Creation (26 page)

Chapter 4: What Is Life?

A good read on the accumulation of information storage and inheritance in molecules is: G. F. Joyce, “Bit by Bit: The Darwinian Basis of Life,”
PLoS Biology
10 (2012) (e1001323. doi:10.1371/).

About various definitions of life: Pier Luigi Luisi,
Origins of Life and Evolution of the Biosphere
28 (1998), pp. 613–22.

Refer to Edward Trifinov's meta-definition of life, based on the words that scientists use. Nineteen retorts can be found in the February 2012 edition of the same journal: Edward N. Trifonov, “Vocabulary of Definitions of Life Suggests a Definition,”
Journal of Biomolecular Structure and Dynamics
29 (October 2011), pp. 259–66.

Both Erwin Schrödinger's and J. B .S. Haldane's books entitled
What Is Life?
(1944 and 1949, respectively) are available online for free, and are both essential reading.

Chapter 5: The Origin of the Code

The theoretical takeover of DNA from RNA in the first genes: Kevin Leu et al., “On the Prebiotic Evolutionary Advantage of Transferring Genetic Information from RNA to DNA,”
Nucleic Acids Research
39 (2011), pp. 8135–47 (doi:10.1093/nar/gkr525).

On Jerry Joyce and Tracey Lincoln's short RNA molecules that have the effect of endlessly reproducing themselves: Tracey A. Lincoln and Gerald F. Joyce,
“
Self-Sustained Replication of an RNA Enzyme,”
Science
32 (February 27, 2009), pp. 1229–32 (doi:10.1126/science.1167856).

On Jack Szostak and David Bartel's classic ribozyme experiment: D. P. Bartel and J. W. Szostak, “Isolation of New Ribozymes from a Large Pool of Random Sequences,”
Science
261 (September 10, 1993), pp. 1411–18.

Admittedly a long way from infinite monkeys, but half a dozen aren't very Shakespearean: David Adam, “Give Six Monkeys a Computer, and What Do You Get? Certainly Not the Bard,”
Guardian
(May 9, 2003).

On the idea of a ribozyme's being the most distant ancestor inspired by the blog
Tales from the Nobel Factory,
written by Alex Taylor: though I have chosen a different ribozyme as a conceptual aboriginal ancestor, I am most grateful to him for this and other bits he helped me with, though not his inability to understand what a collective noun is: http://talesfromthenobelfactory.posterous.com; Aniela Wochner et al., “Ribozyme-Catalyzed Transcription of an Active Ribozyme,”
Science
332 (April 8, 2011), pp. 209–12 (doi:10.1126/science.1200752).

Three papers on the origin of the genetic code with fewer than the four bases of modern life bear reading: Jeff Rogers and Gerald F. Joyce, “A Ribozyme That Lacks Cytidine,”
Nature
402 (November 18, 1999), pp. 323–25 (doi:10.1038/46335); John S. Reader and Gerald F. Joyce, “A Ribozyme Composed of Only Two Different Nucleotides,”
Nature
420 (December 19, 2002), pp. 841–44 (doi:10.1038/nature01185); Julia Derr et al., “Prebiotically Plausible Mechanisms Increase Compositional Diversity of Nucleic Acid Sequences,”
Nucleic Acids Research
(2012) (doi:10.1093/nar/gks065).

John Sutherland's classic synthesis of uracil: Matthew W. Powner, Béatrice Gerland, and John D. Sutherland, “Synthesis of Activated Pyrimidine Ribonucleotides in Prebiotically Plausible Conditions,”
Nature
459 (May 14, 2009), pp. 239–42 (doi:10.1038/nature08013).

This fantastic study demonstrates that the uracil found in the Murchison Meteorite was from space, and not earthly contamination: Zita Martins et al., “Extraterrestrial Nucleobases in the Murchison Meteorite,”
Earth and Planetary Science Letters
270 (2008), pp. 130–36.

Chapter 6: Genesis

On the accumulation of human culture: Adam Powell, Stephen Shennan, and Mark G. Thomas, “Late Pleistocene Demography and the Appearance of Modern Human Behavior,”
Science
324 (June 5, 2009), pp. 1298–1301 (doi:10.1126/science.1170165).

On competition in cell membrane formation: Itay Budin and Jack W. Szostak, “Physical Effects Underlying the Transition from Primitive to Modern Cell Membranes,”
PNAS
(2011) (doi:10.1073/pnas.1100498108).

Jack Szostak's protocell model dominates studies of the emergence of the membrane. Other ideas and experiments have suggested different routes. One recent study by Stephen Mann, Shogo Koga, and colleagues from the University of Bristol puts forth the possibility of microdroplets stuffed with nucleotides and amino acid strings so that they compartmentalize without a physical skin. We await the development of that idea with relish. Shogo Koga et al., “Peptide-nucleotide Microdroplets as a Step towards a Membrane-free Protocell Model,”
Nature Chemistry
3 (2011), pp. 720–24 (doi:10.1038/nchem.1110).

Here's an interesting study from 2011 that shows replication of DNA within self-reproducing protocells and sharing of the DNA between the daughter cells. Although very clearly not the same as in modern cells, the process mimics the outcome of actual cell division: K. Kurihara et al., “Self-reproduction of Supramolecular Giant Vesicles Combined with the Amplification of Encapsulated DNA,”
Nature Chemistry
3 (2011), pp. 775–81 (doi:10.1038/nchem.1127).

Orgel's thoughts on the RNA World: Leslie E. Orgel, “Prebiotic Chemistry and the Origin of the RNA World,”
Critical Reviews in Biochemistry and Molecular Biology
39 (2004), pp. 99–123 (doi:10.1080/10409230490460765).

A 2001 overview of the emerging experiments to emulate abiogenesis: Jack W. Szostak, David P. Bartel, and P. Luigi Luisi, “Synthesizing Life,”
Nature
409 (January 18, 2001), pp. 387–90 (doi:10.1038/35053176).

The first description of the hydrothermal vents of the Lost City: D. S. Kelly et al.,
“
An Off-axis Hydrothermal-vent Field near the Mid-Atlantic Ridge at 30° N,”
Nature
412 (July 12, 2001), pp. 145–49.

If you can get hold of this paper, it is a hoot: Crick and Orgel pondering aliens as the origin of earthly life: F. H. C. Crick and L. E. Orgel, “Directed Panspermia,”
Icarus
19 (1973), pp. 341–46.

Sir Fred Hoyle and Chandra Wickramasinghe's interesting but wrong ideas on panspermia: Sir Fred Hoyle and Chandra Wickramasinghe,
Evolution from Space: A Theory of Cosmic Creationism
(Touchstone, 1984).

There are a handful of papers and reviews by Nick Lane, Mike Russell, Bill Martin and others on proton gradients, and the energetic origin of life in hydrothermal vents. Here are some of the best: N. Lane, W. Martin, “The origin of membrane bioenergetics,”
Cell
151 (2012), pp. 1406–16; W. Martin, “Hydrogen, metals, bifurcating electrons, and proton gradients: the early evolution of biological energy conservation,”
FEBS Letters
586 (2012), pp. 485–93; M. J. Russell (editor),
Origins, Abiogenesis and the Search for Life in the Universe
(Cosmology Science Publishers: Cambridge, MA, 2011), p. 487; N. Lane, J. F. Allen, and W. Martin, “How did LUCA make a living? Chemiosmosis in the origin of life,”
Bioessays
32 (2010), pp. 271-280; W. Martin, J. Baross, D. Kelley, and M. J. Russell, “Hydrothermal vents and the origin of life,”
Nature Reviews: Microbiology
6 (2008), pp. 806–814; W. Martin, M. J. Russell, “On the origin of biochemistry at an alkaline hydrothermal vent,”
Philosophical Transactions
, Royal Society of London (Ser.B) 362 (2007), pp. 1887–1925.

And this is a profile of Mike Russell and his research: John Whitfield, “Origin of life: Nascence man,”
Nature
459 (2009), pp. 316–319 (doi:10.1038/459316a).

Part II: The Future of Life

Chapter 7: Life, Not as We Know It

Craig Venter's paper on building a cell from a fully manufactured genome: Daniel G. Gibson et al., “Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome,”
Science
329 (July 2, 2010), pp. 52–56 (doi:10.1126/science.1190719).

And the patent for the minimal genome of
Mycoplasma mycoides
, or Synthia, as it was nicknamed: http://1.usa.gov/QsssVZ.

Chapter 8: Created, Not Begotten

I first physically encountered Freckles the spider-goat (and her creator, Randy Lewis) during the filming of an episode of the BBC television science series
Horizon
. Parts of this chapter are taken from interviews from that filming, and from an article I wrote for the
Observer
newspaper based on that show: “Synthetic Biology and the Rise of the ‘Spider-goats'” (January 14, 2012).

Here is one of many papers describing the silk-producing genetic modifications: F. Teulé et al., “A Protocol for the Production of Recombinant Spider Silk-like Proteins for Artificial Fiber Spinning,”
Nature Protocols
4:3 (2009), pp. 341–55 (doi:10.1038/nprot.2008.250).

Here is Hamilton Smith's 1970 paper characterizing the restriction enzyme HinDII; it was this technology that enabled all molecular biology that followed: H. Smith and K. W. Wilcox, “A Restriction Enzyme from Hemophilus Influenzae 1. Purification and General Properties,”
Journal of Molecular Biology
51 (1970), pp. 379–91 (doi:10.1016/0022-2836(70)90149-X).

Chapter 9: Logic in Life

The most comprehensive analysis of modern biotechnology is
Biology Is Technology: The Promise, Peril, and New Business of Engineering Life
by Robert H. Carlson (Harvard University Press, 2011), and is a brilliant primer for the science, economics, and politics of this ever-changing field.

Ron Weiss's cancer assassin circuit: Zhen Xie et al., “Multi-Input RNAi-Based Logic Circuit for Identification of Specific Cancer Cells,”
Science
333 (September 2, 2011), pp. 1307–11 (doi:10.1126/science.1205527).

The cancer cells that are targeted and destroyed in this system are called HeLa cells. Due to their unlimited ability to divide—“immortality”—they have been experimented on and distributed innumerable times, and are of immeasurable importance to many aspects of modern biology. They were derived in 1951 from the cervix of Henrietta Lacks, a poor black American who died of her cancer and lies in an unmarked grave. Her tale is told with grace and brilliance by Rebecca Skloot in the book
The Immortal Life of Henrietta Lacks
(Crown, 2010).

The two back-to-back papers that launched the component nature of genetic engineering at the birth of synthetic biology: Michael B. Elowitz and Stanislas Leibler, “A Synthetic Oscillatory Network of Transcriptional Regulators,”
Nature
403 (January 20, 2000), pp. 335–38 (doi:10.1038/35002125); Timothy S. Gardner, Charles R. Cantor, and James J. Collins, “The Construction of a Genetic Toggle Switch in
Escherichia coli
,” Nature 403 (January 20, 2000), pp. 339–42 (doi:10.1038/35002131).

Ten years later, genetic circuits had become significantly more sophisticated. For example: Tal Danino, Octavio Mondragón-Palomino, Lev Tsimring, and Jeff Hasty, “A Synchronized Quorum of Genetic Clocks,”
Nature
463 (January 21, 2010), pp. 326–30 (doi:10.1038/nature08753).

At
Nature,
my colleague Charlotte Stoddart made a short film of the astonishing synthetic synchronization of Hasty's bacteria and published it on YouTube. In it Charlotte's voice-over describes the fluorescing action as a “Mexican wave,” because it closely resembles the metachronal rhythm demonstrated in packed stadiums by sports fans standing, yelling, and sitting down in succession. YouTube viewers are not known for providing the most sophisticated commentary below the videos themselves, but we were surprised to learn that the term
Mexican wave
was primarily a British phrase, as a result of its occurrence at football (soccer) matches in the Mexico World Cup, 1986. It seems that many other people in the world took this as a vaguely racist comment.

On the dangers of a trip to Mars: W. Friedberg et al., “Health Aspects of Radiation Exposure on a Simulated Mission to Mars,”
Radioactivity in the Environment
7 (2005), pp. 894–901.

A good analysis of the claims and hype of synthetic biology: Roberta Kwok, “Five Hard Truths for Synthetic Biology,”
Nature
463 (January 20, 2010), pp. 288–90 (doi:10.1038/463288a).

Chapter 10: Remix and Revolution

My thoughts on copying, creativity, and music in relation to evolution and synthetic biology are influenced, appropriately enough, by a series of online videos by New York filmmaker Kirby Ferguson entitled
Everything Is a Remix,
available in four parts at http://www.everythingisaremix.info/.

Completing the loop, Ferguson used evolution as an introductory metaphor for the genesis of ideas in part 4 of his outstanding piece of work, which he formulated with a very small amount of help from me. I now gleefully extend this idea into the realm of synthetic biology by borrowing and transforming his ideas. I'm pretty sure he won't mind.

The changing nature of creativity, specifically in music, as a result of copyright law is excellently documented by Joanna Demers in
Steal This Music
(University of Georgia Press, 2006).

One of the most striking examples of sampling in music is the innumerable reuses of a short stretch of drum solo from the B-side of a 1969 7-inch single by the Winstons, a largely forgotten funk-soul band. The four-bar section is known as the Amen break, as the song itself was called “Amen, Brother,” and features a dropped and syncopated drum hit known as a breakbeat. In the mid-1980s, it began appearing as samples in tracks on the developing New York hip-hop scene. By the end of the 1980s, it had been sampled widely, by many dance and hip-hop bands, including in “Straight Outta Compton” by the influential group N.W.A. A decade later, the seven-second drum loop had appeared on hundreds of songs ranging from a David Bowie single to the credits of the cartoon
Futurama
. Entire genres of jungle music and drum and bass are based around the Amen break. A database of tracks that use it can be found at http://amenbreakdb.com/.