As we have seen, fossil plants engaged Williamson's attention in his earliest years, when as a mere boy he contributed to Lindley and Hutton's Fossil Flora.

His first important independent work in this field was his paper "On the Structure and Affinities of the Plants hitherto known as Sternbergiae" (1851), in which he proved, for the first time, that these curious fossils, resembling a rouleau of coins, were casts of the discoid pith of Dadoxylon, or, as we should now say, of Cordaiteae—the first step in the reconstruction of this early gymnospermous family. This investigation, to which he appears to have been led almost accidentally, through some good specimens coming into his hands, brought him back, as he says, to his old subject of fossil botany. It was long, however, before he got fairly started on his great course of investigations on Carboniferous plants.

In the meantime he had returned to the Yorkshire Oolitic plants and, about 1847, published a paper in the Proceedings of the Yorkshire Philosophical Society, "On the Scaly Vegetable Heads or collars from Runswick Bay, supposed to belong to the Zamia gigas." His full paper, in which he maintained the Cycadean affinities of the flower-like fossils, was written soon afterwards, but met with a series of misfortunes, and was not finally published till 1870, in the Transactions of the Linnean Society, before which body it had been read in 1868. Williamson was admittedly right in connecting the floral organs with the so-called Zamia foliage, and his interpretation of the complicated structure was as good as was possible in the then state of knowledge. The true nature of these fossils, now known by the name Williamsonia, given them by Mr Carruthers, could only be understood at a much later date in the light of Dr Wieland's famous researches on the American Bennettiteae, and has quite recently been made clear in a memoir by Prof. Nathorst. Perhaps, even now, some points remain doubtful.

Early in the fifties Williamson made some rough sections of a Calamite which came into his hands, and this was the beginning of his most characteristic line of work. A remarkable internal cast of a Calamite, figured by Lyell in his Manual of Geology in 1855, led to a correspondence with M. Grand'Eury, now so famous as the veteran French palaeobotanist. Williamson at that time had no intention of entering on the serious study of Carboniferous plants, for Binney was already in the field. Grand'Eury's letter, however, caused him to look up his old sections, which he found differed from the Calamitean stems figured by Binney. Matters for a time moved slowly, and Williamson's specimen was only described in 1868 in the Manchester Memoirs. This fossil, which he named Calamopitus, is now known as Arthrodendron, and is a distinct type of Calamarian stem, intermediate between the common Calamites or Arthropitys, and the more elaborate Calamodendron of the Upper Coal Measures.

Williamson was now fairly started on his Carboniferous work. His first memoir on the Organisation of the Fossil Plants of the Coal Measures was communicated to the Royal Society on November 11, 1870. It is amusing to find that the secretaries objected to the memoir being called Part I, since it bound the society to publish a Part II! Nineteen Parts were published, the last in 1893.

The first memoir was on the Calamites, and controversy at once broke out. Williamson was from the first impressed by the manifest occurrence of exogenous, or, as we should now call it, secondary growth, both in the Calamites and the Lepidodendreae, groups which he was convinced were cryptogamic. The controversy with the great French school, headed by the illustrious Brongniart, is well known. As Williamson put it: "The fight was always the same; was Brongniart right or wrong when he uttered his dogma, that if the stem of a fossil plant contained a secondary growth of wood, the product of a cambium layer, it could not possibly belong to the cryptogamic division of the vegetable kingdom?[127]"

In England, however, the dispute was on different lines. "In August of 1871," says Williamson, "the British Association met at Edinburgh. At that meeting I brought forward the subject of cambiums and secondary woods in Cryptogams, with the result that my views were rejected by every botanist in the room." There followed a controversy in the pages of Nature, which is of some interest, as showing the state of opinion in England at that time. Williamson tells us in his autobiography the principle by which he was guided in his work: "I determined not to look at the writings of any other observer until I had studied every specimen in my cabinet, and arrived at my own conclusions as to what they taught." In spite of this excellent rule it is probable that he was at first unconsciously influenced by the views of Brongniart, which may have led him to attach too much systematic importance to the occurrence of secondary growth. At any rate he proposed at the Edinburgh meeting "to separate the vascular Cryptogams into two groups, the one comprehending Equisetaceae, Lycopodiaceae and Isoëtaceae, to be termed the Cryptogamiae Exogenae, linking the Cryptogams with the true exogens through the Cycads; the other called the Cryptogamiae Endogenae, to comprehend the Ferns, which will unite the Cryptogams with the Endogens through the Palmaceae[128]."

Plate XXIII