TempEx Junk DNA Notes: A Shakespearean Ferrari Factory

Initial research sources with quick take notes

“Junk or functional DNA? ENCODE and the function controversy”
Pierre-Luc Germain • Emanuele Ratti • Federico Boem
Source: Biology & Philosophy
Date: November 1, 2014

Linking here for documentation’s sake. Will remove link if this is somehow inappropriate or otherwise requested.

Quotes and impressions:

“and that selection is but a useful proxy for relevant functions, which might well be unsuitable to biomedical research.”
(emphasis mine) This is elaborated on at length in the article, but an interesting qualifier to note.

“In order to clarify the debate, we then discuss the most important philosophical accounts of functions and the way they address this problem.”
Haha, I love this. Lets decide the essence of functionality!

“In light of this analysis, we propose that ENCODE’s controversial claim of functionality should be interpreted as saying that 80 % of the genome is engaging in relevant biochemical activities that are very likely to have causal roles in phenomena deemed relevant to biomedical research.”
Seemed like this article was going to be a plain refutation, but really is making qualms about specific wording of claims. “Functionality” does not equal “relevant biochemical activities” in their eyes. Interesting to see how this might mean the world to professional scientists, but is indistinguishable to casual pop science journalism.

“The claim that most of our DNA is junk is relevant in two contexts. One is our broader understanding of genome structure and evolution. The other is the attack on the teaching of evolution by the religiously motivated ‘Intelligent design’ movement. The existence of junk DNA seems at odds Fig. 1 Epistemological strategy in which the ENCODE is embedded… with the view that the genome is as efficient as possible, and, hence, that it is the work of an intelligent force or designer.”
WOW I did not even think of this. They revisit this later at the conclusion. Must be important to them.

“Likewise, the fallacy in Gregory’s onion test is to conclude, from the claim that one could make an onion (or, more precisely, an onion-like morphology and behaviour) with 5 times less DNA, to the claim that 4/5 of the onion’s genome is non-functional. To see better why this argument is flawed, consider the well-known stereotype (whose truth or falsity is irrelevant here) according to which public companies are less efficient, and require much more administration, than private companies. Suppose this were true, and that the inefficiency were real (rather than merely a trade-off with, say, more laudable goals). The claim that a private company would do the same thing as a public company with half of the workforce, and even the claim that specific employees are unnecessary, do not imply that these public employees are not doing anything or do not have a function. Rather, they do have a function, but if the system was differently organized this function might not be needed anymore. The proof is that asking the public company to get rid of half of its workforce would surely cripple it completely13—it would require a major reorganization to survive such a cut.”
A nice way to visualize the functionality discussion. But specifically interesting to me that they invoke capitalistic imagery in order to communicate concepts of functionality, and “usefulness” (even while aware of the tropes at play).

 

There are also points that address history: junk DNA could be DNA that used to be useful. While we evolved past needing it, it is still there. Historical/temporal aspects at play.

 

“Junk DNA: A Journey Through the Dark Matter of the Genome”
Carey, Nessa 2015

“Imagine a written script for a play, or film, or television programme.” “Let’s think about the most famous scriptwriter in history, William Shakespeare.” “Let’s imagine we visit a car factory, perhaps for something high-end like a Ferrari.” “Imagine DNA as a ladder, with each base representing a rung, and…” “To think of it another way, the complete works of Shakespeare are reported to contain 3,695,990 letters.”

… only a few pages into the second chapter and we’re double dipping on the Shakespeare metaphors. The metaphors, dear god the metaphors. They’re everywhere.

“If we extend our alphabet analogy a bit further…”
No
“A gene can be thought of as a sentence of three-letter words…”
please
“We could visualize this as looking a little like a railway track.”
no.more.metaphors.

Only 14 pages in and we have a bounty of metaphors and visualizations. I poke fun a bit, but this seems to be an important aspect to the discussion. This is a complicated and almost invisible subject, so it needs as much metaphor as possible to help us wrap our heads around it. Especially for us non-scientist folk.

What metaphors do the experts prefer?

“…we’ll use the term ‘junk’ to denote any DNA that doesn’t code for protein”
aka, Junk DNA is DNA that doesn’t make proteins. Here is the essential, quick answer when you are asked “what is junk DNA?” at a cocktail party.

Chapter 1 uses certain genetic diseases as a basis for understanding junk DNA. While a way to prove evidence of the action of otherwise “useless” DNA, this also adds a humanitarian and moral dimension to understanding junk DNA.

 

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I found one of the alternate online libraries lets me download the book in pieces. I may wind up finishing it before I hear back from Bobst on an interlibrary loan for the physical copy. But this should be a good resource, less technical and more approachable to casual readers.

I’m in the process of getting in contact with Oliver Medvedik, Director of the Kanbar Center for Biomedical Engineering at Cooper Union.

In terms of project ideas, I am somehow attracted to this mess of metaphors (or maybe I just developed some kind of academic stockholm syndrome). It is tempting to just render out as many as I can come across, perhaps irreverently smashing metaphors together. For example, a Shakespearean styled play about a Ferrari factory where only two people out of 100 actually make the cars. Except that in printing the play I add 98 letters of gibberish for every one letter that was put there on purpose.

Another visualization works on our sense of scale:
“Imagine DNA as a ladder, with each base representing a rung, and each rung being 25cm from the next. The ladder would stretch 75 million kilometres, roughly from earth to Mars”
I’ve felt that VR can be a good use of scale visualization, since the sense of personal physicality can bring more context to a sizing metaphor. If I remember correctly, Qwest Kennelly used this approach last year with his NASA/Space oriented thesis work. Perhaps some VR renderings of these metaphors could be interesting.

But in general, I’m also interested in what some experts use as their main metaphor. I like the idea that metaphors are so important in bringing an idea across. And with the ENCODE controversy article I cited at the top of the post, I see potential philosophical ties to the search for a definition of “function”. What is the true purpose of a thing? What is the true definition, and how much can you shave away before the thing becomes something else entirely? These can be used to determine function, but also to think about building metaphors as well.

 

Functional metaphor: Ladder to Mars
Junk metaphor: Shakespearean play about a Ferrari factory