Debbie Knight

Archive for February, 2012|Monthly archive page

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

In observation on February 29, 2012 at 9:00 am

So, here is a list of five (what I found) amusing search engine terms that lead visitors to Biologyze this month.

Honorable Mention: “craig’s guinea pig” 

Not just any guinea pig. It’s got to be Craig’s.

#5: “how do u get paid to be a human ginny pig”

I’ll admit it, it was the misspelling of guinea that made me chuckle.

#4: “I wish I get serious accident and u care me”

I’m a little scared of this search term. Sounds a little depressive and desperate to me.

 #3: “rhinovirus carrier”

Okay, the first thing that popped into my mind was a rhinoceros being carried in a helicopter sling. I’m not sure why.

#2: “liquids that don’t have chemicals”

I hate to tell you this, dear searcher, but all liquids technically have chemicals in them. Yes, even pure water is a chemical.

And, the top amusing search engine term this month?

#1:  “what is the things that stick out on a rhinovirus”

Ears? Tongue? Antenna? Nubbins? Studs? Sprockets? 

Okay, seriously, they would be called the capsid proteins (named very descriptively as VP1 (VP for viral protein), VP2, VP3, and VP4. Those nubbins (aka viral capsid proteins) interacts with a receptor on the cells that line the upper respiratory tract called epithelial cells. The receptor is called ICAM-1 (or CD54).

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A few others that didn’t quite make the Top Five list:

“bacteria sculpture” —  ?????

“geiger counter university”  — and you majored in what?

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.

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Photo of the week

In photo log on February 28, 2012 at 9:00 am

This is a photo of agar plates used to grow bacteria.

Powdered bacterial medium is measured out and water is added. To make the medium in the petri dishes “gel” (like Jell-O), a material called “agar” is also added to the mix. In the lab, agar starts out as a powdered substance but melts when heated to a boil. As it cools, it “solidifies” or “gels” to something a little firmer than Jell-O at the concentration we use it.

In the photo, the boiled (sterilized) medium in the flask is on the left — it is still a liquid. Some of that liquid was poured into the petri dishes on the right. As the medium cools in those dishes, it will become a food source for cultured bacteria as well as provide a solid surface for their growth. It usually takes a couple of hours for the plates to “set.” After which they can be stored in the refrigerator for about a month before they are used in experiments.

Arsenic and old lace

In observation on February 27, 2012 at 5:37 pm

A news story in the February 25 edition of Science News caught my eye.

The story, “Arsenic-based life finding fails follow-up tests: microbe doesn’t use toxic element as a building block,” offered the findings of a new report by microbiologist Rosemary Redfield’s group that perhaps the bacteria dubbed GFAJ-1 was able to tolerate the presence of arsenic but not incorporate it into its DNA.

The follow-up story placed this new report in context with the resounding splash of the journal article by Felisa Wolfe-Simon et al published in Science online in December 2010 and in print June 3, 2011. That article, “A bacterium that can grow by using arsenic instead of phosphorus,” was very controversial and, like any scientific finding that goes against what is currently “known,” it received much attention and criticism from the scientific community.

But it was the source of the Science News story that caught my attention. It wasn’t until I read the last paragraph, that I realized Redfield’s report had not undergone the scrutiny of other scientists (i.e., peer reviewed) nor had it been published in any scientific journal. Instead it was a manuscript that had been posted onCornellUniversity’s Library website, an open access e-print service called arXiv.org on January 31, 2012. On the website, it was noted that the manuscript had been submitted to the journal Science on January 30, 2012.

So this manuscript is now out in the public domain (the Internet) without having been put through the rigors of the peer-review process.

As a scientist, I have a real issue with this.

But first let me explain how the peer-review process works.

After scientists have studied a phenomenon through experimentation, they write up a technical report, a scientific manuscript. This manuscript is sent to a scientific journal for consideration for publication. In top-tiered journals such as Science or Nature, it is the editor that makes the initial assessment whether the manuscript’s topic, breadth, and timeliness (among many other criteria) is appropriate for their journal. This decision is made pretty quickly. If the editor says “yes,” then he or she will select two or three scientists (sometimes on the editorial board and sometimes not) who can offer an expert critique of the manuscript. These “peers” in the peer review process carefully read the manuscript for its scientific merit and provide feedback to the editor as well as the manuscript’s authors.

The reviewers are anonymous to the manuscript’s authors.

If the manuscript is rejected by the reviewers or the editor, the authors will generally submit their manuscript elsewhere for consideration. This is the most painful outcome.

Sometimes only a few tweaks in wording or an additional experiment is requested before the reviewers and editor will give it a thumb’s up for publication.

And sometimes, they want major revisions. This is also painful because it often involves doing several additional experiments to prove the results shown in the manuscript are real. After the sting of the rebuff has worn off, you put your nose to the grindstone and do those experiments. Of course there are a couple of alternatives. You can withdraw the manuscript and submit it elsewhere, but then you have to go through the review process all over again. Or you can write a well-crafted rebuttal to reduce the number of experiments that need to be done. This route runs the risk of angering the editor or the reviewers, so it’s best to pick your battles carefully if you want your manuscript published.

Is this peer-review system perfect? No, it’s not perfect. Occasionally even a seasoned expert reviewer can miss a detail. And in a rare instance, an anonymous reviewer may be a fierce competitor of the authors and he or she may not give the manuscript an entirely fair assessment.

And the entire review process takes time. With some journals, it can take up to a year from submission and acceptance to publication.

But the system does allow for powerful scrutiny (with a fine-tooth comb and everything) and rigorous review of the research study before it is printed for public consumption.

Even though I have 20 years of research experience, I know I’m not qualified to say if Redfield’s study is robust enough. The general public is even less qualified to do so.

While her motives may have been honorable and the result unintended, Redfield has circumvented this peer-review process by posting her manuscript on arXiv.org. And because it is now in a way “published,” I’m not sure she hasn’t shot herself in the foot. Scientific journals want exclusive rights to a manuscript and will not consider work published elsewhere. It seems likely that posting the manuscript on the website may count as “publishing” and it may somehow void its exclusivity. It will be interesting to see how this plays out.
(Update July 9, 2012: The article was accepted and published online by Science on July 8th)

With the scientific community under increasingly powerful scrutiny from scientists as well as the media and public, its members need to be good stewards of science. They need to stop trying to win the science race at any cost and focus on the quality of their research (I’d like to believe most scientists do the latter)

But two resounding questions remain. Like the arsenate used in Redfield’s study, will posting the manuscript on an open-access website “poison” its acceptance into a peer-reviewed journal? And does such a posting do science a disservice? Only time will tell.

Taking the “yawn” out of a presentation?

In observation on February 23, 2012 at 9:00 am

I was asked by the chief financial officer of our department to spice up his powerpoint presentation on billing that he would be presenting at a national meeting next month.

Let’s just let that sink in for a moment.

A presentation …

… on billing

… by an accountant (no offense to any accountants out there)

… to an audience (this particular audience: clinical lab directors).

How do you take a presentation that is all words (see image below) and turn it into something that won’t put the audience to sleep immediately? Note: I could not change the content, only the display of that content.

An example of the word-heavy slides in the presentation

Yawn, right? He knew this, that’s why he asked for my help.

To further complicate matters, I was locked in by a template the medical center requires for “branding.” There was little wiggle room for creativity.

The medical center's branding title slide (minus specifics, of course)

I had many issues with this title slide, the branding slide. The placement of the talk’s title. The density of image and text. It’s a busy slide! (especially when you add in a lengthy title). Clearly these were personal issues.

But as a researcher, I also had issues with it. It had a series of scientists doing “science” stuff. (That wasn’t the problem). It had senior scientists, people who run labs not work in them, in the images. For example, the guy in the middle photo (of the triple inset image)?  He has a huge lab operation and I highly doubt he has done hands-on bench work in years. While I greatly respect his research, this photo was clearly staged.

So my first instinct was to add some authentic photos. So I went over to our molecular pathology lab, snapped some photos, and inserted them into the branding slide. The result:

My version of the title slide.

I’m still not completely happy with the slide, but I feel it’s more “authentic.”

Oh, the medical center just modified its name (and branding), so I had to make some adjustments — like covering up the old brand in the photo that spans the width of the slide and adding the new logo for the medical center. Easy enough to fix.

I toyed with the idea of using background images on each slide, but with so many words, there was an issue of readability of those words if they were typed over a photo. So I stuck with design elements rather than images — keeping it simple.

So next was tackling the template body slide.

The medical center's template for the body of the talk

All those words on a predominately white background (with only a little color pop) wouldn’t really help jazz up the presentation. So I worked it over a little.

After a few modifications, it's looking a little snazzier.

I think this was a marked improvement, but was it enough?

His talk had four major topics to cover, so the background color changes with each topic to alert the audience it’s a new topic and to add a little interest/variety. I was limited by the color palette built into the template.

New topic, new background color

But could I do more?

Since the theme of the talk was billing codes, I played with numbers, built in some animation so that a few of the numbers fell from the top of the slide to the pile of numbers at the bottom.

The "something more" version -- numbers piled on the bottom of the slide to reflect the numbers in the billing codes

I’m not sure which version he’ll pick, but I think the presentation has been improved from the black-text-on-a-white-background. Hopefully there will be fewer yawns from the (non-accounting) audience.

January rain brings February flowers (???)

In observation on February 22, 2012 at 9:00 am

Snow Drops have been in bloom for at least two weeks now. It's mid-February in Central Ohio. They usually don't come up until early March.

Daffodils are coming up in mid-February in my flowerbeds. They usually don't appear until early April.

Tulips starting to emerge in mid-February. These typically bloom in early May.

Tulips emerging in mid-February. This variety typically emerge in April.

They say timing is everything.

Well, the flower bulbs in my yard are a little confused by the mild winter weather here inCentral Ohio.

  • The snow drops have been in bloom for about two weeks – they usually don’t bloom until March.
  • The daffodils are almost in bloom – they usually don’t bloom until April.
  • And two varieties of tulips, one an early bloomer (typically in April) and the other a late bloomer (typically in May), are both emerging.

What the heck?

This concerns me not because Spring appears to have arrived early (real early) this year in my flowerbeds. After all, a splash of color is always welcome in the gray of winter.

But I can’t help but think what other plant life is out of synch as well. And how that will affect the life cycles of various mammal and insect species that depend on those plants for survival. Will they be forced to migrate farther north for food or will they remain here and adapt?

Is this evidence of climate change or just a fluke?

I’ve been to seminars that discuss how climate change has already begun to affect bird and tree species distribution across North America. And I’ve seen predictions on how their distribution will be affected over then next two decades.

This makes me wonder whether mother nature can adapt quickly enough to climate change? And whether we will lose integral components of our ecological systems?

I guess time will tell.

Photo of the Week

In photo log on February 21, 2012 at 12:30 pm

This is a photo of an agarose gel (think really firm Jell-o) being placed on a ultraviolet light (UV) box which is making the gel “glow.”

The gel has been soaked in a dye that makes the nucleic acids visible (the dye: ethidium bromide actually binds to the nucleic acid and the UV light makes the dye-nucleic acid complex glow).

The nucleic acids in this case were amplified from a few strands of DNA during a procedure called a polymerase chain reaction (commonly called PCR) where a specific probe is used to copy only a certain region of the DNA over and over again until there is enough to see on the gel.

After the PCR is performed, the samples are loaded on one end of the gel, an electrical charge is applied across the gel, and the DNA moves toward the other end of the gel. Small pieces of DNA will travel farther in the gel than larger pieces (similar to how the small crumbs of potato chips seem to end up in the bottom of the bag — they can wiggle through all the spaces and move past the larger pieces).

If this PCR was performed successfully only one size (one band) of DNA will be seen on the gel (the pinkish-whitish stripe across the middle of the gel).

This photo was taken in my department’s Molecular Pathology Lab where diagnostic specimens are tested for genetic mutations.

The journey: clearing out an abandoned lab

In observation on February 15, 2012 at 9:00 am

Over the past month or so, I’ve been involved in cleaning out an abandoned lab. I haven’t done all the work myself — Erin, a medical technologist, was also tapped for the job.

Day 1: The first step was clearing out all the biological specimens — from freezers, fridges, and cabinets. Although many were probably not considered biohazardous, we treated them as such, disposing of them in specially designated biohazard boxes. These cardboard boxes are lined with a bright orange thick plastic bag. It took seven of these boxes to clear out all the biological specimens. This step took about four hours. The next two photos are from the first stage of clean up.

The lab after completing phase 1 of lab clean up.

These biohazard boxes are ready for disposal by our Environmental Health and Safety people.

Day 2:  The next step was carried out a few days later. This involved finding a place to stash all the freezer boxes. Also, during this stage, any unusable lab supplies were placed in the trash. Washed glassware was put away. An inventory of chemicals was sent to Environmental Health and Safety — this is required for them to pick up chemicals for redistribution and disposal. This step took another four hours.

After phase 2 of lab clean up.

Day 3: The next step was to get rid of any tissue samples that were stored in fixative (like formalin) and any tissue sections on microscope slides. We also disinfected all bench tops and lab equipment including fridges and freezers. By doing this, we removed any possible residual biohazards. It is now safe to move any equipment from this lab to another without fear of contaminating the movers or lab personnel. Yet another four hours.

Phase 3 of lab clean up: getting rid of tissue samples.

Day 4: The final stage was to have the chemicals removed from the lab by Environmental Health and Safety personnel. This turned out to be the task of one person. He had to make several trips from the lab to his truck. This step took about 30 minutes.

The lab still has equipment in it — this was done intentionally. The next department member to take this lab space may want the equipment. If we had been doing a complete lab clean out, we would have left only bare benches.

I’m glad it’s finally over. It’s not fun clearing out another researcher’s lab.

Environmental Health and Safety guy taking away the last of the chemicals

The lab is now ready for a new owner. It's not completely cleared out because the new person may want some or all of the equipment.

The last phase from another angle.

Happy Valentine’s Day!

In photo log on February 14, 2012 at 2:46 pm

A friend sent this image to me the other day.

Nothing says Happy Valentine’s Day like an electrophoresis “love” gel.

 

Photo of the week

In photo log on February 14, 2012 at 9:00 am

This is a photo of gloves specially designed to handle really cold stuff in our ultra-low freezers and cryopreservation tanks.

They’re a bit bulky (and quite the fashion statement!), so we don’t always use them when we get small things out of the freezers. But they certainly help prevent frost bite when we need to dig around on a scavenger hunt or have to move freezer racks around. Frost bite under these circumstances is deep — the blister doesn’t really surface for a few weeks. That’s cold!

It is a mystery why we have three gloves (instead of two sets of two).

The grass looks different on the other side

In observation on February 13, 2012 at 1:00 pm

I work in a pathology department. And in my many years, I’ve often picked up research specimens from the surgical pathology lab (pictured above). And while I had noticed the doors to the right over which is written the words “Operating Room,” I hadn’t really thought about what goes on in those surgical suites (except maybe in abstraction) … until this past week.

What was different this time was that my loved one, my husband, was behind those doors, undergoing a four and a half hour surgery.

Oh sure, I’ve been in other waiting rooms at other hospitals waiting to hear news about my mom or my dad. But this time it was different — this time it was where I worked, my stomping grounds, a place where I thought I knew what went on behind the scenes.

But it’s different being on the “other” side, the patient side.

Here I was, worrying about how things were going, hoping there were no surprises, and hoping I would get my husband back in better shape than when he went into that surgical suite. We had surrendered to the skills of his surgical team.

When I’d passed this way before, I hadn’t realize that the people sitting in the chairs on the other side of these double doors were waiting to hear news about their loved ones undergoing surgery. I didn’t understand the tension and emotional roller-coaster was so palpable (had I paid attention) when I had walked past them all those times before. I didn’t understand the hidden personal dramas that were unfolding in surreal (yet real) time … until I sat in those very chairs, for the very same reasons.

Now I understand all this, having sat on the other side of those doors.

And in the future, I will be sure to send out some positive thoughts as I pass by the patients’ families.

Because now I know.

The grass does look different on the other side.