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Evolutionary Biology


Life on Earth is astonishingly complex. There are tens of millions of living species, or kinds of organisms. Some endangered species have just a few individual organisms, while others have quadrillions. Every individual organism is, all by itself, an extremely complicated object, with many interacting parts. Further, organisms interact with other organisms, of the same species and of other species, to form an inconceivably complex network of causes and effects.

Evolutionary biology studies the origin and methods of this complexity. Evolutionary biologists try to answer questions like: Why are there so many species, and how did they come to be? What are the relationships between species and how did these relationships arise? How did organisms develop their intricate structures and ways of life? Why do species become extinct? How did life originate in the first place?

In the last two hundred years, great advances have been made in answering many of these questions. An overarching theory, the theory of evolution by modification and natural selection, first expounded by Charles Darwin in the 1850's, has been very successful at explaining the origin of life's complexity in general, although many puzzling questions remain unanswered.

This book will present our current understanding of how life on Earth got the way it is, and describe current research directions in this profound and fascinating field.

Introduction to the History of Life

It is very interesting that life began from simple chemical molecules. Starting from the formation of the universe from simple elements such as hydrogen and helium 13.7 billion years ago, until now, with Homo sapiens evolving and trying to expand its colony to a new planet, there is one great history of life. To understand those sequences in chronological order, it is important to understand the geologic time scale. There are two ways to represent geologic time: relative time, which deals with divisions and subdivisions of the Earth's geology in a specific order based on relative age relationships, and absolute time, which is usually obtained from radiometric dating methods performed on igneous rocks, such as volcanic ash layers or lava flows, to determine numerical ages. Chemical Origins of Life The study of evolution is incomplete without first a consideration for the origin of life itself. Any theory of biology would be incomplete without a finite and irreducible origin. Life emerging from non-life, or "abiogenesis" is a tricky subject to study because scientists are typically divided as to what precisely constitutes "life." In its simplest possible form, life consists only of simple replicating chemical structures, such as amino acids and short RNA chains. These simple molecules are typically not what people think of when talking about "life", although it does serve as a convenient starting point to further studies of evolution. The atmosphere of earth was significantly different before the advent of living organisms. Without plants and a replicable process of photosynthesis, the atmosphere was almost completely devoid of oxygen. Nitrogen and Carbon rich compounds, such as ammonia and methane, were far more common in the environment then they are now. Combined with excess geothermal heat and lightning, it is hypothesized that genetic building blocks could have formed from these chemicals. Miller-Urey Experiment Wächtershäuser's Hypothesis Chemist Gunter Wächtershäuser put forth a similar hypothesis to Miller and Urey, except that instead of external energy sources of electric arcs and UV radiation, energy required by organic molecule synthesis could have come from redox reactions involving sulfides of Iron. This theory is consistent with the idea that life may have originated near hydrothermal vents in the ocean floor. While Wächtershäuser's experiments did succeed in producing simple and more complicated amino acids, those acid chains were noted to hydrolyze quickly in the surrounding chemical environment. Martin and Russell Based off the Wächtershäuser hypothesis, William Martin and Michael Russell proposed that life could have had hydrothermal origins and microstructural origins. Ocean floor structures known as "black smokers", which provide essentially a mostly-enclosed microcavern filled with iron sulfides would provide both the geothermal energy necessary by Wächtershäuser's hypothesis, but also the security necessary to prevent the amino acid chains from hydrolyzing. In such a black smoker, it is theoretically possible for the various components of life: DNA and RNA chains, protein synthesis, and enzyme interaction could have all formed simultaneously, without having first to develop a lipid cell membrane. The eventual synthesis of a lipid membrane, possibly as a lipid coating of the inside of the black smoker, would have enabled the new protocell to leave the black smoker and travel the ocean independently. It is interesting to note that Archaea, simple single-cell organisms, can be found to live in black smokers. Some recently-discovered forms of bacteria have been found that utilize the faint light of the black smokers for photosynthesis, the first recorded case of photosynthesis occurring without sunlight. "Gene First" and "Metabolism First" There are two competing theories of thought as to the origin of life. The first theory, "Genes First" hypothesizes that self-replicating molecules such as RNA were created from simple amino acids, and later evolved into more complex replicating systems. DNA is not usually considered a candidate, since its replication and formation require the use of complex protein structures to facilitate those tasks, proteins which are unlikely to be produced through non-biological means. This theory suffers from the fact that RNA and similar amino acid structures are sensitive to UV radiation, and they are also prone to hydrolyzing. In essence, a bare RNA chain would have a difficulty surviving both in and out of the ocean. In contrast to the "Genes First" theory, the "Metabolism First" theory speculates that enclosed environments with metabolic pathways existed first, and later served as a secure enclosed location for the synthesis of Amino acid chains. Alexander Oparin hypothesized that primitive chemical structures could have been self-replicating without the need for RNA or other amino acid chains. Some support for this theory stem from the fact that the Acetyl-CoA metabolic pathway utilizes Iron-Nickel-Sulfur compounds (key to Wächtershäuser's hypothesis) and catalyzes key components in a single, simple step. A commonality between these two approaches is seen with a simple analogy. Consider a completed grocery list. The list, analogous to genetic material, conveys a description of the contents of a bag of groceries. The bag itself, however, contains the same vital information, by virtue of its contents. Whereas the list contains the information in a coded fashion, the full bag itself contains the exact same information in physical form. The "metabolism first" theory proposes that this "full bag" scenario is in fact simpler than requiring genetic information prior to the production and assembly of proteins. To further explain the "Metabolism First" theory, it helps to simplify what is meant by metabolism. In the simplest explanation, metabolism is the utilization of energy to construct more complex materials from simpler components. In the "metabolism first" theory, a boundary between the outside environment and the interior of the system is required. The abiosythesis of lipid bilayers similar to those found in the cell membrane of all living cells has been produced in the laboratory, though any physical means of separating the system from the environment at large would suffice. There must also be a source of energy to drive the reaction. This, according to many adherents, would be facilitated by what are known in chemistry as "redox" (an abbreviation of reduction/oxidation) reactions. When one chemical gains electrons, it is said to be reduced, the chemical losing electrons is said to be oxidized. Redox reactions occur in many current biological processes. It is responsible for the transfer of electrons in the light dependent phase of photosynthesis in photosynthetic bacteria and all chloroplast bearing eukaryotes, and the absorption of oxygen in our hemoglobin. However, any source of energy could be a candidate for the earliest forms of energy consumption, including pH differentials, sharp temperature gradients, even radioactivity. Along with energy utilization, some mechanism of coupling must have existed in order to use the energy to drive further chemical reactions. Catalysts are chemicals that work as intermediaries between substrates and products. Consider hydrogen peroxide. Hydrogen peroxide will break down into water and oxygen gas when mixed with a catalyst. The catalyst itself is not consumed in the reaction, but is able to continue functioning after the reaction has taken place. Depending on the substrate, any number of naturally occurring minerals and chemicals can act as catalysts. Catalysts serve to speed up chemical reactions. Hydrogen peroxide will spontaneously degrade into water and molecular oxygen, however, the presence of a catalyst speeds up this reaction to the point that it has been used a fuel source for torpedoes and even spacecraft. With energy extracted from the environment, suitable substrates and a catalyst to speed up the reaction, energy storing intermediate materials could have been produced. These materials could later release their stored chemical energy to facilitate further reactions. Some form of cyclic reaction is established in the "metabolism first" scenario. Consider an organic substrate A. When A is catalyzed and energy is introduced, a new chemical B is produced. B can now be used to carry out further chemical reactions, utilized by C, D, and so forth. In the end, B is reconverted to A, closing the cycle. Cyclic reactions are favorable in this scenario, since the replenishment of A does not require the further extraction of the material from the environment. This ensures that the system will be able to continue to exist even if A becomes scarce in the environment. The increased complexity of a cyclic system also allows for adaptation within the system. If one of the further pathways (C, D, etc.) is adversely affected by environmental conditions, different pathways can be included or take the place of the non-functioning portion. Finally, the system must have some means of growing and reproducing in order to be considered life. To grow, the system must gain materials faster than it loses it, either by diffusion into the surrounding environment, or through some other means, such as precipitation of waste materials. Reproduction can be achieved as an accidental process. Consider a "compartment" of some kind, like a bubble of wax in a Lava Lamp. Within the bubble, the network of pathways extracts energy from the environment, creates some system of reactions that produce more materials for the chemical pathways. The bubble expands with the increase of its contents. Environmental conditions such as current or temperature gradients cause the bubble to pinch off, creating two bubbles containing similar concentrations of materials. If the concentrations are adequate, two separate networks have been formed. These two networks can continue to grow and split off into further networks, allowing them to compete for resources in the environment. This competition for resources is the beginnings of Darwinian evolution. At some point in their evolution, these chemical networks must have made the leap from a content-based information storage to a coded form. As the networks grew in complexity, it would be more favorable to have some means of imprinting the necessary contents. A transferable coded form of information would allow a greater chance of sustainable systems to result from division of the parent system. Mesozoic Era (245 million years ago) The time period between 245 million years ago and 65 million years ago is called Mesozoic Era. Mesozoic Era is mostly known for many dinosaurs, which evolved in the Triassic and became very diverse in Jurassic Period. This Mesozoic Era lasted for about 180 million years and it is some times called the age of reptiles. Similar to the Paleozoic extinction, at the end of Mesozoic Era, dinosaurs became extinct. In this period, there were many changes to the terrestrial vegetation. For example, gymnosperms, such as conifers, were evolved in this Era and the earliest angiosperms were also diversifying in this Era. During Triassic Period, the first dinosaurs appeared. At this time, molluscs were the dominating invertebrates. In the Jurassic Period, many dinosaurs evolved and thrived. The first birds also evolved in this Period, of which the fossil Archaeopteryx is seen as an early example. For plants, the first flowering plant or angiosperms evolved together with gymnosperms. The Mesozoic Era ended with a large extinction of the dinosaurs. Mammalian creatures prospered after this. Cenozoic Era (65 million years ago until now) Compared to the other Eras that lasted for hundreds of million years, the Cenozoic Era spans only for about 65 million years. This era is divided into two major Periods; the Tertiary(now referred to as the Paleogene and Neogene) and Quaternary Periods. The Tertiary Period was when major radiation of mammals and birds occurred. Insects also predominated this Era. Similarly to the Mesozoic Era, angiosperms diversified. Around 35 million years ago, the first primate groups appeared. The first human-like apes appeared around 5 million years ago. The Ice Age marks the end of the Tertiary period and the beginning of the Quaternary period. As temperatures rose, extinctions were common. The Quaternary period is also known for evolution of Homo sapiens.
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