Life is like JavaScript, not like Java

Today most object-oriented programming languages, such as Java, are based around the class concept. The class describes the properties shared by all instances (objects) of that class; and individual objects are created as instances of a particular class. Class-based object-oriented programming originated with Simula and Smalltalk. An alternative is prototype-based object-oriented programming. This is used in JavaScript, and originated with Self. In prototype-based object-oriented programming there are no classes, only instances. New instances are created by copying the properties of an existing instance (the prototype) and adding new properties.

The difference between class-based and prototype-based programming is a useful metaphor for understanding the complexities of the biological concept of Species. Life consists of instances copied from one another (like JavaScript). Species are a class hierarchy (like Java) we try to impose on the instances after the fact -- we forget species is a man-made construct. Nature just does whatever it does, and we try to simplify it by mapping to categories and rules. Certainly species is a useful concept for living in the world. You don't want to take a child to the zoo and say "see the animal instance?" "see the plant instance?" (or just "see the instance?" !). You want to say "see the giraffe?". However, the usefulness of species (or folk categories) does not mean they always obey our expectations.

The difference between class-based and prototype-based programming is also related to the philosophical Problem of Universals. Do classes exist in the real world, or only instances? The most famous theory of real-world classes is Plato's Theory of Forms. In Platonic Idealism pure archetypes for different objects (such as chairs, or giraffes), and ideas (such as justice, or triangles), actually exist in some other space or dimension our minds can contact. This theory was modified, but not completely rejected, by Aristotle's Theory of Universals. Aristotle thought universals were constructed from the common properties of the instances, rather than existing as pure Forms somewhere else. From these Greeks we inherited the idea of dividing the world up into invariant categories, and performing logical operations on them. That works to a point, and makes science possible. But the simplified model is not the real world -- "the map is not the territory".

The psychology of folk-biology, along with folk-psychology, folk-physics, etc. arose naturally through our evolutionary heritage and individual maturation and learning via interaction with the natural world. Even beliefs in the soul, etc. are understandable in this context. A great book on all this is Philosophy in the Flesh : The Embodied Mind and Its Challenge to Western Thought, by George Lakoff and Mark Johnson. Yes, it is a 624 page slog. In part II some of the examples can be skimmed. But if you make it through it will completely change your understanding of what metaphor is and how we think. You will realize that 99% of philosophy is out of date. That we often just trade one set of absolutes for another, without understanding the real biological reasons why we are wired to search for and believe in absolutes in the first place.