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Monday, May 02, 2011

Funny Stories

Lately, the Xconomy folk have been having a hard time coming up with stories to write about the local biotech scene here in Seattle. Since I'm not making a living at it I'd like to share a few stories I've encountered over the years that I think may have something to do with our troubles

There once was a lady who had just receiveed her PhD. During the course of her education she had worked in a lab but she had never dialyzed a protein. We showed her the cassettes and the flotation sponges. The next day we showed up and to our amazement, she had managed to balance the cassettes on top of the sponge, exposed only to the air. The dialysis cassette had not touched the buffer.

Our fermentation scientist (not a PhD) had six 3 liter fermentors. Every two weeks she would set up six runs, usually testing six different methods. When we asked her why she didn't do anything in duplicate she said that it was because she could get more tests done that way. "Ya, but how do you know if the data is reproducible?" "Trust me, it is," she barked at us as she stomped off. Then one day she needed to test only 3 pHs during a particular step. DO EACH ONE TWICE! we begged of her. She did. pH 4 gave very different results, pH 5 both died, and one of the pH 6s gave the best expression. The other pH 6 run died. Conclusion; pH 6 is the best condition but pH 4 could be used in a pinch. pH 5 is lethal.

PS: The six reactors were named after six of the seven dwarfs. Actual conversation: "Which pH 6 run died?" "I think it was Sleepy."

Related story: We had six fifteen liter fermentors. The original process development scientist on the larger fermentors was perusing the fermentation scientists "pH 6" method. The fermentation scientist entered the lab. "What are you doing?" "We're going to try this method at the 15 liter scale." The fermentation scientist snatched the method out of the hands of the process development scientist and stomped out of the room. The process development scientist had to get the method from someone else.

PS: The six 15 liter reactors were named 1, 2... 6.
PSS: The process development scientist was later fired and replaced with an even more experienced scientist. The fermentation scientist was to be a member of his staff. Within the first week of his arrival the he wanted to fire the fermenation scientist. It wasn't allowed. He later left a note reading "Beam me up Scotty, no signs of intelligent life." We never saw him again.

In a Nobel Prize winning lab, they decided to generate antibodies against infectious prions (and not the normal confirmation protein) by denaturing the protein with guanidinium and using phage display technology. As a result of the denaturation, it was impossible to fish out antibodies that adhered to our hopes and dreams. The phage display was done at the Scripps Institute in San Diego. Without testing they sent up numerous samples for western blot analysis. After 3 months it was determined that I (the cargo cult scientist) was incapable of running a proper western blot. In spite of my examples of almost daily western blots using proper antibodies, the job was turned over to another person. They retested my most recent lot. Same result. After a long meeting, my replacement returned to the lab. "How'd it go?" I asked. "You know the step where you boil your sample for 5 minutes prior to running the gel? Well I only boiled for 4 minutes." I responded that I had done that many times and it doesn't really matter. My replacement repeated the work with the 5 minute sample boiling and still obtained the same results. The supervisor was none to happy. She gave us both a dirty look when she saw the same results for the third time.

The ForteBio is a machine that will measure your binding affinity between two proteins. Our ForteBio people tested ten antibodies, 3 times each. In their presentation they listed the 30 results from strongest to weakest binding. A couple of us asked why they had not made a bar chart with the average of each antibody binding affinity and an error bar to show us the deviation of the measurement. The director then took a different tack. On the spot he created an excel spreadsheet and they began using the excel functions to list the 30 antibodies in as many ways as they could think of. Never an average with a deviation measurement. From the strongest to weakest list they selected the one with the first, fifth and 12th strongest binding affinity. It was the best.


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