Pas si mal

Greetings earthlings!

In the previous post, we saw what it was that made a protocol make you feel more frustrated than a dog trying to catch its own tail. This time around, we will take a look at a protocol that is quite all right... until the very end. Like a Hitchcock movie, you know that something bad is lurking around the corner, but even when it hits you, you're surprised it was there. (If this doesn't make any sense to you, don't worry. It was not meant to.)

In the spotlight today is the Size selective DNA precipitation protocol from OpenWetWare.org. At first, it looks like a superior protocol - concise, complete and correct. Look closer, specifically, the last step.

"Dissolve the pellet in a appropriate amount of buffer of choice."

Questions:

1. Is 50 ml appropriate? Or a 1000 gallons? How much is "appropriate"?

2. What if my "buffer of choice" is blood plasma?(Blood plasma contains a bicarbonate - carbonic acid buffer)

[We have overlooked the previous step which is a paradox in itself:

"Carefully remove supernatant not to disturb the pellet, which will be invisible."

(It's like saying "Oh! Be careful with the dangerous pterodactyl that is right behind you! It's angry and invisible!! ")]

The BioCoder version marks this step as a to_do() instruction that will hopefully attract the attention of the person carrying out the protocol with its cheery red color (not to be confused with the red blood cells left over after extracting the blood plasma that we would like to use as our "buffer of choice".)

Also, the place holder for the "buffer of choice" is a generic buffer whose name and properties will have to be changed by the person executing the protocol. (In this case:

Fluid buffer = new_fluid("blood plasma", "bicarbonate + carbonic acid");)

Our final verdict:

2 QMs for this protocol because of ambiguity in two instances in the final step.

(And although we haven't taken the penultimate step into account, if we did evaluate it, it would get 5 QMs for playing with the sentiments of the poor guy/gal carrying out the protocol.)

Until next time, 

VisualAcuity.