Debbie Knight

Archive for November, 2011|Monthly archive page

To err is … biological

In observation on November 29, 2011 at 2:22 pm

A little graphic humor: the error bar (source unknown)

Ah, the error bar.

It can tell us quite a bit about the results of an experiment.

Last week, my lab (a biology lab) had its weekly meeting with the chemists with whom we collaborate. When our graduate student mentioned that she would be setting up each experimental condition in quadruplicate, the chemists seemed a bit surprised.

Now, I don’t know about chemistry experiments, but I do know that when you are working with a biological system (whether it is cultured cell, an animal study, or a human clinical trial), there can be quite a bit of variability. This is why biologists need to repeat each experimental condition, to reduce the effect of that variability. When the results are averaged together, we also determine how much each of those data points is different from that average – which gives the error bar. If that error bar is long, then we know that there is quite a bit of “bounce” in the measurements. Ideally, the measurements would be nearly identical and the error bar’s length short.

But I’ve found that biology is rarely “ideal.”

As it turned out, it was a good thing we performed the experiment in quadruplicate because some conditions had long error bars – which suggested a trend in the data and pointed us in another direction.

I suspect that in the chemistry world (at least in our collaborator’s world), experiments give more precise results than they do in the biology world and that replicates aren’t as critical.

Sometimes I wish that were the case in the experiments I do.

But sometimes that’s where the truly interesting findings are found – in the “bounce” of an error bar.


Crowd sourcing to fund research?

In observation on November 17, 2011 at 6:09 pm

There’s a new trend rising across the Internet  — crowd sourcing (i.e., asking the public to donate money toward a worthwhile cause or project, often through social networking avenues).

And some researchers, as an experiment of sorts, are turning to crowd sourcing as a way to fund those little, difficult-to-fund research projects.

For example, one researcher curious about why a type of male spinner dolphins have a backward dorsal fin. He’s trying to raise money for a CT scan of one such dolphin to gain an understanding why only the males have this quirk.

At one point in history, it was common for scientists to turn to the public for funding. And, as a result, these scientists had to communicate their research clearly and provocatively to an audience of potential benefactors. The topic had to be upbeat, engaging, and perceived as worthwhile.

Obviously scientists still have some of those skills today.  Those skills are needed to convince the government agencies  to fund a grant proposal. But scientists are communicating with other scientists in “science-speak” rather than in a language everyone can understand.

I think crowd sourcing could be a great idea. It could work!

The scientists must effectively communicate their research proposal, clearly and concisely, to a general audience to raise the funding. If they don’t do a good job at this, if it isn’t provocative enough, very few people will be moved to donate.

The public is inspired by the science. They are directly involved in funding the research. They are in control of where their money goes,  rather than a governmental agency investing those  tax dollars  for them.

You may have noted I said  it could be a great idea.

One major problem I see with crowd sourcing is accountability. How do the donors know that their money is actually being used toward the proposed project? When the government invests money (via a grant), there is an accounting structure in place. At my university, that accountability starts at the researcher’s level through the department and university levels. There are audits. That doesn’t mean it’s a perfect system. The university has had to buckle down and enforce rules over the years I’ve been there. Of course, there is a great deal more money involved than what is crowd sourced, but I do want to know my money is going toward what I think I’m investing in.

That being said, I like the idea of crowd sourcing.

It feels like a grass roots movement, which I find appealing.

I feel involved.

And I think it could work!


If you’re looking for a place to start, there are 49 crowd sourcing research projects that you can check out at #SciFund Challenge

“Don’t be such a scientist …”

In observation on November 15, 2011 at 4:54 pm

I had the honor of writing a blog post for the Scientific American Guest Blog, which was published online yesterday. As I dug through the scientific literature preparing for the post, I found I had a difficult time taking off my “scientist” hat and putting on my “writing” cap. As a result, the first draft was way too … “science-y.”

And after reading the book on science communication by former-scientist-turned-filmmaker Randy Olson, “Don’t Be Such A Scientist,” I kept hearing those words echoing through my head as I worked on the post.






Simple words. But it’s hard to actually live by – especially when I’ve basked in “science speak” for so long. I sometimes forget that something that’s obvious to me might not be so obvious to the reader. For example, not everyone might understand the implications of a silver nanoparticle binding to a  strand of DNA (hint: one possible outcome is the nanoparticle might act as a roadblock for the protein that is trying to make a copy of the DNA). And, to be honest, I’m not sure if the “hint” I just gave is simplified enough – I’m still assuming certain terms are understood.

Olson stresses that you should tell a story, create tension, peak the reader’s interest (“arouse the audience” as he puts it) and then fulfill the reader’s expectations. But I think there’s one more element: the reader needs to walk away feeling like she’s learned something.

Before I sent the final draft to the editor, I needed a “test” audience, so I recruited a few friends to read the story.  I picked friends who I hoped would be brutally honest. Two of them said (independent of one another) that they felt they learned something.

That was THE best compliment they could give a writer!

Of course, the happy buzz quickly wore off when my sister said: “It’s so long!” She has absolutely no interest in science, so I felt she was the litmus test. Obviously, I scored pretty low marks in that category. <sigh>

I had hoped the topic was controversial enough to generate discussion on the Guest Blog, but as of this moment, all I hear are crickets chirping. I had toyed with the idea of voicing more opinion in the post — you know, stir the proverbial pot a bit. But I really didn’t want to freak the readers out. My goal was to increase awareness. Hopefully I accomplished that.

I will come back to this topic of science communication in a future blog post. I have more to say … much more.

But in the meantime, I will try to “not be such a scientist.”

A day in the life: November 9, 2011

In research log on November 9, 2011 at 1:48 pm

From time to time, I will give a glimpse into the “glamorous” life of a research associate and talk about what I’m doing in the lab on a particular day. These entries I will call “A Day in the Life…”

This fiscal year, my department had to let three researchers go.  I’ve talked about two of them in previous posts (Dr. V and Dr. T). The third researcher (Dr. G) did not go quietly, judging by a few scathing email messages he sent to everyone in the department.

He left a few months ago.

And as a final nose-thumb, he left his lab … untouched.

Dirty glassware still sit on the benches, formalin-preserved specimens fill the shelves, and bottles of reagents and chemicals fill the cabinets and refrigerators.

It’s pretty much a mess! I know this because I weekly monitor the liquid nitrogen levels in his cryopreservation tanks where his cell lines are kept in suspended animation. (The department will eventually ship those cells to him, once he settles in a new lab).

Because my name and phone number are posted on the door as a contact, I got a call today from an inspector from Environmental Health and Safety – she was scheduled to do a routine inspection of this abandoned lab.

Great! It’s stressful enough to endure my own lab’s inspections (which is due any time), and now I have to endure another lab’s?!

Well, unlike some inspectors, she was pretty understanding and decided to call it an “unofficial inspection” since no one was currently using the lab space. She pointed out a few problems that would need to be remedied (a fume hood that needed certification, a few moldy ceiling tiles that needed replacement, etc) and that was it. Pretty painless.

Of course, during the inspection I realized how much it would take to clean out the lab for another researcher to take over the space. And I sure hope it isn’t assigned to me! There are tissue culture dishes in the incubator, mildew growing like gangbusters in the fridge, an endless sea of culture media and reagents that will need discarding, and chemicals that will need to be inventoried for disposal.

But that’s for another day.