Modeling: The March of Kinesin

 

Each week, the journalist Carl Zimmer writes a science-focus column called “Matter” that appears on Thursday in the New York Times. Last week he asked, “if you can shrink down to the size of a molecule and flying to a cell, what would you see?”

You can see the answer in the 3 minute video, “The Inner  Life of a Cell.”

The material in the video is based on new understandings about cells and protein molecules. These understandings were translated into mathematical algorithms that were processed by large arrays of computers that created the animations that make up the video.

The video shows an immune cell moving along a blood vessel seeking for signs of inflammation (a possible indicator of infection).

Now we are taken into the cell itself and see the response to the information. Genes are switched on that create new proteins. These proteins are collected into a vesicle and hauled along the microtubule to the periphery of the cell by kinesin (a motor protein found in all eukaryotic cells) (“kinesin,” Wikipedia). 

While the kinesin looks so much like an human trudging along a pathway, it is a protein, and a “motor” protein at that.

Of course, it isn’t actually a kinesin either; it is a representation of a kinesin. 

It’s a model of a kinesin. The video shows us a model that explains an aspect of the immune system. 

Science often involves the construction and use of a wide variety of models and simulations to help develop explanations about natural phenomena. Models make it possible to go beyond observables and imagine a world not yet seen. Models enable predictions of the form “if . . . then . . . therefore” to be made in order to test hypothetical explanations. (Framework, p. 50)

The image in the video is an attempt to visualize how the “is a mechanochemical protein capable of utilizing chemical energy from ATP hydrolysis to generate mechanical force “if….”

The video is captivating but what might be more instructive would be to watch the development of the model for that explains how the ”mechanochemical protein” transports materials inside the cell. 

You can see how the model building took place.  On the Duke University’ Cell Biology  Kinesin-1 site you can read about experiments that have been done to work out how the kinesin molecule functions as a motor.  You can see a picture of an experiment involving kinesin molecule pulling microtubule that is attached to a glass rod.  In the experiment it was calculated that the kinesin can exert a maximum force of 5 pN (piconewtons).

We get so accustomed to realistic graphical representations of reality, that it’s easy to miss the real wonder that emerges when we attempt to model the natural world. The real wonder happens when we test our model by constructing an investigation so that we can see how well the model explains the data.

 

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