I did this write up and sketch to help visualize the role of spatial organisation in biological function and anatomy. Most people are aware that DNA contains instructions for proteins and RNA. They may even understand that the components of DNA: water, Adenine, Guanine, Cytosine, Thymine do not inherently contain complex information rather it is how they are placed, their order in the genetic chain that produces instructions for proteins.
Unfortunately once we arrive at the level of proteins and rna all of this understanding collapses. Suddenly proteins become literal deterministic instructions, and the tragedy of this flawed understanding is the reality that the distance between protein to organism is arguably greater than the distance between humans and tiktaalik. Ultimately, proteins, like nucleotides, are dynamic and context dependant structures. The way proteins interact and organize is variable and depending on how they spatially align and lock with eachother, dramatically affects protein function and outcomes. Like nucleotides how proteins are spatially organised affects the information contained within these macromolecular super structures.
This is where the ‘cytoplasm’ comes in, I hate the word cytoplasm, because we associate it with a boring bag of enzymes when the reality is the intracellular matric is extremely organised and spatially complex, much more so than dna. There are far more possible molecular arrangements the ‘cytoplasm’ can produce than nucleotide arrangements can. The organisation of the cytoplasm is self perpetuating, self correcting and determines how proteins and rna function. Even individual proteins can recruit neighbors into copies of itself i.e prions, this molecular recruitment applies to super molecular structures even more so. The spatial organisation of the cytoplasm, thermodynamically and bioelectrically modulates cell behavior, controlling pathways for making sugars and other cell products, responsible for properties of the extracellular matrix. It affects intercellular communication both by regulating outgoing signals and determining how incoming signals are interpreted. This spatial-macromolecular code is as important as the genetic code. It is the reason why cells of different taxa are not interchangeable.
As cells communicate and coordinate multicellularity emerges. Multicellular organisms are essentially self replicating biofilms. The bioelectric and chemical network between cells help reinforce collective states and structures. It is an intercellular feed back loop with constant checks between cells to maintain structures. Some cell cloisters organise into specially shaped chambers which participate in the construction of imperfect copies of the collective state. This is the egg cell or womb. We cannot simply go from a single human cell to a human because it requires communication and interaction with an emergent intercellular environment, in our case the uterus.
Why is all of this important? Because it is important to recognize that organisms are the organisation and behavior of cells, rather than a black box of chemicals. It shows that information arises from how components are organised and this applies equally to nucleotides and other molecules. Information does not end at the genes but is present at every step of the biological hierarchy. This used to be controversial. I was among the first to propose this but it is being rapidly accepted by mainstream biology. Because it is true, and it finally solves the mystery of evolution.