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This self-contained textbook covers fundamental aspects of sequence analysis with special emphasis on evolutionary biology, including sequence alignment, exact matching, phylogeny reconstruction, and coalescent simulation. It addresses these topics through a series of over 800 computer problems, ranging from elementary to research level, to enable learning by doing. Students solve the problems in the same computational environment used for decades in science – the Unix command line. This is available on all four major operating systems for PCs: Windows, macOS, chromeOS, and Linux. To learn using this powerful system, students analyze sample sequence data by applying generic tools, bioinformatics software, and over 50 programs specifically written for this course and available via GitHub. The solutions for all problems are included, making the book ideal for self-study. Problems are grouped into sections headed by an introduction and a list of new terms. By using practical computing to explore sequence data in an evolutionary context, the book enables readers to tackle their own computational problems.

Bioinformatics. --- Evolution (Biology)

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"Many fields of science and engineering have come against the problem of complex design. This occurs when the details become so numerous that computer power alone cannot make progress. For neural networks (aka deep learning), this is known as the NP-completeness problem whereby the amount of computation needed to compute network weights grows in a non-polynomial (i.e. exponential) way as the number of weights increases. For systems biology, it happens when there are too many cell-model parameters to allow for successful estimation. For many engineering fields, it happens when the designs become so complex that integrated testing cannot eliminate faults. Nature solved this complex-design problem using evolution. But exactly how it solved it has been a mystery. Both laboratory experiments and computer-simulation attempts eventually stopped evolving. Something more than Darwin's ideas of heredity, variation, and selection was needed. The solution is that there is a fourth element to evolution and that is ecological change. What happens is that a new variation that is selected can change the ecology and the new ecology can create new opportunities for even more new variations to be selected. By this endless cycle, complexity can grow automatically. This book uses the physics of resource flow to describe in detail how that happens and that knowledge can be used to help overcome the problem of complex design. This book is a monograph that can be used as a textbook on how physics plays a strong role in evolution. The key starting ideas are the flow of energy-and-matter resources, organisms making copies of themselves, and ecological change. From these ideas, quantitative models are developed for many evolutionary processes. Such models include that for selection, multicellularity, coevolution, sexual reproduction, and the Serengeti Rules. Numerous examples of biological phenomena are shown to be in conceptual agreement with the models. In the end, the physics shows how complex design can arise automatically"-- Provided by publisher.

Evolution (Biology) --- Variation (Biology)

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A journey guided by science that explores the universe, the earth, and the story of life For Irwin Shapiro, science starts with questions. This book provides a broad and entertaining survey of major scientific discoveries that have changed our views of nature and, in turn, spawned further questions. Shapiro, an award-winning scientist and beloved teacher, separates his inquiry into three parts: looking up at the universe; looking down at the earth and its fossils; and looking in at the story of life. His framework encourages readers to view science as a detective story-to observe and question nature and natural phenomena, and to base all conclusions on scientific evidence. With his knowledgeable yet conversational approach, Shapiro offers an enjoyable way for the curious to learn about the foundations of a range of scientific topics: the motions of bodies in the cosmos, the history and structure of the earth, the evolution of organisms, and the search for extraterrestrial life and intelligence.

Cosmology. --- Evolution (Biology) --- Earth (Planet)

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A definitive and richly illustrated guide to the botanically unique area of Upper Teesdale in England’s County DurhamTo anyone who loves the wild flowers of Great Britain and Ireland, there are some places that beckon time and again, such as The Lizard in Cornwall, The Burren in Ireland’s County Clare and Ben Lawers in Perthshire, Scotland. Upper Teesdale in England’s County Durham must, however, be included among these jewels of our botanical heritage. This locality, which is within sight of the highest point of the Pennines, has an outstanding and special flora that has been shaped by its altitude, land-use patterns and diverse geology. Many of the plants found here are rare and localized, while others are more common and widespread, but together they form the botanically unique “Teesdale Assemblage.” For this reason, Upper Teesdale is a hotspot for botanists. It is also a scenically beautiful area, located within easy reach of the industrial heartlands of the north-east, and is much visited by walkers and tourists. This book offers visitors unique insights about this area and its botanical riches.Presents the first account to cover together the places, plants and people of this special areaFeatures more than 330 stunning photographsIncludes detailed profiles of 96 plants that make up the “Teesdale Assemblage”Offers a history of Teesdale’s botanical exploration and describes the people who live, work and study plants there todayProvides an overview of environmental threats and what is required to ensure a sustainable future

Plants --- Plant evolution --- Evolution (Biology) --- Evolution. --- Phylogeny

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"Merging recent evolutionary thought, theories of information and signs, and new findings in animal studies, Gary Tomlinson's The Machines of Evolution and the Scope of Meaning offers a groundbreaking account of meaning in our world"--

Meaning (Philosophy) --- Knowledge, Theory of --- Evolution (Biology)