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| . Chemistry escapes me. Too many un-descriptive "historical" names for processes, substances, molecules. Hence chapters 2, 3, and 4 are as difficult to internalize as lists of the crowned heads of Europe (and the wars they started, won, and mostly lost) ---- .'''p001 Chapter 1: A Freak Chemical Accident or a Cosmic Imperative?''' .p022 [[ https://www.brainyquote.com/authors/galileo-galilei-quotes | Galileo: ]] "I do not feel obligated to believe that the same God who has given us our senses, reason, and intelligence, wishes us to abandon their use" ---- .'''p025 Chapter 2: The Origin of Life: The RNA World''' .p033 [[ https://en.wikipedia.org/wiki/Ribonuclease_P | Ribonuclease P ]] !RNase P . broad class of RNA+Protein molecules that cut specific cellular RNAs in [[ https://www.dnatestingexperts.com/what-does-rnase-do-things-students-should-know-about/ | specific ways ]] .p033 The RNA does the work, the attached protein neutralizes the large negative charge of the RNA molecule .p033 [[ https://en.wikipedia.org/wiki/Sidney_Altman | Sidney Altman ]] and colleagues added Mg++ magnesium ions, achieving similar neutralization .p034 discoveries of many self-cleaving RNAs that catalyze chemical reactions .p034 [[ https://en.wikipedia.org/wiki/Walter_Gilbert | Walter Gilbert ]] catchphrase [[ https://en.wikipedia.org/wiki/RNA_world_hypothesis | RNA World ]] .p037 [[ https://en.wikipedia.org/wiki/Thomas_A._Steitz | Yale biochemist Thomas Steitz ]] [[ https://www.science.org/doi/10.1126/science.289.5481.878 | The ribosome is a ribozyme ]] .p038 [[ https://en.wikipedia.org/wiki/Origin_of_DNA | RNA World replaced by more stable DNA ]] ---- .'''p039 Chapter 3: The Origin of Life: From Chemistry to Biology''' .p043 [[ https://en.wikipedia.org/wiki/Formose_reaction | formose synthesis ]], sugar from formaldehyde .p046 British chemist [[ https://en.wikipedia.org/wiki/John_Sutherland_(chemist) | John Sutherland ]] .p048 pH buffer and catalyst makes [[ https://en.wikipedia.org/wiki/2-Aminooxazole | 2-aminooxazole 2AO ]] synthesis efficient, [[ https://en.wikipedia.org/wiki/Systems_chemistry | systems chemistry ]] example .p048 2AO plus [[ https://en.wikipedia.org/wiki/Glyceraldehyde | glyceraldehyde ]] produces [[ https://en.wikipedia.org/wiki/Ribose_aminooxazoline | RAO .p057 Where did SO₂ come from? Volcanic eruptions. [[ https://en.wikipedia.org/wiki/Mount_Pinatubo | Pinatubo ]] released enough SO₂ haze to cool Earth for 2 years. ---- .'''p067 Appendix: Chemical Structures and Reactions''' .'''p073 Chapter 4: The Origin of Life: Amino Acids and Peptides''' ---- .'''p083 Chapter 5: The Origin of Life: The Road to the Protocell''' .p087 dipolar membrane molecules [[ https://en.wikipedia.org/wiki/Amphiphile | amphiphilic ]], hydrophobic and hydrophilic ends, self-assembly of bilayer membranes .p087 early Earth environment origin difficult to explain .p089 [[ https://en.wikipedia.org/wiki/Fatty_acid | fatty acids ]] spontaneously assemble into bilayers in water, model protocells .p091 [[ https://en.wikipedia.org/wiki/Alexander_Oparin | Alexander Oparin ]] proposed [[ https://en.wikipedia.org/wiki/Coacervate | coaverate ]] aggregates of polymers .p091 RNA molecules might have "colonized" the surface of mineral particles, but attraction forces distort them .p092 condensation of nucleotides into chains is endothermic in water, hydrolyzing separation exothermic .p093 Drying RNA in warm CO₂ can polymerize, but carbonic acid breaks bonds .p094 [[ https://en.wikipedia.org/wiki/Leslie_Orgel | Leslie Orgel ]] .p094 [[ https://en.wikipedia.org/wiki/Imidazole | imidazole ]] activated nucleotide release .p094 [[ https://en.wikipedia.org/wiki/Leaving_group | leaving group ]] detaches during reaction .p095 growing ice crystals concentrates dissolved compounds between them .p096 [[ https://en.wikipedia.org/wiki/Soda_lake | alkaline carbonate lakes ]] concentrate dissolved phosphate .p097 perhaps suitable environments for nucleotide and RNA synthesis .p100 [[ https://voices.uchicago.edu/szostaklab/ | Szostak Lab ]] U. Chicago chemistry depertment .p101 non-enzymatic RNA copying very different from biological copying .p101 spending months in the laboratory can save you several hours in the library .p102 [[ https://pubmed.ncbi.nlm.nih.gov/30908802/ | imidazole-activated dinucleotide ]], "bridged substrate" .p103 higher copying at lower concentrations .p104 similarities to replication of simpler RNA viruses infecting bacteria, but simpler .p105 circular genome avoids starting/ending point, [[ https://en.wikipedia.org/wiki/Viroid | viroids ]] .p106 beginning replication methods would not have been complex .p106 [[ https://pmc.ncbi.nlm.nih.gov/articles/PMC7749632/ | virtual circular genome model ]] VCG .p107 temperature cycling separates and joins randomly, copying in different places, eventually complete replication . hypothetical, testing under way .p107 [[ https://en.wikipedia.org/wiki/Albert_Eschenmoser | Albert Eschenmoser ]] hypothetical progenitor nucleic acid that led to RNA .p108 showed a diverse collection of artificial nucleic acids can be viable genetic polymers .p108 [[ https://pubmed.ncbi.nlm.nih.gov/10852702/ | ANA arabinose nucleic acid ]] [[ https://en.wikipedia.org/wiki/Threose_nucleic_acid | TNA threose nucleic acid ]] .p108 Whatever the original nucleic acid, RNA always wins; the copying process preferentially generates RNA .p109 fatty acid membranes highly permeable to inbound nutrients and outbound wastes without evolved pores or channels .p109 experiments demonstrate primordial cells can grow and divide in many different ways .p109 [[ https://en.wikipedia.org/wiki/Micelle | micelles, ]] molecular aggregates that can grow and divide .p110 growing membranes vary in shape, leading to budding and new vesicles .p111 osmotic pressure swells RNA-filled vesicles with water and more RNA .p111 "competitive growth" favors protocells containing RNA that replicates faster .p112 increased concentration outside the protocell reduces osmotic pressure, reshapes the vesicle, perhaps dividing it .p112 divalent [[ https://en.wikipedia.org/wiki/Magnesium_citrate | magnesium citrate ]] can protect a protocell from rupture .p112 doesn't effect fatty acid membranes .p113 membranes also stabilized by ribose and adenine nucleotides .p113 [[ https://chem.washington.edu/people/sarah-l-keller | Sarah Keller University of Washington ]] slkeller@uw.edu, B.A. Physics Rice 1989, PhD Biophysics Princeton 1995 .p117 easiest-to-make amino acids tend to pair-bond strongly .p117 genetic code partly deterministic, partly "frozen historical accident" ---- .'''p119 Chapter 6: Putting it All Together: From Astrophysics and Geology to Chemistry and Biology''' .p135 Many chemical processes only at surface, evidence of surface origin of like, NOT hydrothermal vents .p136 experiment show temperature cycles enable seemingly contradictory requirements. .p136 environment cycling between high and low temperatures seems required for nonenzymatic RNA replication .p137 Darwin's prescient "warm little pond"; volcanic hot springs, and asteroid impact craters .p138 evolving ribozymes requires maintenance of larger genome .p138 hypothetical life on Mars might originate from impact ejecta; [[ https://www2.boulder.swri.edu/~cchapman/2001JE001532.pdf | 12% ]] of Chixhulub ejecta reached Earth escape velocity ---- .'''p141 Chapter 7: Extraterrestrial Life on Solar System Planets?''' .p143 Thin Mars atmosphere (2ppm of Earth mass per square meter, not much more than an industrial high vacuum), no magnetic field. Mars is 2ppm Earth, 999998 ppm Moon, with far less sunlight and similer peak corona mass ejection radiation levels. .p144 Elon Musk wants to die on Mars, just not on impact .p151 1976 [[ https://en.wikipedia.org/wiki/Viking_program | Viking ]] [[ https://en.wikipedia.org/wiki/Viking_lander_biological_experiments#Labeled_release | Labelled Release (LR) experiment ]] .p151 [[ https://en.wikipedia.org/wiki/Gilbert_Levin | Gilbert Levin ]] still insisted that he found life in 2019 Scientific American article. .p152 [[ https://en.wikipedia.org/wiki/Dirk_Schulze-Makuch | Dirk Schulze-Makuch ]] [[ https://www.nature.com/articles/s41550-024-02381-x | suggested life in Martian hygroscopic salts ]], killed by LR water .p152 [[ https://en.wikipedia.org/wiki/Carl_Sagan | Carl Sagan ]] "If there is life on Mars, we should do nothing with Mars. Mars belongs to the Martians, even if the Martians are only microbes." .p156 Martian mineral processes can produce subsurface abiotic methane. .p156 [[ https://en.wikipedia.org/wiki/Sample_Analysis_at_Mars | Sample Analysis at Mars (SAM) ]] on [[ https://en.wikipedia.org/wiki/Mars_Science_Laboratory | Mars Science Laboratory ]] [[ https://en.wikipedia.org/wiki/Curiosity_(rover) | Curiosity Rover ]] found 0.4 ppb methane. .p157 [[ https://en.wikipedia.org/wiki/European_Space_Agency | ESA ]] [[ https://en.wikipedia.org/wiki/ExoMars | ExoMars ]] [[ https://en.wikipedia.org/wiki/Trace_Gas_Orbiter | Trace Gas Orbiter ]] found nothing up to 2019 .p157 [[ https://en.wikipedia.org/wiki/European_Space_Agency | ESA ]][[ https://en.wikipedia.org/wiki/Mars_Express | Mars Express Orbiter ]] reported a [[ https://agupubs.onlinelibrary.wiley.com/doi/full/10.1029/2018JE005824 | methane spike above Gale crater in 2019 ]] .p161 [[ https://en.wikipedia.org/wiki/Perseverance_(rover) | Perseverance ]] samples dried up river delta on west rim of [[ https://en.wikipedia.org/wiki/Jezero_(crater) | Jezero Crater ]] 2022 May, [[ https://en.wikipedia.org/wiki/NASA-ESA_Mars_Sample_Return | sample return mission planned ]] after 2033 ---- .'''p167 Chapter 8: Extraterrestrial Life on Solar System Moons?''' .p172 [[ https://www.space.com/jupiter-moon-europa-water-vapor-confirmed.html | sporadic Europa water vapor plumes (2019) ]] .p174 charged particles bombarding Europa produce [[ https://www.nasa.gov/missions/juno/nasas-juno-mission-measures-oxygen-production-at-europa/ | 40 tonnes of oxygen per hour ]] over Europa's 1e13 square meter surface . Europa surface temperature 50K to 140K, oxygen will be gas, not liquid or solid . Europa escape velocity 2 km/s, rms thermal velocity less than 400 m/s, but charged particle bombardment might remove it . Europa atmospheric density 2.4e18 to 14e18 atoms per square meter, 24 to 140 micrograms per square meter. .p177 [[ | ]] .p178 [[ | ]] .p179 [[ | ]] .p180 [[ | ]] .p180 [[ | ]] .p181 [[ | ]] .p187 [[ | ]] ---- .'''p189 Chapter 9: Life Out There: The Astronomical Quest''' .p194 [[ | ]] .p195 [[ | ]] .p196 [[ | ]] .p197 [[ | ]] .p198 [[ | ]] .p199 [[ | ]] .p199 [[ | ]] .p199 [[ | ]] .p200 [[ | ]] .p200 [[ | ]] .p202 [[ | ]] .p202 [[ | ]] .p203 [[ | ]] .p206 [[ | ]] .p208 [[ | ]] .p216 [[ | ]] .p216 [[ | ]] .p218 [[ | ]] ---- .'''p219 Chapter 10: Life as We Don't Know It: The Design of Natural and Unnatural Life-Forms''' .p221 [[ | ]] .p223 [[ | ]] .p225 [[ | ]] ---- .'''p231 Chapter 11: The Hunt for Intelligence: Preliminary Thoughts''' .p233 [[ | ]] .p233 [[ | ]] .p237 [[ | ]] .p238 [[ | ]] .p242 [[ | ]] .p245 [[ | ]] .p250 [[ | ]] .p251 [[ | ]] .p252 [[ | ]] .p253 [[ | ]] ---- .'''p257 Chapter 12: The Hunt for Intelligence: The Searches''' .p259 [[ | ]] .p259 [[ | ]] .p260 [[ | ]] .p261 [[ | ]] .p261 [[ | ]] .p262 [[ | ]] .p262 [[ | ]] .p262 [[ | ]] .p263 [[ | ]] .p263 [[ | ]] .p264 [[ | ]] .p265 [[ | ]] .p265 [[ | ]] .p266 [[ | ]] .p266 [[ | ]] .p267 [[ | ]] .p268 [[ | ]] .p269 [[ | ]] .p269 [[ | ]] ---- .'''p271 Chapter 13: Epilogue: And Immanent Breakthrough?''' .p272 [[ | ]] .p274 [[ | ]] .p274 [[ | ]] .p275 [[ | ]] .p275 [[ | ]] .p277 [[ | ]] .p278 [[ | ]] .p279 [[ | ]] .p279 [[ | ]] .p279 [[ | ]] .p280 [[ | ]] .p281 [[ | ]] .p282 [[ | ]] .p282 [[ | ]] .p283 [[ | ]] .p283 [[ | ]] .p284 [[ | ]] .p284 [[ | ]] ---- .p285 Acknowledgements ---- .p287 Selected Further Reading .p301 Lustin-Yaeger et. al. 2018, "Detecting Ocean Glint on Exoplanets Using Multiphase Mapping," Astronomical Journal 156 no. 6 December .[[ https://iopscience.iop.org/article/10.3847/1538-3881/aaed3a | summary ]] [[ https://iopscience.iop.org/article/10.3847/1538-3881/aaed3a/pdf | pdf ]] ---- .p311 Index |
Is Earth Exceptional?
The Quest for Cosmic Life
Mario Livio & Jack Szostak . 2024 . 576.83 LIVIO . Cedar Mill Library
- Chemistry escapes me. Too many un-descriptive "historical" names for processes, substances, molecules. Hence chapters 2, 3, and 4 are as difficult to internalize as lists of the crowned heads of Europe (and the wars they started, won, and mostly lost)
p001 Chapter 1: A Freak Chemical Accident or a Cosmic Imperative?
p022 Galileo: "I do not feel obligated to believe that the same God who has given us our senses, reason, and intelligence, wishes us to abandon their use"
p025 Chapter 2: The Origin of Life: The RNA World
p033 Ribonuclease P !RNase P
broad class of RNA+Protein molecules that cut specific cellular RNAs in specific ways
- p033 The RNA does the work, the attached protein neutralizes the large negative charge of the RNA molecule
p033 Sidney Altman and colleagues added Mg++ magnesium ions, achieving similar neutralization
- p034 discoveries of many self-cleaving RNAs that catalyze chemical reactions
p034 Walter Gilbert catchphrase RNA World
p037 Yale biochemist Thomas Steitz The ribosome is a ribozyme
p039 Chapter 3: The Origin of Life: From Chemistry to Biology
p043 formose synthesis, sugar from formaldehyde
p046 British chemist John Sutherland
p048 pH buffer and catalyst makes 2-aminooxazole 2AO synthesis efficient, systems chemistry example
p048 2AO plus glyceraldehyde produces [[ https://en.wikipedia.org/wiki/Ribose_aminooxazoline | RAO
p057 Where did SO₂ come from? Volcanic eruptions. Pinatubo released enough SO₂ haze to cool Earth for 2 years.
p067 Appendix: Chemical Structures and Reactions
p073 Chapter 4: The Origin of Life: Amino Acids and Peptides
p083 Chapter 5: The Origin of Life: The Road to the Protocell
p087 dipolar membrane molecules amphiphilic, hydrophobic and hydrophilic ends, self-assembly of bilayer membranes
- p087 early Earth environment origin difficult to explain
p089 fatty acids spontaneously assemble into bilayers in water, model protocells
p091 Alexander Oparin proposed coaverate aggregates of polymers
- p091 RNA molecules might have "colonized" the surface of mineral particles, but attraction forces distort them
- p092 condensation of nucleotides into chains is endothermic in water, hydrolyzing separation exothermic
- p093 Drying RNA in warm CO₂ can polymerize, but carbonic acid breaks bonds
p094 Leslie Orgel
p094 imidazole activated nucleotide release
p094 leaving group detaches during reaction
- p095 growing ice crystals concentrates dissolved compounds between them
p096 alkaline carbonate lakes concentrate dissolved phosphate
- p097 perhaps suitable environments for nucleotide and RNA synthesis
p100 Szostak Lab U. Chicago chemistry depertment
- p101 non-enzymatic RNA copying very different from biological copying
- p101 spending months in the laboratory can save you several hours in the library
p102 imidazole-activated dinucleotide, "bridged substrate"
- p103 higher copying at lower concentrations
- p104 similarities to replication of simpler RNA viruses infecting bacteria, but simpler
p105 circular genome avoids starting/ending point, viroids
- p106 beginning replication methods would not have been complex
p106 virtual circular genome model VCG
- p107 temperature cycling separates and joins randomly, copying in different places, eventually complete replication
- hypothetical, testing under way
p107 Albert Eschenmoser hypothetical progenitor nucleic acid that led to RNA
- p108 showed a diverse collection of artificial nucleic acids can be viable genetic polymers
- p108 Whatever the original nucleic acid, RNA always wins; the copying process preferentially generates RNA
- p109 fatty acid membranes highly permeable to inbound nutrients and outbound wastes without evolved pores or channels
- p109 experiments demonstrate primordial cells can grow and divide in many different ways
p109 micelles, molecular aggregates that can grow and divide
- p110 growing membranes vary in shape, leading to budding and new vesicles
- p111 osmotic pressure swells RNA-filled vesicles with water and more RNA
- p111 "competitive growth" favors protocells containing RNA that replicates faster
- p112 increased concentration outside the protocell reduces osmotic pressure, reshapes the vesicle, perhaps dividing it
p112 divalent magnesium citrate can protect a protocell from rupture
- p112 doesn't effect fatty acid membranes
- p113 membranes also stabilized by ribose and adenine nucleotides
p113 Sarah Keller University of Washington slkeller@uw.edu, B.A. Physics Rice 1989, PhD Biophysics Princeton 1995
- p117 easiest-to-make amino acids tend to pair-bond strongly
- p117 genetic code partly deterministic, partly "frozen historical accident"
p119 Chapter 6: Putting it All Together: From Astrophysics and Geology to Chemistry and Biology
- p135 Many chemical processes only at surface, evidence of surface origin of like, NOT hydrothermal vents
- p136 experiment show temperature cycles enable seemingly contradictory requirements.
- p136 environment cycling between high and low temperatures seems required for nonenzymatic RNA replication
- p137 Darwin's prescient "warm little pond"; volcanic hot springs, and asteroid impact craters
- p138 evolving ribozymes requires maintenance of larger genome
p138 hypothetical life on Mars might originate from impact ejecta; 12% of Chixhulub ejecta reached Earth escape velocity
p141 Chapter 7: Extraterrestrial Life on Solar System Planets?
- p143 Thin Mars atmosphere (2ppm of Earth mass per square meter, not much more than an industrial high vacuum), no magnetic field. Mars is 2ppm Earth, 999998 ppm Moon, with far less sunlight and similer peak corona mass ejection radiation levels.
- p144 Elon Musk wants to die on Mars, just not on impact
p151 1976 Viking Labelled Release (LR) experiment
p151 Gilbert Levin still insisted that he found life in 2019 Scientific American article.
p152 Dirk Schulze-Makuch suggested life in Martian hygroscopic salts, killed by LR water
p152 Carl Sagan "If there is life on Mars, we should do nothing with Mars. Mars belongs to the Martians, even if the Martians are only microbes."
- p156 Martian mineral processes can produce subsurface abiotic methane.
p156 Sample Analysis at Mars (SAM) on Mars Science Laboratory Curiosity Rover found 0.4 ppb methane.
p157 ESA ExoMars Trace Gas Orbiter found nothing up to 2019
p157 ESAMars Express Orbiter reported a methane spike above Gale crater in 2019
p161 Perseverance samples dried up river delta on west rim of Jezero Crater 2022 May, sample return mission planned after 2033
p167 Chapter 8: Extraterrestrial Life on Solar System Moons?
p174 charged particles bombarding Europa produce 40 tonnes of oxygen per hour over Europa's 1e13 square meter surface
- Europa surface temperature 50K to 140K, oxygen will be gas, not liquid or solid
- Europa escape velocity 2 km/s, rms thermal velocity less than 400 m/s, but charged particle bombardment might remove it
- Europa atmospheric density 2.4e18 to 14e18 atoms per square meter, 24 to 140 micrograms per square meter.
p189 Chapter 9: Life Out There: The Astronomical Quest
p219 Chapter 10: Life as We Don't Know It: The Design of Natural and Unnatural Life-Forms
p231 Chapter 11: The Hunt for Intelligence: Preliminary Thoughts
p257 Chapter 12: The Hunt for Intelligence: The Searches
p271 Chapter 13: Epilogue: And Immanent Breakthrough?
- p285 Acknowledgements
- p287 Selected Further Reading
- p301 Lustin-Yaeger et. al. 2018, "Detecting Ocean Glint on Exoplanets Using Multiphase Mapping," Astronomical Journal 156 no. 6 December
- p311 Index