Part One is focused on how the technique of quasar absorption lines was discovered, how it revolutionized the field of astronomy, and how it has developed into a powerful scientific tool. 

In Chapter 1, we describe the exciting era of the discovery of quasars and how, as cosmologically distant luminous sources, their study has developed into a powerful tool that changed the course of the science of astronomy. This story runs in parallel with technological advances in both light gathering capability and computing power. It is through quasar absorption lines that we are able to study the properties of diffuse gas across the full dynamic range of astrophysical environment out to the highest redshifts.

In Chapter 2, we describe the modern framework and context in which absorption lines are studied. This includes a brief background on the evolutionary stages of the Universe. 

We also describe why certain ions, transitions, and absorption lines are the most commonly studied and what their cosmic visibility is– meaning, what the relationship between the observed redshifted lines is and the cosmic time and era that is probed by them. Finally, we provide a brief overview of the gas phases in the Universe, including the ionization conditions (which are discussed in much more detail in Part Six).

In Chapter 3, we describe various experimental approaches to studying the Universe through the technique of quasar absorption lines, including rudimentary tomography and the use of Gamma-ray bursts. This chapter includes some discussion on the challenges of studying both 1D “core samples” of the Universe as a function of cosmic time and random “pencil beams” probes through individual galaxy halos. We also present an annotated list of “key quantities” measured in absorption line surveys that are used to quantitatively characterize absorbing gas in the Universe.

Part Two is focused on the observations of intervening absorbers. As we learned in Part One, intervening absorbers are those that are cosmologically distributed between the background quasar and Earth; they arise in gas that is not gravitationally or dynamically associated with the quasar environment. We also learned that absorber classes, i.e., DLAs, Mg II, C IV, and O VI absorbers (to name a few), were developed for historical reasons. By arbitrarily segregating absorption into these classes, it does create a false sense that these populations are indeed separate entities when in fact they arise in overlapping astrophysical environments; however, we will adopt the classifications for organizational purposes. And indeed, there is utility in knowing the statistical characteristics of each absorber population.  While describing the observations and growth of astrophysical knowledge, we will attempt to provide historical context. The material necessarily is developed only up to the publication date. Nonetheless, it is hoped that Part Two will provide a useful foundation on which the next generation of researchers might build on the great work of their predecessors. 

In Chapter 4, we focus on Hi absorbers, including the Ly α forest, Lyman-limit systems (LLSs), and damped Lyman-α (DLA) systems. We also cover the Epoch of H I Reionization (EoR). 

Deuterium is an abundant isotope of hydrogen that is deeply informative about Big Bang Nucleosynthesis; we cover the fascinating history and science of deuterium in Chapter 5.  

The 21-cm line due to hyperfine structure in H I informs us about the “cold” phase of hydrogen in the Universe and this is covered in Chapter 6. Next, in Chapter 7, we discuss He II absorption in the Universe, including its power to probe the ultraviolet cosmic background and the Epoch of He II Reionization. 

Low-ionization metal-line absorbers are covered in Chapter 8, including Mg II, Ca II, Na I, O I, and C I absorbers. Intermediate-ionization absorbers are discussed in Chapter 9, including C IV, Si IV C III, and Si III absorbers. 

We then take a detour to discuss the Warm-Hot Intergalactic Medium (WHIM) in Chapter 10, which takes us to the X-ray band.  Finally, in Chapter 11, we cover the high-ionization absorbers such as O VI, NV, and Ne VIII.

Part Three is focused on the relationship between galaxies and their gas. The body of work for the topics covered is so large that it is not possible to represent all efforts or scientific programs. The relationships between galaxies and their gas is complex, and knowledge and theory continue to evolve rapidly. The observational experiments and subsequent results discussed throughout these chapters should first-and-foremost be viewed as examples of observational techniques and methods of inference. The hope is that what is presented serves as a fair representation of the efforts of a large and active community of researchers.

In Chapter 12, we begin by providing a brief history of the discovery of extended gaseous halos surrounding galaxies. We then cover the so-called “baryon cycle” and the basics of dark matter halos and the virial radius. We describe some fundamental theoretical insights and general trends of gaseous halos as a function of halo mass and conclude by discussing the concept of a composite spatial-kinematic model of the baryon cycle. In Chapter 13, we will describe the practical observational methods employed by observers to characterize the connection between “isolated” galaxies and their halo gas, or circumgalactic medium (CGM). 

In Chapter 14, we will summarize selected findings from these studies. We will then consider galaxies in the context of the modern paradigm of hierarchical structure growth in the context of grouped and clustered dark matter halos. The clustering of halos and a basic introduction to the observations and theory of gas in groups and clusters will be discussed in Chapter 15. In Chapter 16, we describe observational and theoretical quasar absorption line studies of group and cluster environments, including some discussion on the difficulties unique to examining the CGM of galaxies residing in these environments.

Finally, we reserve Chapter 17 to discuss the classification of the spectra of starbursts, AGN, and quasars, Chapter 18 to cover black hole accretion and the radiatively-drive winds and outflows of AGN/quasars, and Chapter 19 to describe broad absorption lines (BALs) and narrow absorption lines (NALs) as seen in down-the-barrel associated absorption, as well as what transverse quasar-probing-quasar experiments have revealed about quasar CGM.