In Chapter VI ("Difficulties on Theory") of The Origin of Species Charles Darwin reflects on the challenges that his hypothesis must overcome, and begins with the confession:
Long before having arrived at this part of my work, a crowd of difficulties will have occurred to the reader. Some of them are so grave that to this day I can never reflect on them without being staggered; but, to the best of my judgment, the greater number are only apparent, and those that are real are not, I think, fatal to my theory.
Shortly thereafter Darwin notes:
The crust of the earth is a vast museum; but the natural collections have been made only at intervals of time immensely remote.
In Chapter IX ("On the Imperfection of the Geological Record") he returns to this theme in more detail, concluding with a lovely metaphor:
... Those who think the natural geological record in any degree perfect, and who do not attach much weight to the facts and arguments of other kinds given in this volume, will undoubtedly at once reject my theory. For my part, following out Lyell's metaphor, I look at the natural geological record, as a history of the world imperfectly kept, and written in a changing dialect; of this history we possess the last volume alone, relating only to two or three countries. Of this volume, only here and there a short chapter has been preserved; and of each page, only here and there a few lines. Each word of the slowly-changing language, in which the history is supposed to be written, being more or less different in the interrupted succession of chapters, may represent the apparently abruptly changed forms of life, entombed in our consecutive, but widely separated formations. On this view, the difficulties above discussed are greatly diminished, or even disappear.