In introducing Jefferson’s Notes on the State of Virginia, William Peden declares this mass of information and commentary to be “…the most important scientific...book written by an American before 1785." In Notes, readers find inventories and analyses of stream flow, lakes and coastlines, topography, soils, climate, minerals, plants and animals. Jefferson’s contributions, though not termed geological at the time, are such in a modern sense. His “Rivers” section stands as a prototype of publications produced a century later by the U.S. Geological Survey. His discourse on minerals set the pattern for the mineral commodity surveys now published each year by the U.S. Geological Survey. In Notes Jefferson described field methods he developed to place time lines on layers of soils—an important contribution to stratigraphy, a nascent branch of geology.
With his one book, Jefferson demonstrated he was more than a tabulator and analyzer of information. He also promoted the scientific method and used the occasion to criticize unscientific thinking. This expansion of scope led Jefferson into controversies that stayed with him throughout his lifetime.
In the Paris edition of Notes (1785), Jefferson discussed a chemical theory of the formation of shells found on mountaintops. Bedini relates how the passage "...brought [Jefferson] considerable criticism because it was inconsistent with the Biblical account of Noah’s flood." That criticism was mild compared to what Peden terms the "long and frequently violent controversy" in opposition to the analyses Jefferson presented in the English language edition of Notes, published in 1788. Readers in America could then assume, from Jefferson’s analysis of the physics of the atmosphere, that he was rejecting the literal truth of Noah’s flood. In an attempt seemingly directed at diluting the controversy, Jefferson examined three conflicting explanations of how shells came to present 15,000 feet above sea level, and he discounted all three “explanations” as equally unsatisfactory. He tried to clarify his position by stating a cardinal principle of science: we must be content to acknowledge, that this…is as yet unsolved. Ignorance is preferable to error; and he is less remote from the truth who believes nothing, than he who believes what is wrong. Jefferson’s critics were far from content or satisfied.
Jefferson wrote and perfected Notes when he was in his late thirties—that is, before his involvement in bitter political fights. Historians are in general agreement Jefferson was thin-skinned about criticism and became more so with age. In 1803, Jefferson wrote: Every word which goes from me, whether verbally or in writing becomes the subject of so much malignant distortion, & perverted construction, that I am obliged to caution my friends against…my letters getting into the public…. 
The President Jefferson who retired to Monticello six years later could not escape criticism from determined opponents; but he could act to reduce the power of controversy to defeat his aims. This is most evident in his strong advice on the teaching of geology at the University of Virginia—statements from Jefferson that seem to run contra to his principles.
Jefferson’s proposals of curricula for the fledgling University of Virginia included a recommendation which has been interpreted as de-emphasizing the study of geology. This stance by Jefferson is puzzling, given Jefferson’s pioneering work in several fields of the science.
In writing to the Natural History Professor John Emmet, Jefferson stated his case for de-emphasis, with reference to the purpose of the academic course on geology: To learn, as far as observation has informed us, the ordinary arrangement of the different strata…in the earth….But the dreams about the modes of creation, inquiries whether our globe has been formed by the agency of fire or water, how many millions of years it has cost Vulcan or Neptune to produce…is too idle to be worth a single hour of any man’s life.
On reading that letter, puzzlement grows: Is this the same man who wrote: This institution [University of Virginia] will be based on the illimitable freedom of the human mind. For here we are not afraid to follow truth, wherever it may lead, nor to tolerate any error so long as reason is left free to combat it.
But a plausible explanation is available if we consult biographies of leading geologists of Jefferson’s time, and consider Jefferson’s general aversion to unproductive argument and lessons he learned about avoiding controversy.
Jefferson’s use of the words “Vulcan” and “Neptune” were deliberate; these are the battle flags flying in a bitter controversy raging between geologists throughout the last half of Jefferson’s lifetime. One school of thought, the Vulcanists, led by the eminent Scotch geologist, James Hutton, adhered passionately to the belief that rocks resulted from volcanism; the opposing school, the Neptunists, led by the Saxon mineralogist, Abraham Werner, held unflinchingly to the belief that chemical precipitation was the agent of rock formation. The Fenton’s, in their seminal work on the controversy conclude: [This struggle] …divided geologists into two camps whose members battered each other with words as often as they broke stones with hammer.
Jefferson sought to steer clear of this intellectual war by focusing his university’s scientists on practical matters. Under severe criticism on high priority matters, e.g., faculty and financing, the University could ill afford involvement in one of the major academic controversies of the age. Pragmatism trumped idealism.
 /TJ letter to Edward Dowse, Washington, April 19, 1803
 /See Bedini, Silvio A., Jefferson and Science. Monticello Monograph Series: Thomas Jefferson Foundation (University of North Carolina Press, 2002) pp, 102-103,
 /E.G., Prince, Cathryn j., A Professor, A President, and A Meteor. Amherst, NY: Prometheus, 2010, p.141.
 /TJ letter to Dr. John Emmet, May 2, 1826. L&B, 16: 168-72.
 / TJ letter to William Roscoe, December 27, 1820. L&B, 15: 303.
 / Fenton, C.L. and Fenton, M.A. 1956, Giants of Geology. Doubleday & Company: p.61