What does it mean to understand something in biology?

There are of course Tinbergen's four questions to understand systems in biology. Tinbergen separates explanations into:

  1. What's the function of X, evolutionarily speaking?
  2. How did X evolve?
  3. How does X work?
  4. How does X develop as an organism grows?

So for vision, wikipedia gives the following example:

Four ways of explaining visual perception:

  • Function: To find food and avoid danger.
  • Phylogeny: The vertebrate eye initially developed with a blind spot, but the lack of adaptive intermediate forms prevented the loss of the blind spot.
  • Causation: The lens of the eye focuses light on the retina.
  • Development: Neurons need the stimulation of light to wire the eye to the brain (Moore, 2001:98–99).

But this is too high level. As I've been reading a lot of biology papers recently, initially coming to a new area and reading papers feels like this:


The black bits represent knowledge. Initially there are separate islands, with some extra details around core concepts, but they are disconnected.

Eventually it becomes more like:


One starts to build relations between the different ideas. That's roughly what understanding feels like, to put something in context. With that in mind, and reflecting over my own recent experiences reading these papers, these questions seem like a good framework that approximate the experience of understanding:

  1. What are the functions? (Rarely there is just one)
  2. Is there anything else that plays the same functions?
  3. Where are they made? What's their usual lifecycle?
  4. Are there other things similar to them? Are there subcategories?
  5. What reduces/downregulates the functions of the system?
  6. What enhances/upregulates them?
  7. Is it the same in other animals?
  8. How do we know all that? What kind of measurement devices or assays are usually involved? How robust are they?
  9. Is the evidence base broad and agreed-on, is it based on a handful of old papers, or are there ongoing disputes?
  10. Is this a highly connected concept? Is this a relatively disconnected part of a system that does one thing or is this connected to many other parts, with multiple functions?

You might also find this framework useful in your own explorations of biological systems.