GENESIS: The Scientific Quest for Life’s Origins

Robert Hazen asks "what can Yellowstone tell us
about life’s origins?"

Transcript

1. Robert M. Hazen—Geophysical Lab DCO Summer School-Yellowstone 26 July 2016 GENESIS: The Scientific Quest for Life’s Origins
2. Robert M. Hazen—Geophysical Lab DCO Summer School-Yellowstone 26 July 2016 What can Yellowstone tell us about life’s origins?
3. The Origins of Life By what processes did life arise on Earth (and on other worlds)? How can scientists study these processes in the lab?
4. Chemical Evolution Life arose by a natural process of “emergent complexity,” consistent with natural laws. This hypothesis assumes that life began as a sequence of chemical steps.
5. OUTLINE 1.  Emergent Complexity 2.  Emergence of biomolecules 3.  Emergence of organized molecular systems 4.  Emergence of self-replicating molecular systems 5.  Emergence of natural selection
6. What is Emergent Complexity? Emergent phenomena arise from interactions among numerous individual particles, or “agents.”
7. The Emergence of Slime Mold à Chemical Potential Gradients Dictyostelium
8. The Emergence of Slime Mold Dictyostelium
9. The Emergence of Consciousness à Neural connections and electrical impulses
10. The Emergence of Consciousness
11. Emergent Phenomena – Space
12. Emergent Phenomena – Life
13. Complex Evolving Systems Require Three Things: 1.  The system must possess the potential for combinatorial richness. 2.  There must be mechanisms to generate numerous configurations of the system. 3.  There must be mechanisms for selection (i.e., winnow out confignurations that do not “function”).
14. Geochemical complexities are key to understanding life’s origins: Gradients Cycles Fluxes Interfaces Chemical complexity [Sources of energy]
15. Geochemical Complexity At Yellowstone These environments display all of these phenomena: gradients, cycles, fluxes, interfaces, & chemical complexity
16. Central Assumptions of Origin-of-Life Research The first life forms were carbon-based. Life’s origin was a chemical process that relied on water, air, and rock. The origin of life required a sequence of emergent steps of increasing complexity.
17. Life’s Origins: Four Emergent Steps 1.  Emergence of biomolecules 2.  Emergence of organized molecular systems 3.  Emergence of self-replicating molecular systems 4.  Emergence of natural selection
18. STEP 1: Emergence of Biomolecules The strategy is to use simple molecules to build larger molecules.
19. STEP 1: Emergence of Biomolecules The strategy is to use simple molecules to build larger molecules.
20. STEP 1: Emergence of Biomolecules The strategy is to use simple molecules to build larger molecules.
21. The Miller-Urey Experiment Organic synthesis near the ocean-atmosphere interface.
22. The Miller-Urey Experiment Organic synthesis near the ocean-atmosphere interface.
23. Louis J. Allamandola, NASA-ARC
24. Organic Synthesis in Interstellar “Dense” Molecular Clouds Experiments at NASA Ames simulate this environment.
25. Minerals  and  the  Origins  of  Life:   Catalysis  
26. The Hydrothermal Hypothesis A “BLACK SMOKER”
27. Hydrothermal Organic Synthesis Gold tube reactors Capsules are run in a gas-media pressure apparatus.
28. Hydrothermal Organic Synthesis Hatten S. Yoder, Jr.
29. George D. Cody
34. Carbon-Addition Reactions: Hydrothermal F-T Synthesis (+CH2) •  Reactants: CO 2 + H 2 + H 2 O •  Catalyst: Iron metal •  Conditions: 300oC 500 atm 24 hours
35. Carbon-Addition Reactions: Hydroformylation (+CO)
36. Carbon-Addition Reactions: Hydroformylation (+CO)
37. Carbon-Addition Reactions: Hydroformylation (+CO)
38. Mineral Catalyzed Carbon-Addition Reactions
39. Mineral Catalyzed Carbon-Addition Reactions
40. STEP 1: CONCLUSIONS The prebiotic synthesis of biomolecules occurred with relative ease. Minerals played key roles.
41. STEP 2: The Emergence of Organized Molecular Systems Prebiotic synthesis processes are facile but indiscriminate. Yet a fundamental attribute of life is a high degree of molecular selectivity and organization. What prebiotic processes might have contributed to such selection and organization?
42. Self-Organization •  Reactants: Pyruvic acid + CO2 + H2 O •  Conditions: 200o C 2,000 atm 2 hours •  Products: A diverse suite of organic molecules
43. David Deamer Marilyn Fogel
44. Self-Assembling Amphiphilic Molecules
45. Self-Assembling Amphiphilic Molecules
46. Selection on Mineral Surfaces Mineral surfaces select and concentrate small molecules
47. Adsorption of L-Glu on Rutile solid conc = 20 g/L ; T = 25°C (Jonsson et al., 2009) 0 10 20 30 40 50 60 70 80 3 4 5 6 7 8 9 10 Ads (%) pH [Glu]tot 0.1 mM 0.5 mM 1 mM 2 mM [NaCl] = 0.1 M (constant) 0 10 20 30 40 50 60 3 4 5 6 7 8 9 10 11 pH Ads (%) [L-Glu] = 0.5 mM (constant) [NaCl]tot 0.01 M 0.05 M 0.1 M 0.3 M Estimated error in each data point is ±1 to 3%, based on uncertainties associated with the Glu analysis.
48. Chelating - Monodentate “lying down” QuickTime™ and a TIFF (Uncompressed) decompressor are needed to see this picture. 0 5 10 15 20 25 30 35 40 3 4 5 6 7 8 9 10 Chelating “standing up” pH % adsorption Chelating - Monodentate “lying down” [L-Glu] = 0.5 mM [NaCl] = 0.1 M Solid conc = 20 g/L Jonsson et al. (2009, 2010)
49. Glutamate Adsorption onto Rutile + Ca2+ Add Ca2+ to the system and glutamate adsorbs onto rutile at both low and high pH, also in two competing configurations. [Lee et al. (2014) Envir. Sci. Tech.] No Ca2+ With Ca2+
50. Lysine Adsorbs onto Rutile at High pH Lysine adsorbs to rutile at high pH in two configurations. [Lee et al. (2014) Envir. Sci. Tech.] No Ca2+
51. Suppression of Lysine Adsorption onto Rutile by Ca2+ Add Ca2+ to the system and lysine adsorption is almost completely suppressed at all pH values. [Lee et al. (2014) Envir. Sci. Tech.] With Ca2+ No Ca2+
52. Competitive interaction of pentose sugars: arabinose, lyxose, xylose, and ribose with TiO2 For ribose and lyxose pH dependent adsorption is pronounced at pH > 8. Ribose
53. Selective Amino Acid Adsorption Equimolar mixture of five amino acids adsorbed onto brucite Aspartate Glycine Phenylalanine Lysine Leucine 0 10 20 30 40 50 150 75 50 10 Aspartate Lysine Glycine Leucine Phenylalanine Adsorption % [AA] 0 [Mg2+]= 0.9x10-3 M pH=10.2 25ºC, 1 bar AVERAGE Competitive adsorption on Brucite Estrada et al. (2014) Astrobiology
54. 0 10 20 30 40 50 150 75 50 10 Aspartate Lysine Glycine Leucine Phenylalanine Adsorption % [AA] 0 [Ca2+ ]= 4.1x10-3 M [Mg2+]= 1.1x10-3 M pH=10.2 25ºC, 1 bar AVERAGE Selective Amino Acid Adsorption Amino Acid Adsorption on Brucite 0 10 20 30 40 50 150 75 50 10 Aspartate Lysine Glycine Leucine Phenylalanine Adsorption % [AA] 0 [Mg2+]= 0.9x10-3 M pH=10.2 25ºC, 1 bar AVERAGE Addition of Ca2+ suppresses adsorption of all amino acids studied except aspartate. Estrada et al. (2014) Astrobiology
55. Biological Homochirality The most challenging aspect of molecular selection is handedness 4 2 C 3 1 (L)-enantiomer 4 2 C 3 1 (R)-enantiomer How did life on Earth become homochiral? Annual sales of chiral pharmaceuticals approaches $200 billion.
56. Chiral  Purity  is  Important   Smells like oranges Smells like lemons R-Limonene Mirror L-Limonene
57. Chiral Purity is Important Thalidomide R-enantiomer Analgesic (Good)
58. Chiral Purity is Important Thalidomide R-enantiomer Analgesic (Good) S-enantiomer Teratogen (Bad)
59. Prebiotic Chiral Selection •  But life demonstrates a remarkable degree of chiral selectivity. •  Prebiotic synthesis processes produce mixtures of left and right molecules. What is the mechanism of symmetry breaking?
60. Quartz – SiO2 Quartz is the only common chiral rock-forming mineral Right Left
61. Quartz: Face-Specific Adsorption (10-11) (01-11)
62. Quartz  Crystal  Faces   Courtesy of S. Parker
63. Calcite (214) Faces
64. Minerals and Chiral Selection Mineral surfaces select chiral amino acids
65. (D)-ASP (L)-ASP The most stable configuration found for D- and L-aspartic acid on calcite (214) surface. The D enantiomer is favored by 8 Kcal/mol. Aspartic Acid-Calcite (214) Interactions
66. STEP 2: CONCLUSIONS Prebiotic molecules can be selected and concentrated, both by self-organization and by adsorption on mineral surfaces.
67. STEP 3: The Emergence of Self-Replicating Molecular Cycles The abiotic synthesis of such a “metabolic” cycle represents a “Holy Grail” for our experimental program.
68. The Emergence of Self-Replicating Molecular Cycles Farmer, Kauffman & Packard (1986) Autocatalytic cycles
69. Those who favor genetics first note that RNA can act as both an information- carrying molecule and an enzyme. All cells use RNA; hence the RNA World scenario. Which came first? METABOLISM vs. GENETICS
70. RNA is an implausible prebiotic molecule, because there’s no known way to synthesize it in a prebiotic environment. What happened between the soup and the RNA world? The RNA World Dilemma
71. STEP 3: CONCLUSIONS We haven’t yet synthesized a plausible prebiotic molecule, cycle of molecules, or molecular network that can replicate itself, but we are getting close.
72. STEP 4: The Emergence of Natural Selection At some point a self-replicating system of molecules emerged. Mutations in that molecular system must have occurred from time to time. In such a system, competition and natural selection are inevitable.
73. Is there a “shadow biosphere” that might point to an early domain of life?
74. New data from deep drilling hint at a new domain of life >150°C
75. Deep “Ur-Life” Is there a deep domain of “life” that does not rely on DNA and proteins? >40 km ?
76. CONCLUSIONS The origin of life on Earth is best understood in terms of a sequence of emergent chemical events, each of which added a degree of structure and complexity to the prebiotic world. While we don’t yet know all the details, there is no compelling evidence to suggest that life’s origin was other than a natural process.
78. With thanks to: NASA Astrobiology Institute National Science Foundation Alfred P. Sloan Foundation Carnegie Institution, Geophysical Lab
79. Feedback:  Eye  EvoluBon   Selection rules for model eye evolution: 1. Vary curvature, aperture, and central refractive index randomly by ±1%. 2. If visual acuity (spatial resolution) increases, then retain that variation. D. Nilsson & S. Pelger, “A pessimistic estimate for the time required for an eye to evolve.” Proc. R. Soc. Lond. B 256, 53-58 (1994).
80. Feedback:  Eye  EvoluBon   This evolutionary sequence is continuously driven by selection, which is not random.
81. Jack Szostak, Harvard University Experiments in Molecular Evolution Molecular evolution has been demonstrated in the laboratory!
82. Szostak Lab: Aptamer Evolution 1.  Random RNA pool *1 *2 *3 *4 *5 *6 *7
83. Szostak Lab: Aptamer Evolution 1.  Random RNA pool 2.  In vitro process 3.  Remove nonbinding strands *1 *2 *3 *4 *5 *6 *7
84. Szostak Lab: Aptamer Evolution 1.  Random RNA pool 2.  In vitro process 3.  Remove nonbinding strands 4.  Collect bound RNA *1 *2 *3 *4 *5 *6 *7
85. Szostak Lab: Aptamer Evolution 1.  Random RNA pool 2.  In vitro process 3.  Remove nonbinding strands 4.  Collect bound RNA 5.  Reverse transcriptase 6.  PCR amplify with errors *1 *2 *3 *4 *5 *6 *7
86. Szostak Lab: Aptamer Evolution 1.  Random RNA pool 2.  In vitro process 3.  Remove nonbinding strands 4.  Collect bound RNA 5.  Reverse transcriptase 6.  PCR amplify with errors 7.  Transcribe DNA to new RNA strands 8.  Repeat 1 thru 7 *1 *2 *3 *4 *5 *6 *7
87. Geochemical complexities are key to understanding life’s origins: Gradients Cycles Fluxes Interfaces Chemical complexity [Sources of energy]
88. Aptamer Evolution 1.  Random RNA pool 2.  In vitro process 3.  Remove nonbinding strands 4.  Collect bound RNA 5.  Reverse transcriptase 6.  PCR amplify with errors 7.  Transcribe DNA to new RNA strands 8.  Repeat 1 thru 7 *1 *2 *3 *4 *5 *6 *7
89. Aptamer Evolution 1.  Random RNA pool 2.  In vitro process 3.  Remove nonbinding strands 4.  Collect bound RNA 5.  Reverse transcriptase 6.  PCR amplify with errors 7.  Transcribe DNA to new RNA strands 8.  Repeat 1 thru 7 *1 *2 *3 *4 *5 *6 *7
90. Aptamer Evolution 1.  Random RNA pool 2.  In vitro process 3.  Remove nonbinding strands 4.  Collect bound RNA 5.  Reverse transcriptase 6.  PCR amplify with errors 7.  Transcribe DNA to new RNA strands 8.  Repeat 1 thru 7 *1 *2 *3 *4 *5 *6 *7
91. Aptamer Evolution 1.  Random RNA pool 2.  In vitro process 3.  Remove nonbinding strands 4.  Collect bound RNA 5.  Reverse transcriptase 6.  PCR amplify with errors 7.  Transcribe DNA to new RNA strands 8.  Repeat 1 thru 7 *1 *2 *3 *4 *5 *6 *7
92. Life’s Origins: Four Steps 1. Synthesis of biomolecules 2. Biomolecular selection 3. Replicating molecular systems 4. Molecular natural selection Hazen (2005) Genesis. Joseph Henry Press: Washington ? ? ? ?