第一章　生命的起源

1.　Fyfe W. S. The water inventory of the Earth: fluids and tectonics.Geological Society, London, Special Publications 78: 1–7; 1994.

2.　Holm N. G., et al. Alkaline fluid circulation in ultramafic rocks and formation of nucleotide constituents: a hypothesis. Geochemical Transactions 7:7; 2006.

4.　Kelley D. S., Karson J. A., Fruh-Green G. L. et al. A serpentinite-hosted ecosystem: the Lost City hydrothermal field. Science 307: 1428–34; 2005.

5.　Martin W., Baross J., Kelley D., Russell M. J. Hydrothermal vents and the origin of life. Nature Reviews in Microbiology 6: 805–14; 2008.

6.　Martin W., Russell M. J. On the origin of biochemistry at an alkaline hydrothermal vent. Philosophical Transactions of the Royal Society of London B 362: 1887–925; 2007.

7.　Morowitz H., Smith E. Energy flow and the organisation of life. Complexity 13: 51–9; 2007.

8.　Proskurowski G., et al. Abiogenic hydrocarbon production at Lost City hydrothermal field. Science 319: 604–7; 2008.

9.　Russell M. J., Martin W. The rocky roots of the acetyl CoA pathway. Trends in Biochemical Sciences 29: 358–63; 2004.

10.　Russell M. First Life. American Scientist 94: 32–9; 2006.

11.　Smith E., Morowitz H. J. Universality in intermediary metabolism. Proceedings of the National Academy of Sciences USA 101: 13168–73; 2004.

第二章　DNA

1.　Baaske P., et al. Extreme accumulation of nucleotides in simulated hydrothermal pore systems. Proceedings of the National Academy of Sciences USA 104: 9346–51; 2007.

2.　Copley S. D., Smith E., Morowitz H. J. A mechanism for the association of amino acids with their codons and the origin of the genetic code. PNAS 102: 4442-7 2005.

3.　Crick F. H. C. The origin of the genetic code. Journal of Molecular Biology 38: 367–79; 1968.

4.　De Duve C. The onset of selection. Nature 433: 581–2; 2005.

5.　Freeland S. J., Hurst L. D. The genetic code is one in a million. Journal of Molecular Evolution 47: 238–48; 1998.

6.　Gilbert W. The RNA world. Nature 319: 618; 1986.

7.　Hayes B. The invention of the genetic code. American Scientist 86: 8–14; 1998.

8.　Koonin E. V., Martin W. On the origin of genomes and cells within inorganic compartments. Trends in Genetics 21: 647–54; 2005.

9.　Leipe D., Aravind L., Koonin E.V. Did DNA replication evolve twice independently? Nucleic Acids Research 27: 3389–401; 1999.

10.　Martin W., Russell M. J. On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells. Philosophical Transactions of the Royal Society of London B. 358: 59–83; 2003.

11.　Taylor F. J. R., Coates D. The code within the codons. Biosystems 22: 177–87; 1989.

12.　Watson J. D., Crick F. H. C. A structure for deoxyribose nucleic acid.Nature 171: 737–8; 1953.

第三章　光合作用

1.　Allen J. F., Martin W. Out of thin air. Nature 445: 610–12; 2007.

2.　Allen J. F. A redox switch hypothesis for the origin of two light reactions in photosynthesis. FEBS Letters 579: 963–68; 2005.

3.　Dalton R. Squaring up over ancient life. Nature 417: 782–4; 2002.

4.　Ferreira K. N. et al. Architecture of the photosynthetic oxygen-evolving center. Science 303: 1831–8; 2004.

5.　Mauzerall D. Evolution of porphyrins – life as a cosmic imperative. Clinics in Dermatology 16: 195–201; 1998.

6.　Olson J. M., Blankenship R. E. Thinking about photosynthesis. Photosynthesis Research 80: 373–86; 2004.

7.　Russell M. J., Allen J. F., Milner-White E. J. Inorganic complexes enabled the onset of life and oxygenic photosynthesis. In Energy from the Sun: 14th International Congress on Photosynthesis, Allen J. F., Gantt E., Golbeck J. H., Osmond B. (editors). Springer 1193–8; 2008.

8.　Sadekar S., Raymond J., Blankenship R. E. Conservation of distantly related membrane proteins: photosynthetic reaction centers share a common structural core. Molecular Biology and Evolution 23: 2001–7; 2006.

9.　Sauer K., Yachandra V. K. A possible evolutionary origin for the Mn4 cluster of the photosynthetic water oxidation complex from natural MnO2 precipitates in the early ocean. Proceedings of the National Academy of Sciences USA 99: 8631–6; 2002.

10.　Walker D. A. The Z-scheme – Down Hill all the way. Trends in Plant Sciences 7: 183–5; 2002.

11.　Yano J., et al. Where water is oxidised to dioxygen: structure of the photosynthetic Mn4Ca cluster. Science 314: 821–5; 2006.

第四章　复杂细胞

1.　Cox C. J., et al. The archaebacterial origin of eukaryotes. Proceedings of the National Academy of Sciences USA 105: 20356–61; 2008.

2.　Embley M. T , Martin W. Eukaryotic evolution, changes and challenges. Nature 440: 623–30; 2006.

4.　Koonin E. V. The origin of introns and their role in eukaryogenesis: a compromise solution to the introns-early versus introns-late debate？Biology Direct 1: 22; 2006.

6.　Martin W., Koonin E. V. Introns and the origin of nucleus-cytosol compartmentalisation. Nature 440: 41–5; 2006.

8.　Pisani D, Cotton J. A., McInerney J. O. Supertrees disentangle the chimerical origin of eukaryotic genomes. Molecular Biology and Evolution 24: 1752–60; 2007.

9.　Sagan L. On the origin of mitosing cells. Journal of Theoretical Biology 14: 255–74; 1967.

10.　Simonson A. B., et al. Decoding the genomic tree of life. Proceedings of the National Academy of Sciences USA 102: 6608–13; 2005.

11.　Taft R. J., Pheasant M., Mattick J. S. The relationship between nonproteincoding DNA and eukaryotic complexity. BioEssays 29: 288–99; 2007.

12.　Vellai T., Vida G. The difference between prokaryotic and eukaryotic cells. Proceedings of the Royal Society of London B 266: 1571–7; 1999.

第五章　性

1.　Burt A. Sex, recombination, and the efficacy of selection: was Weismann right? Evolution 54: 337–51; 2000.

2.　Butlin R. The costs and benefits of sex: new insights from old asexual lineages. Nature Reviews in Genetics 3: 311–17; 2002.

3.　Cavalier-Smith T. Origins of the machinery of recombination and sex. Heredity 88: 125–41; 2002.

4.　Dacks J., Roger A. J. The first sexual lineage and the relevance of facultative sex. Journal of Molecular Evolution 48: 779–83; 1999.

5.　Felsenstein J. The evolutionary advantage of recombination. Genetics 78: 737–56; 1974.

6.　Hamilton W. D., Axelrod R., Tanese R. Sexual reproduction as an adaptation to resist parasites. Proceedings of the National Academy of Sciences USA 87: 3566–73; 1990.

7.　Howard R. S., Lively C. V. Parasitism, mutation accumulation and the maintenance of sex. Nature 367: 554–7; 1994.

8.　Keightley P. D., Otto S. P. Interference among deleterious mutations favours sex and recombination in finite populations. Nature 443: 89–92; 2006.

9.　Kondrashov A. Deleterious mutations and the evolution of sexual recombination. Nature 336: 435–40; 1988.

10.　Otto S. P., Nuismer S. L. Species interactions and the evolution of sex. Science 304: 1018–20; 2004.

11.　Szollosi G. J., Derenyi I., Vellai T. The maintenance of sex in bacteria is ensured by its potential to reload genes. Genetics 174: 2173–80; 2006.

第六章　运动

1.　Amos L. A., van den Ent F., Lowe J. Structural/functional homology between the bacterial and eukaryotic cytoskeletons. Current Opinion in Cell Biology 16: 24–31; 2004.

2.　Frixione E. Recurring views on the structure and function of the cytoskeleton: a 300 year epic. Cell Motility and the Cytoskeleton 46: 73–94; 2000.

3.　Huxley H. E., Hanson J. Changes in the cross striations of muscle during contraction and stretch and their structural interpretation. Nature 173: 973–1954.

4.　Huxley H. E. A personal view of muscle and motility mechanisms. Annual Review of Physiology 58: 1–19; 1996.

5.　Mitchison T. J. Evolution of a dynamic cytoskeleton. Philosophical Transactions of the Royal Society of London B 349: 299–304; 1995.

6.　Nachmias V. T., Huxley H., Kessler D. Electron microscope observations on actomyosin and actin preparations from Physarum polycephalum, and on their interaction with heavy meromyosin subfragment I from muscle myosin. Journal of Molecular Biology 50: 83–90; 1970.

7.　OOta S., Saitou N. Phylogenetic relationship of muscle tissues deduced from superimposition of gene trees. Molecular Biology and Evolution 16: 856–67; 1999.

8.　Piccolino M. Animal electricity and the birth of electrophysiology: The legacy of Luigi Galvani. Brain Research Bulletin 46: 381–407; 1998.

9.　Richards T. A., Cavalier-Smith T. Myosin domain evolution and the primary divergence of eukaryotes. Nature 436: 1113–18; 2005.

10.　Swank D. M., Vishnudas V. K., Maughan D. W. An exceptionally fast actomyosin reaction powers insect flight muscle. Proceedings of the National Academy of Sciences USA 103: 17543–7; 2006.

11.　Wagner P. J., Kosnik M. A., Lidgard S. Abundance distributions imply elevated complexity of post-paleozoic marine ecosystems. Science 314: 1289–92; 2006.

第七章　视觉

1.　Addadi L., Weiner S. Control and Design Principles in Biological Mineralisation. Angew Chem Int Ed Engl 3: 153–69; 1992.

2.　Aizenberg J., et al. Calcitic microlenses as part of the photoreceptor system in brittlestars. Nature 412: 819–22; 2001.

3.　Arendt D., et al. Ciliary photoreceptors with a vertebrate-type opsin in an invertebrate brain. Science 306: 869–71; 2004.

4.　Deininger W., Fuhrmann M., Hegemann P. Opsin evolution: out of wild green yonder? Trends in Genetics 16: 158–9; 2000.

5.　Gehring W. J. Historical perspective on the development and evolution of eyes and photoreceptors. International Journal of Developmental Biology 48: 707–17; 2004.

6.　Gehring W. J. New perspectives on eye development and the evolution of eyes and photoreceptors. Journal of Heredity 96: 171–84; 2005.

7.　Nilsson D. E., Pelger S. A pessimistic estimate of the time required for an eye to evolve. Proceedings of the Royal Society of London B 256: 53–8; 1994.

8.　Panda S., et al. Illumination of the melanopsin signaling pathway. Science 307: 600–604; 2005.

9.　Piatigorsky J. Seeing the light: the role of inherited developmental cascades in the origins of vertebrate lenses and their crystallins. Heredity 96: 275–77; 2006.

10.　Shi Y., Yokoyama S. Molecular analysis of the evolutionary significance of ultraviolet vision in vertebrates. Proceedings of the National Academy of Sciences USA 100: 8308–13; 2003.

11.　Van Dover C. L., et al. A novel eye in ‘eyeless’ shrimp from hydrothermal vents on the Mid-Atlantic Ridge. Nature 337: 458–60; 1989.

12.　White S. N., et al. Ambient light emission from hydrothermal vents on the Mid-Atlantic Ridge. Geophysical Research Letters 29: 341–4; 2000.

第八章　热血

1.　Burness G. P., Diamond J., Flannery T. Dinosaurs, dragons, and dwarfs: the evolution of maximal body size. Proceedings of the National Academy of Sciences USA 98: 14518–23; 2001.

2.　Hayes J. P., Garland J. The evolution of endothermy: testing the aerobic capacity model. Evolution 49: 836–47; 1995.

3.　Hulbert A. J., Else P. L. Membranes and the setting of energy demand. Journal of Experimental Biology 208: 1593–99; 2005.

4.　Kirkland J. I., et al. A primitive therizinosauroid dinosaur from the Early Cretaceous of Utah. Nature 435: 84–7; 2005.

5.　Klaassen M., Nolet B. A. Stoichiometry of endothermy: shifting the quest from nitrogen to carbon. Ecology Letters 11: 1–8; 2008.

6.　Lane N. Reading the book of death. Nature 448: 122–5; 2007.

7.　O’Connor P. M., Claessens L. P. A. M. Basic avian pulmonary design and flow-through ventilation in non-avian theropod dinosaurs. Nature 436: 253–6; 2005.

8.　Organ C. L., et al. Molecular phylogenetics of Mastodon and Tyrannosaurus rex. Science 320: 499; 2008.

9.　Prum R. O., Brush A. H. The evolutionary origin and diversification of feathers. Quarterly Review of Biology 77: 261–95; 2002.

10.　Sawyer R. H., Knapp L. W. Avian skin development and the evolutionary origin of feathers. Journal of Experimental Zoology 298B: 57–72; 2003.

11.　Seebacher F. Dinosaur body temperatures: the occurrence of endothermy and ectothermy. Paleobiology 29: 105–22; 2003.

12.　Walter I., Seebacher F. Molecular mechanisms underlying the development of endothermy in birds (Gallus gallus): a new role of PGC-1a? American Journal of Physiology Regul Integr Comp Physiol 293: R2315–22, 2007.

第九章　意识

1.　Churchland P. How do neurons know? Daedalus Winter 2004; 42–50.

2.　Crick F., Koch C. A framework for consciousness. Nature Neuroscience 6: 119–26; 2003.

3.　Denton D. A., et al. The role of primordial emotions in the evolutionary origin of consciousness. Consciousness and Cognition 18: 500–514; 2009.

4.　Edelman G., Gally J. A. Degeneracy and complexity in biological systems. Proceedings of the National Academy of Sciences USA 98: 13763–68; 2001.

5.　Edelman G. Consciousness: the remembered present. Annals of the New York Academy of Sciences 929: 111–22; 2001.

6.　Gil M., De Marco R. J., Menzel R. Learning reward expectations in honeybees. Learning and Memory 14: 49–96; 2007.

7.　Koch C., Greenfield S. How does consciousness happen? Scientific American October 2007; 76–83.

8.　Lane N. Medical constraints on the quantum mind. Journal of the Royal Society of Medicine 93: 571–5; 2000.

9.　Merker B. Consciousness without a cerebral cortex: A challenge for neuroscience and medicine. Behavioral and Brain Sciences 30: 63–134; 2007.

10.　Musacchio J. M. The ineffability of qualia and the word-anchoring problem. Language Sciences 27: 403–35; 2005.

11.　Searle J. How to study consciousness scientifically. Philosophical Transactions of the Royal Society of London B 353: 1935–42; 1998.

12.　Singer W. Consciousness and the binding problem. Annals of the New York Academy of Sciences 929: 123–46; 2001.

第十章　死亡

2.　Barja G. Mitochondrial oxygen consumption and reactive oxygen species production are independently modulated: implications for aging studies. Rejuvenation Research 10: 215–24; 2007.

3.　Bauer et al. Resveratrol improves health and survival of mice on a highcalorie diet. Nature 444: 280–81; 2006.

4.　Bidle K. D., Falkowski P. G. Cell death in planktonic, photosynthetic microorganisms. Nature Reviews in Microbiology 2: 643–55; 2004.

5.　Blagosklonny M. V. An anti-aging drug today: from senescencepromoting genes to anti-aging pill. Drug Discovery Today 12: 218–24; 2007.

6.　Bonawitz N. D., et al. Reduced TOR signaling extends chronological life span via increased respiration and upregulation of mitochondrial gene expression. Cell Metabolism 5: 265–77; 2007.

7.　Garber K. A mid-life crisis for aging theory. Nature 26: 371–4; 2008.

8.　Hunter P. Is eternal youth scientifically plausible? EMBO Reports 8: 18–20; 2007.

9.　Kirkwood T. Understanding the odd science of aging. Cell 120: 437–47; 2005.

10.　Lane N. A unifying view of aging and disease: the double-agent theory. Journal of Theoretical Biology 225: 531–40; 2003.

11.　Lane N. Origins of death. Nature 453: 583–5; 2008.

12.　Tanaka M., et al. Mitochondrial genotype associated with longevity. Lancet 351: 185–6; 1998.

部分图片来源

1.　图1.1、图1.2 来自Kelley, D.S. the mantle to microbes: The Lost City Hydrothermal Field. Oceanography 18(3):32–45, https://doi.org/10.5670/oceanog.2005.23. Figure2

2.　图1.3来自The Lost City Hydrothermal Field Revisited Kelley, D.S., G.L. Früh-Green, J.A. Karson, and K.A. Ludwig. 2007. The Lost City Hydrothermal Field revisited. Oceanography 20(4):90–99, https://doi.org/10.5670/oceanog.2007.09. Figure5

3.　图3.2由杜塞尔多夫大学Klaus Kowallik教授提供。

4.　图3.3由西澳大利亚大学Catherine Colas des Francs-Small博士提供。

5.　图4.5由犹他州立大学Carol von Dohlen教授提供。

6.　图6.1由马萨诸塞大学Roger Craig教授提供。

7.　图6.2由圣地亚哥斯克里普斯研究所David Goodsell博士提供。

8.　图7.1由Dan-Eric Nilsson提供。Michael Land and Dan-Eric Nilsson, Animal Eyes. OUP, Oxford, 2002

9.　图7.2由爱丁堡大学Euan Clarkson教授提供。