Bits and Pieces

I am exhausted!

Today at lunch I did a 2.5 mile outdoor jog/walk. The weather was nice and the run went quickly. After that I came back to the office and packed up for my first move in eight years. We’re implementing a new program that requires co-location of team members, so I moved from a modest desk on the first floor to a much larger cube area on the second floor. It’s pretty sweet. But there was a lot of cleaning up to do – eight years of accumulated business plans, training documentation, hundreds of file folders filled with things that might someday be useful or necessary – but not so necessary that they require formal logging and storage – little gadgets and anniversary doo-dads, and five – count ’em five – separate containers of floss. Five floss barely beat out the four chapstick that  I found squirreled away in different drawers. Many, many trips up and down the stairs.

But now I’m moved in and I have my computer and the internet back up, so life can continue. Gads, my knees are complaining, though.

Tomorrow we’re supposed to get 8-12 inches of snow. Frickin’ Minnesota spring.

Here’s A Thing Going Around the Internet. It looks like it originated on Santa Cruz Biotechnology Facebook page. I apologize for not providing a transcript. This is a very wordy image, a list of 54 “Ways To Tell That You’ve Been in a Lab Too Long” and there’s way too much to type up. But I will type my top six favorites:

1. You use the word “aliquot” in regular sentences. (Oh…this isn’t normal. But…aliquot is such a useful word!)

6. You flinch when you hear the word “significant”. (And “hypothesis” and “theory.”

23. You always seem to use the microscope after the person with the impossible close together eyes.

33. Warning labels invoke curiosity rather than caution

43. You’ve left the lab wearing a piece of PPE because you forgot that you had it on. (It’s always my safety glasses.)

46. You’ve bent down to pick something up off the floor only to scatter the contents of your top pocket under the largest machine in the lab (EVERY. DAMN. TIME).

48. When you start making patterns in your pipette tip box as you take the tips out. (I once made an X-Wing.)

There are a few on here that make me think NOPE.NOPE.NOPE (#25 – I’ve never wanted to drink distilled water from the lab). Also a few that make me think that the person who put this list together has jerkish tendencies (#28 – Who rolls their eyes and talks down to non-scientists who inquire about your work? Not cool.) But overall, I recognize waaaay too many of these.

 And here are a few of my own:

*You’ve argued about whether it’s spelled “pipet” or “pipette”.

*You’ve had to explain the difference between a 1:10, 1/10, 1 in 10 and a 10-fold dilution.

*You’ve gotten annoyed because someone left an empty glove box in the holder.

*It sometimes feels like you have to defend your equipment against your coworkers with a sword and shield.

*Who spilled some unknown white crystalline chemical on the weigh scale and didn’t clean it up? Was it you? It was you, wasn’t it?

*The prospect of of having to explain your mixed study results to a cross-functional team fills you with dread.

Any of you lab people have any to add?

Bits and Pieces

Goodbye, Dear Samples.

When in the Course of sample shelf life stability, it becomes necessary for one person to dissolve the emotional bands which have connected her with these samples, and to assume among the powers of industry science, the separate and equal station to which the Laws of Finance and of Peer-Reviewed Literature entitle her, a decent respect to the opinions of Her Project Manager requires that she should declare the causes which impel her to the separation.

They were old and the integrity of the proteins could no longer be trusted. That’s pretty much it.


I was hired in 2006 to conduct a month-long blood draw that produced thousands of aliquots. I participated as a phlebotomist, a sample processor, and I helped test them and analyze the data that they provided. My successful participation in this project has developed into a happy and fruitful career. Across eight years, numerous projects and the periodic mandated freezer cleanup (the bane of many a laboratory scientist) I have managed to save these characterized samples in the hope that someone, someday would be able to use them. But the end has come: All of the analytes within the serum that might be of use to us have likely degraded. So it was with a heavy heart that this afternoon – on the 26th day of March in the 2014th year of our calendar – I discarded them all.

Goodbye, dear samples. I will remember you fondly.

Eleven freezer canes, filled with sample freezer boxes

Most of these eleven freezer canes contain twelve freezer boxes, each of which contain somewhere between 40 and 80 1mL sample aliquots. That’s about 8,000 vials that were discarded.

Goodbye, Dear Samples.

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

Caution: Water

New labels for the water bottles in the lab. You can never be too safe, kids.

Just…perhaps no ingesting in very large quantities, okay?



(DI Water, Pure Water, Dihydrogen Oxide)

Target Organs: N/A

PRECAUTIONARY MEASURE: GENERALLY CONSIDERED SAFE. Avoid contact with materials which are water reactive. Follow precautionary measures for other materials which are in use.

SYMPTOMS OF EXPOSURE: Ingestion of very large quantities can cause convulsions, tremors, muscle contractions, narcosis, diarrhea, and fever due to dilution of electrolytes in the body.

INSTRUCTIONS FOR IMMEDIATE AID IN CASE OF EXPOSURE: Call a Physician. Determine other causes of illness. If victim is not breathing, give artificial respiration. If breathing is difficult, give oxygen. Seek medical attention to treat symptoms.

SPILL RESPONSE PROCEDURES: Only appropriately trained personnel should respond to spills. Use proper response procedures and maintain appropriate level of fire protection. Dispose of as required by federal, state and local regulations.

CONTAINER HANDLING and STORAGE: Store away from water reactive materials.

MSDS REFERENCE: Refer to Material Safety Data Sheet for more information about this chemical.

Caution: Water

Lab Life is Rough

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


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

Ficoll Fun

Here’s a cool science photo from the lab:

RBCs in Ficoll

What we’re looking at is whole blood that is separating into its various components.

Blood is made up of red blood cells (RBCs), white blood cells (WBCs) and plasma. If fresh, whole blood is left sitting in a tube, the denser RBCs will slowly fall to the bottom, leaving the less dense, pale, yellowish plasma on the top. The WBCs cannot usually be seen unless separated from the red cells by centrifugation.

This particular tube was filled with Ficoll Paque, a chemical that looks and moves like water. It is used to help separate blood into its different components. Ficoll is less dense than RBCs, but more dense than plasma and some of the WBCs. Blood was very slowly and carefully pipetted on top of the Ficoll. You can see where the whole blood was layered and the Ficoll starts – it’s the place where the RBCs begin to “shower down” through the clear layer, making it look speckled. This tube was left sitting on the bench for about 15 minutes and the RBCs are collecting on the bottom of the tube:

RBCs in Ficoll with labels

Neat stuff, huh? Here’s what it looks like after centrifugation:

Separated Cells

The bottom layer is RBCs, followed by a thin layer of granulocytes (the name for  WBCs that have granules in their cytoplasm. The granules make them denser than the Ficoll). Above that is a wide band of the Ficoll, then a thin, translucent layer of white blood cells called mononuclear cells (the name for WBCs that have a single-lobed nucleus. MNCs don’t have granules in their cytoplasm). And at the top of the tube is plasma.

And all we have to do at this point is carefully pipet the different layers that we want separated:

Separate Components

From left to right: the first tube contains plasma, the second tube is comprised of three layers: Ficoll, granulocytes and RBCs, and the third tube holds our prize: the mononuclear cells.

And because I think it’s pretty, here’s one more photo of RBCs drifting down through Ficoll. These three tubes were layered one after the other. The one that was layered first has had the most time to separate, the one that was layered last has had the least:

Ficoll Time Course

Ficoll Fun

6 O’Clock BS: Zen Lab Work

I love doing protein concentration determinations. There’s something calming about calculating dilutions, pipetting precise volumes, being able to trust the objective evidence of the OD280 readings.

Oh, the lies I tell myself when the work day runs long.

Yay! Moar dilutions, moar reps! Blarg. I mean…Oooooohm.

6 O’Clock BS: Zen Lab Work

A Sad Day in the Science Classroom

I opened up the Star Tribune to a sad story. From the Star Tribune:

Thursday morning, ninth-graders in the second-hour science class at Maple Grove Junior High School had turned their desks toward the science table where teacher Matthew Achor conducted experiments for the class final.

The first time the teacher dropped a match into a jug of methanol, Neuberger said the experiment seemed to work. “It made a loud boom and a little flame,” he said. “Everyone thought that was cool and clapped.”

Neuberger looked down at his paper to begin writing down his observations. “I’m pretty sure he was starting it up to do it a second time,” Neuberger said. “And the next thing I know I’m on fire.”

Several students were injured during this science experiment. One of the students, Dane Neuberger, was severely injured with second degree burns to his face.  All of the students are expected to make a full recovery, and according to the article it doesn’t look like Neuberger will need skin grafts. Only minor damage was sustained to the classroom.

Details are slim in the article, but it sounds like the appropriate actions were taken after the explosion. A fire blanket was used to wrap Neuberger and an ambulance was called immediately. The room was evacuated and the fire department was called to investigate. The article doesn’t discuss the type of bottle or the amount or type of methyl alcohol employed in the experiment.

The science behind what was being taught.

The purposes of this experiment could be to demonstrate an exothermic reaction, oxygen supply in combustions (if a narrow-necked bottle is used as heat, flame and gas exits the bottle, fresh oxygen is sucked back into the bottle, re-igniting any remaining methanol vapor), detonation velocity, expansion of gases, etc.

This video shows the experiment as performed on four different alcohols:

The way it works is that liquid methanol is put into a bottle and allowed to evaporate, leaving methanol vapor in the bottle. Heat energy – a match, in this case – is added to the bottle, causing a combustible chemical reaction. Visible flame and a loud whoosh” is heard during the reaction. The methanol vapors are ignited, and liquid by-product (H2O) is left in the bottom of the bottle.

In the article above it’s mentioned that this teacher had been performing this experiment for years, and I found several online mentions of this as an acceptable high-school chemistry-level experiment. Some sites perform the study outdoors, some indoors. I do not remember this experiment performed when I was in junior high or high school.

Science teachers – Do you use this experiment in your classes? What safety precautions do you employ? For the rest of you – Do you remember this experiment from your days in the chemistry classroom? Did you have any larger-than-intended explosions?

A Sad Day in the Science Classroom

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