Why I work late

Oy. Tonight was a long one. Deadlines aren’t always as flexible as one might hope, and science sometimes does not play by human clocks. But it’s all worth it for a chance to piss off the anti-science, pro-God set. One of my secret atheist coworker friends (we have a secret handshake okay no we do not but I’d totally learn one because who doesn’t want to be part of a club that has secret handshakes), gave this to me today:

2014-07-29 13.15.51

Text on a small scrap of paper says: “SCIENCE: The study and investigation of phenomena based on rigorous study and experiment, conducted solely for the purpose of pissing off those who think God did it all.”

Yup. As Fox News has known for years, science-ing is actually part of the Atheist Agenda. I do what I can. You’re welcome.

Why I work late
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Eureka Moments

The most exciting phrase to hear in science, the one that heralds new discoveries, is not “Eureka” but “That’s funny…” —Isaac Asimov (1920–1992).

I had a “Eureka!” moment today. An honest-to-goodness real-all-growed-up-scientist Eureka moment. In my case the particular exclamation wasn’t “that’s funny”, but “NOOOOOOO! What the @%$&*# is that!?” which is a slightly less literary turn of phrase than Asimov gave us, but I think probably more common in the real world.

I saw the weirdness, got my swearing out of the way and then spent about twenty minutes organizing and re-organizing data, then turning my computer upside down to get yet another view. Next I had to go over my methods and try to figure out where I might have screwed something up. And in a moment of absolutely stunning clarity, I found the pattern. And it was a pattern. Everything fit! I actually pulled a passing coworker over to my desk saying “Do you see this?”

I won’t describe it here because it’s boringly specialized and to try to explain it would dull the awesomeness of the moment. But there is a good chance that the finding may help my group further our understanding of the science that’s driving our project.

The thing that I learned today ain’t gonna get me a paper or a patent – some scientist somewhere would undoubtedly look at my announcement and go “Ummm…yeah? We knew that.” But no one in OUR group knew it. This is a special interaction that is (might be) affecting one tiny part of the greater whole of what we’re working on. It wouldn’t be new science, but it would be a new understanding of why we’re seeing the weird things we’ve occasionally been seeing. And hey, it may help us build in controls that will make the final product just a bit better.

Not every Eureka moment leads to the Theory of Special Relativity or Post-It glue, but I think a lot of people – including scientists – feel like if they’re not Einstein or Dr. Gregory House they’re never going to have that moment when a bus drives by and an advert for polka dot bikinis catches your eye and makes you think of the spots that the patient reported seeing, and all sound fades out and you get a stupid blank look on your face and then you shout “SARCCOIDOSIS!”

Nah…For most of us, Eureka moments usually have to be earned with laborious, dull effort. But that means they can be earned with hard work – not just be had by those with innate genius or mad observational and deductive skills.

Annoyingly, Eureka moments also have to be verified. So wish me luck – the results that will support (not prove, mind you) my hypothesis should come off the instrument any moment now!

Eureka Moments

Lab Life is Rough

Busy lab, limited resources. Everyone wants to use the same equipment. Jeepers. Some days.

Mine2

Image shows the scene from “Finding Nemo” where the crab fends off the seagulls (the ones who yell “MINE! MINE!). Text says: “C’mon guys – I got here FIRST!”. The crab is labeled “me”. The seagulls are labeled “The coworkers, they want my instruments!”

Lab Life is Rough

Weekend Report

I was hoping to get a lot of writing done this weekend because there is SO MUCH TO WRITE ABOUT! I got exactly zero writing done, but looking back on my weekend, it turns out I did some pretty cool stuff.

Friday night was supposed to be a night of relaxing and hanging out with the Virtual Drinking Skeptically (VDS) gang. Unfortunately, work setbacks trashed that idea. I didn’t have all my ducks in a row and ended up working until midnight 🙁  Long story short, I grabbed some material (calibrators) for a study and forgot to check the expiration date. After doing all of the set-up on Friday morning, I went to use the calibrators and discovered that they were expired. No problem, I’ll just go grab a new lot, right? Ohhhh…so sad for me: there are no unexpired lots left in the freezer. Luckily, my company makes the darned things on site, so I’ll just go over to manufacturing and pick some up. Three hours later…

At some point during the morning’s series of fiascoes I noted with that sort of inappropriate hilarity that often precludes a mental breakdown that I was going through various stages of grief as my Friday night went up in flames.

  • Shock/Denial: WHAT? How the hell are the calibrators expired? What do you mean we don’t have any extra calibrators in the building? How is that possible? I am NOT letting this get in the way of Virtual Drinking Skeptically tonight.
  • Pain/Guilt: How could I be so stupid as to not check the expiration date before I started!? How could I have everything in place and forget that? I haven’t been to a VDS in months and I feel horrible for not showing up and supporting it because it’s awesome and I can’t believe I’ve ruined my evening like this!
  • Anger/Bargaining: How did NO ONE stock calibrators? Why did this have to happen tonight!? Maybe I could use the expired cals and write some sort of justification. No? Okay, if I can just get the study started, I can sneak away and come in over the weekend to finish things up.
  • Depression/Loneliness: This sucks. I hate working late on Friday nights. Everyone goes home to relax and start their weekend and I’m going to be stuck here pipetting samples until kingdom come. Which isn’t coming, so that means FOREVER. I’m not making it to VDS.
  • Upward Turn: Okay… I have new calibrators. The instruments are all ready to go. Let’s calibrate and see if the controls pass. Samples are thawed, time to start pipetting. If I can load 20 samples per hour and I’ve got 149 samples to load… awwww, man. Wait, calm…I can do this.
  • Acceptance/Hope: Okay, there’s no way I’m getting out of here in time for VDS, but I’ll just have to plan to make the next one. And hey, everything’s running well and I’m going to make it through at least half of these samples today. I’ll come back on Sunday and finish ’em up. And I’ll still have all of Saturday. Every little thing… is gonna be alright.

That’s a whole lot of emotion to go through over the course of a day! Like I said earlier, I left at midnight, but I did get to come home to a sympathetic partner and a whiskey nightcap. So that was nice.

Continue reading “Weekend Report”

Weekend Report

Understanding p-values

A couple of days ago I was trying to nail down p-value, significance levels and null hypotheses. I know that if the p-value is lower than 0.05, the result is significant and the null hypothesis is rejected – but that’s just memorization. I wanted to understand it, know when it should be applied, and be able to explain it to others. I turned to my trusty co-worker, R., to help in this endeavor. (If you prefer you can skip the dorky “Brianne comes to understand p-values” conversation and go right to the “why this shit is important” section below.)

Continue reading “Understanding p-values”

Understanding p-values

Snippets

You know how when you’re doing data analysis, you sometimes get sucked right in? You’re working with the raw data, getting it all organized and pretty so you can drop the whole chunk into a statistics program and watch the Passing-Bablocks and Pearsons fly forth onto the computer screen? But it takes a while to do all the organization, data point exclusions (with valid justifications), reprocessing, manually checking the lines and watching the SD and CV calculations to make sure there are no cut/paste errors, double-checking formulae, making sure no single reps in set of mostly double reps are mucking up the whole scheme, but finally! – you’re ready to define the final data set, you click the analyze button and BAM! SLOPE OF 1.01, R=1.00 BEETCHEZ!

*ahem* So, work went well last night. How about you?

Anyway, after getting home from work and the grocery store at 10:30pm I lazed out on the google reader and blog writing. But here are a few things that I’ve been mulling over.

Continue reading “Snippets”

Snippets

The Poinsettia Mystery

I was a biology major in college. During that time I was a student employee and I got stuck with the mind-numbingly boring and frustrating task had the opportunity and challenge of gluing hundreds of friable, sometimes paper-thin plant specimens into specimen books. I also took a botany course, but it was only one semester long and I believe that the most I’ve retained from that class is an understanding of the differences between deciduous and coniferous trees. Actually, that was one of my big SCI-ENCE! moments. I remember being hugely impressed with needle-bearing evergreens’ adaptive strategies for surviving in nutrient-poor soil, and arid and low-sunlight conditions. Rah! Rah! Evergreens!

Anyway, that’s just a side story. The point is, I’m not a botanist, but I do imagine myself to be a bit of a naturalist and appreciator of ecological science. And what I’m…. Well… Hmmm… What I’m trying to say is that I learned something new, something that’s probably common knowledge and I’m a little embarrassed to have not known this, especially having studied a bit of botany. But on the other hand we all make assumptions about little things that don’t have much to do with out day-to-day needs or experiences, and it’s neat to have those misconceptions or ignorances cleared up. Here’s the story:

We, like many work offices, acquired a poinsettia over the holiday season. You know, one of these:

Image Source

And as is the fate of so many under-appreciated and ignored office plants this one didn’t get nearly as much water as it needed. Eventually all of the green leaves blackened and curled and fell off to their final resting place on the dry soil. For some reason, after the last of the green leaves dropped, the officemates and I were spurred into action. We became poinsettia paramedics, determined to bring this abused plant back from the brink of destruction to which we had driven it.

As we were considering the poinsettia several days later I had this conversation with my office mate, R.

Me: Isn’t it weird that the leaves fell off  before the petals did?

R: I think the red ones are leaves too, not petals. 

Me: No way! Why have two different types of leaves on a plant? And leaves have chloroplasts, and don’t those cause the leaves to be green?

R: (A PhD in virology and rather far removed from his own botany course) I don’t know. Maybe. But I don’t think it’s necessary to be green if you  have chloroplasts.

Me: I don’t know either. I bet the concentration of chloroplasts is less in the red parts than in the green leaves. I wonder how long the plant is going to live without the green leaves. Will it be able to produce enough energy to survive?

R: Hmm. [goes back to his computer]

Me: You know, if only there was someplace where we could easily look all of this stuff up.

R: [Playing with a ROC curve and only half listening to me ramble anymore] Have at it.

To the interwebs! As I knew it would be, the answer was immediately presented:

From the website BiologyReference.com

At first glance one might come to the erroneous conclusions that all leaves are green, and that which is green in nature is a leaf. While often this is the case, there are numerous exceptions. Plant organs are green because of the presence of chloroplasts in the cells near the surface, which reflect green light and absorb other wavelengths as a source of energy for photosynthesis. Certain cells in many leaves contain these organelles , but chloroplasts are also found elsewhere in other organs, such as the stems of cacti of the desert and twigs of sassafras trees in the deciduous forest. In addition, flowers such as the head of broccoli, and fruits such as watermelons also contain chloroplasts.Conversely, many leaves are not green. The winter holiday season brings potted poinsettia plants into many homes. The bright red or pink organs on these plants are not the flowers; they are specialized leaves called bracts, with cells that contain so much pigment that the limited amount of chlorophyll in the chloroplasts is obscured from view. Some poinsettias are white; usually a close look reveals that they have a green tinge due to the presence of a few chloroplasts. Poinsettias do, however, produce flowers. They are less conspicuous small, round yellow and green organs nestled at the apex of the stem, surrounded by the colorful modified leaves.

So – one mystery solved! But why bracts? Wikipedia says that the colorful red leaves serve the function of attracting pollinators. And an article on e-how provided some fascinating insight on why the poinsettia in our office is the way it is:

Why Colored Bracts Form: In nature, the poinsettia plant is deciduous and drops its leaves in the winter. Some of the leaves change color before they fall. Growers carefully control the light exposure of poinsettias cultivated for the home market to mimic this natural cycle and the topmost leaves, or bracts, turn color in response.

Special Breeding and Cultivating: Although all poinsettias have descended from the tall perennial Mexican plant, plant cultivators have bred and selected plants over decades to produce poinsettias with a height and appearance appropriate for inside decoration. In addition to shading leaves to induce color change, growers pinch the plants to produce side shoots for a fuller poinsettia.

Controlling Light Exposure:The amount of light a poinsettia receives controls its ability to produce colored bracts. Growers manipulate this natural process, called photoperiodism, to create colored leaves in time for the Christmas season, by giving the plants at least 12 hours of darkness for eight to 11 weeks.

Thanks, internets. I love when you prove me wrong get me the information I’m seeking!

And our Poinsettia is still hanging in there, although we’ll probably toss it out when it comes time to torture the poor potted Easter Lily that will show up in a couple of months.

The Poinsettia Mystery

Nerd Trash Talk

I headed right up to the lab when I arrived at work this morning, which is a different pattern than I’ve had over the past several weeks. My most recent project has been a long-term study that I’ve been testing it in the later part of the day just because it’s a simple assay that I can throw on as I’m walking out the door at night. But usually I can be found in the lab at all hours of the day or night.

A relatively new coworker (and also my office mate with whom I get along well) saw me in the lab this morning and commented.

Him: What are you doing in the lab? You usually don’t stroll in until sometime after noon.

I’m in work mode and tend to make science jokes because I have a receptive audience here.

Me: Hey, buddy! Your observational data set of my behavior is dangerously small to be making any assumptions.

Him: Hey…I can only work with the data I have.

So, a relatively benign, forgettable, nerdish exchange. But I later realized that I had just asserted – in probably the geekiest way EVAR in all of recorded history:

“Bitch! You don’t know me!”

And I’ve been giggling all morning over that.

Nerd Trash Talk