Representing DNA as code

by | Monday, March 09, 2009

What does it mean to represent something? Sean Nash (of Nashworld) and I have been having some fun at the expense of periodic representations (my post and his response) and even children’s books. I had been wanting to write about this for the past few days but travel, work and illness came in the way. However, I stumbled upon a way of thinking about DNA that prompted (actually forced) me to write this post.

One of the biggest myths of representation is that representations are direct one-on-one mapping of the real world. Nothing could be further from the truth. It is important to understand that all representations are wrong – wrong because they, by necessity, have to distort in order to communicate. A map that had all the details of the real world would not be a map – it would be the world! We need a map to get rid of extraneous details, so that we can focus on the important details. As to what is important depends on the purpose for which the representation is being created. Thus underlying every visualization is a theory, a way of looking at the world.

Another way of saying this is in Alfred Korzybski’s statement that “The map is not the territory.” The wikipedia page devoted to this describes this as follows:

The map is not the territory is a remark by Polish-American scientist and philosopher Alfred Korzybski, encapsulating his view that an abstraction derived from something, or a reaction to it, is not the thing itself, e.g., the pain from a stone falling on your foot is not the stone; one’s opinion of a politician, favorable or unfavorable, is not that person; a metaphorical representation of a concept is not the concept itself; and so on. A specific abstraction or reaction does not capture all facets of its source … and thus may limit an individual’s understanding and cognitive abilities unless the two are distinguished. Korzybski held that many people do confuse maps with territories, in this sense. [Emphasis mine.]

The best example of this is Magritte’s famous painting (shown below) where a painting of a pipe should not be confused with the real object:

There are a couple of important conclusions that emerge from this. First, a representation is by its very nature limited, constrained, and incorrect. Second, a representation is always for a certain purpose and this purpose emphasizes certain aspects of the phenomena being represented, even while it under-emphasizes or ignores others. Third, understanding a representation requires understanding this purpose. Often this means recognizing and understanding the perspective, the point of view, the theory, or framework that led to the creation of the representation.

So what does have all this to do with representing DNA? Well, I have been thinking about issues related to representation for a while now (see this for a good example of how goofy and serious this thinking can get) and was reminded of it when I stumbled upon an article that specifically looks at DNA as computer code: DNA as seen through the eyes of a coder.

That DNA is information is not a new idea. However, it is when we take it to its limit, to see DNA through the eyes of a computer programmer or coder is to truly see it in a new light. In this piece Bert Hubert takes the idea of DNA as code (as a computer program) to its extreme. Consider for instance this statement:

DNA is not like C source but more like byte-compiled code for a virtual machine called ‘the nucleus’.

He continues in this vein, attempting to mine this metaphor to its limit. For instance, see his explanation of “stem cells” or “junk dna.” I found these explanations extremely powerful ways of thinking about DNA.

Of course the usual caveats apply (the map is not the territory, all representations are limited, blah blah blah…). However the power of a new representation as helping us “see” patterns and connections that didn’t make sense before is palpable.

Pretty cool stuff.

A few randomly selected blog posts…

On making computation visible

Here is a cool video about a "a mechanical, binary adding machine that uses marbles to flip the bits" - in other words a computer made of wood, that works at a pace that we can grasp! Marvelous. (HT: Collision Detection). Check out the video: [youtube width="425"...

Teaching to learning styles, what hogwash

There is an article in today's Chronicle titled Matching Teaching Style to Learning Style May Not Help Students. I have been somewhat skeptical of the learning styles literature for a while, not the least for hearing the phrase being bandied about without much...

New TPACK themed book on English Education

My friend Carl Young of NCState recently released an edited volume (co-editor, Sara Kajder a the University of Pittsburgh) titled Research on Technology in English Education. It is a volume in the series: Research Methods for Educational Technology, edited by Walt...

Fear, awe and the algebra of the pendulum

In response to my previous posting titled How artists work, Leigh Wolf pointed out a book (Curious Minds: How a child becomes a scientist). I had not heard of this book before and a quick google search led me to this page. Edited by John Brockman (the brains behind...

Goodbye MSU!

Goodbye MSU!

I started working at Michigan State University on the 15th of August, 1998. Today exactly 18 years later I bid MSU farewell to take up a new position as Associate Dean of Scholarship at the Mary Lou Fulton Teachers College at Arizona State University. These last 18...

SITE08 Keynote YouTubed!

I just found out (via These Apples are Delicious blog, and more specifically this posting: Creative Teachers) that the keynote that Matt and I presented at SITE08 is now available on YouTube! Somebody went through the effort of breaking up the video into 5 parts and...

Teaching TPACK @ BYU

I just found out about IPT287: Instructional Technology for ElEd and ECE a course taught at Brigham Young by Charles Graham (an active TPACK researcher and the adviser of Suzy Cox about whose dissertation I had written about here). Of particular interest to me was a...

The 60 second lecture

I received an email yesterday from the State News (our local university newspaper) about what I thought of the 60 second lecture—a trend sweeping through online courses. Some of my first thoughts about this are below. If you don't know what they are, check out this...


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