Alternative models to the theory of universal common descent have, thus far, been underdeveloped. Our previous work introduced a dependency graph model as an alternative way of explaining the patterns of genetic similarity and diversity among living things. According to this model, different forms of life share similarities because they share function-specific genetic features (modules) that may have dependencies on other genetic features. Here, we introduce a tool ( AminoGraph ) that infers dependency graphs from protein sequence alignments
The vital information carried in the DNA of every organism must be protected from the mutagenic processes that tend to degrade it. Molecular systems that detect and correct chemical alterations and base-pair mismatches form the first line of defense in all kingdoms of life. Natural selection provides a second line of defense. Specifically, purifying selection (or negative selection) is the natural tendency in wild populations for the genetic lines of individuals that suffer impairment from a new mutation to terminate within a few generations of the mutation event. Purifying selection is known to be much more efficient than positive selection, though it becomes less efficient in very small populations. Here, we describe a long-term evolution experiment that tracks fitness in a population of 1,000 computational organisms. We use the previously described Stylus artificial-world model, in which genes encode drawings that have scorable functionality based on the degree to which they resemble one of the Chinese written characters. In our weakest-link minimal-genome model, the fitness of the organism is proportional to the lowest score of its 223 essential genes. Following a population of 1,000 model organisms through 2,000,000 fixation events, we find that fitness declines approximately as a two-phase exponential decay. The long-term result is substantial loss of function for all 223 genes, seen both in a collapse of numerical scores and in loss of legibility. The cause of the collapse is an imbalance in the initial genome: the number of ways for mutations to produce a new worst gene is so much higher than the number of ways to improve the current worst that selection is unable to prevent decline. This result raises the question of genome decay in real organisms. It seems likely that the same imbalance exists there, though life may have ways of averting the decline we describe here.
To perform agile bipedal movement, human feet must meet extremely demanding requirements in terms of compactness, flexibility, strength, joint movements, actuation, and control. These requirements are met through very sophisticated engineering solutions. This paper describes four highly specialised mechanical features of the ankle-foot complex that show a very high degree of complexity and fine-tuning: i) a
Viscosity is inversely related to temperature. The circulatory system of Antarctic icefish may have been designed to prevent high blood viscosity at low temperatures by taking advantage of the increased solubility of oxygen at low temperatures, allowing use of hemoglobin-free blood. This necessitates a high-output, high-velocity, low-pressure, low-resistance circulation. High-velocity flow requires adequate viscosity to minimize loss of laminar flow and increased friction. This creates an interesting design problem: in other animals, hemoglobin determines blood viscosity via the hematocrit, whereas in icefish, blood viscosity is produced largely by antifreeze glycoproteins. The effect of inappropriate blood viscosity on maximal cardiac output is seen in experiments with a related fish, Pagothenia borchgrevinki . In this species, acclimation to a particular temperature involves tailoring blood viscosity to cardiac power, which varies with the availability of oxygen and temperature. The factorial scope for cardiac output—i.e., the ratio of maximal to basal cardiac output—is greater in acclimated than unacclimated fish despite the similar availability of oxygen. Experiments also suggest that blood viscosity determines the maximum tolerable temperature in Antarctic fish. Those experiments demonstrate that blood viscosity is actively controlled. It is part of what the physiologist Claude Bernard called the milieu intérieur . The hemoglobinless phenotype requires simultaneous customization of the heart, vasculature, and blood, including its viscosity
It is well known that the embryonic development of vertebrates from different classes (e.g., fish, reptiles, mammals) pass through a “phylotypic stage” when they look similar, and this apparent homology is widely seen as evidence of their common ancestry. However, despite their morphological similarities, and contrary to evolutionary expectations, the phylotypic stages of different vertebrate classes arise in radically diverse ways. This diversity clearly counters the superficial appearance of homology of the phylotypic stage, and the plain inference is that vertebrates have not evolved from a common vertebrate ancestor. The diversity extends through all stages of early development—including cleavage and formation of the blastula, gastrulation, neurulation, and formation of the gut and extraembryonic membranes. This paper focuses on gastrulation, during which the germ layers originate and the vertebrate body-plan begins to form. Despite its key role in embryonic development, gastrulation occurs in fundamentally different ways in different classes of vertebrates. The inference against common ancestry becomes progressively stronger as more is discovered about the genetic and molecular mechanisms that implement development. It is increasingly evident that these are of such complexity that it is unrealistic to think that undirected variations (random mutations) could produce constructive changes to development, such as those required to account for a diversification of development from that of a common ancestor, especially while retaining a similar phylotypic stage.
This paper, the second of three, takes a systems biology view of the bacterial flagellum. The flagellum is the organelle imparting motility to common bacteria. The first paper was a constructive or top-down view from a systems engineering viewpoint: “An Engineering Perspective on the Bacterial Flagellum, Part 1 – Constructive View”. It detailed the typical environment, the purpose, the required existing and new resources, the necessary functional requirements, various constraints, the control means, and the self-assembly of any kind of bacterial motility organelle. The specification of these requirements was intended to be independent from knowledge about the actual flagellum. A converse approach is detailed in this Part 2. It is an analytical , reductionist , or bottom-up view , which discusses the known 40+ protein components and the observed and inferred structure, control, and assembly of a typical bacterial flagellum. This cellular subsystem is well-researched. Much of that research is reviewed herein. However, the assembly orchestration is illustrated in a form and detail not found elsewhere. Part 3 will compare the two views and will conclude with original observations. Those include an ontology of the exceedingly specific protein binding relationships in the flagellum. The latter observation is new and significant.
This study examines the bacterial flagellum from an engineering viewpoint. This examination concentrates on the structure, proteins, control, and assembly of a typical flagellum, which is the organelle imparting motility to common bacteria. Two very different, independent approaches are applied and then compared in three separate papers: Parts 1, 2, and 3. The first approach is a constructive or top-down approach, covered in this Part 1. It considers the purpose of a bacterial motility system, its typical environment, new and existing required resources, and its physiology. It sets forth the logically necessary functional requirements, constraints, assembly, and relationships. The functionality includes a motility control subsystem and provision for self-assembly. The specification of these requirements is intended to be independent from knowledge of the flagellar structures. This is original material not covered in academic papers on the flagellum. Part 2 will cover the second approach, an analytical or bottom-up approach. It will document the known 40+ protein components and the structure, assembly, and control of a typical flagellum. The bacterial flagellum is a well-researched molecular subsystem. However, in Part 2 the assembly relationships will be illustrated graphically in a form and detail not found in previous literature. Part 3 will compare the two approaches and conclude with several original observations. Those include the coherent assembly orchestration and an ontology of the exceedingly specific protein-binding properties. The latter observation is significant, and it suggests future modeling to elucidate how the strong, coherent, multi-way protein binding is achieved at the molecular level.
The flagellum is the organelle imparting motility to common bacteria. This paper, the third of three, takes a systems engineering and systems biology perspective on the bacterial flagellum. The first paper (Part 1 of the series) provided a constructive or top-down view from a systems engineering viewpoint. It detailed the typical environment, the purpose, the required existing and new resources, the necessary functional requirements, the various constraints, the control means, and the self-assembly for any kind of bacterial motility organelle. The specification of these requirements was intended to be independent of knowledge about the actual flagellum. A converse approach was detailed in the second paper (Part 2 of the series). It was an analytical or bottom-up view, which discussed the known 40+ protein components and the observed and inferred structure, control, and assembly of a typical bacterial flagellum. This cellular subsystem is well researched. Much of that research was reviewed in Part 2 from a systems biology viewpoint, including the chemotaxis feedback control system. Part 2 included a very detailed dependency graph of the orchestrated assembly not found elsewhere. This third paper (Part 3) concludes the three-part study with original observations. The observations include an ontology of the exceedingly specific protein binding relationships in the flagellum. The latter observation is new and significant and suggests research to further elaborate the details of the molecular configurations of the proteins. Part 3 also compares the independent constructive and analytical views, which correlate well. Finally, it is suggested that a motility organelle of this scope and scale seems profoundly unlikely to naturally evolve in the absence of foresight and mindful intent.
In the context of population genetics, active information can be extended to measure the change of information of a given event (e.g., fixation of an allele) from a neutral model in which only genetic drift is taken into account to a non-neutral model that includes other sources of frequency variation (e.g., selection and mutation). In this paper we illustrate active information in population genetics through the Wright-Fisher model.
In the last three decades, several measures of complexity have been proposed. Up to this point, most of such measures have only been developed for finite spaces. In these scenarios the baseline distribution is uniform. This makes sense because, among other things, the uniform distribution is the measure of maximum entropy over the relevant space. Active information traditionally assumes a finite interval universe of discourse but can be extended to other cases where maximum entropy is defined. Illustrating this is the purpose of this paper. Disequilibrium from maximum entropy, measured as active information, can be evaluated from baselines with unbounded support.
In computer search optimization theory, active information is a measurement of a search algorithm’s internal information as it relates to its problem space. While it has been previously applied to evolutionary search algorithms on computers, it has not been applied yet to biological systems. Active information can be very useful in differentiating between mutational adaptations which are based on internally-coded information and those which are the results of happenstance. However, biological systems present many practical problems regarding measuring active information which are not present in digital systems. This paper describes active information, how it can be used in biology, and how some of these problems can be overcome in specific cases.
