Debbie Knight

Archive for December, 2011|Monthly archive page

The list

In observation on December 30, 2011 at 10:46 am

Like Santa, I have a naughty and nice list – only this one is for researchers: ones I would love to work for and ones you couldn’t pay me enough money to work for.

Today, I bumped into a woman who used to work in a lab that offered a service for fee. What that means is Muna’s lab would cut out tiny areas from a thin section of human tissue using a laser for researchers for a certain amount of money. This helps make an extremely expensive piece of equipment a little more affordable for university labs.

The technique she performed is called laser capture microscopic dissection and it takes time to cut enough tissue for analysis in the lab. In my case, I wanted the cells inside blood vessels (easy part) as well as cells that were in certain areas of the tissue (hard part).

The problem was that this technique, once mastered, became boring and tedious for her. She clearly was not happy doing this sort of work.

So, I was glad to hear she is working in a different lab, doing regular lab work which varies on a daily basis. She seems much happier. And that’s good.

When she told me she now works for Dr. B, my heart sank.  I personally would never work for this researcher because of what I’ve heard from people who worked with and around him. But she says it’s much better working for him than her boss in her previous lab, so I guess it’s all relative.

That got me to thinking. Over the years, I have kept a mental list of university researchers I would love to work for (if I needed to find another position) and an extremely long list of researchers I would never work for.

So just how does a researcher get on my “never work for” list?

It’s from my own observations. And it’s from the stories I hear from graduate students, research associates, and other professors. For example, a researcher be a really nice person but expects his lab personnel to put in 12-hour days. I’m not afraid of putting in long days, but I don’t want it to be the norm and I would like it to be voluntary rather than mandatory.

It could be that the researcher does not treat his lab personnel well – like yelling at them or pitting people against one another in an effort to increase productivity.

It could be the researcher has a huge lab – I prefer a smaller lab where it feels more like a family than a factory.

These are just a few examples as to how a researcher gets on that list.

And, of course, I compare all researchers to my current and former bosses – all were great guys to work for.

In the case of Dr. B, he falls into the “mean to his peeps” category. So I was a little surprised that Muna said working with him was an improvement. (I didn’t ask her how he treats her – I didn’t want to disenchant her.)

And although her old boss (Dr. S) was on my “I don’t think I want to work for this guy” list, her assessment has put him squarely on the “never work for” list – especially if she considers Dr. B (already on the list) an improvement.

I’m just beginning to re-assess my mental lists because I may have to look for another position by the end of 2012 when the lab’s funding runs out. That is, unless we secure more grant funding – something that’s not so easy and definitely not guaranteed these days.

But for now, I’ll be happy for Muna. Happy that she found a research position she can be excited about.

Congrats, Muna! And good luck with your research project!


Pride and glory: the publication board

In research log on December 23, 2011 at 7:52 pm

Until about four years ago, I maintained my department’s publication board. I would replace older journal articles published by faculty members with freshly minted ones. It was a great way for the department to show the diversity and breadth of research that went on in the department.

Now, the department has a clinical side and a basic science research side. And back then, the board heavily favored the basic science side – those were the only faculty members who would routinely provide articles for the board.

I left the department for three years when my lab’s grant funding ran out.

In that time, the tumbleweeds rolled in and the board was in shambles.

It was a disgrace.

It was a wall of shame.

After it was clear that no one would step forward to reclaim the publication board, I asked our chairman and vice chairman of research if I could restore the board to its original glory. They were very supportive. And the vice chair of research sent a message to faculty members to help in the endeavor by sending their recently published journal articles. Only four responded.

I waited for more articles to “pour” in.

And waited.

Eventually, I had the vice chair send out another request to the faculty. Maybe they didn’t pay attention to the first message.

One more article dribbled in.

This was a disgrace. I knew that there are more than five faculty members publishing in scientific journals.

So, I stalked them.

Well, cyberstalked them – on a website called PubMed. I typed in each of their names and found a bounty of journal articles to plunder (okay, maybe I just printed them out).

It took me three freaking hours to chase them all down, but I now had dozens of articles.

As I was starting to pin the articles on the bulletin board, my division head passed by. Because there were so many articles from 2011, I had to limit the number of articles per faculty member to four (that just happens to be how many fit vertically on the board). He was not too pleased – he had many more than four publications from this year.

But I stubbornly stuck to my guns. With the current board space, there just wasn’t room for any more.

(I hope he doesn’t remember this when it comes time to do my performance evaluation)

So, the publication board has been restored to all its glory. I wanted to display them a little more artistically (perhaps gently zigzagging as they cascade vertically), but there simply wasn’t room for anything but efficient use of space. I would have preferred to have a vertical slot for each faculty member, but there were simply too many articles and not enough space.

So here the boards are, in all their glory. The open space is for my division head to put his articles – hopefully he’ll understand his need to “edit” his publication selections when he sees the finished product.

One of two publication boards

The publication board on the opposing wall. The gap in the middle is reserved for my division head's journal articles.

With any luck, we’ll get an additional board mounted so we can display more — my division head was not the only faculty member who had more than four articles published this year.

As I looked at the board, I was impressed by the sheer number of articles published by my department’s faculty this year. And I hope the department will once again take pride in displaying its accomplishments on the publication board.

Holiday cookies and the research lab

In observation on December 19, 2011 at 6:54 pm

Since many (including myself) are baking holiday goodies this time of year, I couldn’t help think about some of the similarities of working in the lab and working in the kitchen – and there are quite a few.

Having the right equipment is essential.
In the kitchen: When making cookie batter, it’s really helpful to have an electric beater. Yes, there were cookies before the electric beater, but I can’t help but think how hard that must’ve been, stirring the batter by hand. It’s not really so different in the lab.

In the lab: Sure you can swirl a flask of chemicals you want to go into solution by hand, but it’s so much easier with an electric stir plate and a magnetic stir bar (the stir bar goes inside the flask to stir its contents).

In the kitchen: Having a properly-functioning oven to bake an apple pie to perfection is important. If it runs too warm, the crust gets singed before the apple filling is warm and bubbly. If too cool, it takes forever for the pie to finish baking.

In the lab: The same can be said about the steam sterilizer that labs use to kill any bacteria on some lab equipment or in liquids that will be used to culture animal cells. The sterilizer (also called an autoclave), which looks a little like an oven, uses steam to get the things inside it to the ideal temperature and pressure to kill bacteria. And like the oven, if it runs too warm, it can melt the plastic equipment (like pipet tips and tip boxes) into some interesting shapes I like to call “autoclave art.” If it runs too cool, any bacteria that weren’t successfully killed will grow in the liquids you don’t want them to grow.

Recipes are followed.
In the kitchen: You might have measurements in ounces or cups or teaspoons.

In the lab: The measurements are made in grams and liters. The idea is that if you mix things in the right proportions, using those measurements, you will get a consistent product at the end.

In the kitchen: You might get cookies instead of soufflé (okay, so this is a slight exaggeration, but you get the idea).

In the lab: If the liquid media is not made exactly right, the cells you want to grow simply won’t grow because the conditions are not exactly right.

In the kitchen: You have a little “slop” when you follow a recipe. If you add a mounded teaspoon instead of a leveled teaspoon, the cookies will probably still come out okay.

In the lab: If you add more of chemical A than you intended, it can absolutely ruin the experiment.

One lab director takes this analogy to heart.

When I interviewed for a job in his lab, he asked if I was a good cook. That’s a great screening question. If the person is a lousy cook, they might not be able to follow a laboratory protocol (another kind of “recipe” in the lab) – especially a complicated one such as a multi-stepped Western blot analysis protocol used to analyze proteins in a sample.

I’m a pretty good cook – I follow the recipe to the “t” a few times to get the hang of it. And then, like a scientist, I start experimenting by adding a touch of something not in the original recipe.  Sometimes that works out great … and sometimes the dogs get the honor of eating the failed experiment.

Happy Holidays, Everyone!


The cost of health insurance?

In observation on December 14, 2011 at 1:21 pm

Thankfully I don’t have to resort to being a research experiment in order to afford health care like the rat in the above cartoon.

Working at a university (especially one with a medical center) definitely has it perks — one of which is good health insurance. Of course, the rates will be going up next month, but you won’t find me complaining about it.

There are plenty of people out there who can’t afford it. And one of those people is my sister.

She works at a small daycare that does not offer a health care plan. She simply cannot afford individual health care insurance on her part-time paycheck.

Last month, she felt the costly effects of not having health insurance.

She had a sharp pain on her right side. She suffered until the pain became intense enough to seek medical attention. She went to a fast clinic located inside a grocery store. The nurse practitioner suspected she had gallstones, but the clinic lacked the ability to accurately diagnose this condition and suggested she go to the emergency room.

That gave my sister pause – that would be really expensive. Was her medical condition serious enough to warrant going to the hospital?

Her pain persisted and she eventually decided to go to a nearby hospital.

After an x-ray and blood work, they determined she had pneumonia in the lower right lobe of her lung which was causing the pain.

However, one of her blood tests came back a little “off” which lead the ER doctor to order a $2,500 CT scan to look for possible blood clots – which, thankfully, there were none.

While she was lucky it wasn’t anything more serious (say something that required surgery), she now owes the hospital well over $5,000 (and the bills are still rolling in). Somehow she will have to pay these bills, possibly arranging payments she can afford each month.

Could she have avoided this much out-of-pocket expense by having health insurance? Definitely.

Could she have avoided the emergency room if she had a regular physician? The answer is a resolute “yes.”

But will she do either of these things (buy health insurance and have a regular physician)? The answer is most likely “no” – she simply cannot afford it (especially now that she owes the hospital so much money).

So you might say she’s in a catch 22 situation. And I’m sure she’s not alone.

If she had a regular physician, the doctor could have ordered the x-rays and determined she had pneumonia. But because she was in the ER, the ER doctor had to in good conscience rule out the blood clot. Was this “defensive medicine” on the behalf of the ER doctor? Or simply standard medical practice?

Defensive medicine. Covering one’s medical practicing butt to deflect the slightest whiff of malpractice. Could this be one factor in rising health costs? Is defensive medicine being driven by the medical institution or by the consumer? Do we as Americans expect this privilege? Do we demand the thorough workups, demand the prescription drugs, demand good health care? Do medical professionals rely too heavily on expensive diagnostic tests to make diagnoses? These are tough questions to answer.

I will say that I never appreciated just how expensive health insurance can be until I asked another sister how much she pays for her insurance. She somehow manages to cover the cost of her individual health insurance. It runs her $456 a month at the moment (those rates will be increasing early next year) and she has a $1,000 deductible. She also works at the same day care, but swings the high cost of insurance by picking up babysitting jobs to supplement her income and by living very frugally.

Is it worth her paying $5,472 a year? It could very well be, especially in light of our sister’s recent hospital bills.

My mom, like many retirees, is now on Medicare. And with the changes in coverage, she now faces the decision which prescriptions drugs she can afford to continue taking and which ones she will have to let lapse. I find this unsettling.

Again, I’m grateful that I only pay a small portion of what she pays for health insurance. And I’m grateful that I have really good health care coverage.

I’m not sure what can be done to “fix” the health care system, but I do know that it needs some help.

I had high hopes the health care changes proposed by President Obama and modified extensively by Congress would help people like my sisters – those who make too much money to qualify for Medicaid benefits – but alas, I fear the reform did not go far enough to be effectual. My sisters could really use the help, as well as countless Americans out there.

My sister’s recent experience with the health care system really brings the issue home for me. And I find it both eye-opening and frightening.

Advice to scientists: stop putting your audience to sleep!

In observation on December 13, 2011 at 3:43 pm

Today, I attended our department’s Grand Rounds (which is a seminar series often geared toward the clinical side of the department). I didn’t actually go because I was interested in the topic – although the title was a bit provocative with words like “flesh-eating bacterium” and “novel.”

The actual title was: “Novel Virulence-Regulating and Virulence-Causing Abilities of Eukaryote-Type Cognate Kinase and Phosphatase of ‘Flesh-Eating Bacterium.’”

I attended this seminar because I suspected attendance would be low and they needed bodies to fill the seats.

The researcher’s findings were interesting (and I think they could be woven into a newsworthy story), but his presentation was anything but interesting. At one point, I dozed off, complete with the head bob and arm jerk that woke me up (I hope no one saw that!).

And when I looked around at the others in attendance, I found I wasn’t alone in my brief snooze — about half the people were at various stages of dozing off as well.

One thing I do to keep myself awake and listening is I doodle. I can tell how tough a time I’m having by the number and intricacy of my doodles. Here is one such doodle I did today. I have no idea what it is supposed to be? Perhaps the enzyme the speaker was discussing, perhaps not.

A doodle I made during the seminar.

I realize that he was talking to other researchers and medical doctors, so he could make the talk pretty technical, but I think he forgot that his audience is pretty diverse. It is a pathology department, after all. There is more to pathology than flesh-eating bacteria (For those who want to know, the flesh-eating part is called necrotizing fasciitis, and the bacteria is a member of the Group A Streptococcus family).

So, for such a diverse audience, a speaker needs to take a little time to set the scene, to give a little background. This speaker made assumptions about his audience and jumped into his complicated research, throwing around bacterial gene names like we should know them and not fully explaining how he got the data he was showing.

This is an intelligent guy. Perhaps he was a little too intelligent which lead him to make assumptions about his audience. I don’t know.

He was not very engaging with his audience. He didn’t look at the group or attempt to make eye contact – he was turned away, looking at the screen so he could accurately point his laser pointer and to read his slides. And his slides – they were busy! They often showed several figures at one time so it was difficult to know where to start looking.

Now, his presentation wasn’t all bad. To give him credit, he did sometimes have a summary statement across the top, which helped the audience to quickly figure out what the slide was about.

However, had he simplified those slides, showing one figure at a time, his talk might have been less daunting to audience members.

And his last data slide? A very provocative thought that his research findings could lead to a new cancer treatment. What?? Why didn’t he mention this earlier? It would have enticed the audience to be more attentive.

There are lessons to be learned here.

So, if there are any scientists reading this blog entry, let me give a few pointers for your next talk – whether your talk is to fellow scientists or a general audience:

  • Focus on one aspect of your research. Don’t tell the entire story – you don’t have time to do it justice in a 55-minute talk.
  • Tell a story. Yes, your data tells a story, but you need to add a humanizing element. Add anecdotes. Tell your audience where you got stumped and how you resolved the problem. Give them insight into the research process.
  • Simplify your slides. Just show one figure at a time. You can build several on a single slide, but reveal one at a time to help your audience focus on what you’re talking about.
  • Engage your audience. This might be as simple as looking them in the eye or showing your enthusiasm for your research or asking them rhetorical questions to get them thinking. If they’re engaged, they’ll pay attention and the eyes will stay open.
  • Summarize each result. Write a one sentence (a short one!) across the top of each slide. This helps your audience understand what the data is saying and, in case they lose focus for a moment, helps them quickly get back up to speed.
  • Don’t assume your audience knows everything you do about your topic. Be sure to give an adequate background and definitions of new terms. The audience will appreciate it.
  • Recap what you said. Briefly summarize your results and put them in proper context at the end of your talk. Yes, your talk just covered all those points, but it really helps the audience understand what they just experienced. A friend of mine who took business classes told me she was taught to: tell them what you’re going to talk about, talk about it, and then tell them what you just talked about.
  • Don’t talk too fast (or too quietly). You want your audience to follow you. They can’t do that if you’re speaking at the speed of sound – they need time to process what you’re saying, especially if they are international folks. Slow down. Take a breath. And have a conversation.

Will these pointers keep your audience from snoozing? Who knows.

But I challenge you to think about the worst speakers and the best speakers you’ve ever heard and think about what made them the worst or the best. The data is there! And much can be learned from those experiences so you too can be placed in the “best” category by your future audience.

A day in the life: December 7, 2011

In research log on December 7, 2011 at 12:37 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…”

Tonight is my department’s holiday reception. It’s a time when the clinical faculty and staff mingle with the basic science faculty and staff – something that rarely occurs on such a scale. It’s a little like going to a high school reunion, where you assume the person you don’t know is a classmate’s spouse — only in this case, since I’m from the basic science “side,” I assume those I don’t know are from the “other” side, the clinical side.

Because I spend a great deal of time in the research lab, I rarely see the clinical faculty members and even more rarely see any of the clinical staff, and I’m amazed just how large and diverse the Pathology Department really is.

If the holiday reception is anything like last year, there will be lots of nibble stations filled with hors-d’oeuvres and lots of people.

It’s a really nice soiree. Although in these economic times, it’s been scaled down a bit. Gone is the ice sculpture shaped like a microscope at the martini station where the drink is chilled as it is poured from the top of the sculpture and into the awaiting glass at the base.

Ice sculpture at the 2008 holiday reception for the Department of Pathology.

Gone is the chocolate fountain and fondue station. And gone is the chef-manned make-your-own pasta-creation station.

But that’s okay, it’s not really about the food (okay, maybe a little bit), it’s about hanging out with my departmental family … whoever they are.

A day in the life: December 3, 2011

In research log on December 3, 2011 at 10:31 am

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…”

Back in June, I wrote about the darker side of research and how a supposed collaborator decided to go solo and write a manuscript on the very research we were working on together. We only found out after the manuscript had been accepted by a scientific journal for publication. Well, the article has officially been published in the December issue of the journal.

Part of me did not want to look at it because the whole situation just makes me seething mad.

But like a train wreck, I had to look.

Curiosity killed the scientist?

I had to see what was included in this article, to see if it will affect the data we will parcel into our own manuscript.

Because our supposed (now former) collaborator is a clinician, the published paper does have a clinical bend. So that was a small piece of good news. The lab I work in is a basic science lab, currently focused on ferreting out the mechanisms behind this particular disease process.

As I looked through the article, thinking back on our group discussions we had during the collaboration, I couldn’t help but think this article could have been a much stronger and more complete story had we combined our findings into a single document. It would have been in both our interests to combine our efforts to pool our patient specimens (increasing the number of patients in the study) and execute a more intensive, robust examination of the proteins that may be involved in the disease.

There were no arguments, no falling out, just impatience to get at least some of the story out — no desire to wait while we chased down the details of our collective observations. (sigh).

Alas, it was not meant to be.

Or perhaps I should say, that’s how the collaboration “cookie” crumbles.

The good news is that after my lab completes a few more experiments, we’ll submit our own results to the peer-review process and have the opportunity to tell more of the story. Granted, we’ll have to modify how we tell that story since the collaborator used a few images that stole some thunder – but we’ll get it out there.

In the meantime, while I work on cranking out those experiments, I might look for a photo of our former collaborator and fashion a pinata or dart board – you know, for something to do during breaks.

The cost of research

In observation on December 1, 2011 at 6:55 pm

Through university announcements, I will hear about an individual researcher or research team receiving National Institutes of Health grant funding. That’s always good news to hear, especially with grant funding so difficult to secure these days.

But the amounts of the awards stagger my mind.

It is not uncommon to hear announcements that a researcher received a $1.5 million NIH grant. That seems like a lot of money. But if you break it down: a four-year grant of that size would come to $375,000 per year.

That seems a little more reasonable when you start to consider what the money goes toward.

The first order of business is paying the people to do the research. Personnel salaries and benefits can account for up to 70 percent of the total budget. A large chunk of the money goes toward the principal investigator who directs the research and the e technician, graduate student, and/or post-doctoral researcher who actually perform the experiments.

The rest of the money goes toward the supplies and equipment needed to do the experiments.

And let me tell you, research is expensive!

My former boss used to jokingly say that for research supply costs, just move the decimal over one place (meaning there is an incredible markup of price for supplies purchased from scientific supply companies).

It is understandable that scientific equipment like flow cytometers and gas chromatographs, designed to make very precise measurements, will be expensive. It is also understandable that many of the supplies used specifically for that equipment will also be expensive – especially if the scientific company is the only supplier for those supplies.

But what about the small stuff? The general supplies used by a lab?

You can’t just go down to your local mercantile and buy a case of plastic tubes, culture flasks, reagent-grade chemicals, or antibodies. You have to buy these sorts of items through a scientific supply company.

Many researchers do their best to get the lowest prices, asking vendors for price quotes, buying in bulk, and using vendors that give the university a discounted price, taking advantage of vendor sale specials. But even with these cost-saving measures, the supplies are still expensive.

Admittedly, there are some supplies that could be purchased from a local store much cheaper than from a scientific vendor. However, the university keeps very close tabs on how research grant funding is spent. A researcher can’t just go down to the local grocer and buy supplies such as non-fat dried milk, plastic wrap or aluminum foil and charge it to his research account. This practice is frowned upon by the university because it is difficult to track spending and difficult to prevent fraud. In addition, there is a prohibitive amount of red tape to hack through to do something this simple and cost-saving.

I recently saved my lab (and the American tax payers) a bundle of money.

The list price of nylon mesh from a well-reputed scientific supply company is $359 for three 12-inch squares (we’ll call this 3 square feet, so it costs about $120 per square foot). Admittedly, this mesh is made pretty carefully: the mesh size is very tightly controlled and no human hands have touched it. And some labs may need this amount of precision. But all we will be doing is filtering cells through it, so it doesn’t need to be so pristine. I purchased the mesh (aka silk screen) from a local art supply store where I paid $8.49 per yard. This mesh is about 3 feet wide, so a yard would be about 9 square feet – that’s 94 cents per square foot. Much cheaper! I paid for it out of my own pocket, but that’s okay, I couldn’t justify paying the scientific supply company’s outlandish price.

There are other supplies that fall into this category such as aluminum foil. From the same scientific supply company, a 200-foot roll of Reynold’s aluminum foil costs $37. The university buys it in bulk and sells it to labs for $10. And if I trot down to the local grocery store, it would cost about $6. Now I can’t go buying everything out of my pocket, so in this instance, I go with the university’s pricing.

Sometimes it just takes smart shopping. For example, my former boss just bought a ultra-low freezer (it cools things down to minus 80 degrees Celsius (or minus 112 Fahrenheit), instead of the standard minus 4 degrees Fahrenheit of the home appliance freezer). Instead of paying $11,000 for a new freezer, he saved quite a bit of money by buying a demonstration model from the scientific supply company for $7,000. The demo only had a surface dent on it and he reports that it works perfectly fine.

One researcher set out to equip a home molecular biology lab for $500, buying used equipment from Craig’s List, eBay, and other Internet sites. He was able to find a thermocycler, pipetters, a pH meter, a centrifuge, a scale, a transilluminator and electrophoresis equipment that would have cost ~$7,000 for $453.12 (plus shipping). Granted, the equipment was most likely older and more likely to need repairs sooner than a newer counterpart, but the idea that research can be done on such a shoe-string budget is amazing.

Of course, it’s not uncommon for university labs to go on scavenger missions when news hits that a lab is closing, down-sizing, or just getting rid of equipment that they no longer need. I’ve been on a number of those missions in my career and you can find some really good stuff this way. The price is even right: free!

There is a hidden cost, in addition to supplies, equipment and personnel. This is something the university calls “indirect costs.” These costs include the utilities, maintenance, and administrative costs. In terms of NIH funding, for a $1.5 million grant award, the NIH would give the university an additional $780,000. This means the NIH gives the researcher and university a total of $2.28 million over those four years.

So there you have it. The cost of research. The price tag may look high (especially at first blush) but we need to remember that many great discoveries are generated from this funding.

But with the current funding crisis, there are fewer grant dollars. So there may be an additional cost of research: the loss of scientists and a slowing of scientific discoveries. But that is a topic for another day.