What is Life?:How chemistry becomes biology (25 page)

The network perspective on life might assist in addressing some of the questions concerning life that have been frequently raised over the years. Based on the theory of life proposed here, replication is the essence of life. That might seem to imply that a mule or lone rabbit would not be considered alive, as neither can reproduce. But, of course, mules (and lone rabbits) are alive. It is true that they cannot reproduce but they
are
still part of the replicative network—they are just dead-ends. A road that stops in a dead-end is still a road and part of the road network. Mules
are
replicative entities, not because they can reproduce—they can’t—but because of the replicative process by which they came into being. What about viruses—are they alive? One can conduct lengthy debates on the matter and ultimately the answer would depend on one’s precise definition of a living thing. Clearly viruses are lacking key life characteristics, such as possessing an independent metabolism. Having said that, however, there is no doubting that viruses are also an integral part of the life network. For viruses the question is more philosophic and linguistic than scientific.

The goal of this book has been to demonstrate that answers to several of the most central of life questions, including the classic one posed by Schrödinger, are finally becoming accessible. The extraordinary powers of science and the inductive method in particular, have revolutionized our lives and our understanding of the
world to an extent we could not have foreseen, even a century ago. Thanks to the remarkable scientific progress these past 150 years, from Darwin’s awesome revolution in biological thinking, through to the exciting new developments in systems chemistry, biology and chemistry are finally merging, finally becoming one. The Darwinian revolution may now be nearing its ultimate goal, the one that Charles Darwin already foresaw 130 years ago—the integration of the biological sciences within the physical sciences. That merging of the two sciences means that within the limits that science itself imposes on us, we can begin to understand what is life, why it emerged, how we, a twiglet on the tree of life, together with all other living things on our planet, relate to the material world and the universe as a whole, and why, despite the unforgiving harshness of the Darwinian view, we are committed to one another, why in some deeper sense, we are one. Can that fundamental life connection serve as a ray of hope for the future of humankind, the entity that Stephen Hawking called ‘a chemical scum on a moderate-sized planet’? Only time will tell.

1
. Woese CR, A new biology for a new century.
Microbiol. Mol. Biol. Rev.
68: 173–86, 2004.

2
. Dawkins R,
The Blind Watchmaker.
Norton: New York, 1996.

3
. Gold T, The deep, hot biosphere.
PNAS
89: 6045–9, 1992.

4
. Proctor LM, Karl DM, A sea of microbes.
Oceanography
20: 14–15, 2007.

5
. Soshichi U, Darwin’s principle of divergence. <
http://www.philsci-archive.pitt.edu/1781/1/PrDiv.pdf
>, 2004.

6
. McShea DW, Brandon RN,
Biology’s First Law: The Tendency for Diversity and Complexity to Increase in Evolutionary Systems.
University of Chicago Press: Chicago, 2010.

7
. Haeckel E,
Die Radiolarien (Rhizopoda Radiaria): Eine Monographie.
Druck und Verlag Von Georg Reimer: Berlin, 1862; cited in Pereto J, Bada JF, Lazcano A, Charles Darwin and the origin of life.
Orig. Life Evol. Biosphere
39: 395–406, 2009.

8
. Bohr N,
Nature
131: 458, 1933; cited in Yockey HP,
Information Theory, Evolution, and the Origin of Life.
Cambridge University Press: Cambridge, 2005.

9
. Schrödinger E,
What is Life?
Cambridge University Press: Cambridge, 1944.

10
. Monod J,
Chance and Necessity.
Random: New York, 1971.

11
. Watson JD, Crick FH, Genetical implications of the structure of deoxyribonucleic acid.
Nature
171: 964–7, 1953.

12
. Popper K, Reduction and the incompleteness of science. In Ayala F, Dobzhansky T, eds.,
Studies in the Philosophy of Biology.
University of California Press: Berkeley and Los Angeles, 1974.

13
. Crick FHC,
Life Itself.
Simon and Schuster: New York, 1981.

14
. Popa R,
Between Necessity and Probability: Searching for the Definition and Origin of Life.
Springer: Berlin, 2004.

15
. Dyson FJ, Colloquium at NASA’s Goddard Space Flight Center, 2000.

16
. Kunin V, A system of two polymerases—a model for the origin of life.
Orig. Life Evol. Biosphere
30: 459–66, 2000.

17
. Arrhenius G, Short definitions of life. In Palyi G, Zucchi C, Caglioti L, eds.,
Fundamentals of Life,
17–18. Elsevier: New York, 2002.

18
. Hennet RJC, Life is simply a particular state of organized instability. In Palyi G, Zucchi C, Caglioti L, eds.,
Fundamentals of Life,
109–10. Elsevier: Paris, 2002.

19
. Cleland CE, Chyba CF, Defining life.
Orig. Life Evol. Biosphere
32: 387–93, 2002.

20
. Macaulay TB,
Critical and Historical Essays,
vol. iii. Project Gutenberg eBook #28046, 2009.

21
. Ayala FJ, Dobzhansky T, eds.,
Studies in the Philosophy of Biology: Reduction and Related Problems.
Macmillan: London, 1974.

22
. Noble D,
The Music of Life.
Oxford University Press: Oxford, 2006.

23
. Brenner S, Sequences and consequences.
Phil. Trans. R. Soc. B
365: 207–12, 2010.

24
. Weinberg S,
Dreams of a Final Theory.
Vintage: New York, 1994.

25
. Crick FHC,
Of Molecules and Men.
University of Washington Press: Seattle, 1966.

26
. Cornish-Bowden A,
Perspectives in Biology and Medicine
49: 475–89, 2006.

27
. Mills DR, Peterson RL, Spiegelman S, An extracellular Darwinian experiment with a self-duplicating nucleic acid molecule.
PNAS
58: 217, 1967.

28
. von Kiedrowski G, A self-replicating hexadeoxynucleotide.
Angew. Chem. Int. Ed. Eng.
25: 932–4, 1986.

29
. von Kiedrowski G, Otto S, Herdewijn P, Welcome home, systems chemists!
J. Syst. Chem.
1: 1, 2011.

30
. Dawkins R,
The Selfish Gene.
Oxford University Press: Oxford, 1989.

31
. Grand S,
Creation.
Harvard University Press: Cambridge, MA, 2001.

32
. For recent comprehensive reviews on the origin of life see: (a) Luisi PL,
The Emergence of Life: From Chemical Origins to Synthetic Biology.
Cambridge University Press: Cambridge, 2006; (b) ref. 14; (c) Fry I,
The Emergence of Life on Earth.
Rutgers University Press: Piscataway, 2000.

33
. Wacey D, Kilburn MR, Saunders M, Cliff J, Brasier MD, Microfossils of sulphur-metabolizing cells in 3.4-billion-year-old rocks of Western Australia.
Nature Geoscience
4: 698–702. doi:10.1038/ngeo1238, 2011.

34
. Mojzsis SJ, Arrhenius G, McKeegan KD, Harrison TM, Nutman AP, Friend CRL, Evidence for life on Earth before 3800 million years ago.
Nature
384: 55–9, 1996.

35
. Hanage WP, Fraser C, Spratt BG, Fuzzy species among recombinogenic bacteria.
BMC Biology
3: 6, 2005; Papke RT, Gogarten JP, How bacterial lineages emerge.
Science
336: 45, 2012.

36
. Woese C, Interpreting the universal phylogenetic tree.
PNAS
97: 8392–6, 2000.

37
. Miller SL, A production of amino acids under possible primitive earth conditions.
Science
117: 528–9, 1953.

38
. Waechtershaeuser G, Groundwork for an evolutionary biochemistry: the iron-sulphur world.
Prog. Biophys. Mol. Biol.
58: 85–201, 1992.

39
. Cairns-Smith A,
Genetic Takeover and the Mineral Origin of Life.
Cambridge University Press: London, 1982.

40
. Powner MW, Gerland B, Sutherland JD, Synthesis of activated pyrimi-dine ribonucleotides in prebiotically plausible conditions.
Nature
459: 239–42, 2009.

41
. Szostak JW, Bartel DP, Luisi PL, Synthesizing life.
Nature
409: 387–90, 2001.

42
. Kauffman SA,
Investigations.
Oxford University Press: Oxford, 2000.

43
. Dyson FJ,
Origins of Life.
Cambridge University Press: London, 1985.

44
. Eigen M,
Steps toward Life: A Perspective on Evolution.
Oxford University Press: Oxford, 1992.

45
. Gesteland RF, Atkins, JF,
The RNA World: The Nature of Modern RNA Suggests a Prebiotic World.
Cold Spring Harbor Laboratory Press: Cold Spring Harbor, NY, 1993.

46
. Lifson S, On the crucial stages in the origin of animate matter.
J. Mol. Evol.
44: 1–8, 1997.

47
. Orgel LE, The implausibility of metabolic cycles on the prebiotic earth.
PLoS Biol.
6:e18, 2008.

48
. de Duve C,
Life Evolving: Molecules, Mind and Meaning.
Oxford University Press: Oxford, 2002.

49
. Ganti T, Organization of chemical reactions into dividing and metabolizing units: the chemotons.
BioSystems
7: 189–95, 1975.

50
. Prigogine I, Time, structure and fluctuations.
Science
201: 777–85, 1978.

51
. Collier J, The dynamics of biological order. In Weber BH, Depew DJ, Smith JD, eds.,
Entropy, Information, and Evolution,
227–42. MIT Press: Cambridge, MA, 1988.

52
. Gardner M, Mathematical games: the fantastic combinations of John Conway’s new solitaire game ‘Life’.
Scientific American
223: 120–3, 1970.

53
. Voytek SB, Joyce GF, Niche partitioning in the coevolution of two distinct RNA.
PNAS
106: 7780–5, 2009.

54
. Hardin G, The competitive exclusion principle.
Science
131: 1292–7, 1960.

55
. Maynard Smith J, Szathmary E,
The Major Transitions in Evolution.
Oxford University Press: Oxford, 1995.

56
. Dadon Z, Wagner N, Ashkenasy G, The road to non-enzymatic molecular networks.
Angew. Chem. Int. Ed.
47: 6128–36, 2008.

57
. Lincoln TA, Joyce GF, Self-sustained replication of an RNA enzyme.
Science
323: 1229–32, 2009.

58
. Eigen M, Schuster P,
The Hypercycle: A Principle of Natural Self-Organization.
Springer-Verlag: Berlin, 1979.

59
. Saffhill R, Schneider-Bernloehr H, Orgel LE, Spiegelman S, In vitro selection of bacteriophage Q
β
ribonucleic acid variants resistant to ethidium bromide.
J. Mol. Biol.
51: 531–9, 1970.

60
. Of course, not
all
life complexified over the evolutionary time frame. Microbial life was, and has remained, the most ubiquitous life form. The point is that from a world that was initially populated solely by relatively simple life forms, the evolutionary process did lead to the emergence of highly complex forms.