While thus learning the art of observing, he was at the same time developing his power of thinking. He was by nature fond of argument, and defended with earnestness any opinions which he had been led to adopt. He was very active in the Harrow Scientific Society, reading papers, taking part in the discussions, and exhibiting specimens. He gained in 1867 a prize for an essay on coal, and when, in 1868, Mr Leaf offered a prize (a microscope) "for the best account of some locality visited by the writer during the Easter Holidays," two essays sent in, one by Balfour, the other by his close friend, Mr Arthur Evans, since well known for his researches in Illyria, were found to be of such unusual merit that Prof. Huxley was specially requested to adjudicate between them. He judged them to be of equal merit, and a prize was given to each. The subject of Balfour's essay was "The Geology and Natural History of East Lothian." When biological subjects were discussed at the Scientific Society, Balfour appears to have spoken as a most uncompromising opponent of the views of Mr Charles Darwin, little thinking that in after life his chief work would be to develop and illustrate the doctrine of evolution.
The years at Harrow passed quickly away, Balfour making fair, but perhaps not more than fair, progress in the ordinary school learning. In due course however he reached the upper sixth form, and in his last year, became a monitor. At the same time his exact scientific knowledge was rapidly increasing. Geology still continued to be his favorite study, and in this he made no mean progress. During his last years at Harrow he and his brother Gerald worked out together some views concerning the geology of their native county. These views they ultimately embodied in a paper, which was published in their joint names in the _Geological Magazine_ for 1872, under the title of "Some Points in the Geology of the East Lothian Coast," and which was in itself a work of considerable promise. Geology however was beginning to find a rival in natural history. Much of his holiday time was now spent in dredging for marine animals along the coast off Dunbar. Each specimen thus obtained was carefully determined and exact records were kept of the various 'finds,' so that the dredgings (which were zealously continued after he had left Harrow and gone to Cambridge) really constituted a serious study of the fauna of this part of the coast. They also enabled him to make a not inconsiderable collection of shells, in the arrangement of which he was assisted by his sister Evelyn, of crustacea and of other animals.