This page-by-page annotation is organized by sections, as delineated by the seven squares (sprockets) which separate each section. The page numbers for this page-by-page annotation are for the original Viking edition (760 pages). Editions by other publishers vary in pagination the newer Penguin editions are 776 pages; the Bantam edition is 886 pages.
Contributors: Please use a 760-page edition (either the original Viking edition with the orange cover or the Penguin USA edition with the blue cover and rocket diagram there are plenty on Ebay for around $10) or search the Google edition for the correct page number. Readers: To calculate the Bantam edition use this formula: Bantam page # x 1.165. Before p.50 it's about a page earlier; as you get later in the book, add a page.
Finally, profound thanks to Prof. Don Larsson for providing the foundation for this page-by-page annotation.
Topiary trees line the drive
Topiary is the horticultural practice of training live perennial plants, by clipping the foliage and twigs of trees, shrubs and subshrubs to develop and maintain clearly defined shapes, perhaps geometric or fanciful; and the term also refers to plants which have been shaped in this way. It can be an art and is a form of living sculpture. The word derives from the Latin word for an ornamental landscape gardener, topiarius, creator of topia or "places", a Greek word that Romans applied also to fictive indoor landscapes executed in fresco. No doubt the use of a Greek word betokens the art's origins in the Hellenistic world that was influenced by Persia, for neither Classical Greece nor Republican Rome developed any sophisticated tradition of artful pleasure grounds. 
Cf. Mason & Dixon pg. 722
83.34-37 meddling with another man's mind...Harvard University
During WWII Dr Henry A. Murray, then assistant director of the Harvard Psychological Clinic, joined the OSS in Europe and assisted James Miller in developing psychological profiles of prospective special agents -- so called stress tests. He also analyzed Hitler for the Allies, predicting that if Germany lost the war, Hitler would commit suicide; that Hitler was impotent as far as heterosexual relations were concerned; and that Hitler had possibly participated in a homosexual relationship -- all suggestive of Blicero.
After 1947 and the Cold War it seemed every self-respecting psychologist was doing side jobs for the CIA in "persuasion technologies" including LSD, various other drugs, sleep deprivation, isolation tanks, hypnosis, etc. even, allegedly, unto the death of the "patient". Perhaps best well known was MK Ultraunder the direction of Dr. Sidney Gottlieb.
Murray himself returned to Harvard where he continued his meddling with the minds of others. One of the minds he meddled with from 1958 to 1962 belonged to Theodore Kaczynski. Alston Chase's book Harvard and the Unabomber: The Education of an American Terrorist tells of the psychological experiments which Kaczynski is reported to have undergone at Harvard, under the direction of Murray. Chase connects these experiences in a controversial thesis to Kaczynski's later career as the Unabomber. As is generally well known in Pynchon circles, TRP himself was suspected of being the Unabomber.
And then of course there was the Leary-Alpert led Harvard Psilocybin Project between 1960 and 1962 ...
Watson and Rayner... "Infant Albert"
The Little Albert experiment was a case study showing empirical evidence of classical conditioning in humans. This study was also an example of stimulus generalization. It was conducted in 1920 by John B. Watson along with his assistant Rosalie Rayner. The study was done at Johns Hopkins University. John B. Watson, after observing children in the field, was interested in finding support for his notion that the reaction of children, whenever they heard loud noises, was prompted by fear. Furthermore, he reasoned that this fear was innate or due to an unconditioned response. He felt that following the principles of classical conditioning, he could condition a child to fear another distinctive stimulus which normally would not be feared by a child. 
Darmstadt is a city in the Bundesland (federal state) of Hesse in Germany, located in the southern part of the Rhine Main Area. 
Kekulé's own famous switch into chemistry from architecture
Friedrich August Kekule von Stradonitz a.k.a. August Kekulé (7 September 1829–13 July 1896) was a German organic chemist. From the 1850s until his death, Kekule was one of the most prominent chemists in Europe, especially in theoretical chemistry. He was the principal founder of the theory of chemical structure. 
Larson-Keeler three-variable "lie detector"
A device recording both blood pressure and galvanic skin response was invented in 1921 by Dr. John A. Larson of the University of California and first applied in law enforcement work by the Berkeley Police Department under its nationally renowned police chief August Vollmer. Further work on this device was done by Leonarde Keeler. 
85.25 Edwin Treacle
Although derived from a word meaning an antidote to poison, "treacle" is the British term for molasses and is often used to describe something excessively sweet and sticky.
85.37 Poisson Distribution/Equation
See entry on page 54
Northern region of Belgium bordering the North Sea. At least 60 miles from the English coast.
See page 78.
The Boeing B-17 Flying Fortress is a four-engine heavy bomber aircraft developed in the 1930s for the then-United States Army Air Corps (USAAC). Competing against Douglas and Martin for a contract to build 200 bombers, the Boeing entry outperformed both competitors and more than met the Air Corps' expectations. Although Boeing lost the contract because the prototype crashed, the Air Corps was so impressed with Boeing's design that they ordered 13 more B-17s for further evaluation. From its introduction in 1938, the B-17 Flying Fortress evolved through numerous design advances. 
The nacelle is a cover housing (separate from the fuselage) that holds engines, fuel, or equipment on an aircraft. In some cases—the most notable one being the World War II-era P-38 Lightning airplane—an aircraft's cockpit may also be housed in a nacelle. The covering is typically aerodynamically shaped. 
Poly(methyl methacrylate) (PMMA) is a transparent thermoplastic, often used as a light or shatter-resistant alternative to glass. It is sometimes called acrylic glass. Chemically, it is the synthetic polymer of methyl methacrylate. The material was developed in 1928 in various laboratories, and was first brought to market in 1933 by Rohm and Haas Company, under the trademark Plexiglas. It has since been sold under many different names including Lucite and Perspex. 
Battle of Britain
See page 40.
Dr. Horsley Gantt
A former student and colleague of Pavlov.
88.10 the submontane Venus
That is, the goddess of the Tannhauser legend and opera.
Venus is also the goddess of love, of course.
88.34 yang-yin rubbish
Note that Pointsman here rejects the concept only to become entranced by it later.
91.27 Dr. Bleagh
An expression of disgust. (Try saying it!)
Beyond the Zero
Un Perm' au Casino Herman Goering
In the Zone
279-295, 295-314, 314-329, 329-336, 336-359, 359-371, 371-383, 383-390, 390-392, 392-397, 397-433, 433-447, 448-456, 457-468, 468-472, 473-482, 482-488, 488-491, 492-505, 505-518, 518-525, 525-532, 532-536, 537-548, 549-557, 557-563, 563-566, 567-577, 577-580, 580-591, 591-610, 610-616