Life's Ratchet: How Molecular Machines Extract Order from Chaos (45 page)

Topoisomerase
Enzyme that cuts and reattaches DNA strands to relieve strain and keep DNA from tangling during replication.

transcription
The transferring of information from DNA to messenger RNA.

transfer RNA (tRNA)
RNA–amino acid complexes that contain the key to translate the genetic information into a protein.

transition state
“Uncomfortable” state that molecules find themselves in temporarily as they transform from one stable form to another. Energy associated with the transition state is the activation barrier.

translation
Translating genetic information into a protein. Happens in the ribosome, with the aid of transfer RNA (tRNA).

vesicle
Spherical assembly of lipids; consists of a double-walled sphere separating a water-filled chamber from water on the outside of the vesicle.

v
italism
The belief that life is associated with special forces.

work
The product of force and distance; the expenditure of energy when force acts over a certain distance to move an object. The unit of work is the joule (J), which is equal to a newton-meter (N·m).

X-rays
Highly energetic electromagnetic radiation, generated by bombarding high-speed electrons into a metal target.

This a partial list of sources I used to write the book. Many of these sources were used in multiple chapters. However, to save space, each source is mentioned only once for the chapter in which it was used first. The references are listed alphabetically by last name of author. I listed only the sources that are easily accessible. Unfortunately, many technical papers are both inaccessible to the public and often incomprehensible to the nonexpert.

INTRODUCTION

Monod, Jacques.
Chance and Necessity
. Translated by Austryn Wainhouse. New York: Alfred A. Knopf, 1971.

Schrödinger, Erwin.
What Is Life?
Canto ed. Cambridge: Cambridge University Press, 1992.

Thomson, D’Arcy.
On Growth and Form
. Canto ed. Cambridge: Cambridge University Press, 1992.

CHAPTER 1

Alioto, Anthony.
A History of Western Science
. Englewood Cliffs, N.J.: Prentice-Hall, 1986.

Aristotle.
De Anima
. In
The Basic Works of Aristotle
. New York: Modern Library, 2001.

———.
Physics
. In
The Basic Works of Aristotle
. New York: Modern Library, 2001.

Cahan, David.
Hermann von Helmholtz and the Foundations of Nineteenth-Century Science.
California Studies in the History of Science. Berkeley: University of California Press, 1994.

Darwin, Charles.
The Origin of Species
. Available at
Literature.org
, the Online Literature Library,
www.literature.org/authors/darwin-charles/the-origin-of-species/
.

Debus, Allen George.
Man and Nature in the Renaissance.
Cambridge Studies in the History of Science. Cambridge: Cambridge University Press, 1978.

Descartes, René.
Discourse on Method
. Available at
Literature.org
, the Online Literature Library,
www.literature.org/authors/descartes-rene/reason-discourse/
.

Gay, Peter.
The Enlightenment: The Rise of Modern Paganism
. New York: W. W. Norton, 1995.

Granger, Herbert.
Aristotle’s Idea of the Soul
. Boston: Kluwer, 1996.

Hankins, Thomas.
Science and the Enlightenment.
Cambridge Studies in the History of Science. Cambridge: Cambridge University Press, 1985.

Harris, Henry.
The Birth of the Cell
. New Haven, Conn.: Yale University Press, 2000.

Helmholtz, Hermann.
Über die Erhaltung der Kraft
. Available at The Internet Archive,
www.archive.org/details/berdieerhaltung01helmgoog
.

Henry, John.
The Scientific Revolution and the Origins of Modern Science.
Studies in European History. New York: Palgrave Macmillan, 2008.

Holmes, Richard.
The Age of Wonder: How the Romantic Generation Discovered the Beauty and Terror of Science
. New York: Pantheon, 2009.

Hooke, Robert.
Micrographia
. Available at Project Gutenberg,
www.gutenberg.org/files/15491/15491-h/15491-h.htm
.

La Mettrie, Julien.
Machine Man and Other Writings
. Edited by Ann Thomson. Cambridge: Cambridge University Press, 1996.

La Mettrie, Julien, and Aram Vartanian.
La Mettrie’s L’homme Machine: A Study in the Origins of an Idea
. Princeton, N.J.: Princeton University Press, 1960.

Lenoir, Timothy.
The Strategy of Life: Teleology and Mechanics in Nineteenth-Century German Biology
. Chicago: University of Chicago Press, 1989.

Lindberg, David.
The Beginnings of Western Science: The European Scientific Tradition in Philosophical, Religious, and Institutional Context, Prehistory to A.D. 1450.
Chicago: University of Chicago Press, 2008.

Lucretius.
De Rerum Natura
. Available at The Internet Classic Archive,
http://classics.mit.edu/Carus/nature_things.html
.

McKendrick, John Gray.
Hermann Ludwig Ferdinand von Helmholtz (Masters of Medicine)
. New York: Longmans, Green & Co., 1899.

Mendelsohn, Everett.
Heat and Life: The Development of the Theory of Animal Heat
. Cambridge, Mass.: Harvard University Press, 1964.

Newton, Isaac.
Opticks
. Available at Project Gutenberg,
www.gutenberg.org/files/33504/33504-h/33504-h.htm
.

Rubenstein, Richard.
Aristotle’s Children: How Christians, Muslims, and Jews Rediscovered Ancient Wisdom and Illuminated the Middle Ages
. New York: Houghton Mifflin, Mariner Books, 2004.

Russell, Bertrand.
A History of Western Philosophy
. New York: Simon & Schuster, 1972.

Shelley, Mary Wollstonecraft.
Frankenstein—or the Modern Prometheus
. Available at
Literature.org
, the Online Literature Library,
www.literature.org/authors/shelley-mary/frankenstein/
.

CHAPTER 2

Chardin, Teilhard.
The Phenomenon of Man
. Available at The Internet Archive,
www.archive.org/details/phenomenon-of-man-pierre-teilhard-de-chardin.pdf
.

Eigen, Manfred, and Ruthild Winkler.
Das Spiel—Naturgesetze steuern den Zufall
. Serie Piper, 1996; English edition:
Laws of the Game: How the Principles of Nature Govern Chance.
Princeton, N.J.: Princeton University Press, 1993.

Judson, Horace Freeland.
The Eighth Day of Creation: Makers of the Revolution in Biology
. Plainview, N.Y.: Cold Spring Harbor Laboratory Press, 1995.

Kline, Morris.
Mathematics for the Nonmathematician.
New York: Dover, 1985.

———.
Mathematics in Western Culture.
New York: Oxford University Press, 1964.

Mainzer, Klaus.
Der kreative Zufall—Wie das Neue in die Welt kommt
. Munich, Germany: C. H. Beck, 2007.

Mlodinow, Leonard.
The Drunkard’s Walk: How Randomness Rules Our Lives
, New York: Pantheon, 2008.

Moore, Walter.
Schrödinger: Life and Thought
. Cambridge: Cambridge University Press, 1992.

Timoféeff-Ressovsky, N. W.; K. G. Zimmer; and M. Delbrück.
Über die Natur der Genmutation und der Genstruktur
(the “green pamphlet”). In
Nachrichten von der Gesellschaft der Wissenschaften zu Göttingen.
Berlin: Weidmannsche Buchhandlung, 1935. Available at
www.ini.uzh.ch/~tobi/fun/max/timofeeff ZimmerDelbruck1935.pdf
.

Wykes, Alan.
Doctor Cardano, Physician Extraordinary
. London: Muller, 1969.

CHAPTER 3

Feynman, Richard.
The Feynman Lectures of Physics
. Boston: Addison Wesley Long-man, 1970.

Lindley, David.
Boltzmann’s Atom: The Great Debate That Launched a Revolution in Physics
. New York: Free Press, 2001.

CHAPTER 4

Drexler, K. Eric.
Engines of Creation 2.0
. E-book. WOWIO, 2006. Available at
www.wowio.com/users/product.asp?BookId=503
.

Feynman, Richard. “There’s Plenty of Room at the Bottom.”
Caltech Engineering and Science
23 (February 1960): 22–36. Available at
www.zyvex.com/nanotech/feynman.html
.

Nelson, Philip.
Biological Physics: Energy, Information, Life
. New York: W. H. Freeman, 2008.

Philips, Rob, and Stephen R. Quake. “The Biological Frontier of Physics.”
Physics Today
(May 2006): 38–43.

CHAPTER 5

Feynman, Richard.
Feynman Lectures on Computation
. Reading, Mass.: Perseus, 2000.

Gamow, George.
Mr. Tompkins in Paperback
. Canto ed. Cambridge: Cambridge University Press, 1993.

Mahon, Basil.
The Man Who Changed Everything: The Life of James Clerk Maxwell
. New York: Wiley, 2003.

CHAPTER 6

Astumian, R. Dean. “Making Molecules into Motors.”
Scientific American
(July 2001).

Astumian, R. Dean, and Peter Hänggi. “Brownian Motors.”
Physics Today
(November 2002): 33–39.

CHAPTER 7

Boyer, Paul. “Energy, Life, and ATP.” Nobel Lecture, December 8, 1997. Available at
http://nobelprize.org/nobel_prizes/chemistry/laureates/1997/boyer-lecture.html
.

Cooper, Geoffrey.
The Cell: A Molecular Approach
. Washington, D.C.: ASM Press, 1997.

Hoagland, Mahlon, and Bert Dodson.
The Way Life Works
. New York: Three Rivers Press, 1995.

Walker, John. “ATP Synthesis by Rotary Catalysis.” Nobel Lecture, December 8, 1997. Available at
http://nobelprize.org/nobel_prizes/chemistry/laureates/1997/walker-lecture.html
.

CHAPTER 8

Paley, William.
Natural Theology
. Available at “The Complete Works of Charles Darwin Online,”
http://darwin-online.org.uk/content/frameset?itemID=A142&viewtype=text&pageseq=1
.

CHAPTER 9

Alon, Uri.
An Introduction to Systems Biology
. Boca Raton, Fla.: Chapman & Hall/ CRC, 2007.