Is DNA the “Master Molecule” or just “a valuable resource for the cell”?

Consider the general contractor, hired to build a building. But how does he know which building to build? Will it be Bilbao or McDonald's? The contractor works from a blueprint drawn up by the architect. Does this drawing cause the building? Something like the blueprint is necessary, but we usually look other causes as being more critical: the availability of funds or the need for the building.

Is the blueprint just another valuable resource, then? It is a resource, but of a unique kind: information. While many resources are necessary (ore that can be turned to steel, carpenters, contractors that can read blueprints), the blueprint has a unique role in determining what we end up with.

This story sheds some light on the particular importance of DNA in making us who we are. It is true that DNA is more like a recipe than a blueprint, but DNA is entirely like the blueprint in being an information resource.

Other resources, like the iron ore, are refined and standardized so that they can be shaped according to the information in the blueprint. They lose all their information. The contractor, and his associated ecosystem of tradesmen are also essential parts of the system. Their constructive efforts, and their understanding of how the language of blueprints calls for standard parts such as doors and windows, these are necessary for the building to come about. But if the resulting building isn't what the architect had in mind, then the system has malfunctioned.

In much the same way, living things digest proteins, breaking them down into their constituent amino acids, stripping out the information. Then we stick them back together again according to the patterns written in our DNA.

The blueprint doesn't cause there to be something instead of nothing, but it does determine what we end up with. Because the blueprint was made to be understood by humans, we can look at it and see which particular symbols caused a window to be installed there, and why that wall has no window.

Our DNA was not made to be understood by anyone, but we have figured out some things, like the code for proteins. We don't understand at all well how the information in our DNA directs the our growth from a single cell, developing complex structures such as skeletons, muscles, and brains. Yet even not knowing that, we can be quite confident that our DNA (and perhaps epigenetic annotations) do determine all of the consistently reproduced aspects of our developed structure. This is simply because there is no other information resource available to do that patterning. After we are born, our experiences are another source of information, and the causes of human patterning become less clear.

A good bit of our uniqueness likely also comes from minor decisions that emerged as “good enough” solutions to local structural problems in the self-organizing process of development. The particular solution used could not be predicted from DNA alone. It is a consequence of similar developmental decisions made earlier on and the constant random buffeting of thermal vibration. Similar things happen during construction of a building. The electrician has to route his wires around the plumbing pipes, and this isn't going to be done in exactly the same way twice, even though the lights do go on and the toilet flushes. Does the light switch go in the left, or the fan switch? The blueprint doesn't say. See Wiring the Brain: Nature, nurture and noise.

Is DNA the “master molecule” or just an “important resource”? It's true that DNA by itself isn't a sufficient cause for life–It isn't a “cause for existence”. DNA only functions as part of a cell, and in the case of human cells (or even fungus cells) this is a quite complex system with subparts like organelles, membranes, enzymes and receptors. But all of these parts are either made out of protein and RNA or are made by proteins (enzymes). And we do understand at a high level of detail how RNA is created from DNA and how proteins are built according to a recipe that is written in the DNA.

Not only is DNA a necessary cause of the cell structure, cellular biologists usually proceed with the assumption that all of the essentially cell-like aspects of the cell are determined by the DNA.

What do we mean by “essentially cell-like”? No two cells are exactly the same. The pressures of the surrounding environment affect the cell shape, and the random processes of self-organization mean that the precise locations of membrane molecules are left to chance. The biologist proceeds by the assumption that these differences between cells don't matter.

When you look at cells in detail, you see that DNA exists within a complex regulatory structure. Not all DNA is transcribed in all cells at all times. This control is by transcription factors that bind to the DNA and various kinds of epigenetic markings on the DNA. But all these control processes operate using proteins assembled according to DNA instructions and regulatory sequences directly coded in the DNA (promoters and inhibitors). These regulatory processes are how the cell responds to the challenges and opportunities that the surrounding environment presents.

The cell can't exist in isolation from the surrounding environment, but there is a genuine modularity to cell structure. The membrane is a physical boundary, and the cell goes to considerable effort to control its internal environment, pulling in chemical resources and expelling wastes. In a multicellular organism like a human, the cell's activity is controlled by many different kinds of messenger molecules. Proper functioning of our body depends on our cells maintaining their boundaries and respecting these external signals. In other words, the design of our bodies assumes that cells “of the same type” are interchangeable. This means that the biologist too can consider cells interchangeable. And insofar as those cells are interchangeable, it is because of what is in common between those cells (DNA and epigenetic markers placed by genetically determined processes.) So that is what “essentially cell-like means”.

It's true that without ribosomes and tRNA that “speak the language” of DNA, the DNA wouldn't generate those structural proteins and enzymes, but we can be pretty confident that our DNA wouldn't be a “valuable resource” to a cell that didn't speak this genetic code, which is shared by all life on earth. Given only DNA it would be tricky to reconstruct what the organism looks like, especially without knowing the genetic code, but no other functioning life form could be constructed using that DNA as its genetic code. So all the other necessary causes inside the cell and in the external environment are highly constrained. There are many many other things that need to be correctly aligned for the cell to survive, but if they aren't there, all you have is a dead cell and a boring story. Those other causes can't contribute meaningful variation because all they can do is harm the cell.

One way to understand this puzzle is to see that the cell (as we know it) depends on circular causation. We don't know how the cell got the way it is, but there is some reason to consider the DNA as a sufficient cause for the cell. Certainly the cell is a sufficient cause for another cell (all other things being equal). This is just the chicken and egg problem. We can understand how chickens and eggs work without knowing how the chicken-and-egg system came into being. A chicken farmer doesn't need to solve the problem of “why is there anything instead of nothing at all”. Is an egg a sufficient cause for a chicken or not?

We say the cell “as we know it” depends on circular causation because this is indeed how we understand cells, based on our assumption that cells are interchangeable. In reality there is no circular causation. The first egg that a chicken hatched from was laid by a bird that wasn't a chicken, way back in a long series of sequential causes, where each intervening chicken and egg weren't actually identical, any more than two chickens or eggs today are truly identical.

Where does this leave the idea that an egg is a sufficient cause for a chicken, or that DNA is a sufficient cause for a cell? In the cloudy limbo-land where all sufficient causes live, based on induction and impossible-to-completely-specify assumptions of “all other things being equal”.