While this investigation was going on, Lyell was preparing the fifth edition of his Manual of Geology. He invited Pengelly to suggest corrections to the text, saying that, besides positive mistakes, he would "be glad of any hints and suggestions made freely, which your knowledge of the manner in which beginners are struck may enable you to send us." The criticisms supplied by Mr. Pengelly were adopted by Lyell except where they had already been made unnecessary.
On the accidental discovery by workmen, in 1858, of a cavern in Windmill Hill, overhanging the town of Brixham, Pengelly at once thought of finding what was in it, and what story it might have to tell. He visited the place and applied to the owner for permission to explore it in behalf of the Torquay Natural History Society. But on consultation with Dr. Hugh Falconer it was decided that as that society probably had not means sufficient to bear the expense of the exploration, the Royal and Geographical Societies should be applied to for a grant. This was obtained, and the work was carried on under the superintendence of Professor Prestwich and Mr. Pengelly, on whom, as a resident of the place, the burden substantially fell. The decision to explore the cave was brought about largely by the fact that it was a virgin cave which had been inaccessibly closed during an incalculably long period, the last previous event in its history having been the introduction of a reindeer antler, which was found attached to the upper surface of the stalagmitic floor. It was therefore free from the objection urged against Kent's Cavern that, having been long known and open, it had probably been ransacked again and again. A thorough method of exploration was determined upon, beginning with the examination and removal of the stalagmitic floor; after which the upper bed should be dealt with in a similar manner horizontally throughout the entire length of the cavern, or so far as practicable; then the next lower bed, and so on, till all the deposits had been removed. By this method the general stratigraphical order of the deposits and their characteristics could be learned, all their fossils secured, and the highest possible exactness attained. The excavations were continued through twelve months, at the end of which the cave had been practically emptied. Besides furnishing interesting indications relative to its physical history, the cave yielded sixteen hundred and twenty-one bones and thirty-six flints. While most of the flints were flakes, some of which possibly might not be artificial, three were fairly well made implements of paleolithic type; and it was therefore concluded that man either frequented or at any rate sometimes entered the Brixham Cave while Devonshire was inhabited by various mammals which are now extinct. Previous to the execution of this work, all geological evidence as to the antiquity of man had been received, even by English geologists of the first rank, with what Pengelly called apathy and skepticism. After the work it soon became evident, Pengelly said in an address to the Section of Anthropology of the British Association, in 1883, that this geological apathy had been more apparent than real. "In fact, geologists were found to have been not so much disinclined to entertain the question of human antiquity, as to doubt the trustworthiness of the evidence which had previously been offered to them on the subject." The discoveries are thought to have had a considerable share in disposing Mr. Prestwich to undertake the investigation of the remains at Amiens and Abbeville in France and Hoxne in England, "which added to his own great reputation and rescued M. Boucher de Perthes from undeserved neglect." Prof. Boyd Dawkins says that they established beyond all doubt the existence of paleolithic man in the Pleistocene age, and caused the whole of the scientific world to awake to the fact of the vast antiquity of the human race. Of course, they aroused a theological controversy which was long and bitter, and has only recently died out. Pengelly had no trouble through it all. "Geologists," he said, "see no mode of reconciling the Mosaic account of creation with geological science.... For myself, I am satisfied that science can do nothing for the salvation of the soul, and that the Bible is able, through God's grace, to make us wise unto salvation." No doubts or difficulties could ever undermine his faith as a Christian.