Interesting Questions:

1. What is “function”?

In Biology, there are two main concepts of function:

• A historical concept of function, also referred to as the “selected effect function” or “proper function.”

• A non-historical concept of function, also referred to as the “causal function.”

• For a trait, A, to have a selected effect function, F, it is necessary and (almost) sufficient that the following two conditions hold:

(1) A originated as a “reproduction” (a copy, or a copy of a copy) of some prior entity that performed F (or some function similar to F) in the past.

(2) A exists because of this function.

• For a trait, A, to have a causal or non-historical function, F, it is necessary and sufficient that:

(1) A performs a function.

What is the function of the heart?

The proper function is to pump blood.

The causal functions of the heart are to add 300 grams to body weight, to produce sounds, to be encased in the the pericardium, to partially fill the mediastinum, to provide an inaccurate logo for Valentine Day cards, & to pump blood.

• Most biologists use the proper or selected effect function.

• ENCODE used the causal function.

“Operationally, we define a functional element as a discrete genome segment that encodes a defined product (for example, protein or non-coding RNA) or displays a reproducible biochemical signature (for example, protein binding, or a specific chromatin structure).”

• An example of a function that fits the ENCODE definition: shoes binding chewing gum. The function of shoe soles is to bind sticky stuff in the summer.

“By the logic employed by ENCODE, following a collision between a car and a pedestrian, a car’s bonnet would be ascribed the 'function' of projecting a pedestrian many meters and the pedestrian would have the 'function' of deforming the car’s bonnet.” Laurence Hurst 2013. BMC Biol. 11:58

Bonnet (UK) = Hood (USA)

Interesting Questions:

2. Why do people have “problems” with DNA that has no function?

“… nothing is so alien to the human mind as the idea of randomness.”

John Cohen. 1960. Chance, Skill, and Luck: The Psychology of Guessing and Gambling. Baltimore, MD: Penguin Books.

Inability to deal with randomness

Apophenia /æpɵˈfiːniə/ In psychology: the experience of seeing meaningful patterns or connections in random or meaningless data. A type of mild or incipient schizophrenia. In statistics, apophenia is known as Type I error (false positives).

Klaus Conrad. 1958. Die beginnende Schizophrenie. Versuch einer Gestaltanalyse des Wahns [Incipient

Schizophrenia: An Attempt to Analyze delusion]. Stuttgart: Georg Thieme Verlag.

Consider the term “junk DNA.” Implicit in this term is the view that because the genome of an organism has been cobbled together through a long, undirected evolutionary process, the genome is a patchwork of which only limited portions are essential to the organism. Thus, on an evolutionary view we expect a lot of useless DNA. If, on the other hand, organisms are designed, we expect DNA, as much as possible, to exhibit function.

Creationist William A. Dembski

Ideological/religious opposition

Junk = Heroin“He's been hittin’ that junk, he's all fucked up”

Junk = Male genitalia“Dude you just touched my junk!!... do it again ;)”

Semantic Baggage

Interesting Questions:

3. What is “junk”?

“Some years ago I noticed that there are two kinds of

rubbish in the world and that most languages have

different words to distinguish them. There is the rubbish

we keep, which is junk, and the rubbish we throw

away, which is garbage. The excess DNA in our

genomes is junk, and it is there because it is harmless,

as well as

being useless, and because the molecular

processes generating extra DNA outpace

those getting rid of it.”

Sydney Brenner. 1998. Refuge of spandrels. Current Biology 8:R669.

“Were the extra DNA to become disadvantageous, it

would become subject to selection, just as junk that

takes up too much space, or is beginning to smell, is

instantly converted to garbage by one’s wife, that

excellent Darwinian instrument.”

Sydney Brenner. 1998. Refuge of spandrels. Current Biology 8:R669.

Graur’s garage: Functional, but full of junk A garage in which junk became garbage

A garage according to ENCODE. Such garages do not exist.