Debbie Knight

Archive for January, 2012|Monthly archive page

The January 2012 Top Five List of Amusing Search Engine Terms (that found Biologyze)

In observation on January 31, 2012 at 9:00 am

So, here is a list of five notable search engine terms that lead visitors to Biologyze this month. Some made me laugh. Some left me completely perplexed.

Without further ado, here they are:

Honorable mention: “Malpractices that causes for baking result”

Clearly there is a language barrier lurking in this search. But whatever information this person was looking for (an exploding cake, perhaps?) was not found in this blog.

#5: “What does a medical school cadaver freezer look like?”

Morbid curiosity, perhaps? Or was it “morgue” curiosity? All I know is I don’t want to know the answer.

#4: ugly gorilla with big head”

I think beauty is in the eye of the beholder. Gorillas can be quite beautiful, even if they have a big head. Why this person was looking for this specific topic leaves me befuddled.

#3: “shrimp safety from radiation”

Ah, a very serious problem in a shrimp’s life. I sure hope they have a good radiation safety officer to assure proper safety for these little guys.

#2: stupid students in laboratory”

A question many research scientists have asked throughout the millennia.

A related search also performed this month was: “Why are graduate students so miserable, science”

Ah, the other side of the coin. Well it could be something to do with the long hours for little pay. But those first couple of years are spent banging one’s head on the wall trying to make experiments work – it gets better with time, assuming the student is meant to be a scientist.

And, the top search engine term this month?

#1: “she has flattened my bike”

What did this person do to peeve her off so much, I wonder?

Well, there you have it. The top five list of search engine terms used to find my blog — that I found amusing. Hopefully, you found them amusing as well.

Achoo! The battle within

In observation on January 26, 2012 at 6:50 pm

During my travels over the weekend, I came down with a rhinovirus – the “common” cold.

Although if you ask me, it doesn’t feel so “common” at the moment – it is the focus of my entire existence as I struggle to breathe.

(I know, I know. I’m being a big baby. It is, after all, “just” a cold)

As a scientist, I find it amazing that something so small (something like 30 nanometers in diameter) can impact an adult human’s life so profoundly.

As the immune system wages warfare, launching tiny molecular grenades to blast the infected cells and contain the infection, it also releases tiny molecular flares called cytokines to rally more troops in an attempt to rev up the battle. Some of those troops specialize in engulfing the enemy-laden cells (macrophages do this, for example). Some perform a cellular version of hand-to-hand combat (neutrophils and some lymphocytes do this). Others (like B cells) launch ninja stars (or antibodies) that stick to the surface of the infected cell, marking the cells for destruction. There is quite a bit going on in this microscopic battlefield.

But right now the casualty feels like my body as it aches and groans with every step I take.

Mucus coats nasal passages in response to the invasion, but only serves to annoy me as I must blow my nose every few minutes.

I am impressed with how this virus has evolved to coexist within its host — it only causes a temporary discomfort as it replicates itself like mad. Equally amazing is how the host’s defenses like sneezing help spread the new viral particles to new hosts (although I’m doing my best to keep these little critters to myself).

Image by Marcelo Rampazzo

Viruses are truly amazing entities.

I just wish it would do these amazing things somewhere else.

Photo of the week

In photo log on January 24, 2012 at 9:00 am

This series of photos shows my labmate blasting a solution of tiny nanoparticles with sound waves in a process called sonication. The sound waves are generated at the tip of the probe which is submerged in the solution (top photo). As the sound waves are generated, the solution is displaced/moved (seen in series in the lower two photos). My labmate used this method to break up any clumps of nanoparticles that may have formed. Once evenly dispersed, the solution is added to cultured human cells and the effects observed.

By the way, you must attend!

In observation on January 19, 2012 at 9:00 am

The meeting
My lab received some funding from the USDA’s National Institute of Food and Agriculture (NIFA) in May 2011.

And once a year, the grantees are required to present their findings at a meeting. While mandatory, the grant does not provide any money towards the travel, hotel accommodations, or the registrations costs to attend this meeting. Instead the money to attend this required meeting either comes out of the researcher’s wallet or, if he or she is lucky enough, some other funding source. In our case, it will come from my boss’ departmental discretionary account.

This meeting serves two purposes. One is accountability to the funding agency. It’s sort of like a “live” progress report. The National Institute of Health (NIH) also requires an annual progress report but it’s in writing rather as a formal presentation.

I firmly believe there should be accountability of how grant funding is used and what scientific findings it has yielded. However, I’m not entirely sure it needs to be in the “live” presentation format. It would be more cost-effective to require a written report than to spend the money (and researcher’s time) in a meeting. But to expect the researcher to pay his/her own way to a mandatory meeting? That may be too much.

A second purpose of the meeting is to facilitate an exchange of ideas and forge collaborations amongst grantees. I can see this has the benefit of reducing duplication of research efforts and increasing the return on the research investment.

Last year the meeting was inWashington,D.C.and held at the USDA/NIFA offices. There were no registration costs for this meeting. However, this year the meeting is inOrlando,Floridaat one of the Disney resort hotels, and there are what the organizers call a “modest fee” associated with the meeting. I was a little naïve thinking it would be maybe $50 or less. It turns out to be $200 per attendee. Yes, compared to other conferences supported by scientific societies, this fee might be considered “modest.” But remember, this is coming out of the researcher’s own pocket, not from the grant.

I’m not sure that this meeting should be held any where but at the Washington, D.C.office. Is it appropriate (or necessary) to have it at Disney World Resort? Okay, so it is a food nanotechnology safety meeting and Disney does use the song “It’s a Small World” at its park – perhaps that is the tenuous connection.

 

The preparation
Our research collaborative is already preparing the presentation which will be given sometime during the meeting February 2 through 4.

In my experience with scientists preparing presentations for meetings, this is WAY ahead of schedule – usually it’s the week before (or on the flight to the meeting!), with everyone in the lab scrambling to graph their data to make it, well, presentable.

I think we’re ahead of schedule because it is spear-headed by the chemist of the group. He is worried that we should have made more progress this year. Perhaps this is true. But considering we were told that the grant would start January 1 and  we did not get the actual check until May, we’re not doing too shabby. Without that check, we couldn’t do any experiments because we needed it to buy the supplies to do those experiments. He’s worried that we will be held accountable for the five months of waiting and that the funding will be withdrawn – a valid concern in these economic times for sure.

At last week’s lab meeting, he outlined a 36-slide presentation. A general rule of thumb is to budget one minute per slide. Some slides will be quickly covered (in a few seconds), but others will require explanation (this could take more than one minute). So on average, it comes to one minute per slide. He anticipated our group would have 40 minutes (including audience questions) for the presentation. Not so. We were informed later in the week the talks are only 20 minutes– that means we need to do some serious editing. This is currently underway.

The attendees
Most of the attendees will be the principal investigators. My boss feels that the graduate student on the project and I can learn quite a bit as well as get new research ideas from attending this meeting. So, I think the two of us will be the exception rather than the rule at this meeting.

Again, this comes out of the researcher’s pocket, so this is very generous of my boss to permit us to attend.

There are many a principal investigator who would not feel this way. Often at scientific society meetings, only the principal investigator attends. Sometimes, a graduate student or post-doctoral researcher will be allowed to present his or her data. But rarely does a research associate such as myself get to attend and/or present.

I consider it a privilege to attend the meeting and will therefore do my best to soak in all that is presented.

This will be our graduate student’s first meeting. It will be interesting to see the process through a fresh pair of eyes.

So, what do you think? Should an annual meeting be mandatory from a granting agency without any travel allowance?

Photo of the week

In photo log on January 18, 2012 at 9:00 am

This photo was taken after the completion of phase one  of operation “lab cleanout.” The lab was abandoned and left pretty much “as is” when the faculty member left the university (I talk about this in another post). Hundreds of tubes of cells frozen in suspended animation and other potential biohazardous materials in the lab were placed into  specially marked biohazard boxes. These seven boxes of biohazardous are the result of that effort. They wait in the hall for pick up by environmental health and safety personnel. The boxes are sent to an off-site facilty for proper disposal. The blue bin holds glassware that will be melted down/recycled.

Lab pranks not always safe, part 2

In lab safety on January 17, 2012 at 9:00 am

A graduate student writes her name in flaming ethanol on her lab bench and posts the photo on her Facebook page. (Image stolen from this source)

Any microbiology student (or culinary chef) worth their muster knows that ethanol will burn.

In a restaurant it is often used to make a dramatic table-side display.  But in the laboratory, it is not something that should be done on a whim. Sure the low-temperature blue flame can be pretty. But if there are combustible materials nearby (paper, an open bottle of ethanol, a shirt sleeve), well, that’s how lab fires can happen.

In the photo above, this graduate student wrote her name on her lab bench in ethanol and then lit it. She thought it was funny enough to share with her Facebook friends with the caption, “Trying to write my name in fire … I believe this means my brain is done thinking for the day. Time to go home.”

(I’d say!)

I’m probably her only Facebook friend that found the photo worrisome (her other friends found it funny by evidence of the “likes” they gave). And she’ll probably “unfriend” me once she hears about this blog post. (Update: She did)

But as a laboratory safety officer in a research lab (not her lab, mind you), I bristled at the photo. This is not the sort of thing you want to see from a responsible lab citizen working in your laboratory. In this case, the graduate student has worked several years in the lab now — she should know better. A question that raced through my safety officer mind is if a lab citizen is doing this, what else is he or she doing that I should know about? The last thing a lab safety officer wants to happen on her watch is an incident (like a fire or a chemical spill or an injury). Those kinds of things are reported to the university’s Environmental Health and Safety Department. And then the entire lab may be penalized for that brief moment of “fun.”

Posting her mischief on a social website was not the best idea (perhaps it was her tired state of mind). You never know who will see it, especially as it is passed around the Internet. Call me paranoid, but what if someone from Environmental Health and Safety sees the photo, recognizes her affiliation with a specific lab, and busts her entire lab  for the seemingly innocent prank? It’s a small networked world, you just never know. (And, yes, the irony of posting the picture on my blog has not escaped me — but you will note I’m not using any names here)

But she’s not the only one who has done this. I know another graduate student (from the same lab — hmmm … perhaps pyromaniacs are drawn to this particular lab)(like a flame?) who walked by his labmate’s bench, dumped a jar of ethanol on the bench top and lit it on fire. In this case, there were actually papers on and around the bench top which could have easily caught on fire.

I’m not trying to be a “downer” here. It’s just there are safety rules and guidelines for a reason — someone somewhere did something stupid and, well, they had to make a new rule about it.

As a laboratory safety officer, I think there are enough rules, regulations and guidelines to remember — we don’t need any more! So, please, if you’re working in a lab, stop and think before you give in to that impulse to write your name in flaming alcohol (or something equally as stupid)!

Update 1/19/12: It should be noted that the university’s EHS is taking this situation pretty seriously. I got a phone call from an administrator’s office this morning about this. Yikes! My intention of this blog post was by no means a criticism of the university’s EHS (they do an excellent job)(and I really mean that, they do!) — it was meant to inform the general public of the importance of lab safety. AT ALL TIMES.

Be safe out there!

Update: 3/7/12:  The university’s EHS included an article in the quarterly newsletter reminding lab personnel that horseplay is not a laughing matter. This may or may not have been because of the above incident. Without further ado, here’s the article:

A page from the university environmental health and safety's quarterly newsletter addressing lab pranks and horseplay in the lab published for March 2012.

Happy Birthday! Biologyze is officially one year old today!

In observation on January 10, 2012 at 9:00 am

January 10th

My first blog post and the birth of Biologyze happened exactly one year ago today. It hardly seems like a year. Time has passed quickly (a lot like my past 20 years in research).

I began this blog as an “experiment” … of sorts. And, yes, you were all proverbial guinea pigs. But hopefully you’ve learned some interesting, behind-the-scenes stuff about life in a research lab and issues that affect that life.

The “experiment” is ongoing. But I think it is going well.

I should admit a major reason I started this blog was simply to practice communicating science to a lay audience.

And let me tell you, it’s not easy!

I didn’t realize that I was so immersed in the scientific culture (that I’ve lived in my “ivory tower” for so long) that I speak a completely different language: science-speak. Sure it sounds a little like English (some of the time), but it’s loaded with scientific terms and lab jargon that most people (including my family) can’t understand. I’m still wondering when this happened? But however I got here, I do speak science-speak and I’m trying to overcome it.

A better Biologyze

I want to make the blog better. Communicate science better. Generate stimulating discussions.

And I’ll need your help to do that.

You need to tell me when I use terms you don’t understand or when my posts are too technical. Of course, I have to assume a few biology basics: like everyone knows what a “protein” or “DNA” is.

So, what would you like to see in this blog?

What topics are you interested in regarding an academic biological research lab?

How can I improve this blog to communicate science better?

How can I generate more conversation, more discussion? Sure I’m broadcasting, but I’ve little idea if you are listening (well, except you, Tom and Renaldo).

Is what I’m writing relevant and timely? I certainly hope so.

I will note a couple of features I will add this year:

  • Guests. There will be a few posts by some scientists I know who can offer their unique perspectives about life in scientific research.
  • More posts. There will be more posts per week. Presently, I try to put up a new post at least once a week. I hope to increase this frequency. One way I’ll do this is by adding a “Photo of the Week” where I post a photo of what’s going on in the lab (with a little text for context).

In the future, as readership grows, I hope to include some interviews.

What I’ve learned

As I said earlier, this blog has been an “experiment” … of sorts.

So what have I learned so far? Most of what I’ve learned has been from trial and error.

Most viewed post?
Which Biologyze post got the most views in 2011? “A day in the life: June 9 -10, 2011” This was a post where I demystified the Western blot by giving a step-by-step photo record of that process. I honestly didn’t think this post would get any attention because it was a lab procedure.

Imagine my surprise.
Of course, now I’m thinking I should include more coverage on lab techniques. Maybe it would help someone out there.

The search.
People can stumble upon blogs by searching for scientific images. I’ve done it myself (and, yes, I’m guilty of “borrowing” a few of those images). I assume that any original images that I’ve posted on this blog whether it be photographs or drawings are open access and susceptible to “borrowing.”

And I hope that a few of those borrowers peeked at what I wrote and left with more than an image – perhaps they left with a little nugget of scientific knowledge.

What’s in a name?
Provocative titles can entice readers to visit a blog. I’ve fallen for that myself on Twitter feeds and I’m glad I did – I often learned something interesting in what I found.

Naming blog posts better is something I intend to work on this year.
One of my most popular posts “Like riding a bike – with flat tires” had an unintentional outcome. It was posted on February 4th. But in March I started getting an unusually high number of “hits” as people dragged their bicycles out of moth balls only to find they had flat tires. I can’t tell you how many times WordPress told me that someone used the search engine term “bike with flat tire” or “bicycle flat tyre.” But it was obvious these browsers stumbled upon my blog only to find something completely unrelated to bicycles. Sorry about that.

I had similar experiences with other posts that included the words “white glove test,” “gorilla suit,” the letter “n” and “guinea pig.” These views came from image searches.

I think my first post “Hello, World” (a title suggested by WordPress) got a few inadvertent views because of the Lady Antebellum song of the same title.

Content and search engines.
Search engines really do crawl across the words in a blog post. WordPress tells its bloggers  just what search terms were used to arrive at their blogs. It’s been interesting seeing some of those terms. Some make me laugh while others leave me shaking my head.

Here are a few search terms so far in 2012:

 “she has flattened my bike”
                  (Yikes! Is this a bad breakup or what?)
“if we add antibody before blocking what can happen”
                  (Oops! This person clearly needed some information and fast! Nothing like a slight procedural mistake to send you frantically searching on the Internet.
The answer? You’ll get a lot of non-specific binding of the antibody to your Western blots – it ain’t pretty! How do I know? Let’s just say I’ve heard about these things
and leave it at that, okay?)
“pathology lab waiting and reception”
                    (there is actually such a thing? Well, there isn’t one in my pathology department (not even in the morgue) but maybe there should be)
 “thawing cells protocol”
                      (My blog was no help here, but maybe I should consider adding more protocol explanations – especially since the Western blot post was so popular. Clearly people are looking for help with their procedures.)
“transilluminator tuberculosis”
                  (Huh?!)
“radiation shrimp”
                   (What?! Do I really want to know why someone is looking up this term?)

Just for fun, I will add a few “popular” terms here to see what happens. Like it’s “news” that President Barack Obama’s ears stick out a little, especially more than, say, Mitt Romney’s. Or I can’t believe the video for the song Kolaveri Di has gone viral (within 8 weeks, it’s had over 32 million views). I will admit the song is kind of catchy. And I really like the rhythm – it kind of feels like you’re riding on the back of an elephant.

Okay those were cheap shots, but I’m a scientist and it’s in the name of “research” (of sorts). I’ll let you know how it went.

————————————–

So that’s it. The first year of my blog.

Hopefully 2012 will be a great year for Biologyze.

And please, join in the conversation!

_____________________

Photo of the week

In photo log on January 9, 2012 at 9:00 am

This is a photo of a stack of empty pipet tip boxes.

The reason I took this photo was to show a significant part of the waste stream in many biological research labs. Researchers use the pipet tips and then throw the empty plastic box in the trash bin.

Some cost-conscious and environmental-conscious labs will re-use the tip boxes. And the tip boxes can be re-used a number of times before they become unusable.

But what do they do with them then?

Researchers at my university just received news that we can now place these empty boxes in the recycle bins and they will actually be recycled. Before this announcement last week, many of the various brands of tip boxes could be collected and the university would arrange to send them back to the individual vendors for recycling. Now these boxes will go directly to the recycling plant.

That’s certainly a step in the right direction.

Photo of the week

In photo log on January 5, 2012 at 10:25 am

New year, trying something new. Once a week, I will be posting a photo of what I’m doing in the lab. I’m not promising professional-grade photography here, just a little documentation of my life in the lab.

So, this week’s photo is of my left hand. Why my left hand? Is it really all that interesting?

Well, before I started doing research, my left hand was pretty useless. Oh, it could play the bass lines on the piano or clack away on a computer keyboard. But it lacked the dexterity my right hand had.

Once I began working in a lab, I quickly discovered things went much easier if  my left hand to remove caps from tubes (such as pictured here).  This is something I try to teach new students.

Watching them makes me smile. And I often wonder if I looked just as bumbling and awkward when I started in the lab.

I honestly don’t remember, but I must have.

 

 

 

A day in the life: January 4, 2012

In research log on January 4, 2012 at 1:02 pm

New year and already things are off and running.

You know how some days you have one of those head-slap moments — a “how did I not think of that before” moments.

This week, the first of the year, I had one of those moments.

A few years ago I had been cranking out Western blots (a technique to look at proteins)* and all was going well. Then there was a three-year gap because I was working in another lab. Upon my return to my “old” lab, I started up the ol’ Western blotting operation again — only this time things did not go so smoothly.

The numerous protein bands I had come to expect on the blots just weren’t there. Increasing the amount of protein I added to each sample didn’t help. Making new buffers and new formulations of those buffers didn’t help. Using new reagents to detect those proteins didn’t help.

It wasn’t until I ran out of the nitrocellulose membrane – the paper-like substance the proteins were stuck on – and I opened a new box of membrane that it became obvious what the problem was. The membrane stock I had been using was over four or five years old. Things had happened to that membrane – things like exposure to air and temperature fluctuations – caused the little charges that helped hold the proteins onto the membrane to change in some way and loose their ability to grip the proteins.

This was something I so obviously should have considered when I was trying to figure out why the procedure wasn’t working like it had a few years before.

(D’oh!)

A side-by-side comparison of old and new stocks of nitrocellulose membrane (a paper-like material the hold on to proteins during a laboratory technique called a Western blot). There are more protein bands detected on the new membrane and the proteins are "crisper" compared to those on the old membrane. The Western blots were run on different days for different times which is why the protein bands do not exactly line up with each other even though they are from the same sample. The lines between the two images show where the corresponding protein bands are located.

The proteins are barely detectable on the old membrane.

So, as you can see by the photos I’ve included in this post, there are more protein bands and they are “crispier” on the new membrane than on the old membrane.

I guess, after 20 years in the lab, I still have a few things left to learn.

Go figure!

*If you would like to see how a Western blot is done, see my previous post.