There is no question that with all the knowledge we have attained, the gaps that exist are continually narrowing. Although we may never understand everything we attempt to, our base of knowledge is growing exponentially, and we're covering areas of physics, biology, and chemistry unknown even 50 years prior. A great deal of the current gaps relate to the concept of Emergence, or the phenomena of an Emergent property. Emergence is the phenomenon that relates to how complex systems arise from simple interactions. For example, how do termite colonies develop from the interaction between termites, their genetic programming, and the environment? These Emergent systems are very difficult to understand because there are so many variables involved, and understanding one system, does not make it that much easier to understand others. Emergence exists through all interactions of the universe but differs by mechanism in each system. Although the concept is similar, the technical details and the mechanism for complexity depends on many factors. To understand this aspect of Emergence, one can think of money. In general, the concept of money around the world relates to a certain nation, group of people, economic bloc, etc... agreeing to a common currency, and using this currency as a standard for trade. The currency can greatly vary, being a mix of paper and metal in some places, plastic in others, giant rocks, shellfish, animal teeth, beads, straw bricks, etc... Similarly, Emergence is like the general property we call money, but the actual mechanism and working detail vary, just as currency does for the monetary concept.
To better illustrate Emergence and how it can lessen the impact and reach that religion uses to wedge itself into reason, some examples must be shown to illustrate this phenomenon. The first relates to the concept of the human mind, or what we call consciousness. A good question to ask is how do the interactions between the neurons in our brain relate to the emergent property of the "mind". We know that we need our brains to process the world and communicate with it. Much like a computer, we input data from outside, process it, and output it in various ways. How does such complexity develop from these neural interactions? With the growth of the computer industry, we are slowly and steadily gaining ground in understanding this concept of the mind. One thing we do know is the network within our brains is vastly more complex and flexible then the static network in computers. We are just beginning to realize how complex a single neuron can be, the types of information it can send, and how billions of them can allow for the emergence of consciousness. We do know that other animals, like chimps, dolphins, and even in some experiments, birds (like parrots) have a limited sense of self and consciousness. Since our closest animal relatives are chimps, we must find those changes in our DNA and subsequently our brains that lead us to have a greater sense of self-awareness. Because of this gap in fully comprehending consciousness however, people are able to fill it with non-empirical concepts like the soul, or a universal consciousness, etc... Once we're able to explain how the mind develops from neural connections, we'll be able to completely discard supernatural notions like the soul.
Another example of Emergent behavior is global economics, or to simplify, national economics. How does the interaction between two people, one who has something, and one who needs it, lead to the complex web of economics as we know it today? There are many ways to observe these trends and attempt to understand the emergent properties involved. One is called the "top-down" approach. In this, one must first look at global economics as a single entity. Try to understand how nations deal with each other, and in doing so, perhaps this will lead to a theory which can trickle down towards lower levels. Another approach is called "bottom-up" where simple interaction between two people at the lowest levels can lead to a greater understanding of more complex interactions. Emergent properties seem to develop from looking at things from the bottom-up, while at the same time, noting the point where certain levels of organized, self-perpetuation complexity arise. Both top-down and bottom-up approaches are needed to understand emergent properties, and with economics, one must not only understand how simple supply and demand functions between two people, but how this relates to a whole community, a city, a state, the country, and eventually the world. At some point, economics appears to be an organized, self-perpetuation organism, and that is another example of emergence.
Once one thinks about it, the universe, at every level is in a constant flux of developing emergence. One way to categorize emergence (can't be by mechanism since there are so many individuals variables) is through a hierarchic system ranging from the smallest most miniscule levels to the largest ones imaginable. In this, the lowest levels involve the subatomic/quantum universe. Our whole universe and world, everything that we know and will ever know starts at the quantum level. The first and most pertinent question to ask is how do space and time emerge from the mess that is the quantum universe? That is, the universe at the smallest possible levels and energies (smaller then a subatomic particle). Imagine inventing the most powerful microscope possible, and looking at space. At this level, space has a completely different property then at our relatively large levels. Space in the quantum universe is a foamy mess, with particles popping in and out of existence (called virtual particles), interactions between particles so exotic that it's hard to grasp. A particle can co-exist in two places at once, called entanglement, and without knowing the mass and direction of a particle, it remains a probability, instead of a specific object (called the wave function). This means that light for example can either be a wave, or a particle, but without measuring it, it remains in two possible states at the same time. Only by doing an experiment and measuring it, do we "collapse the quantum wave function" and turn it into a particle. How then does this wild and chaotic quantum world emerge into a more or less predictable universe? By this, I mean how is it that we can't pop in and out of existence, or find ourselves entangled with our twins across the universe, or even remain a wave function until observed, and then collapse into a physical entity? This is one large mystery, with so much complexity that although we're nearing towards a greater understanding, its still a large mountain to ascend. As the physical world at our levels emerges from the quantum world, we also note that chemistry emerges from physics, and subsequently, biology from chemistry. So the lowest level of the Emergence Hierarchy would be the quantum (which would still involve everything in the universe, since the accumulation of quantum processes eventually leads to the birth of stars, galaxies, clusters of galaxies, superclusters of galaxies, and eventually the whole universe.)
As we scale higher levels of Emergence, we reach a point where we find ourselves in the familiar world we live in. Looking at the familiar, emergence can be found in everything. Beginning with life all together, how did certain chemical processes enclose themselves from the external environment and begin the process we call life? Once life started, how did single celled organisms develop the complexity needed to harbor multicellular structures and eventually into the mass of organisms that are required to generate complex life such as trees, mushrooms, birds, dogs, and even human beings? For as long as human beings have been around, god (or gods, ancestors, spirit animals, or any other supernatural entity or entities concerned with our health and welfare) was used as the initiator of this complexity. In fact, not only was god supposed to be the initiator but often the brooding figure that spent every waking moment looking after all, or certain groups of human beings. As our understanding of evolution and the development of complex life has progressed, god has slowly and methodically taken a back seat to natural processes. The emergence of these natural events has become the reason for the flourishing of life. The fight for survival in the form of an evolutionary arms race, where all creatures struggle to balance evolutionary costs and benefits, is but one example.
As an example, figure 1 here shows the nature of an Emergent hierarchy from the Human perspective. As can be seen, it takes many levels of emergence for consciousness to emerge, then language, and afterwords, economics, culture, and eventually, artificial Intelligence, which is another level of Emergence yet to be reached.
Figure 2 here demonstrates an Emergence Hierarchy from the Universal Perspective. The Human Hierarchy is just an offshoot at about the star level.
Almost any object can have a similar Emergence Hierarchy, whilst as mentioned before, the mechanism for emergence can vary. As for the large towering termite mounds, their emergent hierarchy's will mimic ours until the level of Biological, and from then, it would branch into perhaps insectoid, then social cooperation, and eventually a termite mound emerges. With the mechanisms present here, we have a decent understanding of how termite brains are programmed to create such structures. Of course, there are gaps, but these gaps are slowly being filled by science.
As can be seen from these Hierarchies, the need to invoke a divine presence is completely useless in explaining the phenomenon of emergence. It is easy to claim that a god(s) intervened in this emergence, but that would not help us explain our observations. We know that there are many forms of emergence which we can explain, so our goal is to find a scientific and empirically based explanation for those which we have yet to fully explain.