Babies = Disease Vectors

I'm on to my second cold in two weeks. I was happy that I didn't give Baby Girl my cold last week, but I'm sad to see it doesn't work the other way around: I caught my newest cold from her. Immunological properties of breast milk: 1  Me: 0.

The Air Up There: Taking the Fumes out of the Dreamliner

Check out my post on The Bill Nye Effect about Clem Furlong, an awesome researcher in Medical Genetics at the UW who does some interesting Toxicology field work with toxic fumes on airplanes.

While you're there, read some other postings on our blog!

Vicious Cycle

Like politics, research funding, and most everything else, life in the lab seems to run on a cycle. All of the visuals that come to mind-- a pendulum swinging left to right, the peaks and troughs of sinusoidal waves (or a roller coaster, for the less geeky)-- accurately describe the highs and lows of life. Sadly, the commonality of such patterns doesn't make the lows any easier to bear, nor the highs any more lasting.

Things were going well in the lab, and I guess overall, still are. Unfortunately for my sanity, there are still a few outlier experiments that should be working and aren't. And, as in the past, I have no idea why. This is the vicious cycle of lab research: knowing something is wrong but not knowing what it is, which makes it impossible to fix, and ultimately dooms you to repeat the mistakes. Until, perhaps, something magically changes. (Laugh if you will, but it's still the only explanation I have for my experiments beginning to work correctly back in March.)

I feel like a broken record saying all this, but it's so head-slamming-against-the-wall frustrating that I can't help but vent about it. Positive vibes are welcome these days, send them with care to the angry little lab rat.

I feel you, cat.

Feeling the Crunch

I'm having trouble deciding which time crunches in life are real and which are self-inflicted (and likely unnecessary). In my head, it's all about the next thing that has to be done, and it has to be done ASAP. No exceptions. That nagging voice telling me to work faster and walk quicker just doesn't quit. Maybe the academic environment is responsible for this: you're made to constantly worry about not producing enough data, or not fast enough (what if you get scooped?). What if your funding runs out? Many aspects of these things are not controllable, so the one thing that is-- your productivity-- becomes the main object of obsession.

I'm feel like I'm always late, and I'm unsure how important that date really is.

I walked out of a lab meeting today and was immediately stricken with a mix of anxiety and panic. My presented progress was sufficient this time around, so I left relatively unscathed. Regardless, my brain switched to scheduling the next 2 months+ of my lab life the instant I finished discussing my data. No matter how much progress I feel I made, or how hard I had worked in that past month, I ALWAYS walk out of the meeting overwhelmed by how much more I still need to do. Is this me being too hard on myself, or is this really just the reality of being a productive worker? When do you get to the point where you feel like you were productive enough?

For someone who really likes to strike a line through such things, mentally and physically, these lingering loose ends are guaranteed to induce panic. With the nature of lab work-- tedious, relying on cells to grow over the course of days and weeks-- I can't just rush to my desk and bust out the work that needs to be done. I am forced to sit and plan, and work for weeks to finish even one more experiment, one that may work to my benefit...or it may end more tragically (See: cell contamination). It's a horrible lesson in patience that I'm really tired of learning.

Women in Bio

Another great organization for networking with some powerful women in the biotech world and related: Women in Bio.

I went to one of their networking events last week and really enjoyed talking to so many successful, interesting women in the sciences. I tried to make some initial contacts and hope to see some of the same faces again. Especially for anyone on the East coast, this is a great org with some fun events. Check it out!

'Contagion:' Wash Your Hands

"Blogging is not writing. It's graffiti with punctuation." -Dr. Ian Sussman (Contagion)

For a rare night out, C and I went to see 'Contagion' this weekend. The film is frightening because of the subject matter, and jarring in its realism. It's straight-forward almost to the point of dryness, but for most people, uncontrollable viral epidemics are anything but. I loved it. 'Contagion' presents a situation in which a global epidemic occurs due to a series of random and completely plausible events. An unknown virus spreads rapidly through simple contact: touching surfaces on the bus, or sharing a bowl of peanuts at the bar. It's amazing how many things we touch that are in turn touched by millions of people. And then, as Kate Winslet's character points out, we go on to touch our faces some 2,000 times a day(!). Kate's character, as an aside, is sexy because a) she's Kate Winslet and b) because she has an awesome job at the CDC.

What I liked most about the film was its frankness, the reality of it all. There was no ridiculous drama, only understandable reactions of hungry, scared people who were left to fend for themselves due to lack of resources and a shut-down society. Government agencies, like the CDC, are portrayed as practical and even heroic (for once!). The reality of over-worked scientists and the fallible nature of even the most imposing leaders (Fishburne) were highlights in this aspect.


The characters are varied and excellent as well. Jude Law, for instance, plays the conspiracy-theorist, armed with a blog and millions of followers. He is not paranoid. He's smart, but distrustful of science and the government (as many are). His arguments are understandable and shared by many. Unfortunately, with the power of the Internet, he is able to convince people of an effective, alternative treatment for the virus (that's eventually disproved by science), and likely dissuades thousands of people from getting the vaccine. This character exists in real life. They truly believe in what they are saying and doing, and they reach A LOT of people who trust them. Look at what happened with the one misconducted study linking Autism to vaccines (data was forged, sample size was incredibly small, etc.) became popularized. Thankfully, it appears that Jenny McCarthy has since removed her epithets condemning vaccines and the government for requiring them.

For fellow lab rats, 'Contagion' hits all the right spots in its portrayal of lab science. Science is not magic. A vaccine to an unknown entity takes time to be developed. When they first try to make a vaccine in the movie, the virus kills every type of cell they put it in. Trial and error doesn't even begin to describe it. But, the look on the scientist's face when she realizes she does it-- she created a vaccine-- is priceless. It was that remarkable moment when the base-pairs align and your body fills with triumph. She quickly realizes that she needs to test it in humans immediately and, even in emergency situations, some clinical trials would have to be done before approval for mass use. Putting science first (in true devotee fashion) she injects herself with the vaccine. I wanted to cheer for her.

From the origins of the virus to its capacity to spread, the moral of the story was a true testament to the Public Health field: please, remember to wash your hands.

Is race influencing funding opportunities? Look closer.

Cross-posted from Secretlivesofscientists's Weblog::

Interesting commentary on the disparity of blacks funded by NIH grants. Thanks for using your analytical skills outside the lab, Em.

Communicating Science

Exciting news! I am going to be taking a course in the fall dedicating to 'Science Writing for Impact.' It is taught by a local freelance editor and journalist, and will focus on learning to express ideas and thoughts on science in a clear manner for the general public. Besides actual writing exercises and assignments, there are some guest speakers (local writers, etc) set to come throughout the quarter.

I'm really excited about this class; I've been looking for a formalized atmosphere to learn more about the world of science writing, which can be quite different than other types of writing. Living in the world of science research requires a knowledge of what is rightly seen as its own language. There are terms and words used in science that otherwise may not even exist or have very different meanings in other contexts. It is because of this-- the fact that much of scientific research is published in a highly academic and seemingly indecipherable manner-- that some important information often never reaches the people to whom it can be the most useful. In public health field, communicating the science that is being done and the results of such research is extremely important; the work we do is directly linked to the health of people, and understanding this information is necessary for people to protect themselves and their families.

At the very least, it will be a nice change of pace to break up the lab routine. It probably won't hurt for networking either. Otherwise, things are going ok. It's that time for the SOT abstract again, this year it's in San Francisco! Woot.

Yeast

It's good for this:

Not good for neurons and cell cultures, which end up looking like this:

Yeast contamination: Biotechniques.com

Gah!

DP01_Day 11-- Baby Data to Date

The long awaited arrival of Baby Girl has finally come (appx. 11 days ago)-- August 9th, 2011 = a little bundle of awesomeness.

Day 0

Day 5

I've been out of the lab for 2 weeks enjoying and adjusting to parent life and the new slave driver's  baby's schedule. It's been great and exhausting. She sleeps in about 2-3 hour intervals on a 24-hr schedule. It's like a continuous time-course experiment; I collect diapers instead of cells and treat with milk instead of pesticides. It's tough during the nighttime. I have some trepidation about starting work again next week because I feel it will be tough to actually get up to go to work when what I really will need/want is at least another 2 hrs of sleep. Unlike a true time-course, however, at least I'm not sleeping on the (disgusting) couch in Roo. [Ask me in a week if I have been napping there during the day.]

Overall, though, things are going well. She's just so damn cute that it's hard to hold anything against her, even at 3am. For awhile we were charting her every move (diaper changes, soiled diapers, feedings, you name it). This made me feel useful and productive, hitting all the right lab-notebook-esque spots for me to chart the experiment's..er.. baby's progress. As expected, she's doing wonderfully-- gaining weight, eating well, and being super cute. C is also feeling well, better and more mobile every day.

Future directions for this project:

• Continue to feed and change baby at regular intervals
• Watch baby grow
• Squeeze baby for being cute and observe response

Rants, Raves, and Babes

Firstly, I'm hating Seattle today. This weather is crap. Yeah yeah, I know most of the country is suffering from an unbearable heat wave, but really, 60 degrees and raining is NOT ok. Nor is it acceptable to be called "Summer." It's shit, and I'm frankly tired of wearing the same clothes from November of last year. Someone please tell the rest of the country to share their weather and we'll gladly give you some of our cooler winds.

Thanks, Wordpress.

Now that that's out of the way.. the baby is coming oh so soon! August 8th marks the long-awaited arrival of little Lady Peanut. I'm excited and nervous, but mostly just ready to try to tackle this parenting thing instead of simply anticipating it and driving myself a little batty in the process. I've always been much better at handling a situation rather than the anxiety that comes with thinking about it.

Onesie decorated at the Baby Shower. Awesomeness.

News from the lab is in the theme of 'mediocre on the verge of greatness.' Some experiments have been working out rather well these days, yielding results that I expected to see and in a lovely, clear fashion. Yay! +1 Other experiments, of the Western blot persuasion, not so much. It's kind of a mixed bag with Westerns. It's amazing how you can do the same exact thing, with the same exact antibodies, on two different days and come out with two different results. I'm not even talking different trends in your results (although, that is worthy of throwing things out of frustration). I'm talking about having absolutely nothing show up on your blot. Nothing? Why? Are the proteins shy that day? Do they not want to get out of bed? Where the f*ck did they go? Ah, the reliability of Science.

Savage Love

Last night, while eating pizza at Big Mario's (surprisingly good and the closest to NY pizza I've found out here), I saw Dan Savage. I gave him some grated cheese for his pizza that he was looking for. He said "Oh, thanks." That was all. I didn't geek out and say hi or something dumb like "hey you're Dan Savage" (I'm pretty sure he knows who he is). But, to me, he is somewhat of a celebrity, so it was exciting.

Yay Seattle! Also, please check out the It Gets Better Project, created by Savage, contributed to by many, appreciated by so many more.

Animal Crackers

I really love animal crackers. They are delicious. They also have a surprising amount of protein (4g/box) and calcium (20% DV/box). Just to be clear, I'm talking about the REAL animal crackers, the ones in the little red box with the string (the Barnum's Animal Crackers, not the other ghetto crap you buy in a giant tub).

Fig. 1. The real deal (not to be confused with a box of real animals).

I also have very fond memories attached to animal crackers. And I don't mean something like when I was 5 and my grandparents always had animal crackers for me, nothing lame like that. One time in high school (not band camp), my good friend and I wandered into a CVS late one night and decided to buy all of what was left of the animal crackers in the store. It was the first and only time I've ever bought everything of anything in a store. And believe you me, we ate them all. ....Ok, maybe still lame, but it was exciting at the time.

I have noticed, however, that many of these crackers are in the shape of animals that really don't belong in the circus. Barnum is famous for his circuses and the box leads you to believe that this is what you're getting. But sheep in the circus? Really Barnum? I mean, I know it's been a long time since I've been to the circus, but how lame that would be to have sheep there. And what is a poor child to do now when they go to the circus expecting to see sheep. Camels? I guess they're debatable. Spitting animals could be entertaining for some. The elephants and bears make sense, even the gorillas, but I think you need some help on re-learning which animals actually make an appearance under the big top. On occasion, I'll also find this unidentifiable animal, one I used to refer to as "the shaggy dog," for lack of a better guess. Perhaps this is one of the carny's dogs that come along on the circus tour.

Maybe we can suggest some animal changes to Barnum. Any thoughts?

In other news, the lab is boring/frustrating/a black hole of misery these days. I'm hoping the lab gods remember our saluting them and they continue to bestow their blessings on me... maybe they are just on vacation or a vengeful streak.

Fig 2. GlaDos from Portal

Eat, Sleep, and Breathe

The other day I was walking home from my usual bus stop after a wonderfully long day of sitting in the little dark microscope box room and had to do a double-take at the graffiti on the floor. I immediately thought "oh, look, a neuron!" Regardless of  its multiple (beautiful) dendrites, it was, in fact, not a neuron. On second look, I don't think it was even an intentional graffiti, merely a splatter of spray paint next to some inane tag.
This is not the first time this has happened. I see neurons on bumper stickers and glial cells in art work in restaurants. (Actually, I'm still pretty convinced that last one really was an abstract version of neural networks, but who knows). Am I obsessed? Maybe I'm more haunted by my work rather than obsessed. Perhaps, it's a nice unhealthy mixture of both. I suppose all good scientists are somewhat consumed by their work, that they see cell types in cloud formations, or mechanisms in their dreams.

Nevertheless, it reminds me how hopelessly geeky I am. But, never fear, little scientists, we are not alone. Tthe ever amusing author Mary Roach (author of 'Bonk,' 'Spook,' and 'Stiff' to name a few) speaks to this quite nicely in her intro to 'Bonk:'

"I am obsessed with my research, not by nature but serially: book by book and regardless of topic. All good research-- whether for science or for a book-- is a form of obsession. And obsession can be awkward. It can be downright embarrassing."

Halleloo!

Please excuse my extended absence. Apparently, I'm not very good at keeping this updated when things are going at "bat-shit crazy" speed. Here's a brief recap of what's been going on in my life since February:

1. SOT was awesome! How great it is to see this expansive world of science and toxicology outside of this hole I live in, here in the lab. It is so easy to forget why I am putting myself through all this; seeing all this other research and successful professionals really excites me. I was totally nerding out over things like new methodology and mechanisms in neurotox, but I also was cherishing the connections I was able to make. In any event, drinking and going out to jazz clubs with various professors didn't hurt either. Perhaps by simply incorporating people from industry and government into the mix, the science world was given a personality and a human-ness that's severely lacking from my within academia.

2. Peru was, as expected, fantastic. I really can't complain about sunny, 85F weather. It was super relaxing, spent time on the beach and ate a lot. The wedding was great-- a lot of fun, beautiful ceremony at sunset over the water... as you can imagine, it was incredibly difficult to return to rain and lab-slave life.

3. Girlfriend and I also found out the sex of the baby (due in the beginning of August)-- it's a girl! Really amazing, and scary at the same time. Girlfriend is already worrying about her getting pregnant. I'm still worried about changing the diapers. Hmm...

Fig. 1. Baby Girl at 20 weeks. She has fingers and hands and a nose! Yeah!

4. Lastly, things in the lab have actually started to turn around!!.... !!! I am slightly hesistant to really celebrate just yet because I still am only half believing it to be true. I am sort of waiting for the other shoe to drop and for things to go horribly wrong.... I'm pretty sure that won't happen, but really, I have no idea what to expect with my work. I can't tell you what exactly changed, but the experiment I had been doing with little success has finally worked. In addition, the results are showing surprisingly drastic differences between my treatments and controls! To that, I simply have to say, Halleloo! (Please refer to Figure 2 if this saying eludes you).

Fig. 2. Shangela from RuPaul's Drag Race on LOGO. Halleloo!

If you haven't already, please watch RuPaul's Drag Race for some pure entertainment in the form of America's Next Top Drag Superstar. These chicas are sexy. Til next time, 'echa pa'lante.'

Grad School Made Me Blind

I want someone to do a study (or, actually, several studies) on grad students working in labs. Here are some ideas so far::

1. Repetitive Stress: No, I'm not referring to the chronic stress from advisor expectations or the constant disappointments. The ergonomics peeps should study repetitive stress due to pipette use, or overuse as the case may be. It's a legitimate problem I worry about.




Fig. 1. The scariest looking lab worker pipetting something colorful (generally not the case).


2.  Blindness: I'm pretty sure that sitting in a dark room for hours staring into a microscope, scanning for and taking pictures of fluorescent-glowing cells is likely going to cause long-term damage to my perfect vision. Prospective cohort?

Fig. 2. Approximate size of and light availble in the room containing the microscope.

         3. General measures of sanity. I think this might actually be ongoing in certain departments-- the attempt to monitor stress and its effects on certain health outcomes. I believe one was related to cancer, actually... Imagine that headline when the study reaches mainstream media-- "Scientists say, Grad school gives you cancer!"

In Better News

Because my last post was oh so uplifting, I thought I should put a quick new note to state that things are not as miserable as they seemed last week.

The microscope is up and running..good enough for me to use but still with issues, so I'll tread lightly. I'm still in the process of optimizing this new assay, but I am hopeful. Aside from the 12-hour time point deal, it's a fairly simple and easy assay for which I can store my samples and do it as I please. Flexibility is always nice.

As for new data, the results from the latest experiment were a bit different than what I had previously seen (of course). The need to potentially switch directions on my project is still to be determined. Let's all cross our fingers that this doesn't have to happen.

In other news, Girlfriend is pregnant! I'm pretty sure anyone who actually reads this knows this by now, but as this blog follows my life both in and out of grad school, I think this is a relevant and important detail. Now the goal is to do my oral exam before mid-August or else I'll be competing with a newborn for prep time. Eeek! :)

Fig. 1. My reaction to Girlfriend being pregnant. Or, future baby.

Speaking to that end, in more good news, I have officially formed my disertation committee. Yay! Now I just need the data and I can make some progress.... 'Till next time.

...Annnnd We're Back.

I've been back from my Christmas break for a couple weeks now and have been trying to hit the ground running in high gear, with an optimistic attitude towards my work. At least, that was the initial intent. I know exactly what needs to get done between now and the beginning of March (primarily in preparation for the annual Society of Toxicology meeting-- in DC this year!), and I'm trying, desperately, to start moving on those things. Of course, like always (it seems), no matter how hard I try to be proactive, forward thinking, and prepared, things NEVER seem to work like they are supposed to. And please, spare me the "metaphor for life" because this is not life-- it's Science! It's SUPPOSED to be a controlled environment where you can manipulate variables for scientific purposes. Liars.

Read: Despondent: adj, de·spon·dent [ di spóndənt ]

1. Extremely unhappy and discouraged

*Warning* Lab ranting ahead::: 
So far, the microscope I use to photograph and thus analyze all of my cells for the most important part of my project, is broken. The guy in charge cannot figure it out and it has since been 'sent out' to be repaired. Trying to stay ahead of the game, I decided to find another way to get my work done. So, I found another micrscope center to use, was trained to use it, and now... am waiting to simply be put on a list in order to sign up to use said microscope... I cannot tell you how frustrating this is.

I've also started a new assay for a different aspect of my project, one that promises to be more consistent and reliable than the dreaded ROS assay. The downside is it invovles a 12-hour treatment, which there is really no good way to go about. I was in the lab around 8:30pm last night making a buffer, and even such a seemingly simple task-- putting different things together in a tube-- somehow failed. A particularly pesky reagent (SDS) failed to dissolve appropriately once combined with other stuff. After some failed attempts to change the pH, I remade a simplified version of the buffer and had some success. Overall, I'm pretty sure the buffer was not good and the samples will likely be a waste. But, at 11pm, you stop caring about such things, and you just go home.

Now, with that said, I am still, somehow, trying to be optimistic about this being a better, more productive year in the lab. Mostly because it just has to be. I'm in a sink-or-swim type of stage in my career here. Or, at least, that's the way I see it. This goes beyond the semi-unrealistic expectations of my advisor and well into my own expectations for myself... expectations I am currently not meeting. And that is what is truly depressing.