The changes in the state of the soul and in karma are of two different kinds. The soul experiences transformation and is itself the main cause for these changes; karma is the auxiliary cause. As a soul possesses intelligence, it responds to changes in karma intelligently. Karma either bonds or rises (or experiences fruition): these processes are physical and may follow some (still unknown) laws of the physical sciences without any element of natural intelligence. The activities of the soul and karma take place continuously.
For example, let us presume that at any instant the soul is in state S1 and karma is in state K1, as shown in Figure 2. The changes in states S1 and K1 may be brought about by either a change in S1 or a change in K1. A change inS1 is caused by soul processes such as annihilation, subsidence, or annihilation-cum-subsidence of bhava karma, that happen on the initiative of the soul. A change in K1 takes place either by the bonding of new karma or the rise of existing karma. In both cases, yoga, activities of the mind, speech and/or body, and kashaya, emotions and passions, participate in the process. In the case of bonding, these are the cause of the changes; in the case of rise, they are the effects of the changes.
Figure 2 Soul - Karma system
First let us consider the case in which the changes are initiated by the bonding of new karma and the state of the karma body changes from K1 to K2 through the activities of yoga and kashaya. To balance the karma, the state of the soul automatically changes from S1 to S2. The soul responds intelligently to this initial change and then changes its own state from S2 to S3, say by the process of annihilation-cum-suppression, which is common to most souls. Corresponding to this change, the karma state now becomes K3. The change in karma from K2 to K3 will also be associated with some activity of yoga and kashaya, but this activity will be marked by intelligence (meaning that this change will be brought about intelligently).
In the process just described, K2 and S2 are temporary, intermediate stages. In practice, the karma state changes from K1 to K3 and the soul state from S1 to S3, meaning that the two processes occur simultaneously; the soul responds intelligently to the change in the karma states, so this change has an element of the soul's intelligence. Thus, the temporal transformation in the karma states is subjective and not objective or based on physical laws only. This also means that it is not possible to describe the temporal transformations in the karma body by the laws of the physical sciences alone; there is a component of subjectivity (signifying intelligence), which is not a natural property of karma matter. The temporal karma processes are not merely a physical principle; because of karma's association with the soul, they are also intelligent and therefore different from other natural physical processes which are objective and devoid of intelligence.
The transformations that take place with the rise of karma are similar to those that happen with the bonding of karma - except that the rise of karma causes the activities of yoga and kasaya to take place in the gross body. In both cases, the change is initiated by a change in dravya karma, followed by changes in bhava karma. However, there are some exceptions. In the case of the soul processes of annihilation, suppression or annihilation-cum-suppression of karma, the change starts with the bhava karma, followed by the dravya karma. This basic model applies to all cases of changes in karma and hence to all transformations in the soul.
In the system shown in Figure 1, the physical bodies (the karma and gross bodies) work on two principles: first, the principles of the physical sciences for the material they are made of; and second, the intelligence of the soul that flows to the physical bodies through the temporal changes in karma. Intelligence is supposed to have the role of regulating these physical processes. This means that although the work is done by the physical units, the directions are provided by the faculties of the soul. By this consideration, the physical units are slaves and the soul, through its faculties, is the master. The physical units, through genes, know "how to do" and the master knows "what to do." Together, the two manage the system. Both the soul and the physical units are essential for the system to function.
The type and quality of work that is done depends on the skill of the slaves. For high-quality output, high skill is required. This explains the role of genes in the gross body. Low-quality genes produce a low level of structure; high-quality genes produce a superior structure. This means that the genes in human beings are of a superior quality to those of animals. By the same logic, the genes in one-sense beings are of the lowest quality. This also implies that the genes of lower beings cannot accomplish the functions that are required in higher organisms. The intelligence required to direct the work of the slaves depends on their skill. The higher the skill, the more intelligence is required to provide proper directions. The human soul, therefore, manifests more intelligence as faculties than animal souls do. This points to the compatibility of the system components; all components of the system must maintain appropriate standards for the system to function efficiently in the desired way. The soul and the physical units together determine the performance of the system.
For successful operation of the system, the directions have to be in real time. We mentioned earlier that the karma body is a form of energy field, implying that its processes are likely to take place at the speed of light. The directions, therefore, should be at least as fast as the karma processes. This is a pointer to the level of intelligence of the soul that can function at that high speed. In Jainism, the soul is supposed to possess infinite intelligence, not all of which is manifested in normal human beings; still, the level of manifested intelligence is mind-boggling.