuts. Studies are sensationalized, taken out of context, and misrepresented. I blame scientists.

The scientific community is reclusive. We publish in journals with specific audiences that only people affiliated with an organization with the resources to pay for expensive subscriptions can read. We speak is jargon and acronyms. We are best at communicating with other scientists and often expect people who are not in the community to know what we are talking about.  

This needs to stop. The focus needs to change.

We need to learn to communicate with the outside world. We need to stop having journalist reading our papers and try to translate them for a wider audience. We need to write in a way that needs no translation. We need to be more approachable. I argue that if scientist were better at communicating there would be no question to the validity of global warming, parents would vaccinate and people wouldn’t think that stem cell research is equivalent to killing babies.  

I recently published my first paper. I thought it was pretty good. I thought it was written well. I thought my family would be able to read it and understand it. I was wrong. Reading it now I realize that being apart of academia has made me lose touch with ‘normal’ people’s understanding. The average person doesn’t know (and has no need to know) what a transcription factor is or the importance of signaling pathway analysis.

I want to become a better writer. I want to communicate clearer and reach a wider audience.

I have made a personal goal of writing everyday (well, every weekday). I hope that by writing everyday my communication skills will improve and writing will come more naturally (and, cross your fingers, make writing my thesis go a little faster).
Oh, and maybe this experiment will help me get my dream job of being a science correspondent for NPR... hahahaa

My first challenge: Rewriting my paper for a blog audience!

A carrot is a carrot is a carrot...?

I spend about 50% of my day listening to WBEZ. My commute is mostly done standing on a moving bus and my experiments are highly repetitive. I need the company of NPR to get me through it all. Don't get me wrong, I LOVE NPR, but I've become that annoying person that starts all new topics of conversation with "I was listening to NPR..." or "I heard an interesting interview on NPR..." or "I must be supper smart because a guy on NPR believes the same thing as me..." or "Blah, blah, blah..." That being said, I heard an interesting interview on NPR discussing the role of cooking in evolution. The simplified hypothesis from this interview states that Humans evolved the way that we did (ie developing smaller mouths, smaller intestines, smarter brains compared to our primate cousin) and gained evolutionary advantage (function at a higher level) as a result of the fact that we cook our food. Basically, cooking makes us human. There is a little bit of the chicken or the egg feeling in this argument, but for the sake of this post lets go with it.

Cooking our food allows us humans to actually obtain more net energy from our food because we don't have to send hours gnawing at a hunk of raw meat or processing leafy greens. The anthropologist described two studies to back up his story. The first paper he alluded to was a study (Oka et al., 2003) of two groups of rats. Group 1 was fed normal pellets and group 2 was fed a softer, air puffed version of the same pellet. Both group were fed the same total number of Calories and all results were normalized to exercise. At the end of 26 weeks, it turns out that the soft food group was (statistically) significantly fatter than the control. The post-eating temperature of the soft-fed rats were lower than the hard-fed, suggesting that the metabolism of the hard-fed rats is 'working harder.' The conclusions drawn by the actual researchers and the NPR dude from this experiment are slightly different. The rat guys hypothesize that the different in weight comes more from neurological cues from the act of eating the different textured pellets and Mr. NPR says that the lower temperature comes from the little rat body not having to work as hard to process the softer pellet. I find both interpretations interesting.

The second scientific article (Evenepoel et al., 1999) that is mentioned was slightly more relevant to the argument that cooking food changes the caloric energy that is obtained by humans from food. The researchers in the study labeled eggs and tracked them through human digestion and determined the amount of protein absorbed by the small intestines as a function of whether or not the egg was cooked. There was a 30% difference in the amount of protein that escaped digestion within the small intestine between the two eggs, with the cooked egg having almost 95% of labeled proteins digested in the small intestine. This brings up the question of what cooking food actually does to the nutritional or energy value of foods. According to this thinking, the old dogma of 'a calorie is a calorie is a calorie' does not quite hold up. Cooking may change the amount of net energy we get from food whether the caloric discrepancy comes from our metabolism working harder with uncooked foods or that the energy from the harder to metabolize raw food isn't processed during the relatively short time it is in our digestive tract.

So what does all this mean? Well as with all science, especially science covered in the media, these results and hypotheses should be taken with a grain of salt. What I take from this discussion is an affirmation that we need to be more cognizant of what we eat and how we eat it. I am by no means at all saying that we should al be on the "raw foods diet." Our bodies evolved to eat cook food and we need it to get the energy necessary to function properly (as mentioned in the podcast, women on the "raw foods diet" often stop menstruating because they do not get sufficient energy from their diet). I do think, however, that we need to cut back on the processed foods and let our bodies do some of the processing. Those mashed up, freeze dried carrots that are puffed into chip like things are probably not as good for your body as an unprocessed carrot, period. Anyways, I thought this was interesting food for thought.

The Dreaded Giggle Loop

The Time Traveler's Wife made me cry. Scratch that, it made me bawl. The end got me even though I knew everything that was going to happen in the movie before I even took the turkey sandwiches that we had smuggled in to the theatre out of my oversized purse. So here I am in a crappy theatre on a Tuesday night (free small popcorn night), surrounded by a theatre of women (with a strangely high percentage of lesbians), sitting next to my boyfriend with my nose running and tears streaming down my face. Then it happened, the giggle loop. I took one look at Mike and he saw the helpless embarrassment behind my shameless tears and we both started to giggle. The giggles got worse and before I knew it, we where laughing. The inappropriate nature of our laughing made us laugh harder. I was uncontrollably laughing between uncontrollable sobs, Mike was just laughing. Yup, we were the jackasses laughing out loud during the tragic climax of a chick flick. Damn you Giggle Loop!

Best of Chicago

As of today I have been an official Chicago resident for one year. It’s amazing, I move 5 miles and the city opened up to me. In Evanston I was bound by the silly Purple line and going into the city almost seemed like a chore. Now we explore. The city buses no longer intimidate me. I feel a connection to my neighborhood. We go on missions to seek out the best sandwich, the best pizza in the city.

So to commemorate my city living, I present you my 2009 best of Chicago.

Best Coffee Shop

Metropolis @ 1039 W. Granville Avenue, Edgewater

This little coffee shop roasts their own beans, has rotating local art on the walls and is less than a mile's walk from our apartment. Metropolis will also go down in our history books as the location where Mike wrote most of his doctoral thesis.

Best Restaurant

Lula Cafe @ 2537 N. Kedzie Boulevard, Logan Square

I love Lula. It has fresh, local food put together with ease. Their menu has a good mix of higher end and more affordable food. The best food in Chicago without any pretension along with it.

Favorite Shop or Boutique

Andersonville Galleria @ 5247 N Clark St, Andersonville

With four floors and 90 merchants, the Galleria is like a mini Chicago Etsy shoved into a sun-filled old warehouse. If I had more money I'd shop here all the time, get handmade clothes, jewelery, make-up, art.

Favorite Chicago Tourist Attraction

Millennium Park @ N. Michigan Avenue & the Lake, Downtown

The architecture, the concerts, the people watching, a marvelous view of the skyline and now a bridge to the new modern wing of the Art Institute; Millennium Park has it all.

Hidden Treasure

Chicago Cultural Center @ 78 E Washington St, Downtown

Now home to the Chicago Cultural Center, the old public library is beyond beautiful. If all libraries were this magical cartoons would be unnecessary and every kid would be an avid reader.

Favorite Sports Team

The Chicago Blackhawks

Although Wrigley Field is pretty awesome, I still like the Blackhawks better than the Cubs.

More to come.....

Not funny, Yet hysterical.

I think that phdcomics are very funny and very unfunny at the same time. Sometime the comics on that page satirize my life a little too well, hit too close to home. I know this is the second comic I've shared in as many posts, but honestly I can't help it. I believe this comic is a direct paraphrase from a conversation I had last week with my sister... except that conversation didn't seem so silly and included stress filled tears. At least I can use the comic to give me a little prospective if not a laugh.

False Assumptions

Often in science, when trying to solve a difficult problem or model a complex system, researchers make simplifying assumptions. A good scientist will constantly reevaluate their assumptions to make sure they are still valid. As a community of scientist and researchers we need to begin to question whether the main assumption governing the current structure of academia is legitimate. We assume that because a person is smart enough to get a PhD, land a good postdoc position, publish some papers in high impact journals makes them a qualified teacher, manager and mentor. Currently, university faculty receive little to no direct training on how to be a professor. I actually find it had to believe that in most states you need a postgraduate degree in education to instruct kindergartners on how to say their ABCs but no training on effective teaching is needed to teach the future doctors, engineers, business superheros the intricacies of their respective trades. Tenured track university facility are also expected, immediately upon hiring, to create, run and fund a productive lab. From experience and observation, many principle investigators lack the managerial know how to effectively coordinate the efforts of their students. If research facility was given training on how to effectively run a lab research endeavors would progress forward at a far faster pace. AND if college professors were forced to focus on how to improve their teaching, the students that graduate from college and grad school will be better informed and possibly better members of society.

New things in the R.P.

Over the past few weeks Rogers Park has seen the opening of a few new things. Is this a sign of the economy getting better? I guess we will just have to wait to see.

First up, Royal Coffee. Good cheap coffee but the same old sandwiches as the previous cafe.

Next, the movie theatre that I wrote about in January has reopened. The New 400 is a dollar more expensive, doesn't have the BYOB (bring your own bag) but it's nice having a movie theatre that you can go to on a weeknight and be in bed 7 min after the movie ends.

Third, CVS opened right where I pick up the bus for work. I don't know why I am so excited about this opening but I AM! Their prices seem a little steep though...



No wonder my parents wouldn't buy us lunchables, they ARE expensive.

Finally, Rogers Park now has a Five Guys. Is it possible to overdose on French fries?

iPhone app

In order to try and update more I impulse bought an iPhone app to help. I like BlogPress so far.


It even let's me easily post pictures. Alright back to work.... I get distracted easily when I try to work form home.

Orphaned blog

I know it's been a LONG time.... I bet the select few who actually read this blog thought that it had become part of the 95%... poor abandoned blogs. Well, my new goal is for a new post every week. Lets see if I can parent this blog again.

Turning Over a New Leaf

I love my neighborhood and after an accidental discovery made yesterday by Mike and me, I think I'm going to love it a bit more. Yesterday, after what has turned out to be our bi-Saturday trip to get fresh roasted coffee and to our local butcher (not to mention a quick stop at the fabric shop), we took a different route home and stumbled upon a tiny organic grocery shop. New Lief Grocery itself wasn't that exciting, a very small amount of organic fruits and veggies and a lot of packaged soy and gluten free products. However, the store is basically just a front for an organic co-op that offers weekly boxes of assorted fruits and vegetables for only $15 for 1-2 people. Awesome! You just put in your order a week ahead of time and BAAAM a assorted selection of locally grown produce. Hopefully this will help Mike and me be a bit more diverse and healthy in our weekly eating habits. I can't wait to pick up our first box but we will have to wait a week because we head to California to visit my Dad and Stepmom on Wednesday night! I'll try to give updates during our trip from my new fancy dancy iphone.

Graphophobia?

Sorry for the hiatus in entries but I have really been trying to focus on lab work lately. Mostly, I have been trying to put together and write a paper. The key word in the previous sentence is ‘trying’. It has really been a struggle to just get words on paper and I feel that the words I have been able to spit out are inadequate. I feel my words and my work needs to be meatier but I’m having trouble beefing it up. I think that some of my graphophobia results from this being my first first-author publication and firsts always scare me a bit. As I admitted in my 16 facts, I’m afraid of being wrong or of people figuring out that I am not as smart as they believe me to be. I think a small neurotic part of me feels like this paper (or my inability to put it together) will be the proof that my fears are grounded in some sort of reality and it is really a mistake that I’ve made it this far in science. Okay, so I’m a little dramatic and have anxiety problems, I know, but it doesn’t make these feelings any less real. Well, either way, this has to get done soon. I’m hoping to have a rough draft to my adviser by Friday (I just have half the results and all of the discussion to write, blurg). Oh and I was told today that I have to present at group meeting next Wednesday. So, long story short, I probably wont be updating the blog much in the next week or so. Sorry.

Send me energy.

Over it

Snow was once magical; it was powerful and mysterious. Snow could cause the world to stop or at least substantially slow down. The thought of impending snow had the ability to cancel school and clear grocery store shelves. I loved snow and welcomed it with open arms. As a child, and even a teen, I would even go as far as trying to invite snow to visit by wearing my pajamas inside out and backwards. The sight of snow made me giddy and made me feel as though anything could happen.

Not any more. Chicago has sucked away all of snow’s power and stripped away its magic. Snow is now just a nuisance, something that makes life more difficult and cold. Snow, I am so over you.