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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.

i-5c0c71757bdb3bad05fc4f02bc3b7e2f-sequence.gif

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

Copyright Geospiza, Inc.

Comments

  1. #1 Greg Laden
    February 2, 2007

    Great post!

    A vector in biology can have the same meaning as in physics. In studying bird behavior, for instance, one measures the vector of departure when the ducks leave the pond.

    There are dictionaries of archaeological terms. This is necessitated mainly because arcaheologists love to make up hard words and often do them in non-English languages (which is understandable since most of the French words, for instance, are made up by French archaeologists.)

    For example, the little beak shaped “striking platform” one makes when using the Levallois technique to make a flake is called the Chapeaux Gendarmerie after the funny hat that some French police wear.

    These very obscure and odd terms virtually guarantee that there will be no confusion between archaeology and any actual science!

  2. #2 Sandra Porter
    February 2, 2007

    Thanks Greg! Good example with the ducks. Sometimes a word does the mean thing in multiple disciplines.

  3. #3 Paul Orwin
    February 2, 2007

    Nice. Always funny (not always ha ha) when terms overlap.

    Off topic; I just downloaded FinchTV from your website (Geospiza). Fantastic program!!!

  4. #4 Sandra Porter
    February 3, 2007

    Thanks Paul! We’ve had a lot of good feedback on FinchTV. After all, it makes viewing trace files fun!

  5. #5 KevinC
    February 3, 2007

    I always saw the disease vector as an extension of the physics meaning, i.e., the disease follows a certain path (direction) and time frame (magnitude).

    There is a dictionary that translate all of those, Oxford English Dictionary. It gave all the definitions for vector; math, physics, computing, medical/bio and genetics. Of course it is behind a wall online and runs 20+ vols in print.

  6. #6 Sandra Porter
    February 4, 2007

    I always saw the disease vector as an extension of the physics meaning, i.e., the disease follows a certain path (direction) and time frame (magnitude).

    Could be. I found another place for looking up defintions to science words. I’ll write about it later this week.

  7. #7 Gerry Ward
    January 12, 2009

    We’ve all heard the line that Biologists claim that some organisms multiply by dividing. Science educators often spend time talking about the difference between operational definitions and conceptual definitions. There are many great examples and you have given us some additional ones. I always thought an artifact was something on the microscope slide caused by the glue or a bubble, then I found out that it was an old piece of pottery found at an archeology dig.

  8. #8 Sandra Porter
    January 12, 2009

    Hi Gerry: It’s both. Wikipedia has about 19 definitions for the word artifact and an alternative spelling, artefact.

    Half of the definitions describe an artifact as some kind of an error or misrepresentation and the other half as some kind item produced by humans.

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