Biology,  Physics,  Research

The Structure-Function Debate in Biology

Modern science grew out of the idea that the universe is comprised of independent parts, and a complex system can be reduced to these parts without loss of completeness. The independence of parts became the basis of reductionism―the idea that the whole is simply a linear sum of parts. Sometimes, this reduction fails, and then it becomes necessary to postulate that the parts are indeed interdependent.  The reason for this interdependence, however, has not been very apparent. I will describe the reasons in this post, and connect them to the “systems approach” which views a system as a collection of interrelated parts rather than mutually independent parts.

The Basis of Reductionism

It is not difficult to find macroscopic objects that comprise many parts. Common examples of such macroscopic objects are houses, cars, and people, and we draw boundaries around these macroscopic objects, to give them conceptual names such as a house, car, or person. Reductionism supposes that these boundaries are unreal. They are just conveniences by which fundamental particles are aggregated into the useful instruments of our daily life, but these boundaries have no real existence in the world. If there is no boundary that demarcates a macroscopic object, then the object is simply a collection of smaller parts, all the way down to indivisible parts. Only the indivisible parts have a boundary, and their macroscopic aggregations do not.

The theoretical basis of reductionism is thus the rejection of boundaries in nature. We suppose that there are material objects, but there are no boundaries. Note that boundaries could also be scientific constructs, since they are entities that can exist in space and time, but they would be not material entities in the conventional sense of things that can be measured or observed.

But if boundaries cannot be observed, how can we suppose they even exist? The answer is that if boundaries exist, then reduction is false. By reducing a system to its parts, we will lose the boundary, and the properties of this boundary cannot be attributed to any of the parts within the boundary.

Boundaries and Meanings

A simple example of this loss is meaning in language. If you take the alphabets of a text individually, and measure their physical properties (supposing that these alphabets are independent), then you can never see these alphabets as symbols or representations of ideas. However, if you draw boundaries around these alphabets, thereby forming words, phrases, sentences, and paragraphs, then you see a growth in meaning.

The exact meaning attributed to words or sentences is, however, not given simply by their compositions. Rather, these entities are given meaning in relation to the next higher level of organization. For instance, a word gets its meanings in relation to the sentence, the sentence in relation to the paragraph, the paragraph in relation to a chapter, and so forth.

If, therefore, you discard the boundary, a symbol of meaning becomes a physical object. If you add a boundary, the same physical object becomes a representation of meaning. The problem of reduction is therefore that it converts symbols with meaning into things without meaning. The essential property being lost in reduction is not physical but semantic. That is, you don’t lose the total amount of mass, charge, energy, momentum, or any such physical property by removing a boundary. However, by removing the boundary, we change the organization or distribution of these properties.

The Matter Distribution Problem

All reductionist theories of nature suffer from the problem that the theory describes matter in the aggregate but the exact manner in which the aggregate properties are distributed in nature cannot be predicted. For instance, if you were given a certain amount of paper and ink, there are infinite different ways in which you could use the ink and paper to produce different kinds of books. From a physical perspective, all these books conserve the total physical properties, but they are clearly not identical. The differences between these books is empirical but it cannot be theoretically explained in a reductionist theory. Such a theory, therefore, becomes incomplete: it cannot explain all the observations.

The matter distribution problem is symptomatic of meanings: different books may have the same mass, but they denote different ideas. This makes all classical physical theories also indeterministic because the theory’s predictions are compatible with many possible matter distributions and do not predict which of these distributions is real.

Reduction in Biology

Biology encounters many problems with a reductionist approach because while the materialist reduces a living being to chemicals, he or she does not know how to assemble such beings from chemicals. Despite many advances in decoding the chemical composition of cells, even the simplest unicellular living beings cannot be chemically synthesized. The key reason for this shortfall is that the living being is not just the chemicals, but also a boundary that constitutes the molecules into a whole.

This boundary is also an object, which means that it has physical properties such as energy, mass, momentum, etc. However, these physical properties are only tangentially relevant to the meaning. For example, “animal” and “donkey” are two words with the same number of letters, so their physical properties are similar, but their meanings are completely different. One word (animal) is more abstract than another (donkey). In arriving at this conclusion, we don’t look at the physical properties of the words, but rather at their meanings. In fact, these physical properties are almost entirely irrelevant to the question of meaning, because we could express the same idea through other words. The “boundary” in question is therefore another space-time object, which is higher in meaning. We can sensually perceive the existence of this object because it too can exist as a word. However, we cannot know the meaning of the word by sensual perception.

The result of this difference is that the behaviors of these objects can differ radically even when they have similar physical properties. We cannot explain the observed differences in behaviors if we only measure physical properties and it seems that the physical explanation is incomplete. Therefore, even to explain all the sensual observations, we have to postulate meanings. For example, we can see that the bodies of the living beings function quite differently than the non-living assemblage of the same set of chemicals. If science understood the fact that physical properties are less relevant than meanings, then it would be able to explain how the bodies are created, modified and destroyed. The study of the living bodies would then be more scientific and much less mysterious.

The Debate on Intelligent Design

Today there is a raging debate between reductionists and holists about whether the parts of a living being must be described in terms of their physical structures or in terms of the biological functions. The reductionist equates the biological functions (e.g., hearing) with the physical structure (i.e., the chemical composition of the hearing apparatus―the ear). The holist argues that the ear is too complex to be created from the parts automatically and randomly, unless explicit design considerations are applied to this aggregation.

Both reductionists and holists agree that since the parts can be assembled into wholes in many ways, there must be something due to which one among the many possible assemblies becomes real. They only differ in what they think that selection mechanism is. The design theorist argues that this selection is an act of design by an intelligent agency. The reductionists are fundamentally opposed to this idea of design, since the intelligent agency that designs these wholes can be construed to be a supernatural being who creates life―i.e. God―which renders science incomplete. The reductionists argue that many possible assemblies are automatically eliminated by natural selection which essentially decimates the numerous possibilities―many of which are non-living.

The reductionist argument for natural selection and the design argument for holism are equally flawed if there are indeed meanings in nature. The design argument, under such a situation, would appear to overreach and attribute a natural property to an act of God. Similarly, without the existence of meanings, claims about natural selection are flawed because selection can only occur at the boundary between an organism and its environment and reductionism entails that there isn’t any such boundary. The design argument is thus unnecessary, and the reductionist argument is insufficient.

Deconstructing Natural Holism

There is a better alternative to intelligent design and natural selection in which a new kind of natural entity―boundaries―are seen as the mechanism that creates systems.

A system, in this view, is deconstructed into three components: (1) parts, (2) wholes, and (3) the relation between the whole and the part. The parts are the material objects, which are currently described as physical properties. The wholes are the boundaries or the contexts in which these parts are contained. As noted above, these wholes are individual objects too, but they represent abstract meanings. Finally, the relation between the whole and the part is the space-time location of the part in relation to the whole.

If the form of the whole is altered, the functions of all the parts in that whole would be altered even though the physical properties of these parts would be unchanged. Similarly, if the space-time location of the parts within the whole is altered, the functions of the parts would be altered. The function of a part, therefore, depends on the form of the whole and the location of the part in the whole. This location, however, cannot be described in a universal manner. Rather, it must be described in a context-sensitive manner such that the boundary represents the coordinate system origin in relation to which parts are located. If the form of the boundary is defined, then the coordinate system is also fixed.

I have previously illustrated how this kind of coordinate system represents a hierarchical space-time similar to postal addresses and clock times. In a postal address, the state is inside the country, and a city is inside the state. The states in the country are therefore named not universally, but contextually: two countries can use the same name for different states because the name for a state acquires a significance only in relation to the country. Similarly, two cities in different states or countries can have the same name because the name resolution is not universal, but contextual.

The Language of Types

In the hierarchical space-time structure, parts, wholes and the relation between wholes and parts must be described using a language of types rather than quantities. The whole may therefore be called a “body”, the part can be called the “stomach”, the relation between whole and part is that the stomach is in the “middle” of the body. Similarly, the whole may be the “head”, the part may be the “eye”, and the relation between whole and part is that the eyes are in the “front” of the head.

Note how the hierarchical space-time structure shifts the focus of science from quantities to qualities. We are no longer measuring physical properties, registering their numerical values, and locating objects in a space-time whose locations are defined as numerical quantities. Rather, the whole (space-time), the parts (objects in that space-time) and the relation between whole and part (the object’s location in that space-time) are all described in a language of types instead of quantities. Since each object in the space-time can also be treated as another space-time or whole which is in turn comprised of more parts, the system of parts and wholes constructs a hierarchical structure of types or meanings.

The location of the parts in the whole constitutes a structure. This location gives meaning to the parts, but that meaning depends upon the form of the whole and the form of the parts, aside from the location of the part in relationship to the whole. Structure and function can therefore be equated in the semantic scheme, in the sense that the location of a object (which defines its structure) also defines the functionality. This equation emerges only in a hierarchical space-time, and not in the physical description of nature.

The debate between structure and function is, in one sense, misconstrued because the two can be equated. However, this equation is semantic and not physical, and shifts in scientific notions about space and time must occur before this equation is achieved.

The Comprehension of Living Beings

An understanding of life requires the treatment of boundaries as ideas more abstract than the objects within that boundary. For instance, the idea of a house is more abstract relative to the rooms in it, and the idea of a city is more abstract relative to the houses in it. The whole living being is therefore more abstract relative to the body parts, which are more abstract than the cells in them.

A living being is built upon multiple layers of abstractions relative to the smallest cells and molecules, and these abstractions are given meaning in relation to even more abstract constructs such as society, economy, and nationality. Today, the study of biology is divorced from social sciences, and biology is only loosely coupled with physics, mathematics, and computing. The semantic view changes this understanding of living beings―treating their consciousness and mind as being part of the same structure as their bodies―while not reducing the mind or consciousness to their bodies.