Tales from the Bench (Lab Life)

               8 times out of 10, the experiments a scientist does fail.  So much of science is trial and error.  This does not mean that we don’t know what we’re doing; rather it means that we have fifty hypotheses to follow up on and only one is correct.  The other 49 times, we’re wrong.  How fast we find the correct answer is influenced by our experiences, our breadth of literature knowledge, plain old luck and, most importantly, by the lab gods (they are finicky bunch).  

                Experiments fail for all kinds of reasons: wrong hypothesis, improper controls, improper interpretations of previous results, complete failure of the scientist to do the experiment correctly (sometimes you just add the wrong thing or accidently knock stuff over.  It happens.  There’s no shame in repeating an experiment because you’re an idiot.).  

However, the most egregious failures are when the lab gods decide to hate you.  It doesn’t happen often, but when it does, everything you do in lab that week will fail for reasons completely beyond your control.  Hypothesis correct, experiment planned well, you actually drink enough coffee to pay attention to your protocols, but the lab gods still decide that you aren’t worthy and they break your experiments in downright miraculous ways.  This happened to me during the week of March 1^st.  I won’t go into all the problems, but I will tell you about the last straw.  The failure that made me say, “Okay.  I get it.  I GET IT.  You hate me.”

Earlier in the week, I had discovered that a particular protein I was working with had a minor error in it.  Unfortunately, this meant that I had to repeat a bunch of experiments I had done before Christmas.  It happens.  I was angry for about ten minutes and then got over it.  I ran a very simple experiment to change the protein to what I needed (the protein was too long so I had to clip off a small part).  This is a very standard thing to do and I’ve done it approximately four hundred times during my career.

When I was done clipping my protein, the protein was very dilute.  For later experiments and long term storage of the protein, I needed to increase its concentration.  Figure 6.1 shows what a dilute and concentrated protein sample look like.  In short, I wanted many more protein molecules in the same volume.

This is a common problem and the company Millipore manufactures concentrators.  They are two tubes that stack inside each other (Figure 6.2).  You put your dilute protein in the top tube.  The base of the top tube has a filter.  This filter is full of very small holes that allow small things (such as water molecules) to pass through but larger molecules (such as my protein) cannot pass.  If you apply a force to the whole tube, the dilute protein sample will be forced downward towards the filter and what can fit through will flow into the bottom tube.  Whatever cannot pass through will remain in the top tube.  We apply a force to these tubes by spinning them at a high speed (centrifugation).  

Okay.  I’ve done this more times that I seriously can count.  My entire Ph.D. involved purifying proteins, concentrating proteins and performing experiments with them.  In fact, a tremendous amount of biochemistry involves this procedure.  I’ve used Millipore concentrators for seven years.  

On Friday, when the centrifuge had spun for 15 minutes, I went to pull out my concentrator and to check how things were going.  Imagine my surprise when I found my concentrator shattered (Figure 6.3).  The top tube had broken loose, spun to the bottom of the second tube, and cracked the entire unit.  My solution of protein was all over the bottom of the centrifuge.  My boss asked me if I could get it out anyway.  Um, that’s like trying to recover your spilled soup from a trashcan.  Gross.

In seven years, neither I nor anyone in my lab had ever seen a concentrator break so badly.  I did everything correctly with the clipping of the protein, purified it properly, spun the concentrator at the proper speed, but I still have to repeat the experiment because of something that no amount of ability could have avoided.  Freakish freakish accidents are just the most annoying of all.

P.S. – I pulled some more protein out the freezer on Monday, March 7^th, clipped it, and purified it.  This time it went perfectly.  Clearly, I needed a weekend break.

Centrifuge: an apparatus that spins rotors at high speeds and creates centrifugal force on the samples inside.

Rotor: the apparatus that holds sample tubes for high speed spins

References

Me, myself, and I.

If you’d like to see a real concentrator, courtesy of Millipore: http://www.millipore.com/catalogue/module/c7715

They have pretty pink caps.  They used to be blue – I have no idea why it changed!

NOTE: Originally, this post should have been #9, hence why the figures are actually labeled 9.1, 9.2 and 9.3  I moved it up in the order (to #6) and while I changed the numbering in the text, I forgot to change it in the figures.  Sorry about that.