A Systems View of Life: A Grander Order in the Complexity of Life

Design has been a key and yet elusive word in the areas of science and philosophy for many years. It seemed to reach its apex in 1802 with Paley’s Natural Theology. However, in the wake of Darwin’s Origin the recognition of design as part of a biological research paradigm has been greatly undermined. Design as expressed in Natural Theology is equivalent to that of a highly tuned machine. The parts are idealized and their relationships are synchronized and static. Although we see design of this type in nature, it has limitations when dealing with dynamic, complex interactions between components of a system. Component interaction can range from that of an organism within a biosphere to that of an organelle within the cell. Could there be a broader definition of design that can provide useful insights into the study of the creation and in turn become part of a fruitful research paradigm? Here systems theory is used to develop a framework for defining design in a broader fashion. General systems theory, developed in the 1930s by Ludwig Bertalanffy, proposes the existence of properties or laws that describe the interactions between systems. These laws of interaction apply not only to biological systems, but also to social, political and mechanical systems. Cybernetics, a subdiscipline of systems theory, treats each component of a system as a black box. The black box interacts with its environment through inputs and outputs. Although the outputs of a component are dependent on its environment and internal state, it is possible to study component interaction without knowing the internal function of the component. This is a more holistic approach and provides a context from which to study adaptation, complexity and optimal design. In recent years computer scientists have gained experience working with the design of complex systems. One fruitful approach to software design is Object Oriented Programming (OOP). In this approach complex programs are broken into smaller interacting components. By restricting the amount of interaction between components, the programmer is able to better anticipate the complexities of the system’s behavior and, therefore, control and hopefully eliminate errant behavior. Out of OOP came the concept of design patterns, which are rules of “best practices” when solving certain software problems. Gamma et al. (1995) identified twenty-three such design patterns. Assuming these patterns capture the essence of design in a broader sense, a comparison can be made to biological systems. From this comparison there is at least an analogous correspondence between OOP and biological systems. This gives confidence that design patterns provide a starting point for developing an inter-disciplinary language of design. As a research paradigm, a design language provides potential solutions to classes of biological problems. Although it does not prescribe the particular solution, it does restrict the number of viable solutions for a well behaved system. As biologists are able to recognize and communicate design concepts effectively, new patterns can be discovered, which can benefit the OOP community as well as others. As a specific application, systems theory and design patterns can be applied to the study of limits of variability in the creation. Thinking of an organism as a collection of interacting components, it is possible to differentiate between components exercising global control and those exercising only local control. Likewise a distinction can be made between components of interdependent function and components of peripheral function. Although the loss of a peripheral component is not lethal, it may reduce the ability of an organism to adapt to its environment. Assuming there has been a systemic degradation of each holobaramin since the fall, it may be possible to restore some of the adaptive capabilities of an organism by comparing current members of a particular holobaramin

Modeling Holistic Behavior of Biological Systems for Analysis by Systems Theory

Due to the complexity of biological systems it is not possible to capture the richness of their interactions by purely studying the individual parts. Only a subset of all possible interactions between individual parts results in functional behavior. This restriction of functional possibilities is sometimes described as an emergent property of the system and emphasizes a holistic approach to the study of biological systems. By using concepts from systems theory a systemic approach to modeling biological systems is possible. This approach is currently used successfully in such areas as niche theory and organism biology. This presentation looks at a framework for modeling biological systems as Complex Functional Units (CFU’s). With this level of abstraction it is possible to model systems from intracellular processes to ecological environments. Focusing on the number and quality of interactions between CFU’s it is possible to determine criteria for the interchangeability of CFU’s with similar functionality, but different implementation. Adaptability of CFU’s to changing conditions can also be studied to evaluate possible limits to variation. In order to demonstrate the applicability of CFU’s to biology, several examples will be presented. The first is a comparison of C3 and C4 photosynthetic processes. Both perform similar functions, but have differences in their implementation. Modeled as CFU’s the degree of difference in implementation will be evaluated and applied to C3−C4 intermediates. The second example looks at immunology in light of CFU’s. This is a preliminary exploration with the goal of evaluating the benefit of a more detailed study in the future

What Is the Eternal?

Apologetics arguments related to the creation account in Genesis have ranged from evidential proofs for a young creation to the presuppositional consistency of the biblical worldview. Each of these arguments has its place, but the effectiveness varies depending on the audience’s background. A fundamental assumption for all arguments is that God exists and that he has purposefully communicated with his creation through special revelation. Those not holding this faith commitment resort to other answers that they feel are scientifically based. What they overlook are the faith commitments underlying their scientific answers. This paper poses the question “What is the Eternal?” to expose the faith basis for all answers related to origins issues. For the purpose of this paper, the “Eternal” is defined to be that which is before all things and will persist after all other things are gone. It is the foundation or basis for all that is real. From the author’s perspective there are five distinct responses to this question. All other possible responses are syntheses of these basic five. 1. This is a ridiculous question. This response denies the need to address first causes. 2. Everything came from nothing. This response is not an argument for ex nihilo creation, but for the spontaneous creation of the universe from nothingness. 3. The material universe is eternal. This response retains the foundations of atomism, but adds other assumptions to address the expansion of the universe. 4. The eternal is a metaphysical essence or cosmic consciousness. This response resorts to impersonal forces beyond the physical to explain the fine-tuning of the universe and the complexity of life. 5. The eternal is a self-existent, omnipotent, personal creator. This response corresponds to traditional theism and posits that the existence of the universe is the result of a purposeful choice of a Creator, who desires relationship with His creation. The argument outlined in this paper has historical roots predating Paul’s defense on Mar’s Hill. The originality of this approach hopefully is in its ability to expose syncretic thinking in a culture that makes science the ultimate authority. Historically creationists have debated evolution using a two-model approach: theism vs. materialism. However, it is becoming clear to the author that metaphysical explanations appear with increasing frequency in scientific literature to skirt the philosophical and moral barrenness of materialism. Presenting an audience with the distinction between “What is the Eternal” and “Who is the Eternal” will help them to respond to the One “to whom we must give account.” (Heb. 4:13

Deep Ocean Interaction in a Post-Flood Warm Ocean Scenario

Explanations for the Pleistocene Ice Ages in the context of a recent creation have ranged from denial of the existence of ice ages to a single contracted ice age with multiple surges. This second position mentioned in The Genesis Flood (Whitcomb and Morris, 1961) and modified by Oard (Oard, 1979) relies on a warm ocean in the wake of a global flood. The warm ocean provides a ready source of water vapor, which can be deposited over cold polar land masses as snow. Since a warm ocean prevents land masses from cooling sufficiently to accumulate snow, it is necessary to propose a cooling mechanism to offset the heat flux from the ocean. The most likely mechanism is reflection of sunlight by high concentrations of volcanic aerosols in the atmosphere. Two validity studies of this scenario were performed by Spelman and Vardiman. Spelman looked at the sensitivity of atmospheric parameters to different sea surface temperature distributions (Spelman, 1996) and Vardiman studied the enhancement of precipitation due to hot mid-ocean ridges (Vardiman, 1998). Over the past decade no additional simulations have been published using this scenario. Simulation of climate has progressed significantly over the past ten years and a number of models are available to study the validity of a rapidly developing ice age due to warm oceans. Current climate models not only simulate the circulation of the atmosphere, but also the circulation of the ocean, build up of sea ice and response of land surfaces. Two models from the Goddard Institute of Space Studies (GISS) are used for this study. GISS Model II (Hansen, 1983) simulates the atmosphere at a resolution comparable to the studies done by Spelman and Vardiman. This earlier model can also be run efficiently on a desktop computer in order to explore a number of preliminary scenarios. The GISS Model E (Schmidt, 2006) is designed to be more flexible and makes it easier to use different ocean models and aerosol parameterizations. To limit the scope of this study, only the heat flux from the ocean surface and between the ocean mixed layer and deep ocean is studied. The mixed layer includes the first 50 - 100 meters of the ocean’s surface. It varies with latitude and season and is mixed by thermal gradients and wind-shear. The deep ocean interacts weakly with the mixed layer due to stability of the lower ocean beginning at the thermocline. Regions of sinking and upwelling through the mixed layer do exist due to the thermohaline circulation and interaction with continental boundaries; however, in modern day oceans this interaction has a minimal effect on climate variability over the time period of centuries. If the deep ocean was warmer in the recent past, then there would be an enhanced vertical circulation over the full depth of the water column. If the full depth of the ocean were treated as a mixed layer, the thermal adjustment timescale would be 40 years (Marshall, 2008). Model II and Model E are used to calculate the heat flux entering the mixed layer from the deep ocean. By comparing current ocean heat fluxes with that of a warm deep ocean it is possible to verify the cooling rate of the deep ocean and to infer an enhanced interaction between the deep ocean and the mixed layer. This enhanced interaction not only includes heat transport, but also nutrient transport, which may have implications for the ocean biome

Initial Conditions for a Post-Flood Rapid Ice Age

In the early years of the modern creationist movement questions were raised as to the role of ice ages in explaining geological data. Beginning with Whitcomb and Morris (1961) and formalized by Oard (1979), a proposed scenario of warm oceans and volcanic activity would provide the needed conditions to initiate a post-flood ice age. During the 1990’s Vardiman used the Community Climate Model (CCM) to study the impact of warm oceans on global air circulation and precipitation patterns. Following Vardiman’s lead this study uses the Goddard Institute of Space Studies (GISS) Model E climate model. The first part of the study uses a fixed 30 ºC sea surface temperature to validate against work done by Spelman (1996). The second part of the study incorporates a dynamic ocean as well as increased volcanic aerosol levels to determine the initial conditions needed to provide snowfall rates of significant intensity to initiate accumulation for an ice age. Given initial sea surface temperatures of 30 ºC, extensive volcanic activity is needed to offset the heat flux provided by warm oceans. The Model E simulations had run times of six years and did not achieve the conditions needed for extensive snowfall at high latitudes. Using a dynamic ocean and volcanic aerosol optical depths of 2.00 give promise of sufficient cooling if the simulation were to extend to several decades. Given the limited run times, these simulations can only provide information about the sensitivity of the climate model and the thermodynamic balance over a limited time scale. Future work using century long runs will provide more conclusive results about the validity of the initial conditions proposed here. Extended runs will also provide valuable information about climate shifts as well as changes in circulation patterns within the ocean, which can then be compared to geological strata associated with the Pleistocene

Modeling Biochemical Processes as Designed Systems

Being in the post-genomic era, there is a need for new methodologies from an interdisciplinary perspective, which can complement current genomics research. Bioinformatics and systems biology are rapidly growing research areas that are meeting this need. Operating with the assumption that there is design with a purpose, creationists provide a unique perspective for discovering order in the complexity of genes, regulatory networks, and biochemical reactions. Since the genome acts as an information storage system, it seems reasonable to apply design concepts, originating from computer and network programming, to make sense of genomic information. One such concept is that of design patterns, which has been formalized by programmers and analysts working with object-oriented programming (OOP). Several patterns are introduced and related to biochemical systems in the cell. A more detailed analysis of the observer pattern is made in the context of galactose metabolism in Saccharomyces cerevisiae. Since design patterns embody good OOP practice and do not specify a specific implementation, it is possible to explore a variety of implementations that can achieve regulation of galactose metabolism. This methodology can complement current research approaches by clarifying what is meant by system homology at the biochemical level

Modeling Biochemical Processes as Designed Systems

Being in the post-genomic era, there is a need for new methodologies from an interdisciplinary perspective, which can complement current genomics research. Bioinformatics and systems biology are rapidly growing research areas that are meeting this need. Operating with the assumption that there is design with a purpose, creationists provide a unique perspective for discovering order in the complexity of genes, regulatory networks, and biochemical reactions. Since the genome acts as an information storage system, it seems reasonable to apply design concepts, originating from computer and network programming, to make sense of genomic information. One such concept is that of design patterns, which has been formalized by programmers and analysts working with object-oriented programming (OOP). Several patterns are introduced and related to biochemical systems in the cell. A more detailed analysis of the observer pattern is made in the context of galactose metabolism in Saccharomyces cerevisiae. Since design patterns embody good OOP practice and do not specify a specific implementation, it is possible to explore a variety of implementations that can achieve regulation of galactose metabolism. This methodology can complement current research approaches by clarifying what is meant by system homology at the biochemical level