Complexity Explorer Santa Few Institute

Origins of Life (Summer 2022)

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Unit 1 – Introduction

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1.1 Welcome to the Course

1.2 Life

            Easy or Hard?

                        References: Selection and the origin of cells (Baum 2015)

                        Potentially biogenic carbon preserved in 4.1 billion-year-old zircon (Bell et al. 2015)

                        On the origin of biochemistry at an alkaline hydrothermal vent (Martin & Russell 2007)

                        Before enzymes and templates: theory of surface metabolism (Wächtershäuser 1988)

            What is the meaning of ‘life’?

                        References: Selection and the origin of cells (Baum 2015)

                        Foreword: Origins of Life: The central concepts (Joyce 1994; book)

                        The Origins of Life: A Review of Scientific Inquiry (Cleaves 2020; Templeton Foundation)

1.3 Constraining Chemical Complexity to Form Life

            Constraining Chemical Complexity to Form Life

                       Suggested Reading: Constrained Location Examples -

                       Hydrothermal Vents: On the origin of biochemistry at an alkaline hydrothermal vent (Martin & Russell 2007)

                       Atmosphere: Endogenous production, exogenous delivery and impact-shock synthesis of organic molecules: an

                       inventory for the origins of life (Chyba & Sagan 1992)

                       Organic compound synthesis on the primitive earth (Miller & Urey 1959)

                       Constrained Reactant Examples -

                       Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions (Powner et al. 2009)

                       The cradle chemistry of life: on the origin of natural products in a pyrite-pulled chemoautotrophic origin of life

                       (Wächtershäuser 1993)

                       Borate minerals and origin of the RNA world (Grew et al. 2011)

                       Constrained Energy Examples -

                       Serpentinization, carbon, and deep life (Schrenk et al. 2013)

                       Prebiotic chemistry and atmospheric warming of an early Earth by an active young Sun (Airapetian et al. 2016)

                       Radiolytic Synthesis of Cyanogen Chloride, Cyanamide, and Simple Sugar Precursors (Ruiqin et al. 2018)

                       Estimating the capacity for production of formamide by radioactive minerals on the prebiotic Earth (Adam et al. 2018)

1.4 Geological Conditions, Change, and Chaos

            Geological Conditions, Change, and Chaos

                       Suggested Reading: Growth, destruction, and preservation of Earth's continental crust (Spencer et al. 2017)

                       NASA Astrobiology Strategy Document (2015)

1.5 Pattern Formation in Chemical Systems

            Reaction Diffusion Systems

                       Simulation - The Gray-Scott System (Brockmann 2019)

1.6 The Central Dogma of Biology

            An Introduction

                       Supplemental Reading: Woese and Fox: Life, rearranged

            Efficiency of the Central Dogma

                       Supplemental Reading: The thermodynamic efficiency of computations made in cells across the range of life

                       (Kempes et al. 2017)

1.7 Biological Similarity

            Biological Similarity

                       Supplemental Reading: The Origin and Amplification of Biomolecular Chirality (Bonner 1991)

                       Lateral gene transfer as a support for the tree of life (Abby et al. 2012)

1.8 What is Life?

            Constraining the Definition of Life

                        References: What is Life (Schrödinger 1944)

            Weird Life

                        References: Life without a cell membrane: Challenging the specificity of bacterial endophytes within

                        Bryopsis (Hollants et al. 2011)

                        Life without a cell membrane: regeneration of protoplasts from disintegrated cells of the marine green alga

                        Bryopsis plumose (Kin et al. 2001)

                        Why Water? Toward More Exotic Habitats (2007)

                        Dynamics of Chemotactic Droplets in Salt Concentration Gradients (Cejková et al. 2014)

1.9 Earth's Early Atmosphere

           Earth's Early Atmosphere

                    References: Bolide impacts and the oxidation state of carbon in the Earth's early atmosphere (Kasting 1990)

                     Earth's early atmosphere (1993)

                     Atmospheric composition of Hadean-early Archean Earth: The importance of CO. (Kasting 2014)

                     How climate evolved on the terrestrial planets (Kasting et al. 1988)

                     A production of amino acids under possible primitive Earth conditions (Miller 1953)

                     Production of some organic compounds under possible primitive Earth conditions (Miller 1955)

                     The Origin of Life (Oparin 1938)

                     Geological history of seawater. An attempt to state the problem (Rubey 1951)

                     The onset and early evolution of life (Russell & Hall 2006)

                     Core formation and the oxidation state of the Earth (Wade & Wood 2005)

Unit 2 – Chemical Origins

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2.1 Unit 2 Introduction

2.2 What did Early Earth Look Like?

            Chemistry and Energy Sources

                        References: Origins of building blocks of life: a Review (Kitadai & Maruyama 2018)

                        Did life originate from a global chemical reactor? (Stüeken et al. 2013)

                        A Field Trip to the Archaean in Search of Darwin’s Warm Little Pond (Damer 2016)

                        Organic Compound Synthesis on a Primitive Earth (Miller & Urey 1959)

                        Astrophysical and Astrochemical Insights into the Origin of Life (Ehrenfreund et al. 2002)

                        Incubating life: Prebiotic sources of organics for the origin of life (Dalai et al. 2016) - Page 401

                        Comets as a Source of Prebiotic Organic Molecules for the Early Earth (Chyba & Sagan 1997)

            Early Earth Bombardment History

                        Suggested Reading: The Lunar Cataclysm: Reality or “Mythconception”? (Norman 2009)

                        Cataclysm no more: New views on the timing and delivery of lunar impactors (Zellner 2017)

                        Bashing holes in the tale of Earth’s troubled youth

                        Fossil Discoveries Challenge Ideas About Earth’s Start

                        References: Potentially biogenic carbon preserved in a 4.1 billion –year-old zircon (Bell et al. 2015)

                        Evidence for early life in Earth’s oldest hydrothermal vent precipitates (Dodd et el. 2017)

                        Earliest signs of life on land preserved in ca. 3.5 Ga hot spring deposits (Djokic et al. 2017)

                        The bombardment history of the Moon as recorded by 40Ar-39Ar chronology (Fernandes et al. 2013)

                        Origin of the cataclysmic Late Heavy Bombardment period of the terrestrial planets (Gomes et al. 2005)

                        Terrestrial and lunar flux of large meteorites in the last two billion years (Hartmann 1965)

                                   Early lunar cratering (Hartmann 1966)

                        The time-dependent intense bombardment of the primordial Earth/Moon system (Hartmann et al. 2000)

                        Spherule beds 3.47-3.24 billion years old in the Barberton Greenstone belt, South Africa: A record of the large

                                   meteorite impacts and their influences on early crustal and biological evolution (Lowe et al. 2003)

                        Impact frustration of the Origin of Life (Maher & Stevenson 1988)

                        Refining lunar impact chronology through high spatial resolution Ar40/Ar39 dating of impact melts

                                   (Mercer et al. 2015)

                        High resolution U-Pb ages of Ca-Phosphates in Apollo 14 breccias: Implications for the age of

                                   Imbrium impact (Merle et al. 2014)

                        A sawtooth-like timeline for the first billion years of lunar bombardment (Morbidelli et al. 2012)

                        Annihilation of ecosystems by large asteroid impacts on the early Earth (Sleep et al. 1989)

                        The Sculptured Hills of the Taurus Highlands: Implications for the relative age of Serenitatis, basin chronologies,

                                   and the cratering history of the Moon (Spudis et al. 2011)

                        Zircon Thermometer Reveals Minimum Melting Conditions on Earliest Earth (Watson & Harrison 2005)

                        Evidence from detrital zircons for the existence of continental crust and oceans on the Earth 4.4 Gyr ago

                                   (Wilde et al. 2001)

2.3 Likely Environments for Studying Origins of Life

            Likely Environments for Studying Extremophiles

                        Suggested Reading: Life’s Engines: How Microbes Made Earth Habitable (Falkowski)

                        Microbes From Hell (Forterre)

                        Life in the Universe (Bennett & Shostak)

                        References: Ecophysiology of “Halarsenatibacter silvermanii (Blum et al. 2009)

                        Turnstiles and bifurcators: the disequilibrium converting engines that put metabolism on the road

                                   (Branscomb & Russell 2013)

                        Astrobiology and the Possibility of Life on Earth and Elsewhere (Cottin et al. 2017)

                        The Astrobiology Primer (Domagal-Goldman et al. 2016)

                        Astrobiology: An Introduction (Longstaff 2015)

                        Earth as a Tool for Astrobiology – A European Perspective (Martins et al. 2017)

                        Living at the Extremes: Extremophiles and the Limits of Life in a Planetary context (Merino et al. 2019)

                        Bacterial growth at -15 C; molecular insights from the permafrost bacterium Planococcus halocryophilus

                                   (Mykytczuk et al. 2013)

                        Picrophilus oshimae and Picrophilus torridus; Two Species of Hyperacidophilic, Thermophilic, Heterotrophic,

                                   Aerobic Archaea (Schleper et al. 1996)

                        SIMS analyses of the oldest known assemblage of microfossils document their taxon-correlated carbon isotope

                                   compositions (Schopf et al. 2018)

                        Physiological and genomic features of highly alkaliphilic hydrogen-utilizing Betaproteobacteria from a

                                   continental serpentinizing site (Suzuki et al. 2014)

                        Cell proliferation at 122 C and isotopically heavy CH4 production by a hyperthermophilic methanogen

                                   under high-pressure cultivation (Takai et al. 2008)

            Cuatro Ciénegas Special Feature

                        References: Leptolyngbya CCM 4, a Cyanobacterium with Far-Red Photoacclimation from Cuatro

                                   Ciénegas Basin, Mexico (Gomez-Lojero et al. 2018)

                        The Lost World of Cuatro Ciénegas Basin, a Relictual Bacterial Niche in a Desert Oasis (Souza et al. 2018)

                        The Geographic Structure of Viruses in the Cuatro Ciénegas Basin, a Unique Oasis in the Northern Mexico,

                                   Reveals a Highly Diverse Population on a Small Geographic Scale (Taboada et al. 2018)

                        Variability of rRNA Operon Copy Number and Growth Rate Dynamics of Bacillus Isolated from an

                                   Extremely Oligotrophic Aquatic Ecosystem (Valdivia-Anistro et al. 2016)

2.4 Chemistry and The Origins of Life

            Chemistry and The Origins of Life

                        Suggested Reading: List of interstellar and circumstellar molecules


                        The 1953 Stanley L. Miller experiment: fifty years of prebiotic organic chemistry (Lazcano & Bada 2003)

2.5 Why Nature Chose Phosphates

            Why Nature Chose Phosphates

                        Suggested Reading: LibreTexts: Chapter 10: Phosphoryl transfer reactions

                        Remnants of an Ancient Metabolism without Phosphate

                        Phosphorus (P) and the Origins of Life

                        References: Why nature chose phosphates (Westheimer 1987)

                        Organic Chemistry with a Biological Emphasis Volume I (Soderberg 2016)

                        Remnants of an ancient metabolism without phosphate (Goldford et al. 2017)

                        Opening and closing the metabolite gate (Törnroth-Horsefield et al. 2008)

                        Are polyphosphates or phosphate esters prebiotic reagents? (Keefe & Miller 1995)

2.6 Why Water, Why Carbon

            Why Water, Why Carbon

                        Suggested Reading: Carl Sagan’s Cosmic Connection: an Extraterrestrial Perspective (Sagan 2000)

                        The limits of organic life in planetary systems (Baross 2006)

                        References: Abundance in Earth’s Crust (2007)

                        The search for life on other planets: Sulfur-based, silicon-based, ammonia-based life (Rampelotto 2010)

                        Many chemistries could be used to build living systems (Bains 2004)

2.7 Macromolecules

            Proteins and Lipids

                       Suggested Reading: The Grayness of the Origin of Life (Smith et al. 2021)

                       LibreText: Chapter 25.9: Proteins

                       LibreText: Chapter 14.2: Lipids and Triglycerides

            Nucleic Acids and Sugars

                       Suggested Reading: LibreText: Chapter 19.S: Nucleic Acids (Summary)

2.8 Chemical Cycles and Chaos

            An Introduction


                       Suggested Reading: Dynamics of the Brusselator (Ault & Holmgreen 2003)


Unit 3 – Chemical Commonalities


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3.1 Unit 3 Introduction

3.2 DNA as Information

            DNA as Information Part 1

                        References: Covalently modified DNA nucleobases

                        Bacteriophages of Bacillus subtilis (Hemphill & Whiteley 1975)

                        The RNA Modification Database

            DNA as Information Part 2

                        Suggested Reading: DNA Replication Fidelity (Kunkel 2004)

                        References: MutS/MutL crystal structure reveals that the MutS sliding clamp loads MutL onto DNA (Groothuizen et

                        al. 2015)

3.3 Water as a Driving Force for Organization

            Water as a Driving Force for Organization

                        Suggested Reading: All About Water

                        Water is an active matrix of life for cell and molecular biology (Ball 2017)

3.4 Kinetic vs. Thermodynamics – Assembly Constraints

            Kinetic vs. Thermodynamics – Assembly Constraints

                        Suggested Reading: How and why kinetics, thermodynamics, and chemistry induce the logic of biological evolution

                        (Pross & Pascal 2017)

                        Autocatalytic, bistable, oscillatory networks of biologically relevant organic reactions (Semenov 2016)

                        How can a chemical system act purposefully? Bridging between life and non-life (Pross 2008)

                        References: Comparing the energy landscapes for native folding and aggregation of PrP (Dee & Woodside 2016)

                        On the emergence of biological complexity: life as a kinetic state of matter (Pross 2005)

                        How can a chemical system act purposefully? Bridging between life and non-life (Pross 2008)

                        Autocatalytic, bistable, oscillatory networks of biologically relevant organic reactions (Semenov 2016)

                        How and why kinetics, thermodynamics, and chemistry induce the logic of biological evolution (Pross & Pascal 2017)

3.5 Chemical Configurations: Proteins and DNA

            Chemical Configurations: Proteins and DNA

                        References: Origin of organic molecules and biomolecular homochirality (Podlech 2001)

                        Large enantiomeric excesses in primitive meteorites and the diverse effects of water in cosmochemical evolution

                        (Pizzarello et al. 2012)

                        The origin of biologically coded amino acids (Cleaves 2010)

                        Permeation of Membranes by Ribose and Its Diastereomers (Wei & Pohorille 2009)

3.6 Early Metabolisms

            An Introduction

                        Suggested Reading: A survey of carbon fixation pathways through a quantitative lens (Bar-Even et al. 2011)

                        Alternative pathways of carbon dioxide fixation: insights into the early evolution of life? (Fuchs 2011)

                        The physiology and habitat of the last universal common ancestor (Weiss et al. 2016)


                        References: Metabolic Versatility in Methanogens (Costa & Leigh 2014)

                        Native iron reduces CO2 to intermediates and end-products of the acetyl-CoA pathway (Varma et al. 2018)

                        The Origin of Life in Alkaline Hydrothermal Vents (Sojo et al. 2016)

3.7 Energy Harvesting

            Diversity of Energy Harvesting Across Membranes

                        References: Essential Cell Biology

                        The organization of proton motive and non-proton motive redox loops in prokaryotic respiratory systems (Simon et

                        al. 2008)


3.8 Systematics and Limits of Metabolic Rates

            Systematics and Limits of Metabolic Rates

Unit 4 - Early Life

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4.1 Introduction

4.2 Protocells


                        References: The Role of Lipid Membranes in Life’s Origin (Deamer 2017)

                        Primitive Membrane Formation, Characteristics, and Roles in the Emergent Properties of a Protocell

                        (Maurer & Monnard 2011)

                        The Lipid World (Segre et al. 2001)

                        The Origin of Life in Alkaline Hydrothermal Vents (Sojo et al. 2016)

                        Programmable RNA-binding protein composed of repeats of a single modular unit (Adamala et al. 2016)

                        Current Ideas about Prebiological Compartmentalization (Monnard & Walde 2015)

                        Photochemically driven redox chemistry induces protocell membrane pearling and division (Zhu et al. 2012)

                        The emergence of competition between model protocells (Chen & Szostak 2004)

4.3 LUCA

            What Did LUCA Look Like

                        Suggested Reading: The nature of the last universal common ancestor (Penny & Poole 1999)

                        The physiology and habitat of the last universal common ancestor (Weiss et al. 2016)

                        Piecing together cell-like systems (Torino et al. 2013)

4.4 Chemical signatures for identifying life in the geological record       

            Chemical signatures for identifying life in the geologic record

                        Suggested Reading: Isotope Geology (Allégre 2008)

                        Principles of Stable Isotope Geochemistry (Sharp 2017)

                        References: Potentially biogenic carbon preserved in 4.1 billion-year-old zircon (Bell et al. 2015)

                        13C-Depleted Carbon Microparticles in >3700-Ma Sea-Floor Sedimentary Rocks from West

                        Greenland (Rosing 1999)

                        Evidence from fluid inclusions for microbial methanogenesis in the early Archaean era (Ueno et al. 2006)

                        Isotopic evidence for microbial sulphate reduction in the early Archaean era (Shen et al. 2001)

                        2-Methylhopanoids as biomarkers for cyanobacterial oxygenic photosynthesis (Summons et al. 1999)

                        Megascopic eukaryotic algae from the 2.1-billion-year-old negaunee iron-formation (Han & Runnegar 1992)

4.5 RNA

            The RNA World

                        Suggested Reading: The origins of the RNA world (Robertson & Joyce 2012)

                        Protocells and RNA Self-Replication (Joyce & Szostak 2018)

                        Searching for lost nucleotides of the pre-RNA World with a self-refining model of early Earth (Hud 2018)

                        Hachimoji DNA and RNA: A genetic system with eight building blocks (Hoshika et al. 2019)

            Molecular Evolution in the Lab

                        Suggested Reading: Forty years of in vitro evolution (Joyce 2007)

                        Selection and evolution of enzymes from a partially randomized non-catalytic scaffold (Seelig & Szostak 2007)

                        References: Ribozyme catalysis of metabolism in the RNA world (Chen et al. 2007)

                        Aptamers and the RNA world, past and present (Gold et al. 2012)

                        In vitro selection with artificial expanded genetic information systems (Sefah et al. 2014)

                        Synthetic genetic polymers capable of heredity and evolution (Pinheiro et al. 2012)

                        Structure and evolutionary analysis of a non-biological ATP-binding protein (Mansy et al. 2007)

                        Isolation of new ribozymes from a large pool of random sequences (Bartel & Szostak 1993)

                        Limits of neutral drift: Lessons from the in vitro evolution of two ribozymes (Petrie & Joyce 2014)

                        Mapping a systematic ribozyme fitness landscape reveals a frustrated evolutionary network for self-aminoacylating

                        RNA (Pressman et al. 2019)

4.6 Autocatalysis

            Autocatalytic Sets: A Cooperative Origin of Life

                        Suggested Reading: The origin of life: A selfish act or a cooperative effort? (Hordijk 2017)

                        Chasing the tail: The emergence of autocatalytic networks (Hordijk & Steel 2017)


                        References: Self replicating systems (Patzke & Kiedrowski 2007)

                        Spontaneous network formation among cooperative RNA replications (Vaidya et al. 2012)

                        Design of a directed molecular network (Ashkenasy et al. 2004)

                        The structure of autocatalytic sets: Evolvability, enablement, and emergence (Hordijk et al. 2012)

                        Autocatalytic sets in E. coli metabolism (Sousa et al. 2015)

            Reaction Networks and Autocatalysis

                        Suggested Reading: Generic strategies for chemical space exploration (Anderson et al. 2013)

                        Mechanosensitive self-replication driven by self-organization (Carnall et al. 2010)

                        Self-organization of matter and the evolution of biological macromolecules (Eigen 1971)

                        Symbiosis and the origin of life (King 1977)

                        Recycling, reproduction, and life’s origins (King 1982)

                        The evolution of replicators (Szathmáry 2000)

                        Evolution before genes (Vasas et al. 2012)

                        Compositional genomes: prebiotic information transfer in mutually catalytic noncovalent assemblies

                        (Segré et al. 2000)

                        Evolvable physical self-replicators (Virgo et al. 2012)

                        Complex autocatalysis in simple chemistries (Virgo et al. 2016)

                        A self-replicating hexadeoxynucleotide (Kiedrowski 1986)

4.7 Evolutionary Theory

            An Introduction

                        Suggested Reading: The Origins of Life (Maynard Smith & Szathmary 1999)

                        Evidence for de novo production of self-replicating and environmentally adapted RNA structures by bacteriophage

                        Qbeta replicase (Sumper & Luce 1975)

                        References: Prebiotic chemistry and the origin of RNA world (Orgel 2004)

                        Self organization of matter and the evolution of biological macromolecules (Eigen 1971)

                        Real ribozymes suggest a relaxed error threshold (Kun et al. 2005)

                        Experimental Evolution of Multicellular Complexity in Saccharomyces cerevisiae (Ratcliffe & Travisano 2014)

            A Recipe for Adaptation

                        References: Chemical Ecosystem Selection on Mineral Surfaces Reveals Long-Term Dynamics

                        Consistent with the Spontaneous Emergence of Mutual Catalysis (Vincent et al. 2019)

                        Selection and the origin of cells (Baum 2015)

                        The origin and early evolution of life in chemical composition space (Baum 2018)

                        The Intelligent Universe (Hoyle 1984)

                        Evolution of Cooperation on Spatial Network with Limited Resource (Wang & Wang 2015)

            Chance and Change

                        References: Molecular evolution over the mutational landscape (Gillespie 1984)

                        The NK model of rugged fitness landscapes and its application to maturation of the immune response (Kauffman

                        & Weinberger 1989)

                        The neutral theory of molecular evolution (Kimura 1983)

                        Origins of the coalescent: 1974-1982 (Kingman 2000)

                        The fixation probability of beneficial mutations (Patwa & Wahl 2008)

                        Empirical fitness landscapes reveal accessible evolutionary paths (Poelwijk et al. 2007)

                        Genealogical trees, coalescent theory and the analysis of genetic polymorphism (Rosenberg & Nordborg 2002)

4.8 Niche Construction

            Niche Construction

                        Suggested Reading: Experimental Evolution and the Nature of Biodiversity (Kassen 2014)

                        Experimental Evolution (Garland & Rose 2009)

                        References: Evolution of Escherichia coli during growth in a constant environment (Helling et al. 1987)

                        Spatial structure leads to ecological breakdown and loss of diversity (Saxer et al. 2009)

                        Ecological perspectives on synthetic biology: insights from microbial population biology (Escalante et al. 2015)

                        Adaptive radiation in a heterogeneous environment (Rainey & Travisano 1998)

                        Santa Rosalia revisited: Why are there so many species of bacteria? (Dykhuizen 1998)

                        The Influence of Interspecific Competition and Other Factors on the Distribution of the Barnacle Chthamalus

                        Stellatus (Connell 1961)

                        Homage to Santa Rosalia or Why Are There So Many Kinds of Animals? (Hutchinson 1959)

Unit 5 – Evolution

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5.1 Introduction

5.2 Origins of Eukaryotes

            Origins of Eukaryotes

                        References: An inside-out origin of the eukaryotic cell (Baum & Baum 2014)

                        Presence of a mitochondrial-type 70-kDa heat shock protein in Trichomonas vaginalis suggests a very

                        early mitochondrial endosymbiosis in eukaryotes (Germot 1996)

                        Recognizing and interpreting the fossils of early eukaryotes (Javaux et al. 2003)

                        The energetics of genome complexity (Lane & Martin 2010)

                        Complex archaea that bridge the gap between prokaryotes and eukaryotes (Spang et al. 2015)

                        An evolutionary network of genes present in eukaryote common ancestor polls genomes on eukaryotic

                        and mitochondrial origin (Thiergart et al. 2012)

5.3 Phylogenetics

            Using Phylogenetics to Travel in Time

                        Further Reading: Phylogenetic inferences (Swofford et al. 1996)

                        Molecules as documents of evolutionary history (Zuckerkandl & Pauling 1965)

                        Assessing the accuracy of ancestral protein reconstruction methods (Williams et al. 2006)

                        On the evolution of cells (Woese 2002)

            A Deeper Dive into Phylogenetics

                        Suggested Reading: MRBAYES: Bayesian inference of phylogenetic trees (Huelsenbeck & Ronquist 2001)

                        Phylogeny estimation and hypothesis testing using maximum likelihood (Huelsenbeck & Crandall 1997)

                        A new view of the tree of life (Hug et al. 2016)

                        Heterotachy and long-branch attraction in phylogenetics (Philippe et al. 2005)

                        The SILVA ribosomal RNA gene database project: improved data processing and web-based tools (Quast et al. 2012)

                        R8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock

                        (Sanderson 2003)

                        Evolutionary rates vary among rRNA structural elements (Smit et al. 2007)

5.4 Macroscopic Theories in Biology

            Macroscopic Theories of Biology

                        References: Allometric scaling of mammalian metabolism (White & Seymour 2005)

                        A general model for the origin of allometric scaling laws in biology (West et al. 1997)

                        Predicting maximum tree heights and other traits from allometric scaling and resource limitations

                        (Kempes et al. 2011)

                        Evolutionary tradeoffs in cellular composition across diverse bacteria (Kempes et al. 2016)

5.5 Selection


                        References: On the Origin of Species (Darwin 1859)

5.6 Selection Theory

            Selection Theory I

                       Supplemental Reading: Fitness Landscapes (Stadler 2002)

                       The utility of fitness landscapes and big data for predicting evolution (Visser et al. 2018)

            Selection Theory II

            Quasispecies and Error Catastrophe

                        Gain Visual Intuition with this Interactive Simulation from Complexity Explorable's

                       Description of Variables Used

5.7 Artificial Life Theory

            Artificial Life Theory

                        References: Theory of Self-Reproducing Automata (Von Neumann 1966)

                        The computer and the brain (Von Neumann 1958)

                        Is there a physically universal cellular automation or Hamiltonian (Janzing 2010)

                        A physically universal cellular automation (Schafer 2014)

Unit 6 – Astrobiology & General Theories of Life

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6.1 Unit 6 Introduction

6.2 Origins of Life and Astrobiology

            Origins of Life and Astrobiology

                        Suggested Reading: New Approach Could Boost the Search for Life in Otherworldly Oceans (Elliot 2021)

6.3 Exoplanets

            The Habitable Zone

                        Suggested Reading:

                        NASA NExSS ‘Many Worlds’ blog

                        Exoplanet Biosignatures: Observational Prospects (Yuka Fujii et al. 2018)

                        References: Unique Spectroscopy and Imaging of Mars with JWST (Villaneuva et al. 2015)

                        Habitable zones around main sequence stars (Kasting et al. 1993)

                        Habitable zones around main sequence stars: new estimates (Kopparapu et al. 2013)

                        NASA Exoplanet Archive

            Exoplanet Atmospheric Characterization

                        Suggested Reading: A search for life on Earth from the Galileo Spacecraft (Sagan et al. 1993)

                        How to Characterize Habitable Worlds and Signs of Life (Kaltenegger 2017)

                        Exoplanet Biosignatures: Observational Prospects (Fujii et al. 2018)

                        References: The Exoplanet Orbit Database (

                        Earth as an Extrasolar Planet: Earth Model Validation Using EPOXI Earth Observations (Robinson et al. 2011)

                        Images of a fourth planet orbiting HR 8799 (Marois et al. 2010)

                        GPI Spectra of HR 8799 c, d, and e from 1.5 to 2.4 um with KLIP Forward Modeling (Greenbaum et al. 2018)

                        Infrared Transmission Spectroscopy of the Exoplanets HD 209458b and XO-1b Using the Wide Field Camera-3 on

                        the Hubble Space Telescope (Deming et al. 2013)

                        A map of the day-night contrast of the extrasolar planet HD 189733b (Knutson et al. 2007)

6.4 Abstract and general Models for Life

           Abstract and General Models for Life

                        References: Vocabulary of definitions of life suggests a definition (Trifonov 2011)

                        Beyond prebiotic chemistry (Cronin et al. 2016)

6.5 The Multiple Origins of Life

            The Argument

                     References: SFI researchers publish new theory on life's multiple origins (Kempes & Krakauer 2021)

            Reversing the Arrow of Time

            The Theory of the Adaptive Arrow of Time

                        References: The Cultural Evolution of National Constitutions (Rockmore et al. 2017)

            Evolutionary Agents

6.6 Evolutionary Computation

            Evolutionary Computation

                        Further Reading: A biological perspective on evolutionary computation (Miikkulainen & Forrest 2021)

                        An Introduction to Genetic Algorithms (Mitchell 1996)

                        An Introduction to Evolutionary Computing (Eiben & Smith 2015)

                        Adaptation in Natural and Artificial Systems: An Introductory Analysis with Applications to Biology (Holland 1992)

                        Genetic algorithms: principles of natural selection applied to computation (Forrest 1993)

                        References: Automatic Bug Repair (Hardesty 2015)

                        De-Novo Learning of Genome-Scale Regulatory Networks in S. cerevisiae (Ma et al. 2014)

                        The evolution of morphogenetic fitness landscapes: conceptualizing the interplay between the developmental

                        and ecological drivers of morphological innovation (Marshall 2014)

6.7 Scaling


                        References: Altered dynamics of forest recovery under a changing climate (Anderson-Teixeira et al. 2012)

                        Population density and body size in mammals (Damuth 1981)

                        Allometric scaling of plant energetics and population density (Enquist et al. 1998)

                        Land plants: new theoretical directions and empirical prospects (Enquist & Bentley 2012)

                        Scaling and Power-Laws in Ecological Systems (Marquet et al. 2005)

                        Scaling: Why is Animal Size so Important? (Schmidt-Nielsen 1984)

                        Life history (Sibly 2012)

                        Evolutionary Predictors of Mammalian Home Range Size: Body Mass, Diet and the Environment: Home

                        Range-Body Mass Patterns: Are Mammals Equal? (Tucker et al. 2014)

                        A general model for the origin of allometric scaling laws in biology (West et al. 1997)

                        Methodological tools (White et al. 2012)

6.8 Energy


                        References: Energy Basis for Man and Nature (Odum & Odum 1976)

                        Systems Ecology: An Introduction (Odum 1983)

                        Animal Physiology: Adaptation and Environment (Schmidt-Nielsen 1997)

                        Toward a metabolic theory of ecology (Brown et al. 2004)

                        Metabolic Ecology; A Scaling Approach (Sibly et al. 2012)

                        Energetics of Microbial Growth (Battley 1987)

                        Thermodynamic and metabolic effects on the scaling of production and population energy use (Ernest et al. 2003)

                        The predominance of quarter-power scaling in biology (Savage et al. 2004)

                        Systematic variation in the temperature dependence of physiological and ecological traits (Dell et al. 2011)

                        The thermodynamic efficiency of computations made in cells across the range of life (Kempes et al. 2017)

6.9 Nonequilibrium Physics

            Nonequilibrium Physics

                       More to Explore: Large-deviation principles, stochastic effective actions, path entropies, and the structure and

                       meaning of thermodynamic descriptions (Smith 2011)

                       Lectures on phase transitions and the re-nromalization group (Goldenfeld 1992)

                       McCloskey Speaker Series - New Theories on the Origin of Life

                       The Origin and Nature of Life on Earth: The Emergence of the Fourth Geosphere (Smith & Morowitz 2015)

                       References: Atomistic aspects of fracture (Bitzek et al. 2015)

                       The Microbial Engines that Drive Earth's Biogeochemical Cycles (Falkowski et al. 2008)

                       Modelling the Diversity of Extrasolar Terrestrial Planets (Meadows 2005)

6.10 Search for Life in Our Solar System

           The Search for Life on Mars

           The Search for Life on Icy Moons

                     References: Europa’s differentiated internal structure: Inferences from four Galileo encounters (Anderson et al. 1998)

                     Composition and stability of salts on the surface of Europa and their oceanic origin (Zolotov & Shock 2001)

                     Sodium chloride on the surface of Europa (Trumbo et al. 2019)

                     Galileo magnetometer measurements: A stronger case for a subsurface ocean at Europa (Kivelson et al. 2000)

                     NASA’s Europa Clipper—a mission to a potentially habitable ocean world (Howell & Pappalardo 2020)