p. 2 a veritable city of an organism: J.T. Bonner, First Signals: The Evolution of Multicellular Development (Princeton, NJ: Princeton University Press, 2000), p. 56; S.F. Gilbert, Developmental Biology, 7th ed. (Sunderland, MA: Sinauer, 2003), p. 34.

p. 2 Others, known as “gonidia”: D.L. Kirk, The ontogeny and phylogeny of cellular differentiation in Volvox, Trends in Genetics 4(1988):32–36; D.L. Kirk, Volvox: The Molecular-Genetic Origins of Multicellularity and Cellular Differentiation (Cambridge: Cambridge University Press, 1998), pp. 33; 115–116.

p. 2 dormant until next year’s spring rains: Kirk, Volvox, pp. 51; 126–127; Gilbert, Developmental Biology, pp. 36–38.

p. 2 the Oxford Dictionary definition of a society: The Oxford Dictionary and Thesaurus, American Edition (New York: Oxford University Press, 1996).

p. 3 “some coordination, some integration or communication”: J.T. Bonner, Cells and Societies (Princeton: Princeton University Press, 1955), p. 4.

p. 3 the gonidia, the reproductive cells: A. Hallman, K. Godl, and M. Sumper, The highly efficient sex-inducing pheromone system of Volvox, Trends in Microbiology 6(1998):185–189.

p. 5 a structure known today as the cell nucleus: A comprehensive account of the discovery of the cell and the evolution of the “cell doctrine”—the idea that living organisms are composed of cells—one of the central tenets of biology, can be found in H. Harris, The Birth of the Cell (New Haven, CT: Yale University Press, 1999).

p. 10 textbooks refer to as the “random walk”: H.C. Berg, Random Walks in Biology (Princeton, NJ: Princeton University Press, 1983).

p. 10 “before opening your eyes becomes irresistible?”: R. Llinas, I of the Vortex: From Neurons to Self (Cambridge, MA: The MIT Press, 2001), p. 18.

p. 14 its five senses: F.W. Dahlquist, Amplification of signaling events in bacteria, Science’s STKE 2002 (2002), online at www.stke.org/cgi/content/full/OC_sigtrans;2002/132/ pe24; R.B. Bourret and A.M. Stock, Molecular information processing: Lessons from bacterial chemotaxis, Journal of Biological Chemistry 277 (2002):9625–9628. The Science Signal Transduction Knowledge Environment (STKE; www.stke.org) is a must-see resource for anyone interested in cell signaling research. In addition to an electronic publication featuring original articles as well as reviews on a wide range of topics relevant to signaling research, the STKE also offers a library of “Connections Maps” illustrating the components of critical signaling pathways and their interrelationships, a directory of signaling researchers, a guide to upcoming meetings devoted to signaling, and full-text access to relevant articles from the medical literature. Access to the entire STKE database requires an individual subscription ($69 per year), but a number of the features are free to anyone who registers at the website. A similar “knowledge portal” devoted to cell signaling is maintained by the journal Nature (Nature Signaling Gateway, at www.signaling-gateway.org). More information on the Signaling Gateway can be found in the notes for Chapter 6.

p.14 a pair of identical polypeptide subunits: S.A. Chervitz and J.J. Falke, Molecular mechanism of transmembrane signaling by the aspartate receptor: A model, Proceedings of the National Academy of Sciences 93(1996):2545–2550.

p. 16 add the nuance of context: Bourret and Stock (2002).

p. 17 the tails of chemotactic receptors: Dahlquist (2002); Bourret and Stock (2002).

p. 17 over five orders of magnitude: A.M. Stock, A nonlinear stimulus-response relation in bacterial chemotaxis, Proceedings of the National Academy of Sciences 96(1999):10945–10947.

p. 17 a primitive form of memory: J.B. Stock, M.N. Levit, and P.M. Wolanin, Information processing in bacterial chemotaxis, Science’s STKE 2002 (2002), http://www.stke.org/cgi/content/full/OC_sigtrans;2002/132/pe25.

p. 18 “The modern era begins”: J. Barzun, From Dawn to Decadence: 500 Years of Western Cultural Life (New York: HarperCollins, 2000), p. 3.

p. 20 culture the beach along with the bacteria: T. Kaerberlein, K. Lewis, and S. Epstein, Isolating “uncultivable” microorganisms in pure culture in a simulated environment, Science 296(2002):1127–1129.

p. 22 squid avoids becoming someone else’s: E.G. Ruby, Lessons from a cooperative bacterial-animal association: The Vibrio fischeri-Euprymna scolopes light organ symbiosis, Annual Review of Microbiology 50(1996):591–624. A recent study suggests that the bacteria not only populate their safe haven, but also engineer it: a bacterial peptide, tracheal cytotoxin, released by V. fischeri promotes the development of the

light organ. See T.A. Koropatnick, J.T. Engle, M.A. Apicella, et al., Microbial factor-mediated development in a host-bacterial mutualism, Science 306(2004):1186–1188.

p. 22 “N-(3-oxohexanoyl)-homoserine lactone”: C. Fuqua, M.R. Parsek, and E.P. Greenberg, Regulation of gene expression by cell-to-cell communication: Acylhomoserine lactone quorum sensing, Annual Review of Genetics 35(2001):439–468.

p. 22 the expression of the luciferase gene: K.H. Nealson, T. Platt, and J.W. Hastings, Cellular control of the synthesis and activity of the bacterial luminescent system, Journal of Bacteriology 104(1970):313–322.

p. 23 both receptor and response regulator: S. Schauder and B.L. Bassler, The languages of bacteria, Genes & Development 15(2001):1468–1480; M.B. Miller and B.L. Bassler, Quorum sensing in bacteria, Annual Review of Microbiology 55(2001): 165–199.

p. 25 acyl-HSLs for short: Miller and Bassler (2001); S.C. Winans and B.L. Bassler, Mob psychology, Journal of Bacteriology 184(2002):873–883.

p. 25 controlling critical genes: Schauder and Bassler (2001); Miller and Bassler (2001); Winans and Bassler (2002).

p. 25 Gram-positive bacteria … also count heads: Schauder and Bassler (2001); Miller and Bassler (2001); Winans and Bassler (2002).

p. 27 “the development of multicellular organisms”: Winans and Bassler (2002).

p. 27 “one language and few words”: Gen. 11:1 Revised Standard Version.

p. 27 and undermines diplomacy: B.Wuethrich, Learning the world’s languages before they vanish, Science 288(2000):1156–1159.

p. 27 a Polish doctor, Ludwig L. Zamenhof: The Esperanto League for North America Homepage, The ELNA/Esperanto FAQ List, www.esperanto-usa.org/elnafaq.html.

p. 27 and 20 times easier than Chinese: Esperanto Homepage; Esperanto: FAQs, The Virtual Esperanto Library, www.esperanto.net/veb/faq-2.html.

p. 28 perhaps 2 million speakers worldwide: Virtual Esperanto Library.

p. 29 the causative agent in bubonic plague: Schauder and Bassler (2001); Miller and Bassler (2001); Winans and Bassler (2002).

p. 30 an unusual bolt: a boron atom: X. Chen, S. Schauder, N. Potier, et al., Structural identification of a bacterial quorum-sensing signal containing boron, Nature 415(2002):545–549.

p. 32 call a “biofilm”: J.W. Costerton, Z. Lewandowski, D.E. Caldwell, et al., Microbial biofilms, Annual Review of Microbiology 49(1995):711–745; G. O’Toole, H.B. Kaplan, and R. Kolter, Biofilm formation as microbial development, Annual Review of Microbiology 54(2000):49–79.

p. 33 draining away dissolved waste products: Single-species biofilms generated in the laboratory are often just one cell thick. But in natural settings, biofilm thickness varies widely, depending on the number of species contained in the biofilm and the stage of formation, among other factors.

p. 33 “Chefs and grocers may settle”: P. Watnick and R. Kolter, Biofilm, city of microbes, Journal of Bacteriology 182(2000):2675–2679.

p. 34 to excavate its interconnected canals: D.G. Davies, M.R. Parsek, J.P.

Pearson, et al., The involvement of cell-to-cell signals in the development of a bacterial biofilm, Science 280(1998):295–298; M. Whitely, K.M. Lee, and E.P. Greenberg, Identification of genes controlled by quorum sensing in Pseudomonas aeruginosa, Proceedings of the National Academy of Sciences 96(1999):13904–13909; C. Fuqua and E.P. Greenberg, Listening in on bacteria: Acyl-homoserine lactone signaling, Nature Reviews Molecular Cell Biology 3(2002):685–695.

p. 34 architectural detail or social convention: Davies, et al. (1998); M. Chicurel, Slimebusters, Nature 408(2000):284–286.

p. 34 and recruit passersby: S. Schauder and B.L. Bassler (2001); Chicurel (2000).

p. 34 solid foundation is an anchor in a storm: Another advantage for the bacteria (but not their host) is that living in a biofilm seems to confer resistance to antibiotics. The reasons behind this invincibility may be architectural—the biofilm structure impedes the penetration of the antibiotic or reduces its efficacy because of regional variations in nutrient availability or waste concentration—or physiological—within the biofilm, bacteria may divide more slowly or differentiate into a drug-insensitive state. Biofilm-mediated antibiotic resistance is thought to play a critical role in the persistence of chronic infections, such the recurrent lung infections characteristic of cystic fibrosis. See: J.W. Costerton, P.S. Stewart, and E.P. Greenberg, Bacterial biofilms: A common cause of persistent infections, Science 284(1999):1318–1322; and B. Schachter, Slimy business—The biotechnology of biofilms, Nature Biotechnology 21(2003):361–366.

p. 34 “If the bacteria were unable to escape”: Watnick and Kolter (2000).

p. 35 “deeply rooted in the nature of things”: C. Alexander, S. Ishikawa, and M. Silverstein with M. Jacobson, I. Fiksdahl-King, S. Angel, A Pattern Language: Towns, Buildings, Construction (New York: Oxford University Press, 1977), p. xvii.

p. 35 “In a gothic cathedral”: C. Alexander, The Timeless Way of Building (New York: Oxford University Press, 1979), p. 86.

p. 35 “each sidewalk … includes”: Ibid., p. 73.

p. 36 a problem that “occurs over and over again”: Alexander, et al., A Pattern Language, p. x.

p. 36 “a deep and inescapable property”: Ibid., p. xiv.

p. 36 “patterns which specify connections between patterns”: Alexander, The Timeless Way, p. 187.

p. 36 “features that bear a particular relationship to each other”: Ibid., p. 88.

p. 39 the sophisticated biological sentences of higher organisms: “Conservation,” in this case, refers to the preservation of mechanisms; the actual signaling molecules used by bacteria and animal cells differ.

p. 42 significant improvement in energy efficiency: B. Alberts, A. Johnson, J. Lewis, M. Raff, K. Roberts, and P. Walker, Molecular Biology of the Cell, 4th ed. (New York: Garland Science, 2002), pp. 824–826.

p. 42 “it was the horse’s value as a mount”: S. Budiansky, The Nature of Horses: Exploring Equine Evolution, Intelligence, and Behavior (New York: The Free Press, 1997), p. 55.

p. 42 we know today as mitochondria: Alberts, et al. Molecular Biology of the Cell, pp. 29–33; M.W. Gray, G. Burger, and B.F. Lang, Mitochondrial evolution, Science 283(1999):1476–1481.

p. 43 permitted them to move freely about: Alberts, et al., Molecular Biology of the Cell, pp. 29–33; J Gerhart and M. Kirschner, Cells, Embryos, and Evolution: Toward a Cellular and Developmental Understanding of Phenotypic Variation and Evolutionary Adaptability (Malden, MA: Blackwell Science, 1997), pp. 9–15.

p. 43 forswore rigid walls that prevented real intimacy for good: Gerhart and Kirschner, Cells, Embryos, and Evolution, pp. 9–15.

p. 46 “the one realm … available to escape competition”: J.T. Bonner, First Signals: The Evolution of Multicellular Development (Princeton, NJ: Princeton University Press, 2000): pp. 51–52.

p. 46 “better coordination of the adhering cells”: Bonner, First Signals, p. 7.

p. 46 life’s first true tissue: Gerhart and Kirschner, Cells, Embryos, and Evolution, p. 244.

p. 48 black bile, dark and inert as earth: S. Finger, Minds Behind the Brain: A History of the Pioneers and Their Discoveries (New York: Oxford University Press, 2000), p. 31.

p. 49 “each gland … is the workshop”: A.Q. Maisel, The Hormone Quest (New York: Random House, 1965), p. 7.

pp. 49–50 “A diseased condition” of the adrenal glands: Addison’s original description of the disease which bears his name, quoted here, is reproduced in R. LeBaron, Hormones: A Delicate Balance (New York: Pegasus, 1972), pp. 65–66.

p. 50 a stranger with a vial … the boy’s radial artery: H.M. Leicester, Development of Biochemical Concepts from Ancient to Modern Times (Cambridge, MA: Harvard University Press, 1974), pp. 226–227; “Sharpey-Schafer, Edward Albert (born Schäfer),” http://www.cartage.org.lb/en/themes/Biographies/MainBiographies/S/Sharpey-Schafer/l; Finger, Minds Behind the Brain, p. 261; B.D. Gomperts, P.E.R. Tatham, and I.M. Kramer, Signal Transduction (San Diego: Academic Press, 2002), pp. 8–9. Gomperts notes that accounts of the incident differ somewhat, with Schäfer’s own description rather more clinical than the exuberant recollections of some of his colleagues.

p. 51 “So, Professor Schafer makes the injection …”: J.C. Krantz, Jr., John J. Abel and Epinephrine—The First Hormone, in Historical Medical Classics Involving New Drugs (Baltimore: Williams & Wilkins, 1974), pp. 42–48.

p. 51 “adrenaline” after the gland that secreted it: Krantz, et al. (1974); J.K. Aronson, “Where name and image meet”—The argument for “adrenaline,” British Medical Journal 320(2000):506–509. The substance isolated by Abel was, in fact, not the pure hormone, but the benzoyl derivative (the benzoyl moiety was accidentally introduced during the extraction procedure). Takamine learned the process while a visiting scientist in Abel’s laboratory; upon returning to his own laboratory, he treated the final product with dilute ammonia to remove the impurity. Takamine patented his substance and subsequently transferred the rights to the pharmaceutical firm Parke,

Davis & Co., which marketed it under the trade name “Adrenalin,” to denote its origin. Although Abel’s term “epinephrine” is preferred in the United States, historically, “adrenaline,” as Aronson notes, is probably more correct. Along the same lines, the chemical precursor of adrenaline—a signal in its own right—can be called either “norepinephrine” or “noradrenaline.”

Takamine was a gracious ambassador as well as a skilled chemist. Upon learning of President Taft’s wife’s infatuation with cherry trees, he conspired with the mayor of Tokyo to arrange a gift of 3,000 Japanese cherry trees. Planted along the Tidal Basin, they became the inspiration for Washington’s annual Cherry Blossom Festival.

p. 53 the names of the bones: L.E. Limbird, Cell Surface Receptors. 1. Historical perspective (Boston: Martinus Nijhoff, 1986), pp. 3–6; J.C. Krantz, Jr., Paul Ehrlich and the magic bullet arsphenamine, in Historical Medical Classics Involving New Drugs (Baltimore: Williams & Wilkins, 1974), pp. 51–57; P. DeKruif, The Microbe Hunters (New York: Harvest Books, 1966), pp. 334–358.

p. 53 the recipient of dozens of honorary awards: Gomperts et al., Signal Transduction, pp. 15–16; Limbird, Receptors, pp. 3, 5–6.

p. 53 explanation for such specificity: Limbird, Receptors, p. 3.

p. 54 both vied for this same target: Limbird, Receptors, p. 5.

p. 54 “Corpora non agunt nisi fixata”: quoted in Limbird, Receptors, p. 5.

pp. 54–55 able to deconstruct the polymer: Glycogen is also stored in the muscles; this resource is the first tapped. But when muscle glycogen is exhausted by protracted effort, the body turns to the glycogen stored in the liver for sustenance until the crisis has passed.

p. 55 the alarm clock that actually rouses glycogen phosphorylase: J.A. Beavo and L.L. Brunton, Cyclic nucleotide research—Still expanding after half a century, Nature Reviews Molecular Cell Biology 3(2002):710–717; G.A. Robison, R.W. Butcher, and E.W. Sutherland, cAMP (New York: Academic Press, 1971); E. Krebs and E. Fischer, The phosphorylase B to A converting enzyme of rabbit skeletal muscle, Biochimica Biophysica Acta 1989(1956):302–309.

p. 55 as robust as that found in a living cell: Robison, et al. (1971); J. Berthet, T.W. Rall, and E.W. Sutherland, The relationship of epinephrine and glucagon to liver phosphorylase. IV. Effect of epinephrine and glucagon on the reactivation of phosphorylase in liver homogenates, Journal of Biological Chemistry 224(1957):463–475.

p. 56 “cyclic AMP” for short: E.W. Sutherland and T.W. Rall, Fractionation and characterization of a cyclic adenine ribonucleotide formed by tissue particles, Journal of Biological Chemistry 232(1958):1077–1091.

p. 57 a paper in the prestigious journal: R.J. Lefkowitz, J. Roth, W. Pricer, et al., ACTH receptors in the adrenal: Specific binding of ACTH-¹²⁵I and its relation to adenyl cyclase, Proceedings of the National Academy of Sciences 65(1970):745–752.

p. 58 “without seriously hurting the organism”: Krantz (1974).

p. 58 membranes from heart and brain: R.J. Lefkowitz, Identification and regulation of alpha- and beta-adrenergic receptors, Federation Proceedings 37(1978):123–129; M.G. Caron and R.J. Lefkowitz, Catecholamine receptors: Structure, function, and regulation, Recent Progress in Hormone Research 48(1993):277–319; R.J. Lefkowitz, M.G. Caron, and G.L. Stiles, Mechanisms of membrane-receptor

regulation. Biochemical, physiological, and clinical insights derived from studies of the adrenergic receptors, New England Journal of Medicine 310(1984):1570–1579.

p. 59 adrenergic receptors … had multiple personalities: R. P. Ahlquist, A study of the adrenergic receptors, American Journal of Physiology 153(1948):568–586.

p. 59 α receptors into two groups … β receptors into three: Caron and Lefkowitz (1993); R.J. Lefkowitz, A. De Lean, B.B. Hoffman, et al., Molecular pharmacology of adenylate cyclase-coupled α- and β-adrenergic receptors, Advances in Cyclic Nucleotide Research 14(1981):145–161.

p. 59 had corralled the β₂-adrenertgic receptor: R.G.L. Shorr, R.J. Lefkowitz, and M.G. Caron, Purification of the beta-adrenergic receptor. Identification of the hormone binding subunit, Journal of Biological Chemistry 256(1981):5820–5826.

p. 59 proof that receptor subtypes were actually distinct proteins: R.G.L. Shorr, M.W. Strohsacker, T.N. Lavin, et al., The beta 1-adrenergic receptor of the turkey erythrocyte. Molecular heterogeneity revealed by purification and photoaffinity labeling, Journal of Biological Chemistry 257(1982):12341–12350; R.J. Lefkowitz, The superfamily of heptahelical receptors, Nature Cell Biology 2(2000):E133–E136; R.A.F. Dixon, B.K. Kobilka, D.J. Strader, et al., Cloning of the gene and cDNA for mammalian beta-adrenergic receptor and homology with rhodopsin, Nature 321(1986): 75–79.

p. 60 watery environment on either side: Lefokowitz (2000); Dixon, et al. (1986); H.G. Dohlman, J. Thorner, and M.G. Caron, et al. Model systems for the study of seven-transmembrane-segment receptors, Annual Review of Biochemistry 60(1991):653–688.

p. 60 the most important ingredient in your standard cell membrane: For the information on the life and work of Martin Rodbell, I am especially indebted to “The Martin Rodbell Collection” in Profiles in Science, a website maintained by the National Library of Medicine at http://profiles.nlm.nih.gov/GG/Views/Exhibit/narrative/cells.html.

p. 60 “is in essence a communication device”: Rodbell Collection.

p. 61 which had been christened “adenylyl cyclase,” was the amplifier: M. Rodbell, Signal transduction: Evolution of an idea, Nobel lecture, presented December 8, 1994.

p. 61 carried out under the same conditions: Rodbell, ibid.; M. Rodbell, H.M.J. Krans, S.L. Pohl, et al., The glucagon-sensitive adenyl cyclase system in plasma membranes of rat liver: Effects of guanylnucleotides on binding of ¹²⁵I-glucagon, Journal of Biological Chemistry 246(1971):1872–1876.

p. 61 “I tested many [other] types … of nucleotides”: Rodbell, ibid.

p. 61 it quit making cyclic AMP: M. Rodbell, L. Birnbaumer, S. Pohl, et al., The glucagon-sensitive adenyl cyclase system in plasma membranes of rat liver: An obligatory role of guanylnucleotides in glucagon action, Journal of Biological Chemistry 246(1971):1877–1882.

p. 62 distinct from the binding site for glucagon: Y. Salomon and M. Rodbell, Evidence for specific binding sites for guanine nucleotides in adipocyte and hepatocyte plasma membranes: A difference in fate of GTP and guanosine 5′-(beta, gamma-imino) triphosphate, Journal of Biological Chemistry 250(1975):7245–7250.

p. 62 turn GTP into guanosine diphosphate, GDP: D. Cassel, H. Levkovitz, and Z. Selinger, The regulatory GTPase cycle of turkey erythrocyte adenylate cyclase, Journal of Cyclic Nucleotide Research 3(1977):393–406; D. Cassel and Z. Selinger, Catecholamine-stimulated GTPase activity in turkey erythrocyte membranes, Biochimica Biophysica Acta 452(1976):538–551.

p. 62 an extended family of such G proteins: A.G. Gilman, G proteins: Transducers of receptor-generated signals, Annual Review of Biochemistry 56(1987):615–649; Gomperts, et al., Signal Transduction, pp. 71–105.

p. 63 “the only person who was ever named after a textbook”: “Alfred G. Gilman—Autobiography,” Nobel e-Museum Website, www.nobel.se/medicine/laureates/1994/gilman-autobio.html.

p. 63 fate seemed to have hitched his star to adenylyl cyclase: Ibid.; A.G. Gilman, G proteins and regulation of adenylyl cyclase, Nobel lecture, delivered December 8, 1994.

p. 63 they died in their dishes: V. Daniel, G. Litwack, and G.M. Tomkins, Induction of cytolysis of cultured lymphoma cells by adenosine 3′,5′-cyclic monophosphate and the isolation of resistant variants, Proceedings of the National Academy of Sciences 70(1973):76–79.

p. 64 the enzyme was fine: P.A. Insel, M.E. Maguire, A.G. Gilman, et al., Beta adrenergic receptors and adenylate cyclase: Products of separate genes? Molecular Pharmacology 12(1976):1062–1069; T. Haga, E.M. Ross, and H.J. Anderson, et al., Adenylate cyclase permanently uncoupled from hormone receptors in a novel variant of S49 mouse lymphoma cells, Proceedings of the National Academy of Sciences U.S.A. 74(1977):2016–2020; E.M. Ross and A.G. Gilman, Resolution of some components of adenylate cyclase necessary for catalytic activity, Journal of Biological Chemistry 252(1977):6966–6969.

p. 64 plenty of fully functional adrenergic receptors: Insel, et al. (1976); Haga, et al. (1977); Ross and Gilman (1977).

p. 64 a confederacy of three polypeptides: Gilman (1987); Gomperts, et al., Signal Transduction, pp. 71–105; J.K. Northup, P.C. Sternweis, M.D. Smigel, et al., Purification of the regulatory component of adenylate cyclase, Proceedings of the National Academy of Sciences U.S.A. 77(1980):6516–6520; P.C. Sternweis, J.K. Northup, M.D. Smigel, et al., The regulatory component of adenylate cyclase. Purification and properties, Journal of Biological Chemistry 256(1981):11517–11526.

p. 65 X-ray diffraction patterns and magnetic resonance spectra: D.G. Lambright, J. Sondek, A, Bohm, et al., The 2.0 A structure of a heterotrimeric G protein, Nature 379(1996):311–319; J. Sondek, A. Bohm, D.G. Lambright, et al., Crystal structure of a G-protein beta gamma dimer at 2.1A resolution, Nature 379 (1996):369–374; M. Wall, et al., The structure of the G protein heterotrimer Gi alpha 1 beta 1 gamma 2, Cell 83(1995):1047–1058; D.E. Clapham, The G-protein nanomachine, Nature 379(1996):297–299.

p. 65 “Biological communication” … “consists of a complex meshwork”: Rodbell, Nobel lecture (1994).

p. 66 the same seven-helix, membrane-spanning structure: K.L. Pierce, R.T. Premont, and R.J. Lefkowitz, Seven-transmembrane receptors, Nature Reviews Molecular Cell Biology 3(2002):639–650. Maps of representative G-protein pathways can

be found online at the Science Signal Transduction Knowledge Environment (STKE) Website at www.stke.org.

p. 66 the G-protein-coupled light receptor, rhodopsin, were look-alikes: Dixon, et al. (1986).

p. 67 than with any other introductory word or phrase: Alberts et al., Molecular Biology of the Cell, p. 852.

p. 69 then works with the others to complete the job: Ibid., pp. 140–141; 145–146.

p. 69 Domains … may have started off as proteins themselves: Ibid.

p. 69 a “consensus sequence” on another protein: T. Pawson and P. Nash, Assembly of cell regulatory systems through protein interaction domains, Science 300 (2003):445–452.

p. 69 the pool of potential partners: Ibid.

p. 70 “expanding the possibilities for combinatorial association”: M. Ptashne and A. Gann, Genes and Signals (Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press, 2002), p. xvi.

p. 70 the mutation that transformed c-fps into v-fps: I. Sadowski, J.C. Stone, and T. Pawson, A noncatalytic domain conserved among cytoplasmic protein-tyrosine kinases modifies the kinase function and transforming activity of Fujinami sarcoma virus P130^gag-fps, Molecular and Cellular Biology 6(1986):4396–4408.

p. 71 including Src: Ibid.

p. 71 blocking access to the enzyme’s active site: S.R. Hubbard, M. Mohammadi, and J. Schlessinger, Autoregulatory mechanisms in protein-tyrosine kinases, Journal of Biological Chemistry 273(1998):11987–11990.

p. 71 “SH2,” for “Src-homology 2”: Sadowski, et al. (1986); T. Pawson, G.D. Gish, and P. Nash, SH2 domains, interaction modules, and cellular wiring, Trends in Cell Biology 11(2001):504–511; T. Pawson, Protein modules and signaling networks, Nature 373(1995):573–580.

p. 71 catalyzed by a trio of kinases: R. Triesman. Regulation of transcription by MAP kinase cascades, Current Opinion in Cell Biology 8(1996):205–215; C. Widmann, S. Gibson, M.B. Jarpe, et al., Mitogen-activated protein kinase: Conservation of a three-kinase module from yeast to human, Physiological Reviews 79 (1999): 143–180; L. Chang and M. Karin, Mammalian MAP kinase signaling cascades, Nature 410(2001):37–40.

p. 72 a GTPase known as Ras: Pawson, et al. (2001); Widmann, et al. (1999).

p. 72 by src-homology interaction domains: Pawson, et al. (2001); Pawson (1995); J.D. Scott and T. Pawson, Cell communication: The inside story, Scientific American, June 2000:72–79.

p. 74 in retaliation for their expulsion by Gα: Pierce et al. (2002); S.J. Perry and R. J. Lefkowitz, Arresting developments in heptahelical receptor signaling and regulation, Trends in Cell Biology 12(2002):130–138.

p. 74 a prelude to exile or even execution: Ibid.

p. 74 turns them over to the care of another G protein: Ibid.

p. 75 dressed up as an adaptor: Ibid.

p. 75 “Patterns” … “need the context of others to make sense”: C. Alexander, The Timeless Way of Building (New York: Oxford University Press, 1979), p. 312.

pp. 75–76 Begin your building project … and maintain an optimal population density: C. Alexander, S. Ishikawa, and M. Silverstein with M. Jacobson, I. Fiksdahl-King, S. Angel, A Pattern Language: Towns, Buildings, Construction (New York: Oxford University Press, 1977), pp. 21–25; 70–74; 304–309; 468–472; 508–512; 614–617; 828–832; 893–899; 1006–1008; 1018–1022; 1100–1104.

p. 76 “helps to complete those larger patterns”: Ibid., p. xii.

p. 76 “where we most expect to find variation, we find conservation”: Gerhart and Kirschner, Cells, Embryos and Evolution, p. 1.

p. 77 hand in hand with the evolution of these organisms: Ibid., pp. 45–89.

p. 78 Sixteen different genes … encoded by five…. Twelve genes specify γ subunits: Gomperts, et al., Signal Transduction, pp. 79–82.

p. 79 to the diversity of these organisms: Gerhart and Kirschner, Cells, Embryos, and Evolution, pp. 45–89.

p. 79: “Patterns have enormous power and depth”: Alexander, The Timeless Way, p. 98.

p. 79 “a few thousand gene products”: Specificity in signal transduction, Samuel Lunenfeld Research Institute website, www.mshri.on.ca/pawson/research2.html.

p. 81 the apical ectodermal ridge: J.W. Saunders Jr. The proximo-distal sequence of the origin of the parts of the chick wing and the role of the ectoderm, Journal of Experimental Zoology 108(1948):363–403.

p. 81 at right angles to its normal orientation: Saunders (1948); D.A. Summerbell, A quantitative analysis of the effect of excision of the AER from the chick limb bud, Journal of Embryology and Experimental Morphology 32(1974):651–660; D.A. Rowe and J.F. Fallon, The proximodistal determination of skeletal parts in the developing chick leg, Journal of Embryology and Experimental Morphology 68(1982):1–7; E. Zwilling, Interaction between limb bud ectoderm and mesoderm in the chick embryo. I. Axis establishment, Journal of Experimental Zoology 132(1956): 157–171.

p. 82 indistinguishable from a normal limb: G. R. Martin, The roles of FGFs in the early development of vertebrate limbs, Genes & Development 12(1998):1571–1585; L. Niswander, C. Tickle, A. Vogel, et al., FGF-4 replaces the apical ectodermal ridge and directs outgrowth and patterning of the limb, Cell 75(1993):579–587; J.F. Fallon, M.A. López, M.P. Ros, et al., FGF-2: Apical ectodermal ridge growth signal for chick limb development, Science 264(1994):104–107.

p. 82 in the space between wing and leg: Martin (1998); M.J. Cohn, J.-C. Izpisúa-Belmonte, H. Abud, et al., Fibroblast growth factors induce additional limb development from the flank of chick embryos, Cell 80 (1995):739–746; A. Vogel, C. Rodriguez, and J.-C. Izpisúa-Belmonte, Involvement of FGF-8 in initiation, outgrowth and patterning of the vertebrate limb, Development 122(1996):1737–1750.

p. 83 cells can be substituted for the bead: H. Ohuchi, T. Nakagawa, M.

Yamauchi, et al., An additional limb can be induced from the flank of the chick embryo by FGF-4, Biochemical and Biophysical Research Communications 204(1995): 809–816; H. Ohuchi, T. Nakagawa, A. Yamamoto, et al., The mesenchymal factor, FGF10, initiates and maintains the outgrowth of the chick limb bud through interaction with FGF8, an apical ectodermal factor, Development 124(1997):2235–2244.

p. 83 in mammals as it is in birds: H. Min, D.M. Danilenko, S.A. Scully, et al., Fgf-10 is required for both limb and lung development and exhibits striking functional similarity to Drosophila branchless, Genes and Development 12(1998):3156–3161; K. Sekine, et al., Fgf10 is essential for limb and lung formation, Nature Genetics 21(1999):138–141.

p. 83 instruct the optic vesicle to make a retina: Y. Furata and B.L.M. Hogan, BMP4 is essential for lens induction in the mouse embryo, Genes and Development 12(1998):3764–3775; A. Vogel-Höpker,T. Momose, H. Rohrer, et al., Multiple functions of fibroblast growth factor-8 (FGF-8) in chick eye development, Mechanisms of Development 94(2000):25–36.

p. 83 given you a duplicate set of fingers: A. López-Martinez, et al., Limb-patterning activity and restricted posterior localization of the amino-terminal product of sonic hedgehog cleavage, Current Biology 5(1995):791–796.

p. 84 “this is normally impossible in architecture”: J.J. Coulton, Ancient Greek Architects at Work (Ithaca, NY: Cornell University Press, 1997), p. 53.

p. 84 “to communicate the architect’s intention to the builders”: Ibid.

p. 84 a technique to specify proportions: Ibid., pp. 54–55.

p. 84 “Ex ovo omnia”: C. Singer, A History of Biology to About the Year 1900: A General Introduction of the Study of Living Things, 3rd ed. (London: Abelard-Schuman, 1962), p. 466.

p. 85 “as we read in the poems of Orpheus”: Quoted in G.W. Greg, The organizer, Scientific American 197(1957):79–88.

p. 85 “If organic form is not original”: W. Coleman, Biology in the 19th Century: Problems of Form, Function, and Transformation (New York: Wiley, 1971), p. 42.

p. 85 the movement of the stars or the actions of gravity: Singer, History of Biology, pp. 465–467; L.N. Magner, A History of the Life Sciences, 2nd ed. (New York: Marcel Dekker, 1994), pp. 171–186; S.F. Gilbert, Developmental Biology, 7th ed. (Sunderland, MA: Sinauer, 2003), pp. 6–7.

p. 86 when they peered into their microscopes: Singer, History of Biology, pp. 506–507; Magner, History of the Life Sciences, pp. 176–178.

p. 86 one of the first of these revisionists: Singer, History of Biology, pp. 469–471; Coleman, p. 41.

p. 86 how the tadpole got its eyes: S.F. Gilbert, A selective history of induction II: Spemann’s induction experiments, online at http://www.devbio.com.

p. 87 developed on that side of the embryo: Gilbert, Selective history of induction; C. Fulton and A. O. Klein, Explorations in Developmental Biology (Cambridge, MA: Harvard University Press, 1976), pp. 284–287.

p. 87 “by which the genes of a zygote” … “morphogens”: A.M. Turing, The chemical basis of morphogenesis, Philosophical Transactions of the Royal Society of London B 327(1952):37–72.

p. 88 might translate into biological structure: Turing (1952); Gilbert, Developmental Biology, pp. 20–21; P. Ball, The Self-made Tapestry (New York: Oxford University Press, 1999), pp. 78–83.

p. 88 “a technique of design”: Coulton, Ancient Greek Architects, p. 53.

p. 88 in the early rounds of cell division: Gilbert, Developmental Biology, pp. 59–60.

p. 89 that biologists call “transcription factors”: Comprehensive summaries of eukaryotic gene expression can be found in several leading textbooks; see, for example B. Alberts, A. Johnson, J. Lewis, et al., Molecular Biology of the Cell, 4th ed. (New York: Garland Science, 2002), pp. 379–415; or T.D. Pollard and W.C. Earnshaw, Cell Biology (Philadelphia: Saunders), pp. 215–237.

p. 90 use the information stored in its genome selectively: F. Jacob and J. Monod, Gene regulatory mechanisms in the synthesis of proteins, Journal of Molecular Biology 3(1961):318–356.

p. 92 “A man modeling a clay figure”: Coulton, Ancient Greek Architects, p. 53.

p. 93 “ensure that the lower parts of the building”: Ibid.

p. 93 a “kind of living developmental fossil”: J.T. Bonner, First Signals: The Evolution of Multicellular Development (Princeton, NJ: Princeton University Press, 2000), p. 74.

p. 94 “a directional arrow that points down the slope”: Ball, Self-Made Tapestry, p. 100.

p. 95 a replica of the French flag: L. Wolpert, R. Beddington, J. Brockes, et al., Principles of Development (Oxford: Oxford University Press, 1998), pp. 19–20.

p. 95 one of its most significant challenges: In addition to the technical challenges posed by the isolation and identification of morphogens themselves, it is increasingly clear that gradient formation in the living embryo is more complicated than prototypes like the “French flag model” might suggest. Passive diffusion, for example, is not the only way to create a gradient; an ambitious organism—or a morphogen-maker’s meddling neighbors—can hand-carry the morphogen from cell to cell or bind and impede its movement to shape local concentrations in highly precise ways. Moreover, cells exposed to the morphogen can only respond after they perceive and interpret the signal. As a result, the distribution and affinity of morphogen receptors or other signaling elements can also influence the final pattern set up by the morphogen. See J.B. Gurdon and P.Y. Bourillot, Morphogen gradient interpretation, Nature 413(2001):797–803, or A.A. Teleman, M. Strigini, and S.M. Cohen, Shaping morphogen gradients, Cell 105(2001):559–562 for more information.

p. 96 “‘Death’ is a difficult phenotype”: S.F. Gilbert, Christiane Nüsslein-Volhard and Drosophila embryogenesis, online at www.devbio.com. As Gilbert notes, conceptual and historical factors also comprised the progress of developmental genetics in this otherwise highly regarded model organism.

p. 96 rendered their impenetrable shells transparent: Ibid.

p. 96 a gene they christened “bicoid”: C.N. Nüsslein-Volhard, The bicoid morphogen papers (I): Account from CNV, Cell S116(2004):S1–S5.

p. 96 all-important task of orienting the embryo: H.G. Frohnhöfer and C. Nüsslein-Volhard, Organization of anterior pattern in Drosophila embryo by the maternal gene bicoid, Nature 324(1986):120–125.

p. 96 encodes one of these maternal morphogens: W. Driever and C. Nüsslein-Volhard, A gradient of bicoid protein in Drosophila embryos, Cell 54 (1988):83–93; W. Driever and C. Nüsslein-Volhard, The bicoid protein determines position in the Drosophila embryo in a concentration-dependent manner, Cell 54 (1988):95–104; D. St. Johnston and C. Nüsslein-Volhard, The origin of pattern and polarity in the Drosophila embryo, Cell 66(1992):201–219.

p. 97 a gradient that points from tail to head: St. Johnston and Nüsslein-Volhard (1992); R. Lehmann and C. Nüsslein-Volhard, The maternal gene nanos has a central role in posterior pattern formation in the Drosophila embryo, Development 112(1991):679–691.

p. 97 more or less evenly throughout: Gilbert, Developmental Biology, p. 272.

p. 97 Bicoid activates hunchback: W. Driever and C. Nüsslein-Volhard, The Bicoid protein is a positive regulator of hunchback transcription in the early Drosophila embryo, Nature 337(1989):138–143; G. Struhl, K. Struhl, and P.M. Macdonald, The gradient morphogen bicoid is a concentration-dependent transcriptional activator, Cell 57(1989):1259–1273.

p. 97 the Caudal protein to the tail end of the embryo: S.K. Chan and G. Struhl, Sequence-specific RNA binding by Bicoid, Nature 388(1997):634; R. Rivera-Pomar, D. Niessling, U. Schmidt-Ott, et al., RNA binding and translational suppression by bicoid, Nature 379(1996):746–749; D. Niessing, W. Driever, F. Sprenger, et al., Homeodomain position 54 specifies transcriptional versus translational control by Bicoid, Molecules and Cells 5(2000):395–401.

p. 97 renders it indecipherable: D.D. Barker, C. Wang, J. Moore, et al., Pumilio is essential for function but not for distribution of the Drosophila abdominal determinant, Nanos, Genes and Development 6(1992):2312–2326; C. Wreden, A.C. Verrotti, J.A. Schisa, et al., Nanos and pumilio establish embryonic polarity in Drosophila by promoting poster deadenylation of hunchback mRNA, Development 124(1997):3015–3023.

p. 97 gradient that backs up Nanos: Gilbert, Developmental Biology p. 274.

p. 97 a mist of Dorsal protein: St. Johnston and Nüsslein-Volhard (1992); A.J. Courey and J.-D. Huang, The establishment and interpretation of transcription factor gradients in the Drosophila embryo, Biochimica Biophysica Acta 1261(1995):1–18; S. Roth, D. Stein, and C. Nüsslein-Volhard, A gradient of nuclear localization of the dorsal protein determines dorsoventral pattern in the Drosophila embryo, Cell 59(1989):1189–1202.

p. 98 until it’s liberated from its minder: S. Roth, Y. Hiromi, D. Godt, et al., cactus, a maternal gene required for the proper formation of the dorsoventral morphogen gradient in Drosophila embryos, Development 112(1991):371–388.

p. 98 Dorsal can gambol into nuclei: Courey and Huang (1995).

p. 98 from the bottom of the embryo to its back: Roth, et al. (1989); C.A. Rushlow, K. Han, J.L. Manley, et al., The graded distribution of the dorsal morphogen is initiated by selective nuclear transport in Drosophila , Cell 59(1989):1165–1177; R. Steward, Relocalization of the dorsal protein from the cytoplasm to the nucleus correlates with its function, Cell 59(1989):1179–1188.

p. 98 “a coordinate system … to specify positions”: Gilbert, Developmental Biology, p. 297.

p. 99 known collectively as the gap genes: Ibid., p. 279; C. Nüsslein-Volhard and E. Weischaus, Mutations affecting segment number and polarity in Drosophila, Nature 287(1980):795–801.

p. 99 expressed in seven alternating stripes: Gilbert, Developmental Biology, pp. 281–283.

p. 99 segmental pattern of the fly larva: A. Martinez-Arias and P.A. Lawrence, Parasegments and compartments in the Drosophila embryo, Nature 313(1985):639–642.

p. 99 dividing one from the other: Gilbert, Developmental Biology, pp. 285–290; P.W. Ingham, A.M. Taylor, and Y. Nakano, Role of Drosophila patched gene in positional signaling, Nature 353(1991):184–187; J. Mohler and K. Vani, Molecular organization and embryonic expression of the hedgehog gene involved in cell-cell communication in segmental patterning in Drosophila, Development 115(1992):957–971.

p. 100 the structures they specify: Gilbert, Developmental Biology, pp. 285–290; E.B. Lewis, A gene complex controlling segmentation in Drosophila, Nature 276(1978):565–570; K. Harding, C. Wedeen, W. McGinnis, et al., Spatially regulated expression of homeotic genes in Drosophila, Science 229(1985):1236–1242; M.E. Akam, The molecular basis for metameric patterning in the Drosophila embryo, Development 101(1987):1–22; J. Gerhart and M. Kirschner, Cells, Embryos, and Evolution: Toward a Cellular and Developmental Understanding of Phenotypic Variation and Evolutionary Adaptability (Malden, MA: Blackwell Scientific, 1997), pp. 314–325.

p. 101: chanting “Decapentaplegic, Decapentaplegic”: C Neumann and S. Cohen, Morphogens and pattern formation, BioEssays 19(1997):721–729; R.D. St. Johnston and W.M. Gelbart, Decapentaplegic transcripts are localized along the dorsal-ventral axis of the Drosophila embryo. Embo Journal 6(1987):2785–2791; V.F. Irish and W.M. Gelbart, The decapentaplegic gene is required for dorsal-ventral patterning of the Drosophila embryo, Genes & Development 1(1987):868–879; E.I. Ferguson and K.V. Anderson, Decapentaplegic acts as a morphogen to organize dorsal-ventral pattern in the Drosophila embryo, Cell 71(1992):451–461; K.A. Wharton et al., An activity gradient of decapentaplegic is necessary for the specification of dorsal pattern elements in the Drosophila embryo, Development 117(1993):807–822.

p. 101 their felicitous effects on bone growth: B.L.M. Hogan, Bone morphogenetic proteins: Multifunctional regulators of vertebrate development, Genes & Development 10(1996):1580–1594; Y. Shi and J. Massagué, Mechanisms of TGF-β signaling from cell membrane to the nucleus, Cell 113(2003):685–700.

p. 101 “like an open hand”: Hogan (1996).

p. 101 have activated the genes twist and snail: A. Stathopoulos and M. Levine, Dorsal gradient networks in the Drosophila embryo, Developmental Biology 246(2002):57–67; R. Steward and S. Govind, Dorsal-ventral polarity in the Drosophila embryo, Current Opinion in Genetics and Development 3(1993):556–561.

p. 102 and silences it immediately: Neumann and Cohen (1997); Hogan (1996); S.D. Podos and E.I. Ferguson, Morphogen gradients: New insights from DPP, Trends in Genetics 15(1999):396–402.

p. 104 an entirely new family of tissues: Gilbert, Developmental Biology, p. 46; Gerhart and Kirschner, Cells, Embryos, and Evolution, pp. 351–352.

p. 104 “greater mobility and larger bodies”: Gilbert, Developmental Biology, p. 46.

p. 104 the three so-called germ layers … the endoderm: Ibid., p. 8; Magner, History of the Life Sciences, p. 211. The names “ectoderm,” “mesoderm,” and “endoderm” for the germ layers were introduced in 1855 by another embryologist, Robert Remak.

p. 104 “although already destined for different ends”: Quoted in Gilbert, S.F., A selective history of induction: I. Early concepts of embryonic induction, online at www.devbio.com.

p. 105 “cells required for the formation of specific organs”: Gerhart and Kirschner, Cells, Embryos, and Evolution, p. 476.

p. 106 “The first experiment”: H. Spemann, Nobel lecture, delivered December 12, 1935, online at www.nobel.se/medicine/laureates/1935/spemann-lecture.html.

p. 106 “… It became apparent”: Ibid.

p. 106 an embryo of a light-colored species: Ibid.; Greg (1957); H. Spemann and H. Mangold, Induction of embryonic primordial by implantation of organizers from a different species, translated from the German by Victor Hamburger and reprinted in Fulton and Klein, Explorations, pp. 287–325.

p. 108 secreted chemical signals, not direct contact: Greg (1957).

p. 108 where the sperm pierces the egg: E.M. DeRobertis, J. Larrain, M. Oelgeschläger, et al., The establishment of Spemann’s organizer and patterning of the vertebrate embryo, Nature Reviews Genetics 1(2000):171–181.

p. 108 will be the dorsal side of the embryo: Ibid.; J.R. Miller, B.A. Rowning, C.A. Larabell, et al., Establishment of the dorsal-ventral axis in Xenopus embryos coincides with the dorsal enrichment of Dishevelled that is dependent on cortical rotation, Journal of Cell Biology 146(1999):427–437.

p. 109 “Xenopus … Nodal-related” proteins: DeRobertis, et al. (2000); A.F. Schier and M.M. Shen, Nodal signaling in vertebrate development, Nature 403 (2000):385–389. Developmental biologists know the signaling center based in the endoderm as the “Nieuwkoop center,” after Pieter Nieuwkoop, who, along with Osamu Nakamura, demonstrated its critical role in the induction of the mesoderm and the formation of the organizer. See, for example, P.D. Nieuwkoop, The “organization center” of the amphibian embryo: Its origin, spatial organization and morphogenetic action, Advances in Morphogenetics 10(1973):1–310.

p. 109 fond memories of Hans Spemann: DeRobertis, et al. (2000); E.M. Agius, O. Oelgeschläger, C. Wessely, et al., Endodermal Nodal-related signals and mesoderm induction in Xenopus, Development 127(2000):1151–1159; Gilbert, Developmental Biology, p. 326.

p. 109 that will form the head structures: Ibid., p. 313.

p. 110 unless it’s told otherwise: A. Hemmati-Brivanlou and D.A. Melton, Vertebrate embryonic cells will become nerve cells unless told otherwise, Cell 88(1997):13–17.

p. 110 synonyms … at the ectoderm: DeRobertis, et al. (2000); E.L. Ferguson, Conservation of dorsal-ventral patterning in arthropods and chordates, Current Opinion in Genetics & Development 6(1996):424–431; S.A. Holley and E.I. Ferguson, Fish

are like flies are like frogs: Conservation of dorsal-ventral patterning mechanisms, BioEssays 19(1997):281–284.

p. 110 “Chordin! … Or “follistatin!”: DeRobertis, et al. (2000); Ferguson (1996); Holley and Ferguson (1997); W.C. Smith and R.M. Howland, Expression cloning of noggin, a new dorsalizing factor localized to the Spemann organizer in Xenopus embryos, Cell 70(1992):829–840; Y. Sasai, B. Lu, H. Steinbeisser, et al., Xenopus chordin: A novel dorsalizing factor activated by organizer-specific homeobox genes, Cell 79(1994):779–790; A. Hemmati-Brivanlou and D.A. Melton, Inhibition of activin signaling promotes neutralization in Xenopus, Cell 77(1994):273–281.

p. 110 tissues of the placenta: Gilbert, Developmental Biology, pp. 345–384.

p. 111 the dorsal side of a chick embryo: Ibid.

p. 111 neural ectoderm or epidermal ectoderm: Holley and Ferguson (1997); R.S.P. Beddington and J.C. Smith, Control of vertebrate gastrulation: Inducing signals and responding genes, Current Opinion in Genetics & Development 3(1993):655–661.

p. 111 the induction of the mesoderm: A. Streit, A.J Berliner, C. Papnayoutou, et al., Initiation of neural induction by FGF signaling before gastrulation, Nature 406(2000):74–78; J. Akai and K. Storey, Brain or brawn: How FGF signaling gives us both, Cell 115(2003):510–512.

p. 111 “The most important event of your life”: L. Wolpert, 1986, quoted in S.F. Gilbert, Developmental Biology, 4th ed. (Sunderland, MA: Sinauer Associates, 1994), p. 202.

p. 113 “Setting up a graded positional cue”: M. Osterfield, M.W. Kirschner, and J.G. Flanagan, Graded positional information: Interpretation for both fate and guidance, Cell 113(2003):425–428.

p. 113 “it is not surprising that evolution”: Ibid.

p. 114 begins life as part of a larger precursor: P.W. Ingham and A.P. McMahon, Hedgehog signaling in animal development; Paradigms and principles, Genes & Development 15(2001):3059–3087; J.J. Lee, S.C. Ekker, D.P. von Kessler, et al., Autoproteolysis in hedgehog protein biogenesis, Science 266(1994):1528–1537.

p. 114 and a molecule of cholesterol: P.W. Ingham, Hedgehog signaling: A tale of two lipids, Science 294(2001):1879–1881; J.A. Porter, K.E. Young, and P.A. Beachy, Cholesterol modification of hedgehog signaling proteins in animal development, Science 274(1996):255–259; R. Nusse, Wnts and Hedgehogs: Lipid-modified proteins and similarities in signaling mechanisms at the cell surface, Development 130(2003):5297–5305.

p. 115 exactly where it’s needed: Ingham and McMahon (2001); Nusse (2003); R. Burke, D. Nellen, M. Bellotto, et al., Dispatched, a novel sterol-sensing domain protein dedicated to the release of cholesterol-modified hedgehog from signaling cells, Cell 99(1999):803–815.

p. 115 so is its receptor, Patched: Ingham and McMahon (2001); Nusse (2003); J. Quirk, M. van den Huevel, and D. Henrique, The smoothened gene and Hedgehog signal transduction in Drosophila and vertebrate development, Cold Spring Harbor Symposia 62(1997):217–226.

p. 115 rather than a gene activator: Ingham and McMahon (2001); Nusse (2003).

p. 116 known as the neural plate: Gilbert, Developmental Biology, pp. 391–402.

p. 117 grown up and done with baby talk: R.E. Keller, Vital dye mapping of the gastrula and neurula of Xenopus laevis. II. Prospective areas and morphogenetic movements of the deep layer, Developmental Biology 51(1976):118–137.

p. 118 pointing in a ventral-to-dorsal direction: Y. Tanabe and T.M. Jessell, Diversity and pattern in the developing spinal cord, Science 274(1996):1115–1123; T.M. Jessell, Neuronal specification in the spinal cord: Inductive signals and transcriptional codes, Nature Reviews Genetics 1(2000):20–29.

p. 118 the bone morphogenetic proteins BMP4 and BMP7: Tanabe and Jessell (1996); Jessell (2000); K.F. Liem Jr., T.M. Jessel, and J. Briscoe, Regulation of the neural patterning activity of Sonic hedgehog by secreted BMP inhibitors expressed by notochord and somites, Development 127(2000):4855–4866.

p. 118 “Contingency plans are part and parcel of development”: E.C. Lai, Notch signaling: Control of cell communication and cell fate, Development 131(2004):965–973.

p. 119 daring to expose only its head and shoulders … in one gulp: S. Artavanis-Tsakonas, M.D. Rand, and R.J. Lake, Notch signaling: Cell fate control and signal integration in development, Science 284(1999):770–776; G. Weinmaster, The ins and outs of Notch signaling, Molecular and Cellular Neuroscience 9(1997): 91–10; G. Weinmaster, Notch signaling: Direct or what? Current Opinion in Genetics & Development 8(1998):436–442; R. Kopan, Notch: A membrane-bound transcription factor, Journal of Cell Science 115(2002):1095–1097.

p. 119 regulating so-called proneural genes: Lai (2004); Weinmaster (1997); Kopan (2002).

p. 119 touch receptors in our skin: J.B. Skeath and S.B. Carroll, Regulation of proneural gene expression and cell fate during neuroblast segregation in the Drosophila embryo, Development 114(1992):39–946; A.L. Parks and M.A.T. Muskavitch, Delta function is required for bristle organ determination and morphogenesis in Drosophila melanogaster, Developmental Biology 157(1993):484–496; P. Heitzler and P. Simpson, The choice of cell fate in the epidermis of Drosophila, Cell 64(1991):1083–1092; I. Greenwald and G.M. Rubin, Making a difference: The role of cell-cell interactions in establishing separate identities for equivalent cells, Cell 68(1992):271–281.

p. 121 which will change their minds: T. Gridley, Notch signaling in vertebrate development and disease, Molecular and Cellular Neuroscience 9(1997):103–108.

p. 121 with superfluous neurons: A. Chitnis, D. Henrique, J. Lewis, et al., Primary neurogenesis in Xenopus embryos regulated by a holologue of the Drosophila neurogenic gene Delta, Nature 375(1995):761–766.

p. 122 spitting out tickets at the end of each round: O. Pourquié, The segmentation clock: Converting embryonic time into spatial pattern, Science 301(2003):328–330.

p. 122 the center of the mechanism: Pourquié (2003); C. Jouve, T. Imura, and O. Pourquié, Onset of segmentation clock in the chick embryo: Evidence for oscillations in the somite precursors in the primitive streak, Development 129(2002):1107–1117.

p. 122 that suppresses Notch signaling: Pourquié (2003).

p. 122 the growth factor FGF: Pourquié (2003); J. Dubrelle, M.J. McGrew, and O. Pourquié, FGF signaling controls somite boundary position and regulates segmentation clock control of spatiotemporal Hox gene activation, Cell 106(2001): 219–232; A. Sawada, M. Shinya, Y.-J. Jiang, et al., Fgf/MAPK signaling is a crucial positional cue in somite boundary formation, Development 128(2001): 4873–4880.

p. 123 in particular the Wnt proteins: H.M. Stern, A.M.C. Brown, and S.D. Hauschka, Myogenesis in paraxial mesoderm: preferential induction by dorsal neural tube and by cells expressing Wnt-1, Development 121(1995):3675–3686; M. Ikeya and S. Takada, Wnt signaling from the dorsal neural tube is required for the formation of the medial dermomyotome, Development 125(1998):4969–4976.

p. 123 the first Wnt to be discovered: K.M. Cadigan and R. Nusse, Wnt signaling: A common theme in animal development, Genes & Development 11(1997): 3286–3305. An excellent resource for more information on the Wnt signaling pathway is the Wnt Gene Homepage, online at http://www.stanford.edu/rnusse/wntwindow.html.

p. 123 embellished with a fatty acid, palmitate: Nusse (2003).

p. 123 spelling out “dorsal” in the amphibian embryo: Cadigan and Nusse (1997); W.J. Nelson and R. Nusse, Convergence of Wnt, β-catenin, and cadherin pathways, Science 303(2004):1483–1487; A. Wodarz and R. Nusse, Mechanisms of Wnt signaling in development, Annual Review of Cell and Developmental Biology 14(1998):59–88.

p. 123 before it ever gets near the nucleus: Cadigan and Nusse (1997); Wodarz and Nusse (1998).

p. 123 disperses the Degradation Complex: Ibid.

p. 123 the transcription factors MyoD and Myf-5: Gerhart and Kirschner, Cells, Embryos, and Evolution, pp. 254–260; Gilbert, Developmental Biology, pp. 473–474.

p. 124 every time they say “FGF”: Martin (1998).

p. 124 each has its own nuance: D.M. Ornitz and N. Itoh, Fibroblast growth factors, Genome Biology 2(2001): reviews3005.1–3005.12, online at http://genomebiology.com/2001/2/3/reviews/3005.

p. 124 “fibroblast growth factor eight” (FGF8): P.H. Crossley, G. Minowada, C.A. MacArthur, et al., Roles for FGF8 in the induction, initiation, and maintenance of chick limb development, Cell 84(1996):127–136.

p. 124 it has two things to say: Ohuchi, et al. (1997).

p. 125 just above the apical ectodermal ridge: Martin (1998); G. Martin, Making a vertebrate limb: New players enter from the wings, BioEssays 23 (2001): 856–868; R.D. Riddle, M. Ensini. C. Nelson et al., Induction of the LIM homeobox gene Lmx 1 by Wnt7a establishes dorsoventral pattern in the vertebrate limb, Cell 83(1995):631–640.

p. 125 where the bud leaves the body wall: R.D. Riddle, R.L. Johnson, E. Laufer, et al., Sonic hedgehog mediates the polarizing activity of the ZPA, Cell 75(1993):1401–1416.

p. 125 to keep the words flowing: Vogel, et al. (1996); Ohuci, et al. (1995); Crossley, et al. (1996); L. Niswander, S. Jeffrey, G.R. Martin, et al., A positive feed-

back loop coordinates growth and patterning in the vertebrate limb, Nature 371(1994):609–612.

p. 125 the proximal-distal pattern of the developing limb: D. Summerbell, J.H. Lewis, and L. Wolpert, Positional information in chick limb morphogenesis, Nature 244(1973):492–496.

p. 127 stopped them in their tracks: A.T. Dudley, M.A. Ros, and C.J. Tabin, A re-examination of proximodistal patterning during vertebrate limb development, Nature 418(2002):539–544.

p. 129 a death that was quiet, orderly, even dignified: J.F.R. Kerr, A.H. Wylie, and A.R. Currie, Apoptosis: A basic biological phenomenon with wide ranging implications in tissue kinetics, British Journal of Cancer 26(1972):239–257.

p. 129 the availability of precious resources: R.E. Ellis, J. Yuan, and H.R. Horvitz, Mechanisms and function of cell death, Annual Review of Cell Biology 7(1997):663–698.

p. 130 scavenge the remains of the dead one: M. Barinaga, Death by dozens of cuts, Science 280(1998):32–34; N.A. Thornberry and Y. Lazebnik, Caspases: Enemies within, Science 28(1998):1312–1316; M.O. Hengartner, The biochemistry of apoptosis, Nature 407(2000):770–776.

p. 130 “Caspases are members of the society too”: Y. Lazebnik, “Enemies Within or the Biochemistry of Apoptosis,” presentation at the 164th national meeting of the American Association for the Advancement of Science, February 16, 1998.

p. 130 the demise of the enzyme’s unfortunate landlord: Hengartner (2000); D.D. Newmeyer and S. Ferguson-Miller, Mitochondria: Releasing power for life and unleashing the machineries of death, Cell 112(2003):481–490; D.R. Green and J.C. Reed, Mitochondria and apoptosis, Science 281(1998):1309–1311.

p. 131 cell savers Bcl-2 and Bcl-x_L: Hengartner (2000); Newmeyer and Ferguson-Miller (2003); T. Chittenden, BH3 domains: Intracellular death-ligands critical for initiating apoptosis, Cancer Cell 2(2002):165–166; J.M. Adams and S. Cory, The Bcl-2 protein family; Arbiters of cell survival, Science 281(1998):1322–1325.

p. 131 a cell’s decision to live or die: Ellis, et al. (1997); G. Evan and T. Littlewood, A matter of life and cell death, Science 281(1998):1317–1321.

p. 131 the collective suicide of thousands of cells: L. Grotewold and U. Ruther, Bmp, Fgf, and Wnt signaling in programmed cell death and chondrogenesis during vertebrate limb development: The role of Dickkopf-1, International Journal of Developmental Biology 46(2002):943–947; R. Merino, Y Gañán, D. Macias, et al., Bone morphogenetic proteins regulate interdigital cell death in the avian embryo, Annals of the New York Academy of Sciences 887(1999):120–132; Y. Yokouchi, J. Sakiyama, T. Kameda, et al., BMP-2/-4 mediate programmed cell death in chicken limb buds, Development 122(1996):3725–3724; H. Zou and L. Niswander, Requirement for BMP signaling in interdigital apoptosis and scale formation, Science 272(1996):738–741.

p. 131 A ring of death … behind a BMP antagonist: Merino, et al. (1999); Yokouchi, et al. (1996); Zou and Niswander (1996); Y. Gañán, D. Macias, M. Duterque-Coquillaud, et al., Role of TGFP and BMPs as signals controlling the posi-

tion of the digits and the areas of cell death in the developing chick autopod, Development 122(1996):2349–2357; R. Merino, Y. Gañán, D. Macias, et al., Morphogenesis of digits in the avian limb is controlled by FGFs, TGFβs, and Noggin through BMP signaling, Developmental Biology 200(1998):35–45.

p. 131 the cartilage template for future bone: Merino, et al. (1999); Merino, et al. (1998).

p. 132 BMP actually means “build”: Grotewold and Ruther (2002); Merino, et al. (1998).

p. 132 “BMP” means “go kill yourself”: Grotewold and Ruther (2002); Merino, et al. (1999); J.A. Montero, Y. Gañán, D. Macias, et al., Role of FGFs in the control of programmed cell death during limb development, Development 128(2001):2075–2084.

p. 132 “is a social phenomenon”: M.C. Raff, “Death wish,” The Sciences July/August (1996):36–40.

p. 132 as well as the MAP kinases: L.C. Cantley, The phosphoinositide 3-kinase pathway, Science 296(2002):1655–1657.

p. 133 half of which are actually needed: M.C. Raff, B.A. Barres, J.F. Burne, et al., Programmed cell death and the control of cell survival: Lessons from the nervous system, Science 262(1993):695–700.

p. 133 out of the head like rising bread dough: K. Kuida, et al., Decreased apoptosis in the brain and premature lethality in CPP32-deficient mice, Nature 384(1996):368–372.

p. 133 face certain death by apoptosis: J. Yuan and B.A. Yankner, Apoptosis in the nervous system, Nature 407(2000):802–809.

p. 133 Discovered in the 1950s by Rita Levi-Montalcini: S. Cohen, R. Levi-Montalcini, and V. Hamburger, A nerve growth-stimulating factor isolated from sarcomas 37 and 180, Proceedings of the National Academy of Sciences USA 40(1954):1014–1018.

p. 133 binds to a receptor tyrosine kinase called TrkA: E. Huang and L. Reichardt, Trk receptors: Roles in neuronal signal transduction, Annual Review of Biochemistry 72(2003):609–642.

p. 134 Instead, the TrkA receptor … to act as the courier: F.D. Miller and D.R. Kaplan, TRK makes the retrograde, Science 295(2002):1471–1473; B.L. MacInnis and R.B. Campenot, Retrograde support of neuronal survival without retrograde transport of nerve growth factor, Science 295(2002):536–1539; D.L. Senger and R.B. Campenot, Rapid retrograde tyrosine phosphorylation of trkA and other proteins in rat sympathetic neurons in compartmented cultures, Journal of Cell Biology 138(1997):411–421.

p. 134 and kill themselves in despair: Dudley, et al. (2002).

p. 136 “The embryo inherits a rather compact ‘tool kit’”: Gilbert, Developmental Biology, pp. 149–150.

p. 136 “Genes expressed during formation of one part”: M. Ptashne and A. Gann, Genes and Signals (Cold Spring Harbor, NY: Cold Spring Harbor Press, 2002), p. 3.

p. 136 even this lowly creature … can mouth a Wnt sentence: B. Hobmayer,

F. Rentzsch, K. Kuhn, et al., WNT signaling molecules act in axis formation in the diploblastic metazoan hydra, Nature 407(2000):186–189.

p. 136 the Wnt signaling relay, in plants: V. Amador, E. Monte, J. Garcia-Marinez, et al., Gibberellins signal nuclear import of PHOR1, a photoperiod-responsive protein with homology to Drosophila armadillo, Cell 106(2001):343–354.

p. 137 fly wings by Hedgehog and Wingless: M. Stringini and S.M. Cohen, Formation of morphogen gradients in the Drosophila wing, Seminars in Cell and Developmental Biology 10(1999):335–344.

p. 137 30,000 different words to compose his plays: “A man of many words,” online at http://shakespeare.about.com/b/a/020320.html.

p. 140 “the fell blows of circumstance”: W. Cannon, The Wisdom of the Body (New York: W.W. Norton, 1929), p. 244.

p. 140 “continue to live and carry on their functions”: Cannon, Wisdom, pp. 22–23.

p. 140 “the coordinated physiological processes”: Cannon, Wisdom, p. 24.

p. 140 possible only because biological processes are so elastic: Cannon, Wisdom, pp. 21, 24.

p. 141 the exchange of chemical signals was also apparent: Cannon, Wisdom, p. 255.

p. 141 “what influences the signal” … “has disclosed the facts”: Cannon, Wisdom, p. 289.

p. 141 “the unstable stuff of which we are composed”: Cannon, Wisdom, p. 23.

p. 142 at about 120 to be exact: B. Alberts, A. Johnson, J. Lewis, M. Raff, K. Roberts, and P. Walter, Molecular Biology of the Cell, 4th ed. (New York: Garland Science), p. 1292.

p. 143 are not always identical twins: Ibid., p. 1262; C.S. Potten, M. Loeffler, Stem cells: Attributes, cycles, spirals, pitfalls, and uncertainties. Lessons for and from the crypt, Development 110(1990):1001–1020.

p. 144 “than any other tissue in the body”: Alberts, et al., Molecular Biology of the Cell, p. 1260.

p. 144 “You there!” they shout … “Platelet-derived growth factor!”: T.D. Pollard and W.C. Earnshaw, Cell Biology (Philadelphia: Saunders, 2002), pp. 547–548; S. Werner and R. Grose, Regulation of wound healing by growth factors and cytokines, Physiological Reviews 83(2003):835–870; W.J.H. Kim, Cellular signaling during tissue regeneration, Yonsei Medical Journal 41(2000):692–703; R.A. Clark, Regulation of fibroplasia in cutaneous wound repair, American Journal of Medical Science 306 (1993):42–48.

p. 144 fibroblast growth factors FGF2 and FGF7: Werner and Grose (2003); Kim (2000).

p. 144 pull the edges of the wound together: Pollard and Earnshaw, Cell Biology, pp. 547–548; Werner and Grose (2003); Clark (1993).

p. 144 the keratinocytes and their progenitors: Werner and Grose (2003).

p. 144 encouraging them to divide: Werner and Grose (2003); Kim (2000).

p. 144 raise a roof over the wound: Werner and Grose (2003); Kim (2000); G. Zambruno, P.C. Marchisio, A. Marconi, et al., Transforming growth factor-beta 1 modulates beta 1 and beta 5 integrin receptors and induces the de novo expression of the alpha v beta 6 heterodimer in normal human keratinocytes: Implications for wound healing, Journal of Cell Biology 129(1995):853–865.

p. 145 an entire network of new capillaries: Werner and Grose (2003); S. Frank, G. Hübner, G. Breier, et al., Regulation of vascular endothelial growth factor expression in cultured keratinocytes: Implications for normal and impaired wound healing, Journal of Biological Chemistry 270(1995):12607–12613.

p. 145 poked around the primordial aorta: S.F. Gilbert, Developmental Biology, 7th ed. (Sunderland, MA: 2003), p. 507; M. Kondo, A.J. Wagers, and M.G. Manz, Biology of hematopoietic stem cells and progenitors: Implications for clinical application, Annual Review of Immunology 21(2003):759–806.

p. 146 give up their wandering ways: Kondo, et al. (2003); D.E. Wright, A.J. Wagers, and A.P. Gulati, Physiological migration of hematopoietic stem and progenitor cells, Science 294(2001):1933–1936.

p. 146 dividing and replenishing: T. Reya, A.W. Duncan, L. Ailles, et al., A role for Wnt signaling in self-renewal of haematopoietic stem cells, Nature 423(2003): 409–414.

p. 146 another synonym for “stay young”: F.N. Karanu, B. Murdoch, L. Gallacher, et al., The notch ligand jagged-1 represents a novel growth factor of human hematopoietic stem cells, Journal of Experimental Medicine 192(2000):1365–1372; B. Varnum-Finney, L. Wu, M. Yu, et al., Pluripotent, cytokine-dependent, hematopoietic stem cells are immortalized by constitutive Notch1 signaling, Nature Medicine 6(2000):1278–1281.

p. 146 Sonic hedgehog is a third: G. Bhardwaj, B. Murdoch, D. Wu, et al., Sonic hedgehog induces the proliferation of primitive human hematopoietic cells via BMP regulation, Nature Immunology 2(2001):172–180.

p. 146 as much as tenfold: Kondo, et al. (2003).

p. 147 of that fateful choice: Kondo, et al. (2003); A.J. Wagers, J.L. Christensen, and I.L. Weissman, Cell fate determination from stem cells, Gene Therapy 9(2002):606–612; Gilbert, Developmental Biology, pp. 508–509; Alberts, et al., Molecular Biology of the Cell, pp. 1283–1296.

pp. 147–148 rather than endocrine glands: W.J. Leonard, Type I cytokines and interferons and their receptors, in W.E. Paul (ed), Fundamental Immunology, 4th ed. (Philadelphia: Lippencott-Raven, 1999), pp. 741–774.

p. 148 is a separate protein: D.E. Levy and J.E. Darnell, Jr., STATs: Transcriptional control and biological impact, Nature Reviews Cell and Molecular Biology 3(2002):651–662; A. Ziemiecki, A.G. Harpur, and A.F. Wilks, Jak protein tyrosine kinases: Their role in cytokine signaling, Trends in Cell Biology 4(1994):207–212; C. Schinder and J.E. Darnell, Jr., Transcriptional responses to polypeptide ligands: the Jak-STAT pathway, Annual Review of Biochemistry 64(1995):621–651; J.N. Ihle, B.A.

Witthuhn, F.W. Quell, et al., Signaling through the hematopoietic cytokine receptors, Annual Review of Immunology 13(1995):369–398.

p. 148 interleukin-3, and interleukin-9: Gilbert, Developmental Biology, p. 508.

p. 148 secreted by the kidney: E. Goldwasser, Erythropoietin: A somewhat personal history, Perspectives in Biology and Medicine 40(1996):18–32; J.W. Fisher, A quest for erythropoietin over nine decades, Annual Review of Pharmacology and Toxicology 38(1998):1–20; W.S. Alexander, Cytokines in hematopoiesis, International Review of Immunology 16(1998):651–682.

p. 149 quickly lose their will to live: Reya, et al. (2003).

p. 149 role in stem cell apoptosis: Wagers, et al. (2002).

p. 150 stem cells of normal mice: J. Domen and I.L. Weissman, Hematopoietic stem cells need two signals to prevent apoptosis; BCL-2 can provide one of these, Kit1/c-Kit signaling the other, Journal of Experimental Medicine 192(2000):1707–1718; J. Domen, S.H. Cheshier, and I.L. Weissman, The role of apoptosis in the regulation of hematopoietic stem cells: Overexpression of Bcl-2 increases both their number and repopulation potential, Journal of Experimental Medicine 191(2000):253–264.

p. 150 “the body has no protection”: Cannon, Wisdom, p. 319.

p. 150 veterinarians call it: Interview transcript, John Incardona, in Rediscovering Biology: Unit 7, Genetics of Development, online at www.learner.org/channel/courses/biology/units/gendev/experts/incardona.html.

p. 151 incidence of cyclopia: Ibid.

p. 151 appropriately enough, “cyclopamine”: Ibid.; R.F. Keeler and W. Binns, Teratogenic compounds of Veratrum californicum (Durand). V. Comparison of cyclopean effects of steroidal alkaloids from the plant and structurally related compounds from other sources, Teratology 1(1968):5–10.

p. 151 also born with cyclopia: C. Chiang, Y. Litingtung, E. Lee, et al., Cyclopia and defective axial patterning in mice lacking Sonic hedgehog gene function, Nature 383(1996):407–413.

p. 151 the mirror image of cyclopia: “Basal cell nevus syndrome,” Diseases and Conditions, online at http://health.allrefer.com/health/basal-cell-nevus-syndrome-info.html.

p. 151 signaling pathway is never quiet: A.E. Bale and K.P. Yu, The hedgehog pathway and basal cell carcinoma, Human Molecular Genetics 10(2001):757–762; H. Hahn, et al., Mutations of the human homolog of Drosophila patched in the nevoid basal cell carcinoma syndrome, Cell 85(1996):841–851; R.L. Johnson, et al., Human homolog of patched, a candidate gene for the basal cell nevus syndrome, Science 272(1996):1668–1671.

p. 152 “and its somatic milieu”: D.R. Green and G.E. Evan, A matter of life and death, Cancer Cell 1(2002):19–30.

p. 153 in two ways: Alberts, et al., Molecular Biology of the Cell, p. 1333; D. Hanahan and R.A. Weinberg, The hallmarks of cancer, Cell 100(2000):57–70; B.A.J. Ponder, Cancer genetics, Nature 411(2001):336–341.

p. 153 legitimate growth signals: P. Blume-Jensen and T. Hunter, Oncogenic kinase signaling, Nature 411(2000):355–365.

p. 153 one out of every four human cancers: Alberts, et al., Molecular Biology of the Cell, p. 1335; M. Barbacid, Ras genes, Annual Review of Biochemistry 56(1983):779–827.

p. 153 and multiple myeloma: Blume-Jensen and Hunter (2000).

p. 153 no longer begins with Hedgehog: Aberrations in Hedgehog signaling have now been implicated in a number of other cancers as well, including cancers of the digestive tract, prostate, lung, and bladder. An overview of the role of the Hedgehog pathway in cancer can found in Beachy, Karhadkar, and Berman (2004).

p. 154 “They are the only cells … that live long enough”: Cancer as a stem cell disease. For a recent review of the “cancer stem cell” concept, see P.A. Beachy, S.S. Karhadkar, and D.M. Berman, Tissue repair and stem cell renewal in carcinogenesis, Nature 432(2004):324–331.

p. 154 The fourth most common type of cancer: “Cancer Facts and Figures 2004,” American Cancer Society, online at www.cancer.org.

p. 154: mitogen and morphogen Wnt: B. Vogelstein and K.W. Kinzler, The multistep nature of cancer, Trends in Genetics 9(1993):138–141; K.W. Kinzler and B. Vogelstein, Lessons from hereditary colorectal cancer, Cell 87(1996):159–170.

p. 154 70 percent of colorectal cancers: Alberts, et al., Molecular Biology of the Cell, p. 1352.

p. 155 $2,200 to repair the damage: “White-tailed Deer in Pennsylvania,” report by the Bureau of Wildlife management, Pennsylvania Game Commission, July 2003, online at http://www.pcg.state.pa.us/lib/pgc/deer/pdf/Management_Plan6.03.pdf.

p. 155 appease frustrated sportsmen: Ibid.

p. 155 Today, 1.5 million deer: Ibid.

p. 155 into a space big enough for thirty: “Deer Info Page,” The Pennsylvania Audubon Society, online at http://pa.audobon.org/deerinfopage.html.

p. 155 have more babies: “Deer Biology,” presentation by Dr. Gary Alt at the Conference on the Impact of Deer on the Biodiversity and Economy of the State of Pennsylvania, January 6, 2004, transcript available online at http://pa.audobon.org/chapter/pa/pa/Alt.html.

p. 156 twins or even triplets every spring: Pennsylvania Game Commission, “White-tailed Deer” (2003).

p. 156 “The cancer cell is a renegade”: R. Weinberg, One Renegade Cell (New York: Basic Books, 1999), p. 97.

p. 157 command them to commit suicide: Green and Evan (2002); G.I. Evan and K.H. Vousden, Proliferation, cell cycle and apoptosis in cancer, Nature 411(2001):342–348.

p. 157 blocking the death program: Ibid.

p. 158 on which all cancers are built: Green and Evan (2002).

p. 158 “If it were not permitted to expose our lives”: G. Minois, History of Suicide: Voluntary Death in Western Culture, translated by L.G. Cochrane (Baltimore: The Johns Hopkins University Press, 1999), p. 71.

p. 160 protect the community at large: B. Vogelstein, D. Lane, and A.J. Levine, Surfing the p53 network, Nature 408(2000):307–310; A.J. Levine, p53, the cellular gatekeeper for growth and division, Cell 88(1997):323–331.

p. 160 almost as soon as it’s off the ribosome: Vogelstein, et al. (2000).

p. 160 of its civic duty to die: Vogelstein, et al. (2000); N.E. Sharpless and R.A. DePinho, p53: Good cop/bad cop, Cell 110(2002):9–12; J.C. Reed, Dysregulation of apoptosis in cancer, Journal of Clinical Oncology 17(1999):2941–2953.

p. 160 kill themselves the next: Green and Evan (2002); Evan and Vousden (2001); G. Evan and T. Littlewood, A matter of life and cell death, Science 281(1998): 1317–1322.

p. 160 PIP3 as its direct object: Green and Evan (2002); L.C. Cantley, The phosphoinositide 3-kinase pathway, Science 296(2002):1655–1657; also available online at Science’s Signal Transduction Knowledge Environment website, http://www.stke.org/cgi/cm.CMP_6557; A. Kauffmann-Zeh, P. Rodriguez-Viciana, E. Ulrich, et al., Suppression of c-Myc-induced apoptosis by Ras signaling through PI(3)K and PKB, Nature 385(1997):544–548.

p. 160 operating the cell cycle: D.L. Levens, Reconstructing MYC, Genes & Development 17(2003):1071–1077.

p. 160 dividing cells to the police: Green and Evan (2002); Evan and Vousden (2001); Evan and Littlewood (1998).

p. 160 certain to trigger suicidal ideation: Ibid.

p. 160 releasing deadly cytochrome c: P. Juin, A.O. Hueber, T. Littlewood, and G. Evan, c-Myc-induced sensitization to apoptosis is mediated through cytochrome c release, Genes & Development 13(1999):1367–1381.

p. 160 they cut so beautifully: Green and Evan (2002); Evan and Vousden (2001); Evan and Littlewood (1998).

p. 162 researchers call “death ligands”: A. Ashkenazi and V.M. Dixit, Death receptors: Signaling and modulation, Science 281(1998):1305–1308.

p. 163 resembled the worm protein: N.A. Thornberry and Y. Lazebnik, Caspases: Enemies within, Science 281(1998):1312–1316; M. Barinaga, Forging a path to cell death, Science 273(1996):735–737.

p. 163 discovery of the first caspase: Barinaga (1996).

p. 163 molecular arms dealers: Ashkenazi and Dixit (1998).

p. 163 cell survival rather than cell death: B.C. Barnhart and M.E. Peter, The TNF receptor 1: A split personality complex, Cell 114(2003):148–150. O. Micheau and J. Tschopp, induction of TNF receptor 1-mediated apoptosis via two sequential signaling complexes, Cell 114(2003):181–190.

p. 164 a second signaling complex: Ibid.

p. 164 compromising treatment: R.W. Johnstone, A.A. Ruefli, and S.W. Lowe, Apoptosis; A link between cancer genetics and chemotherapy, Cell 108(2002):153–164; A.S. Baldwin, Control of oncogenesis and cancer therapy resistance by the transcription factor NF-κB, Journal of Clinical Investigation 107(2001):241–246.

p. 164 shielding the tumors from its lethal effects: R.M. Pitti, S.A. Marsters, D.A. Lawrence, et al., Genomic amplification of a decoy receptor for Fas ligand in lung and colon cancer, Nature 396(1998):699–703. Mutations in death ligand signaling pathways are not the only way to derail apoptosis, freeing a cell to pursue delusions of immortality. Overexpression of anti-apoptotic factors like Bcl-2, for example, upsets the balance of power at the mitochondrial membrane; as a result, even a cell that’s well aware that it’s on the road to malignancy cannot access cytochrome c. The

name “Bcl,” in fact, comes from the discovery of such mutations in human follicular B cell lymphoma, a blood cancer. See Green and Evan (2002) and Y. Tsujimoto, L.R. Finger, J. Yunis, et al., Cloning of the chromosome breakpoint of neoplastic B cells with the t(14; 18) chromosome translocation, Science 226(1984):1097–1099.

p. 167 “Insofar as the constancy of the fluid matrix”: Cannon, Wisdom, p. 302.

p. 167 can also poison them: M. Brownlee, Biochemistry and molecular cell biology of diabetic complications, Nature 414(2001):813–820.

p. 167 retina, kidney, and peripheral nerves: Ibid.

p. 168 glycogen or fatty acids: J.E. Pessin and A.R. Saltiel, Signaling pathways in insulin action: Molecular targets of insulin resistance, Journal of Clinical Investigation 106(2000):165–169; J.E.-B. Reusch, Focus on insulin resistance in type 2 diabetes: Therapeutic implications, Diabetes Educator 24(1999):188–193; B.B. Kahn and J.S. Flier, Obesity and insulin resistance, Journal of Clinical Investigation 106(2000):473–481.

p. 168 18 million Americans: American Diabetes Association, “National Diabetes Fact Sheet,” online at http://www.diabetes.org/diabetes-statistics/national-diabetes-fact-sheet-jsp.

p. 168 metabolic disease in the world: A. Dove, Seeking sweet relief for diabetes, Nature Biotechnology 20(2002):977–981.

p. 168 increases the risk of heart attack … limb amputation: Diabetes Fact sheet; Dove (2002).

p. 168 an estimated $100 billion annually: Diabetes Fact Sheet.

p. 168 children … account for an increasing proportion: Diabetes Fact Sheet; American Diabetes Association, “Diabetes Facts and Figures,” online at http://www.diabetes.org/ada/facts.asp.

p. 168 expected to double over the next 25 years: Dove (2002).

p. 169 discovered the pancreas: “History of the Pancreas,” online at http://www.pancreasclub.com/history.

p. 169 in the fourth century BC: Ibid.

p. 169 date back to 1500 BC: Ibid.; Canadian Diabetes Association, “The History of Diabetes,” online at www.diabetes.ca/Section_about/timeline.asp.

p. 169 coursing through the trunk: “History of the Pancreas”; A.Q. Maisel, The Hormone Quest (New York: Random House, 1965), p. 6.

p. 169 initial segment of the small intestine: “History of the Pancreas.”

p. 170 was an exocrine gland: Ibid.

p. 170 under the microscope: Ibid.; M. Bliss, The Discovery of Insulin (Chicago: The University of Chicago Press, 1982), p. 25.

p. 170 the unfortunate animal developed diabetes: Maisel, The Hormone Quest, p. 24; Bliss, Discovery of Insulin, pp. 25–26; C. Singer and E.A. Underwood, A Short History of Medicine (New York: Oxford University Press, 1962), p. 553.

p. 170 the deficiency theory was correct: Maisel, The Hormone Quest, pp. 25–26; Bliss, Discovery of Insulin, pp. 25–26; J.C. Krantz, Jr., Frederick G. Banting, Charles H. Best, and insulin, in Historical Medical Classics Involving New Drugs (Baltimore: Williams & Wilkins, 1974), pp. 58–65.

p. 170 did not respond to insulin: H.P. Himsworth, Diabetes mellitus: Its

differentiation into insulin-sensitive and insulin-insensitive types, Lancet 1(1936):117–121.

p. 171 rather than alarmingly low: R.S. Yalow and S.A. Berson, Plasma insulin concentrations in nondiabeteic and early diabetic subjects, Diabetes 4(1960):254–260.

p. 171 does such a great cover-up job: A.R. Saltiel, The molecular and physiological basis of insulin resistance: Emerging implications for metabolic and cardiovascular diseases, Journal of Clinical Investigation 106(2000):163–164; K.S. Polonsky, J. Sturis, and G.I. Bell, Non-insulin-dependent diabetes mellitus—A genetically programmed failure of the beta cell to compensate for insulin resistance, New England Journal of Medicine 334(1996):777–783; B.B. Kahn, Type 2 diabetes: When insulin secretion fails to compensate for insulin resistance, Cell 92(1998):593–596; M.K. Cavaghan, D.A. Ehrmann, and K.S. Polonsky, Interactions between insulin resistance and insulin secretion, Journal of Clinical Investigation 106(2000):329–333.

p. 172 a cartoon … to accompany a review article: C.R. Kahn, What is the molecular basis for the action of insulin? Trends in Biochemical Sciences 4(1979): N263–N266.

p. 172 a pair of β subunits that constitute the kinase: A.R. Saltiel and C.R. Kahn, Insulin signaling and the regulation of glucose and lipid metabolism, Nature 414(2001):799–805.

p. 172 a phosphate or two themselves: M.F. White, The IRS-signaling system: A network of docking proteins that mediate insulin action, Molecular and Cellular Biochemistry 182(1998):3–11.

p. 172 and then a second, IRS-2: Ibid.; M.F. White, R. Maron, and C.R. Kahn, Insulin rapidly stimulates tyrosine phosphorylation of Mr-185,000 protein in intact cells, Nature 318(1985):183–186.

p. 173 in the signaling relay: M.F. White, Insulin signaling in health and disease, Science 302(2003):1710–1711. For an illustration of the current state of insulin signaling, see the “Insulin Signaling Pathway” Connections Map at the Science STKE website: www.stke.sciencemag.org/cgi/cm/cmp_12069.

p. 174 fleet of membrane-bound vesicles: P.R. Shepherd and B.B. Kahn, Glucose transporters and insulin action, New England Journal of Medicine 341(1999): 248–257. The GLUT4 transporter is actually one member of a group of five homologous glucose transport proteins; of the five, it is the one most important to insulin-mediated glucose uptake.

p. 174 actin fibers of the cytoskeleton: Saltiel and Kahn (2001).

p. 175 IRS protein—PI3kinase—PIP3—Akt: Ibid.; A.R. Saltiel and J.E. Pessin, Insulin signaling pathways in time and space, Trends in Cell Biology 12(2002):65–71; C.A. Baumann and A.R. Saltiel, Spatial compartmentalization of signal transduction in insulin action, BioEssays 23(2001):215–222.

p 175 biologists call “lipid rafts”: Saltiel and Kahn (2001); Saltiel and Pessin (2002); C.A. Baumann, V. Ribon, M. Kanzaki, et al., CAP defines a second signaling pathway required for insulin-stimulated glucose transport, Nature 407(2000):202–207.

p. 175 a protein called CAP: Saltiel and Kahn (2001); Saltiel and Pessin (2002); Baumann and Saltiel (2001); Baumann, et al. (2000).

p. 175 GLUT4 and its vesicles: Saltiel and Kahn (2001); Shepherd and Kahn (1999); J. Alper, New insights into type 2 diabetes, Science 289(2000):37–39; G.I. Shulman, Cellular mechanisms of insulin resistance, Journal of Clinical Investigation 106(2000):171–176.

p. 176 More than 80 percent … are obese: J.S. Flier, The missing link with obesity?, Nature 409(2001):292–293.

p. 176 currently thought to be overweight: National Institute for Diabetes, Digestive and Kidney Disorders, “Prevalence statistics related to overweight and obesity,” online at http://win.niddk.nih.gove/statistics/index.htm#preval. Figures quoted are for 2000. What’s worse, this battle of the bulge now seems to encompass even the youngest members of society—recent data from the American Heart Association indicate that approximately 10% of children between the ages of 2 and 5 can be classified as overweight.

p. 176 and eventually diabetes: P. B j örntorp, Abdominal obesity and the development of noninsulin-dependent diabetes mellitus, Diabetes/Metabolism Reviews 4(1988):615–622; H.E. Lebovitz, Pathogenesis of type 2 diabetes, Drug Benefit Trends 12(suppl A, 2000):8–16; S.E. Kahn, R.L. Prigeon, R.S. Schwartz, et al., Obesity, body fat distribution, insulin sensitivity and islet β-cell function as explanations for metabolic diversity, Journal of Nutrition 131(2001):354S–360S.

p. 176 their response to insulin improves: J.F. Bak, N. Moller, O. Schmitz, et al., In vivo insulin action and muscle glycogen synthase activity in type 2 (non-insulin-dependent) diabetes mellitus: Effects of diet treatment, Diabetologia 35(1992): 777–784.

p. 176 blindness and kidney failure decrease: According to the National Institute for Diabetes and Digestive and Kidney Diseases, every 1 percent reduction in the protein HbA1c (now thought to be the best indicator of glucose tolerance) results in a 40% decrease in the risk of complications. What’s more, weight loss can actually delay or even prevent the development of type 2 diabetes in susceptible individuals. In a recent study of “pre-diabetic” individuals (i.e., patients with insulin resistance and impaired glucose tolerance that had not yet reached pathological levels), a loss of just 5 to 10 pounds, coupled with regular exercise, reduced the incidence of type 2 diabetes by 58% over a three-year period. See Knowler WC, E. Barrett-Connor, S.E.Fowler, et al., Reduction in the incidence of type 2 diabetes with lifestyle intervention or metformin, New England Journal of Medicine 346(2002):393–403.

p. 177 $30 billion to $50 billion spent each year: Weight-control Information Network, “Statistics related to overweight and obesity,” online at http://win.niddk.nih.gov/statistics/#econ.

p. 177 90 percent will eventually gain it all back: J.M Friedman, A war on obesity, not the obese, Science 299(2003):856–858; G. Kolata, “How the Body Knows When to Gain or Lose,” New York Times, October 17, 2000, Science Times section.

p. 178 a prodigious appetite to go with it: D.L. Coleman, Obese and diabetes: Two mutant genes causing diabetes-obesity syndromes in mice, Diabetologia 14(1978):141–148; G.A. Bray and D.A. York, Hypothalamic and genetic obesity in experimental animals: An autonomic and endocrine hypothesis, Physiological Reviews 59(1979):719–809.

p. 178 an ob/ob mouse transfused with blood: D.L. Coleman, Effects of parabiosis of obese with diabetes and normal mice, Diabetologia 9(1973):294–298.

p. 178 succeeded in cloning the ob gene: Y. Zhang, R. Proenca, M. Maffei, et al., Positional cloning of the mouse obese gene and its human homologue, Nature 372(1994):425–432.

p. 178 the maturation of hematopoietic stem cells: J.M. Friedman and J.L. Halaas, Leptin and the regulation of body weight in mammals, Nature 395(1998): 763–770; B.C. Moon and J.M. Friedman, The molecular basis of the obese mutation in ob^2J mice, Genomics 42(1997):152–156; T. Madej, M.S. Boguski, and S.H. Bryant, Threading analysis suggests that the obese gene product may be a helical cytokine, FEBS Letters 373(1995):13–18.

p. 179 other fat cell hormones: G. Frühbeck, J. Gómez-Ambrosi, F.J. Muruzábal, et al., The adipocyte: A model for integration of endocrine and metabolic signaling in energy metabolism, American Journal of Physiology, Endocrinology, and Metabolism 280(2001):E827–E847; A.R. Saltiel, You are what you secrete, Nature Medicine 7(2001):887–888.

p. 179 One, adiponectin, increases sensitivity: Saltiel (2001); P.E. Scherer, S. Williams, M. Fogliano, et al., A novel serum protein similar to C1q, produced exclusively in adipocytes, Journal of Biological Chemistry 270(1995):26746–26749; E. Hu, P. Liang, and B.M. Spiegelman, AdipoQ is a novel adipose-specific gene dysregulated in obesity, Journal of Biological Chemistry 271(1996):10697–10703; T. Yamauchi, et al., The fat-derived hormone adiponectin reverses insulin resistance associated with both lipoatrophy and obesity, Nature Medicine 7(2001):941–946.

p. 179 resistin … triggers insulin resistance: C.M. Steppan, S.T. Bailey, S. Bhat, et al., The hormone resistin links obesity to diabetes, Nature 409(2001):307–312; R.R. Banerjee, S.M. Rangwala, J.S. Shapiro, et al., Regulation of fasted blood glucose by resistin, Science 303(2004):1195–1198.

p. 179 like adiponectin and resistin: Saltiel (2001); Banerjee (2004).

p. 179 Studies of … animals and … patients: Saltiel (2001); Steppan (2001).

pp. 179–180 The balancing act upset: The discovery of resistin came about as part of Lazar’s search for the mechanism of action of a novel class of oral medications for the treatment of type 2 diabetes. Known as thiazolidinediones (TZDs), or glitazones, these agents increase insulin sensitivity and bind to receptors on fat cells called PPAR-γ, for “peroxisome proliferator activated receptor, γ subvariety.”

If the insulin receptor and its baroque intracellular signaling mechanisms are an example of the eloquence of mammalian cells, the PPAR-γ receptor is a testament to their brevity. Like the LuxR receptor of light-producing bacteria, PPAR-γ combines binding site and transcription factor in a single protein, a signaling strategy also employed by steroid hormones such as estrogen and progesterone. TZDs, Lazar found, bind to this so-called nuclear receptor and downregulate the expression of the resistin gene; as resistin levels fall, insulin sensitivity improves.

Unlike other anti-diabetic medications currently on the market, which block the absorption or synthesis of glucose or goad an already overworked pancreas to secrete even more insulin, TZDs make existing insulin more effective, introducing the voice of reason to addled discussions surrounding the fate of dietary glucose. “If you have a

broken phone connection, you can shout louder or fix the problem. Other drugs shout louder. TZDs fix the connection,” says Lazar. Unfortunately, Rezulin, the first TZD introduced in the early 1990s, had to be withdrawn by the manufacturer after reports of severe liver toxicity. However, two other TZDs with a better safety record, Avandia (GlaxoSmithKline) and Actos (Eli Lilly), are currently available and others are in the pipeline.

p. 180 svelte in no time: Friedman and Halaas (1998); M.A. Pellymounter, M.J. Cullen, M.B. Baker, et al., Effects of the obese gene product on body weight regulation in ob/ob mice, Science 269(1995):540–543; J.L. Halaas, K.S. Gajiwala, M. Maffei, et al., Weight-reducing effects of the plasma protein encoded by the obese gene, Science 269(1995):543–546; L.A. Campfield, F.J. Smith, and Y. Guisez, Recombinant mouse OB protein: Evidence for a peripheral signal linking adiposity and central neural networks, Science 269(1995):546–549.

p. 182 dozens of diets they’d tried: S.B. Heymsfield, A.S. Greenberg, K. Fujioka, et al., Recombinant leptin for weight loss in obese and lean adults: a randomized, controlled, dose-escalation trial, Journal of the American Medical Association 282(1999):1568–1575; M. Chicurel, Whatever happened to leptin? Nature 404(2000):538–540.

p. 182 the effects of leptin as well: J. Marx, Cellular warriors at the battle of the bulge, Science 299(2003):846–849.

p. 182 known as the arcuate nucleus … a loss of appetite and weight loss: Ibid.; M.W. Schwartz, S.C. Woods, D. Porte, et al., Central nervous system control of food intake, Nature 404(2000):661–671; J. Flier and E. Maratos-Flier, Energy homeostasis and body weight, Current Biology 10(2001):R215–R217.

p. 183 and the pounds stay on: J.M. Friedman, Obesity in the new millennium, Nature 404(2000):632–634.

p. 183 without aggressive intervention: Friedman (2003); Friedman (2000).

p. 182 in different environments: Friedman (2003).

p. 183 “depends on the premium placed on obesity”: Friedman notes that his argument is an elaboration of that advanced by biogeographer and author Jared Diamond. Interested readers are encouraged to consult Diamond’s 1997 book Guns, Germs and Steel: The Fates of Human Societies (New York: Norton) or J. Diamond, The double puzzle of diabetes, Nature 423(2003):599–602 for more information.

p. 183 “In modern times, obesity and leptin resistance”: Friedman (2003).

p. 185 “Buildings keep being pushed around”: S. Brand, How Buildings Learn: What Happens After They’re Built (New York: Viking, 1994), p. 5.

p. 186 “They’re designed not to adapt”: Ibid., p. 2.

p. 186 will have to do to accommodate those developments: Ibid., pp. 178–189.

p. 186 “A good strategy ensures”: Ibid., p. 178. Notable examples of buildings that implement a user-friendly strategy include a number of prominent scientific research facilities. For example, Brand describes the Lewis Thomas Molecular Biology Laboratory at Princeton University, built in 1986, as “A … research building that works very well, thanks to intelligent programming…. The generous width of the corridors, designed for conviviality, turned out to be essential for materials-handling on flatbeds and glassware carts (that was a surprise not designed for), and the labs designed to share technical equipment—for conviviality as well as economy—were able to absorb many more users than expected when the building population grew from the anticipated 100 people to 300.” Tony Hunter, a signaling researcher at the University of California San Francisco, cites the Salk Institute in La Jolla as “a good example of a research building where all the space is totally flexible because the laboratory floors have no internal structural walls (the services are in a separate floor above each working floor) and can therefore be configured in any way that is needed—and has been over the 40 years since the building was opened.”

p. 188 a new type of cell, the neuron: Neurons, in fact, are probably one of the oldest types of specialized cells in multicellular animals, present in all metazoans except the sponges (Phylum Porifera).

p. 190 And in the Spanish city … our understanding of neuronal communication: S. Ramon y Cajal, Recollections of My Life, translated by E. Horne Craigie with J. Cano (Cambridge, MA: MIT Press, 1996), p. 251.

p. 190 in the laboratory of his histology professor: Ibid., pp. 249–252.

p. 190 such a scurrilous profession: S. Finger, Minds Behind the Brain: A History of the Pioneers and Their Discoveries, (New York: Oxford University Press, 2000), p. 207.

p. 191 Gleaning what he could from journals … illustrated a histology textbook: Cajal, Recollections, pp. 275–303.

p. 191 “In my systematic explorations”: Ibid., p. 304.

p. 191 “To know the brain”: Ibid., p. 305.

p. 191 “Nobody could answer this simple question”: Ibid.

p. 191 what it was that inspired these individuals: Finger, Minds, pp. 301–310.

p. 191 “The truly great scientists”: Ibid., p. 308.

p. 192 “He treated the microscopic scene”: W.M. Cowan and E.R. Kandel, A brief history of synapses and synaptic transmission, in W.M. Cowan, T.C. Südhof, and C.F. Stevens, Synapses (Baltimore: The Johns Hopkins University Press, 2001), pp. 1–87.

p. 192 the German biologists Jacob Schlieden and Theodor Schwann: Ibid.; Finger, Minds, p. 201; C. Sotelo, Viewing the brain through the master hand of Ramón y Cajal, Nature Reviews Neuroscience 4(2003):71–77.

p. 193 a new technique he had learned in Paris: Cowan and Kandel (2001); Sotelo (2003); Cajal, Recollections, pp. 307–309; Finger, Minds, p. 208.

p. 193 more detailed images of neurons: Finger, Minds, pp. 203–205.

p. 193 somewhere between 1 and 3 percent: Ibid.; Cowan and Kandel (2003).

p 193 the “tool of revelation”: Cajal, Recollections, p. 308.

p. 194 “Two methods come to mind”: Ibid., p. 324.

p. 194 “the nerve cells, which are still relatively small”: Ibid.

p. 194 like “ivy or lianas to the trunks of trees”: Ibid., p. 332.

p. 194 two historic conclusions: Cowan and Kandel (2001); Finger, Minds, pp. 210–212; R.R. Llinás, The contribution of Santiago Ramón y Cajal to functional neuroscience, Nature Reviews Neuroscience 4(2003):77–80.

p. 195 stay at his house afterward: Cowan and Kandel (2003); Cajal, Recollections, pp. 417–419.

p. 195 “it is convenient to have a term”: Cowan and Kandel (2003).

p. 196 the gut or the adrenal gland: P. De Camilli, V. Hauke, K. Takei, et al., The structure of synapses, in W.M. Cowan, T.C. Südhof, and C.F. Stevens, Synapses (Baltimore: The Johns Hopkins University Press, 2001), pp. 89–133.

p. 196 refilling them locally: P. de Camilli, V.I. Slepnev, O. Shupliakov, et al., Synaptic vesicle endocytosis, in W.M. Cowan, T.C. Südhof, and C.F. Stevens, Synapses (Baltimore: The Johns Hopkins University Press, 2001), pp. 217–274.

p. 197 at a moment’s notice: De Camilli, et al. (2001); K.M. Harris and P. Sultan, Variation in the number, location, and size of synaptic vesicles provides an anatomical basis for the nonuniform probability of release at CA1 hippocampal synapses, Neuropharmacology 34(1995):1387–1395.

p. 198 pawing in the starting gate: De Camilli, et al. (2001); F.E. Bloom and G.K. Aghajanian, Cytochemistry of synapses: Selective staining for electron microscopy, Science 154(1966):1575–1577; A. Peters, S.L. Palay, and H. deF. Webster, The Fine Structure of the Nervous System : The Neurons and Supporting Cells (Philadelphia: Saunders, 1976), pp. 132–135.

p. 198 concentrated at the active zone: De Camilli, et al. (2001); N. Hirokawa, K. Sobue, K. Kanda, et al., The cytoskeletal architecture of the presynaptic terminal and molecular structure of synapsin 1, Journal of Cell Biology 108 (1989): 111–126.

p. 198 to channel calcium ions: T.C. Südhof and R.H. Scheller, Mechanism and regulation of neurotransmitter release, in W.M. Cowan, T.C. Südhof, and C.F. Stevens, Synapses (Baltimore: The Johns Hopkins University Press, 2001), pp. 177–215.

p. 198 apparatus of the presynaptic neuron: De Camilli, et al. (2001); Peters, et al., The Fine Structure of the Nervous System, pp. 136–142.

p. 198 by the type known as “AMPA”: V.N. Kharazia and R.J. Weinberg, Tangential synaptic distribution of NMDA and AMPA receptors in rat neocortex, Neuroscience Letters 238(1997):41–44.

p. 198 hooks and loops of Velcro: T.C. Südhof, The synaptic cleft and synaptic cell adhesion, in W.M. Cowan, T.C. Südhof, and C.F. Stevens, Synapses (Baltimore: The Johns Hopkins University Press, 2001), pp. 275–313.

p. 199 identifying an appropriate partner: A.M. Fannon and D.R. Colman, A model for central synaptic junctional complex formation based on the differential adhesive specificities of the cadherins, Neuron 17(1996):423–434.

p. 199 “parasynaptic” cadherins: Südhof (2001).

p. 199 was not actually awarded: V. Hamburger, S. Ramón y Cajal, R.G. Harrison, and the beginnings of neuroembryology, Perspectives in Biology and Medicine 23(1980):600–616, available online from the Developmental Biology website at

http://www.devbio.com/article.php?ch=13&id=145; J.A. Schiff, “An Unsung Hero of Medical Research,” Yale Alumni Magazine, February 2000, available online at http://www.yalealumnimagazine.com. “America’s most famous unknown scientist,” according to an article in Fortune (notes Schiff) and certainly one of the unluckiest, Harrison was nominated for the Nobel a second time, in 1935. This time he was passed over in favor of fellow developmental biologist Hans Spemann, on the grounds that “opinions diverged and in view of the rather limited value of the method … an award [to Harrison] could not be made.” Harrison’s “limited method”—tissue culture—has become, of course, one of the mainstays of the modern cell biology laboratory.

p. 199 also intrigued the master: Hamburger (1980); Cajal, Recollections, pp. 365–370.

p. 200 a ring of wax on a microscope slide: G.W. Gray, The organizer, Scientific American 197(1957):79–88.

p. 200 “appeared as a concentration of protoplasm”: Cajal, Recollections, p. 369.

p. 201 possessing “an exquisite chemical sensitivity”: Ibid.

p. 202 set about building a synapse: J. R. Sanes and T. M. Jessell, The guidance of axons to their targets, in E.R. Kandel, J.H. Schwartz, and T.M. Jessell, ed., Principles of Neural Science, 4th ed. (New York: McGraw-Hill, 2000), pp. 1063–1086.

p. 202 opposite side of the spinal cord: M. Tessier-Levigne and C.S.Goodman, The molecular biology of axon guidance, Science 274(1996):1123–1132; S.F. Gilbert, Developmental Biology, 7th ed. (Sunderland, MA: Sinauer Associates, 2003), p. 447.

p. 204 “netrins” which direct the growth cone: Sanes and Jessell (2000); Tessier-Levigne and Goodman (1996); T. Serafini, T.E. Kennedy, M.J. Galko, et al., The netrins define a family of axon-outgrowth-promoting proteins homologous to C. elegans UNC-6, Cell 78(1994): 49–360; T.E. Kennedy, T. Serafini, J.R. de la Torre, et al., Netrins are diffusible chemotropic factors for commissural axons in the embryonic spinal cord, Cell 78(1994):425–435; U. Drescher, Netrins find their receptor, Nature 384(1996):416–417; T.E. Kennedy, Cellular mechanisms of netrin function; Long-range and short-range function, Biochemistry and Cell Biology 78(2000):569–575; X. Li, M. Meriane, I. Triki, et al., The adaptor protein Nck-1 couples the netrin-1 receptor DCC (deleted in colorectal cancer) to the activation of the small GTPase Rac1 through an atypical mechanism, Journal of Biological Chemistry 277(2002):37788–37797. The name “netrin,” incidentally, comes from a Sanskrit word netr, meaning “one who guides” (H. Lodish, A. Berk, S.L. Zipursky, et al., Molecular Cell Biology, 4th. ed. [New York: W.H. Freeman, 2000], p. 1036).

p. 204 toward the center of the floor plate: Gilbert, Developmental Biology, p. 447; Serafini, et al. (1994); Drescher (1996); S.A. Colamarino and M. Tessier-Levigne, The role of the floor plate in axon guidance, Annual Review of Neuroscience 18(1995):497–529.

p. 204 the bone morphogenetic proteins: F. Charron, E. Stein, J. Jeong, et al., The morphogen Sonic hedgehog is an axonal chemoattractant that collaborates with netrin-1 midline axon guidance, Cell 113(2003):11–23; A. Augsberger, A. Schuchardt, S. Hoskins, et al., BMPs as mediators of roof plate repulsion of commissural neurons, Neuron 24(1999):127–141.

p. 204 “Shh and BMPs, which initially cooperate”: Charron, et al. (2003).

p. 204 rolled out for them across the midline: Tessier-Levigne and Goodman (1996).

p. 205 matrix that coats their surfaces: J. Cohen, J.F. Burne, C. McKinlay, et al., The role of laminin and the laminin/fibronectin receptor complex in the outgrowth of retinal ganglion axons, Developmental Biology 122(1987):407–418; P. Liesi and J. Silver, Is astrocyte laminin involved in axon guidance in the mammalian CNS? Developmental Biology 130(1988):774–785.

p. 205 to intracellular signal transduction relays: Sanes and Jessell (2000a); R.O. Hynes, Integrins: Bidirectional allosteric signaling machines, Cell 110(2002): 673–687; F.G. Giancotti and E. Ruoslahti, Integrin signaling, Science 285(1999): 1028–1032.

p. 205 comparable to Gα: Hynes (2002).

p. 205 a short tail that spans the membrane: Hynes (2002); Giancotti and Ruoslahti (1999).

p. 205 that allow them to read it: Cohen, et al. (1987); Liesi and Silver (1988).

p. 206 ephrin A2 and A5: Sanes and Jessell (2000a); J. Frisen, P.A. Yates, T. McLaughlin, et al., Ephrin-A5 (AL-1/RAGS) is essential for proper retinal axon guidance and topographic mapping in the mammalian visual system, Neuron 20(1998): 233–243; J.G. Flanagan and P. Vanderhaeghen, The ephrins and EPH receptors in neural development, Annual Review of Neuroscience 21(1998):309–345.

p. 206 backwards into the signaling cell: A.W. Boyd and M. Lackmann, Signals from Eph and Ephrin proteins: A developmental tool kit, Science’s STKE (2001):1–6, available online at www.stke.org/cgi/content/full/OC_sigtrans;2001/112/re20.

p. 206 retreats to the ephrin-free anterior tectum … the posterior tectum’s ephrin insults: Sanes and Jessell (2002a); J. Walter, S. Henke-Fahle, and F. Bonhoeffer, Avoidance of posterior tectal membranes by temporal retinal axons, Development 101 (1987):909–913; Frisen, et al. (1998); Flanagan and Vanderhaeghen (1998).

p. 206 on its way to a lifetime partnership: In the developing brain, repulsion and attraction are not mutually exclusive. On city streets, red always means stop and green always means go, but on the extracellular highways traveled by emergent axons and infant neurons, some signals can mean both. Take a trip through the trochlear nerve that controls eye movements, for example; the limbic system, central to the regulation of emotional behavior; or the cerebral cortex during their development and you’re certain to hear some form of the word “semaphorin,” the collective name for seven distinct classes of signaling molecules featuring a common protein module, the sema domain. To many listeners, the semaphorins are variations on “no.” But to young pyramidal neurons in the cortex, one, semaphorin 3A, means “come here” as well as “go away.” Located three, five, or even six cell layers below the convoluted cortical surface, these cells face a unique developmental challenge: each has not only an axon, but also a distinctive elongated dendrite which must find its way to targets in the more superficial layers. Both processes rely on a top-to-bottom gradient of semaphorin 3A to navigate. But while pyramidal axons respond in the negative, growing away from the source of the semaphorin 3A signal, the so-called apical dendrites stretch up toward it like seedlings seeking sunlight.

Semaphorin 3A means different things to different parts of a pyramidal cell because pyramidal axons and apical dendrites complete a semaphorin sentence two different ways. Dendrites, but not axons, contain an intracellular signaling molecule, guanylate cyclase. Only dendrites, therefore, can insert this word after “neuropilin-1”(the semaphorin 3A receptor)—and that little addition, apparently, is enough to transform semaphorin 3A signal from a repellant into an attractant. See F. Polleux, T. Morrow, and A. Ghosh, Semaphorin 3A is a chemoattractant for cortical apical dendrites, Nature 404(2000):567–573. For more information on the role of semaphorins as axon guidance cues in the central nervous system, see A. Sahay, M.E. Molliver, D.D. Ginty, et al., Semaphorin 3F is critical for the development of limbic system circuitry and is required in neurons for selective CNS axon guidance events, Journal of Neuroscience 23(2003):6671–6680.

p. 208 take charge of its life: S. Cohen-Cory, The developing synapse: Construction and modulation of synaptic structures and circuits, Science 298(2002):770–776; J.R. Sanes and T.M. Jessell, The formation and regeneration of synapses, in E.R. Kandel, J.H. Schwartz, and T.M. Jessell, ed., Principles of Neural Science, 4th ed. (New York: McGraw-Hill, 2000), pp. 1087–1114; A.M. Craig and J.W. Lichtman, Synapse formation and maturation, in W.M. Cowan, T.C. Südhof, and C.F. Stevens, Synapses (Baltimore: The Johns Hopkins University Press, 2001), pp. 571–612.

p. 208 a cytoskeletal protein called rapsyn: Sanes and Jessell (2000b); J.R. Sanes and J.W. Lichtman, Development of the vertebrate neuromuscular junction, Annual Review of Neuroscience 22(1999):389–442.

p. 208 to fill out each cluster: A.W. Sandrock, S.E. Dryer, K.M. Rosen, et al., Maintenance of acetylcholine receptor number by neuregulins, Science 276(1997): 599–603.

p. 208 receptor making or gathering: Sanes and Jessell (2000b).

pp. 208–209 reinforce the protein scaffolding: Ibid.

p. 209 grow up and start releasing neurotransmitter: Ibid.; B.L. Patton, J.H. Miner, A.Y. Chiu, et al., Localization, regulation and function of laminins in the neuromuscular system of developing, adult and mutant mice, Journal of Cell Biology 139(1997):1507–1521.

p. 209 growth and survival factors: Sanes and Jessell (2000b).

p. 209 acetylcholine receptors in muscle fibers: Ibid.; Cohen-Cory (2002); Craig and Lichtman (2001).

p. 209 the mystery signals collect them: Sanes and Jessell (2000b); Craig and Lichtman (2001). The name of the protein is “gephyrin,” and its similarity to rapsyn is strictly functional; it is structurally unrelated to the muscle protein.

p. 209 time to assemble synaptic vesicles: P. Scheiffele, J. Fan, J. Choih, et al., Neuroligin expressed in noneuronal cells triggers presynaptic development in contacting axons, Cell 101(2000):657–669.

p. 209 all but one axon withdrawn: Craig and Lichtman (2001); J.W. Lichtman and H. Colman, Synapse elimination and indelible memory, Neuron 25(2000):269–278.

p. 212 stimulates the postsynaptic cell to action: M. H.-T. Sheng, The postsynaptic specialization, in W.M. Cowan, T.C. Südhof, and C.F. Stevens, Synapses

(Baltimore: The Johns Hopkins University Press, 2001), pp. 315–355; M.B. Kennedy, Signal-processing machines at the postsynaptic density, Science 290(2000):750–754.

p. 212 earliest stages of synapse formation: C. Lüscher, R.A. Nicoll, R.C. Malenka, et al., Synaptic plasticity and dynamic modulation of the postsynaptic membrane, Nature Neuroscience 3(2000):545–550.

p. 212 AMPA receptors … calcium as well as sodium and potassium: E. R. Kandel and S.A. Siegelbaum, Synaptic integration, in E.R. Kandel, J.H. Schwartz, and T.M. Jessell, ed., Principles of Neural Science, 4th ed. (New York: McGraw-Hill, 2000), pp. 207–227.

p. 213 widespread than calcium: M.J. Berridge, M.D. Bootman, and P. Lipp, Calcium—A life and death signal, Nature 395(1998):645–648; B. Alberts, A. Johnson, J. Lewis, et al., Molecular Biology of the Cell, 4th ed. (New York, Garland Science, 2002), pp. 861–865.

p. 213 The most ubiquitous … is called calmodulin: Alberts, et al., Molecular Biology of the Cell, pp. 863–865.

p. 213 CAM kinases for short: Ibid.

p. 213 of only 20,000 neurons: E.R. Kandel, Cellular mechanisms of learning and the biological basis of individuality, in E.R. Kandel, J.H. Schwartz, and T.M. Jessell, ed., Principles of Neural Science, 4th ed. (New York: McGraw-Hill, 2000), pp. 1247–1279; E.R. Kandel, The molecular biology of memory storage: A dialogue between genes and synapses, Science 294 (2001):1030–1038.

p. 213 for days or even weeks: Ibid.

p. 214 synapses on a sensory neuron … and regulates its activity: Kandel (2000).

p. 214 the activation of protein kinase A: Ibid.; Kandel (2001); J.H. Byrne and E.R. Kandel, Presynaptic facilitation revisited: State and time dependence, Journal of Neuroscience 16(1996):425–435.

p. 215 it complains to the MAP kinase: Kandel (2000); Kandel (2001); D. Michael, K.C. Martin, R. Seger, et al., Repeated pulses of serotonin required for long-term facilitation activate mitogen-activated protein kinase in sensory neurons of Aplysia, Proceedings of the National Academy of Sciences 95(1998):1864–1869.

p. 215 the addition of new synapses: C.H. Bailey and E.R. Kandel, Structural changes accompanying memory storage, Annual Review of Physiology 55(1993):397–426.

p. 215 “long term potentiation,” or LTP: T.V.P. Bliss and T. Lomø, Long-lasting potentiation of synaptic transmission in the dentate gyrus of the anesthetized rabbit following stimulation of the perforant path, Journal of Physiology (London) 232(1973):331–356.

p. 216 Like sensitization in Aplysia … an effect that lasts two to three hours: Lüscher, et al. (2000); Kandel (2000); Kandel (2001); C. Lüscher, et al., Role of AMPA receptor cycling in synaptic transmission and plasticity, Neuron 24(1999): 649–658; S.H. Shi, et al., Rapid spine delivery and redistribution of AMPA receptors after synaptic NMDA receptor activation, Science 284(1999):1811–1816; R.C. Malenka and S.A. Siegelbaum, Synaptic plasticity: Diverse targets and mechanisms for regulating synaptic efficacy, in W.M. Cowan, T.C. Südhof, and C.F. Stevens, Synapses (Baltimore: The Johns Hopkins University Press, 2001), pp. 393–453.

So-called silent synapses—excitatory synapses that lack functional AMPA receptors at the surface but have such receptors sequestered within the postsynaptic neuron—can be converted to functional synapses by LTP induction, presumably because the induction message includes a directive to move the internal AMPA receptors to the surface of the postsynaptic membrane.

p. 216 Once again … that will last at least 24 hours: Lüscher, et al. (2000); Kandel (2000); Kandel (2001); Malenka and Siegelbaum (2001); R.C. Malenka and R.A. Nicoll, Long-term potentiation—A decade of progress? Science 285(1999):1870–1874; M. Sheng and M.J. Kim, Postsynaptic signaling and plasticity mechanisms, Science 298(2002):776–780.

p. 217 carry out local protein synthesis: K.C. Martin, M. Barad, and E.R. Kandel, Local protein synthesis and its role in synapse-specific plasticity, Current Opinion in Neurobiology 10(2000):587–592; J.P. Pierce, K, van Leyen, and J.B. McCarthy, Translocation machinery for synthesis of integral membrane and secretory proteins in dendritic spines, Nature Neuroscience 3(2000):311–313.

p. 217 will now be allowed to use them: Kandel (2001); Sheng and Kim (2002); Martin, et al. (2000); A. Casadio, K.C. Martin, M. Giustetto, et al., A transient, neuron-wide form of CREB-mediated long-term facilitation can be stabilized at specific synapses by local protein synthesis, Cell 99(1999):221–237; K.C. Martin, A. Casadio, H. Zhu, et al., Synapse-specific, long-term facilitation of Aplysia sensory to motor synapses: A function for local protein synthesis in memory storage, Cell 91(1997):927–938.

p. 218 “the anatomical equivalent of city hall”: D.L. Niehoff, The Biology of Violence: How Understanding the Brain, Behavior, and Environment Can Break the Vicious Circle of Aggression (New York, The Free Press, 1999), p. 96.

p. 218 older memories (courtesy of the hippocampus) intersect: Ibid.; E. Halgren, Emotional physiology of the amygdala within the context of human cognition, in A.P. Aggleton, ed., The Amygdala: Neurobiological Aspects of Emotion, Memory, and Mental Dysfunction (New York, Wiley-Liss, 1992), pp. 191–228.

p. 219 its heart pounding and its blood pressure soaring: J.E. LeDoux, Emotion, memory, and the brain, Scientific American 270(1994):32–39; J.E. LeDoux, Information flow from sensation to emotion: Plasticity in the neural computation of stimulus value, in M. Gabriel and J. Moore, Neuroscience: Foundation of Adaptive Networks (Cambridge, MA: MIT Press, 1990), pp. 3–51; J.E. LeDoux, In search of an emotional system in the brain: Leaping from fear to emotion and consciousness, paper presented at the McDonnell-Pew Conference on Cognitive Neuroscience, Lake Tahoe, CA, 1993.

p. 219 can reawaken it: Le Doux (1990).

p. 219 induces LTP in the hippocampus: R.C. Malenka and R.A. Nicoll, Never fear, LTP is hear, Nature 390 (1997): 552–553; M.T. Rogan, U.V. Stäubli, and J.E. LeDoux, Fear conditioning induces associative long-term potentiation in the amygdala, Nature 390(1997):604–607; M.G. McKernan and P. Shinnick-Gallagher, Fear conditioning induces a lasting potentiation of synaptic currents in vitro, Nature 390(1997):607–611.

p. 219 exposed to the tone but never shocked: Rogan, et al. (1997).

p. 220 “If you want a building to learn”: Brand, How Buildings Learn, p. 190.

p. 220 Denise is another example: Not her real name.

p. 220 including alterations in gene expression: S.E. Hyman and E.J. Nestler, Initiation and adaptation: A paradigm for understanding psychotropic drug action, American Journal of Psychiatry 153(1996):151–162.

p. 221 changes in the structure and function of neurons: E.J. Nestler, Molecular basis of addictive states, The Neuroscientist 1(1995):212–220; S.E. Hyman and R.C. Malenka, Addiction and the brain: The neurobiology of compulsion and its persistence, Nature Reviews Neuroscience 2(2001):695–703; J.Chao and E.J. Nestler, Molecular neurobiology of drug addiction, Annual Review of Medicine 55(2004):113–132; N.D. Volkow and T.K. Li, Drug addiction: The neurobiology of behavior gone awry, Nature Reviews Neuroscience 5(2004):963–970. One of the proteins altered by repeated exposure to drugs of abuse is the transcription factor CREB, confidante of cyclic AMP during the late phase of long-term potentiation. The induction of addiction, in other words, appears to involve at least some of the same molecules and mechanisms as those implicated in the storage of explicit memory.

p. 221 particularly so-called reward pathways: Nestler (1995); Hyman and Malenka (2001); Chao and Nestler (2004); Volkow and Li (2004); A.R. Childress, P.D. Mozley, W. McElgin, et al., limbic activation during cue-induced cocaine craving, American Journal of Psychiatry 156(1999):11–18; G. DiChiara and A. Imperato, Drugs of abuse preferentially stimulate dopamine release in the mesolimbic system of freely moving rats, Proceedings of the National Academy of Sciences 85(1988):5274–5278.

p. 222 “Not all adaptations”: S.E. Hyman, presentation at the American Psychiatric Association Annual Meeting, May 1996.

p. 224 synonyms for “help”: C. Nathan, Points of control in inflammation, Nature 420(2002):846–852.

p. 224 and devour them alive: C.A. Janeway and P. Travers, Immunobiology: The Immune System in Health and Disease, 3rd ed. (New York: Garland Publishing, 1997), pp. 9:10–9:12; C.A Janeway and R. Medzhitov, Innate immune recognition, Annual Review of Immunology 20(2000):197–216; R. Medzhitov and C.A. Janeway, Innate immunity, New England Journal of Medicine 343(2000):338–344.

p. 224 to issue a call for reinforcements: Nathan (2002); Janeway and Travers, Immunobiology, pp. 9:13, 9:18–9:19; S. Werner and R. Grose, Regulation of wound healing by growth factors and cytokines, Physiological Reviews 83(2003):835–870.

p. 224 Known collectively as chemokines: Janeway and Travers, Immunobiology, pp. 9:18–9:19; J.G. Cyster, Chemokines and cell migration in secondary lymphoid organs, Science 286(1999):2098–2102; G. Gerard and B.J. Evans, Chemokines and disease, Nature Immunology (2001):108–115.

p. 225 into the infected tissue: Janeway and Travers, Immunobiology, pp. 9:15–9:16; P.J. Delves and I.M. Roitt, The immune system: Part 1, New England Journal of Medicine 343(2000):37–49.

p. 225 leak into the tissue in the process: Nathan (2002).

p. 225 a handful of features common to … microorganisms: Janeway and Travers, Immunobiology, pp. 9:10–9:12; Janeway and Medzhitov (2002); Medzhitov and Janeway (2000).

p. 226 RAG proteins: D.J. Laird, A.W. De Tomaso, M.D.Cooper, et al., 50

million years of chordate evolution: Seeking the origins of adaptive immunity, Proceedings of the National Academy of Sciences 97(2000):6924–6926. The authors note that the precipitous evolution of RAG-mediated adaptive immunity has had such a profound influence on the evolutionary success of the vertebrate lineage some immunologists have referred to it as the “Immunological Big Bang.”

p. 226 waiting around for evolution to do it: Laird, et al. (2000); E.E. Max, Immunoglobulins: molecular genetics, in W.E. Paul, Fundamental Immunology, 4th ed. (Philadelphia: Lippincott-Raven, 1999), pp. 111–182.

p. 226 immunoglobulins and one near relative: The designer proteins produced by white blood cells, the immunoglobulins and the constituent subunits of the so-called T lymphocyte receptor, are members of a gargantuan family of proteins known as the “immunoglobulin (Ig) supergene family,” all of which contain a characteristic structural feature called the Ig fold. In addition to these superstars of the immune system, the Ig supergene family includes several well-known cell adhesion molecules, as well as the DCC receptors that bind netrins and ephrin receptors.

p. 226 millions of bacterial and viral features: Janeway and Travers, Immunobiology, p. 1:15.

p. 227 Lymphocytes come in two flavors: Delves and Roitt (2000a); W.E. Paul, The immune system: An introduction, in W.E. Paul, Fundamental Immunology, 4th ed. (Philadelphia: Lippincott-Raven, 1999), pp. 1–18.

p. 227 but they are not immunoglobulins: Paul (1999).

p. 227 sent to boarding school in the thymus: Detailed discussions of the selection, development, and activation of B and T lymphocytes can be found in any standard textbook of immunology. See, for example, chapters 5–8 in Janeway and Travers, Immunobiology or chapters 6, 7, 11, and 12 in Paul, Fundamental Immunology.

p. 227 commit suicide as soon as possible: E. Palmer, Negative selection—Clearing out the bad apples from the T-cell repertoire, Nature Reviews Immunology 3 (2003):383–391; J.T. Opferman and S.J. Korsmeyer, Apoptosis in the development and maintenance of the immune system, Nature Immunology 4(2003):410–415.

p. 229 hence their name: dendritic cells: J. Banchereau and R.M. Steinman, Dendritic cells and the control of immunity, Nature 392(1998):245–252.

p. 229 educators, mentors, motivators, counselors, and dispatchers: Banchereau and Steinman (1998); R.M. Steinman and M.C. Nussenzweig, Avoiding horror autotoxicus: The importance of dendritic cells in peripheral T cell tolerance, Proceedings of the National Academy of Sciences 99(2002):351–358; R.M. Steinman, Dendritic cells, in W.E. Paul, Fundamental Immunology, 4th ed. (Philadelphia: Lippincott-Raven, 1999), pp. 547–573.

p. 229 the so-called major histocompatibility complex: Janeway and Travers, Immunobiology, pp. 1:24–1:25, 4:2–4:3; P.J. Delves and I.M. Roitt, The immune system, Part 2, New England Journal of Medicine 343(2000):108–117.

p. 229 a so-called costimulatory signal as well: Delves and Roitt (2000b); Janeway and Travers, Immunobiology, pp. 7:8–7:9. Engagement of a T cell’s receptor in the absence of a costimulatory signal is a dead giveaway that the cell in question is binding to a self antigen, rather than a bacterial protein. Such misfirings trigger a failsafe reaction known as anergy, in which the offending cell is stripped of its ability to respond to antigen and condemned to a permanent state of suspended animation.

p. 230 job title is “professional antigen presenting cell”: Banchereau and Steinman (1998); Steinman (1999).

p. 230 start looking for a partner: Ibid.

p. 230 a supply of the essential costimulator: Banchereau and Steinman (1998); Steinman (1999); Steinman and M.C. Nussenzweig (2002).

p. 232 to talk to the B cells they activated: P.A. van der Merwe and S.J. Davis, The immunological synapse—A multitasking system, Science 295(2002):1479–1481; W.E. Paul and R.E. Sader, Lymphocyte responses and cytokines, Cell 76(1994):241–251.

p. 232 the T cell contacted its signaling partner: C.R. Monks, B.A. Freiberg, H. Kupfer, et al., Three-dimensional segregation of supramolecular activation clusters in T cells, Nature 395(1998):82–86; A. Grakoui, S.K. Bromley, C. Sumen, et al., The immunological synapse: A molecular machine controlling T cell activation, Science 285(1999):221–227; J.P. Roberts, Dissecting the immunological synapse, The Scientist 17(2003), available online at www.the-scientist.com/yr2003/may/research1_030505.html.

p. 232 like a bull’s-eye: Monks, et al. (1998); Grakoui, et al. (1999); Roberts (2003); M.L. Dustin and A.S. Shaw, Costimulation: Building an immunological synapse, Science 283(1999):649–651; J. Delon, The immunological synapse, Current Biology 10(2003):214; M.L. Dustin and D.R. Colman, Neural and immunological synaptic relations, Science 298(2002):785–789.

p. 232 the active zone in a neural synapse: Grakoui, et al. (1999); Roberts (2003); Delon (2003); Dustin and Colman (2002); C. Wülfing and M.M. Davis, A receptor/cytoskeletal movement triggered by costimulation during T cell activation, Science 282(1998):2266–2269.

p. 233 before construction of the synapse is finished: van der Merwe and Davis (2002); Roberts (2003); K-H. Lee, A.D. Holdorf, M.L. Dustin, et al., T cell receptor signaling precedes immunological synapse formation, Science 295(2002):1539–1542.

p. 233 to match the level of antigen: K-H. Lee, A.R. Dinner, C. Tu, et al., The immunological synapse balances T cell receptor signaling and degradation, Science 302(2003):1218–1222.

p. 234 later stages in the T cell activation process: Dustin and Colman (2002).

p. 234 chatting like social equals: D.T. Fearon and R.M. Locksley, The instructive role of innate immunity in the acquired immune response, Science 272(1996):50–54.

p. 234 are likely to be pathogenic: Banchereau and Steinman (1998).

p. 234 to the infection site: Nathan (2002).

p. 234 from attack mode to healing mode: Ibid.; T.R. Mosmann, H. Cherwinski, M.W. Bond, et al., Two types of murine helper T cell clone. I. Definition according to profiles of lymphokine activities and secreted proteins, Journal of Immunology 136(1986):2348–2357; H.L. Weiner and D.J. Selkoe, Inflammation and therapeutic vaccination in CNS diseases, Nature 420(2002):879–883.

p. 235 has had to sacrifice infallibility: Fearon and Locksley (1996).

p. 235 picked up self antigens during their travels: Banchereau and Steinman (1998); Steinman and M.C. Nussenzweig (2002).

p. 235 limit their interactions with the immune system: Janeway and Travers, Immunobiology, p. 12:32.

p. 236 known collectively as myelin basic protein: J.H. Schwartz and G.L. Westbrook, The cytology of neurons, in E.R. Kandel, J.H. Schwartz, and T.M. Jessell, ed., Principles of Neural Science, 4th ed. (New York: McGraw-Hill, 2000), pp. 67–87.

p. 236 that body has chosen to ignore: R. Hohlfeld and H. Wekerle, Autoimmune concepts of multiple sclerosis as a basis for selective immunotherapy: From pipe dreams to (therapeutic) pipelines, Proceedings of the National Academy of Sciences 101(2004):14599–14606.

p. 237 the smallest, most lipid-loving molecules: R. Hohlfeld, Biotechnological agents for the immunotherapy of multiple sclerosis: Principles, problems, and perspectives, Brain 120(1997):865–916; H. Wekerle, C. Linington, H. Lassmann, et al., Cellular immune reactivity in the CNS, Trends in Neurosciences 9(1986):271–277.

p. 237 activates myelin-reactive T cells: Hohlfeld and Wekerle (2004); Hohlfeld (1997); R.T. Johnson, The virology of demyelinating diseases, Annals of Neurology 36(1994):S54–S60.

p. 237 in the brain, spinal cord, and optic nerves: Hohlfeld and Wekerle (2004); Hohlfeld (1997).

p. 237 described this autoimmune catastrophe in 1868: D.A. Hafler, Multiple sclerosis, Journal of Clinical Investigation 113(2004):788–794.

p. 237 between the ages of 20 and 40: Hohlfeld and Wekerle (2004); R.D. Adams, M. Victor, and A.H. Ropper, Principles of Neurology, 6th ed. (New York: McGill-Hill, 1997), p. 906.

p. 237 in the Th1 direction: Weiner and Selkoe (2002); R.R. Voskuhl, R. Martin, C. Bergman, et al., T helper (Th1) functional phenotype of human myelin basic protein-specific T lymphocytes, Autoimmunity 15(1993):137–143.

pp. 237–238 precede the attack by several weeks: P. Rieckmann, M. Albrecht, B. Kitze, et al., Tumor necrosis factor-alpha messenger RNA expression in patients with relapsing-remitting multiple sclerosis is associated with disease activity, Annals of Neurology 37(1995):82–88.

p. 238 an MS patient is likely to be: M.K. Sharief and R. Hentges, Association between tumor necrosis factor-alpha and disease progression in patients with multiple sclerosis, New England Journal of Medicine 325(1991):467–472.

p. 238 the rate of disease progression: Ibid.

p. 238 endothelial cells don adhesive molecules: H.P. Hartung, K. Reiners, J.J. Archelos, et al., Circulating adhesion molecules and tumor necrosis factor receptor in multiple sclerosis: Correlation with magnetic resonance imaging, Annals of Neurology 38(1995):186–193.

p. 238 were intent on attacking: D.H. Miller, O.A. Khan, W.A. Sheremata, et al., A controlled trial of natalizumab for relapsing multiple sclerosis, New England Journal of Medicine 348(2003):15–23.

p. 239 a 2-year clinical trial in more than 900 MS patients: “FDA grants accelerated approval of Tysabri^® formerly Antegren^® for the treatment of multiple sclerosis,” press release available online, along with additional information about Tysabri^®, on the Biogen Website: www.biogen.com.

p. 239 sales were suspended … “But I knew it was going to happen”: “Biogen

Idec and Elan Announce Voluntary Suspension of Tysabri^®”, press release available online at www.elan.com/News/full.asp?ID=679361; A.W. Pollack, “Sales Halted in Biotech Drug Because of Link to a Death,” New York Times, March 3, 2005, Business Day section.

p. 239 “survival is impossible”: K.J. Tracey, The inflammatory reflex, Nature 420(2002):853–859.

p. 239 “‘Change is suffering’ was the insight”: Brand, How Buildings Learn, p.167.

p. 242 “the big question of how they all work together”: A. Abbott, Alliance of US labs plans to build map of cell signaling pathways, Nature 402(1999):219–220.

p. 242 “Sequencing the genome is enabling us”: K. Devine, Cell signaling alliance gets underway, The Scientist 14(2000):1,12.

p. 242 catalog and publish as an electronic database: Responsibility for coordinating peer review and publication of the Molecule Pages has been assumed by the editors of the journal Nature. In collaboration with the AfCS, Nature also maintains an online resource, the Signaling Gateway (www.signaling-gateway.org), featuring news updates, review articles, and links to the scientific literature. More information about the AfCS, including regular newsletters highlighting recent progress and news from the Alliance’s annual meeting, can be accessed via the Signaling Gateway as well.

p. 243 The annual budget … totals around $10 million: Abbott (1999).

p. 245 “signaling pathways interact with one another”: U.S. Bhalla and R. Iyengar, Emergent properties of networks of biological signaling pathways, Science 283(1999):381–387.

p. 246 “Complexities can only be understood”: J. Maddox, What Remains to Be Discovered: Mapping the Secrets of the Universe, the Origins of Life, and the Future of the Human Race (New York: The Free Press, 1998), p. 184.

p. 246 scientists realize three benefits: E. Werner, In silico cell signaling underground, Science’s STKE (2003), online at www.stke.org/cgi/content/full/sigtrans;2003/170/pe8.

p. 246 “Models … can be used to plan”: Ibid.

p. 246 “force a new perspective on the subject matter”: Ibid.

p. 246 to appreciate the value of model building: Maddox, What Remains to Be Discovered, pp. 184–189.

p. 247 “Each word carries the whisper,”: C. Alexander, S. Ishikawa, M. Silverstein with M. Jacobson, I. Fiksdahl-King, and S. Angel, A Pattern Language (New York: Oxford University Press, 1977), p. xliii.

p. 248 “a modern-day plague” … “a legion of recondite diseases” … “a terrifying alien entity”: D.R. Green and G.I. Evan, A matter of life and death, Cancer Cell 1(2002):19–30.

p. 248 Herceptin, is a monoclonal antibody: Y. Yarden, J. Baselga, and D.

Miles, Molecular approaches to breast cancer treatment, Seminars in Oncology 31(2004):6–13; R.S. Finn and D.J. Slamon, Monoclonal antibody therapy for breast cancer: Herceptin, Cancer Chemotherapy and Biological Response Modifiers 21(2003):223–233; N. Wade, “Scientists View New Wave of Cancer Drugs,” New York Times, May 29, 2001, Science Times section.

p. 248 extra copies of the her2/neu gene: R. Roskosi, Jr., The ErbB/HER receptor protein-tyrosine kinases and cancer, Biochemical and Biophysical Research Communications 319(2004):1–11; J.S. Ross, J.A. Fletcher, G.P. Linette, et al., The her-2/neu gene and protein in breast cancer 2003: Biomarker and target of therapy, Oncologist 8(2003):307–325.

p. 248 Gleevec silences an aberrant kinase: B.J. Druker, Perspectives on the development of a molecularly targeted agent, Cancer Cell 1(2002):31–36; B.J. Druker, M. Talpaz, D. Resta, et al., Efficacy and safety of a specific inhibitor of the Bcr-Abl tyrosine kinase in chronic myeloid leukemia, New England Journal of Medicine 344(2001):1031–1037; B.J. Druker, C.L. Sawyers, H. Kantarjian, et al., Activity of a specific inhibitor of the Bcr-Abl tyrosine kinase in the blast crisis of chronic myeloid leukemia and acute lymphoblastic leukemia with the Philadelphia chromosome, New England Journal of Medicine 344(2001):1038–1042. The disrupted chromosome was discovered in 1960 by scientists at the Wistar Institute in Philadelphia and is called the “Philadelphia chromosome” as a consequence (see P.C. Nowell and D.A. Hungerford, A minute chromosome in human chronic granulocytic leukemia, Science 132[1960]:1497–1501). Bcr-Abl, the tyrosine kinase encoded by the fused chromosome segments is thought to stimulate proliferation and/or survival of hematopoietic progenitor cells (see M.W. Deininger, J.M. Goldman, and J.V. Melo, The molecular biology of chronic myeloid leukemia, Blood 96[2000]:3343–3356).

p. 248 Gleevec blocks a mutant receptor tyrosine kinase called c-kit: B.J. Druker and N.B. Lydon, Lessons learned from the development of an abl tyrosine kinase inhibitor for chronic myelogenous leukemia, Journal of Clinical Investigation 105(2000):3–7; D.A. Tuveson, N.A. Willis, T. Jacks, et al., STI571 inactivation of the gastrointestinal stromal tumor c-KIT oncoprotein; Biological and clinical implications, Oncogene 20(2001):5054–5058.

p. 248 it also inhibits the platelet-derived growth factor receptor: Druker (2002); Druker and Lydon (2000). In fact, Gleevec was originally synthesized as part of a program directed at inhibiting the platelet-derived growth factor receptor, known to be activated in the brain cancer glioblastoma and present in a number of other solid tissue tumors.

pp. 248–249 90 percent of patients with CML … have their cancers go into remission: Druker (2002); L.K. Altman, “Cancer Doctors See New Era of Optimism,” New York Times, May 22, 2001.

p. 249 mutations in the growth factor receptor itself: T.J. Lynch, D.W. Bell, R. Sordella, et al., Activating mutations in epidermal growth factor receptor underlying responsiveness of non-small-cell lung cancer to gefitinib, New England Journal of Medicine 350(2004):2129–2139; J. Marx, Why a new cancer drug works well, in some patients, Science 304(2004):658–659.

p. 249 to prevent the EGF receptor from phosphorylating itself: Lynch, et al.

(2004); T. Hollon, The current status of cancer treatment, The Scientist 17(2003), available online at www.the-scientist.com/yr2003/sep/feature8_030923.html.

p. 249 “We have only two options to collapse”: Green and Evan (2002).

p. 249 “Alternatively,” … “we could reinstate the defective apoptosis”: Ibid.

p. 250 drugs designed to interfere with growth factor signaling: Ibid.

p. 250 only 25 to 30 percent of breast cancer patients: Ross, et al. (2003); Wade (2001).

p. 250 An even smaller number of lung cancer patients: Lynch, et al. (2004); Marx (2004).

p. 250 patients with advanced disease in the acute, or “blast-crisis” phase: M.E. Gorre, M. Mohammed, K. Ellwood, et al., Clinical resistance to STI-571 cancer therapy caused by BCR-ABL gene mutation or amplification, Science 293(2001):876–880; F. McCormick, New age drug meets resistance, Nature 412(2001):281–282.

p. 251 “When success does occur”: Nature Reviews Drug Discovery GPCR Questionnaire Participants, The state of GPCR research in 2004, Nature Reviews Drug Discovery 3(2004):577–626.

p. 251 “We are still at the stage”: Ibid.

p. 258 “wholeness,” a quality he attributes to entities he calls “centers”: C. Alexander, The Nature of Order: An Essay on the Art of Building and the Nature of the Universe. Book One: The Phenomenon of Life (Berkeley, CA: The Center for Environmental Structure, 2002), pp. 79–108.

p. 258 “a physical set that occupies a certain volume in space”: Ibid., p. 84.

p. 258 “I notice the sunny part of the garden”: Ibid., p. 95.

p. 258 has identified 15 fundamental structural properties: Ibid., pp. 144–242.

p. 259 “deep interlock and ambiguity”: Ibid., pp. 195–199.

p. 259 “not separateness”: Ibid., pp. 230–235.

p. 259 “Nature too is understandable in terms of wholeness”: Ibid., p. 244.

p. 259 “the fifteen properties appear as geometric features”: Ibid., p. 246.

p. 259 Deep interlock and ambiguity … appear in the pattern: Ibid., pp. 270–271.

p. 259 not-separateness is an integral feature of any ecosystem: Ibid., pp. 288–289.

p. 259 “make buildings by stringing together patterns”: Alexander, et al., A Pattern Language, p. xli.

p. 259 “very dense; it has many meanings”: Ibid.

p. 260 “buildings which are poems”: Ibid., p. xliv.