Discovering Biology in a Digital World

Vizzini: He didn't fall? Inconceivable!

Inigio: You keep using that word. I do not think it means what you think it means.

- William Goldman, The Princess Bride

Excuse me while I temporarily interrupt the genome sequencing series to define a word.

Artifacts in the classroom

It's disorienting. You learn a word in certain context. You're sure of it's meaning and then you end up in a situation where people use the word in a completely unexpected way and no one else seems bothered by this!

I had this happen once with the word "artifact." I had organized a conference and some workshop presenters were talking about students and protein gels. It was a dark room and there were on things on mind, which, I confess, began to wander a bit. At least it did, until the presenter said that students could use a photocopier and take home artifacts to show their parents.

What!

In molecular biology, an experimental artifact is a bad thing. It's something that you see sometimes in experiments and it isn't a real, meaningful result. In fact, it can be very misleading. For example, imagine that you're trying to extract ancient DNA from a bug caught in amber, and someone's pet fly buzzes through the lab and drowns in your test tube.

You would get a result from this experiment all right.

You would find that ancient amber contains DNA from Drosophila.

That result would be an artifact.

So, I was stunned to hear someone, in a science education workshop no less, speaking of artifacts as if they were GOOD things.

We were using different definitions. It blows my my mind, but it turns out that the education world defines an artifact as a piece of evidence.

Lost in translation?
Vector is one another word that makes me think we need a special dictionary that translates science words between science disciplines. This would work like an English French dictionary that takes an English word (or vice versa) and finds the French counterpart. Except in this case, we would take a perfectly respectable word that's used in both disciplines and find what the word means in the other discipline.

Heck, you can see from our efforts to define a gene, that sometimes we need a contextual dictionary to translate words within that same discipline. Such a dictionary would allow us to take a perfectly respectable molecular biology word, like "vector," and find out what it means in physics or epidemiology.

What is a vector, anyway?
In physics, a vector is a straight line with a direction and magnitude.

In epidemiology, a vector is something that can spread disease. Things like rats, flies, mosquitoes, birds, and lice, can be vectors. A tsetse fly bites a person with sleeping sickness, picks up some parasites and passes the parasites onward when it bites a new person. In this case the tsetse fly is serving as a vector.

In molecular biology, a vector is something that we use to move nucleic acids (usually DNA) into a new cell or organism. Vectors are either plasmids or viruses. If I sequence a DNA and obtain a read, I can use sequence comparison programs to identify which parts of the sequence are vector and which parts are not.

This image is from the Finch® Suite. The blue letters are from the vector. The black letters represent the DNA sequence of the insert.