The affinities of all the beings of the same class have sometimes been represented by a great tree.I believe this simile largely speaks the truth. The green and budding twigs may represent existing species; and those produced during former years may represent the long succession of extinct species. At each period of growth all the growing twigs have tried to branch out on all sides, and to overtop and kill the surrounding twigs and branches, in the same manner as species and groups of species have at all times overmastered other species in the great battle for life. The limbs divided into great branches, and these into lesser and lesser branches, were themselves once, when the tree was young, budding twigs; and this connection of the former and present buds by ramifying branches may well represent the classification of all extinct and living species in groups subordinate to groups. Of the many twigs which flourished when the tree was a mere bush, only two or three, now grown into great branches, yet survive and bear the other branches; so with the species which lived during long-past geological periods, very few have left living and modified descendants. From the first growth of the tree, many a limb and branch has decayed and dropped off; and these fallen branches of various sizes may represent those whole orders, families, and genera which have now no living representatives, and which are known to us only in a fossil state. As we here and there see a thin straggling branch springing from a fork low down in a tree, and which by some chance has been favoured and is still alive on its summit, so we occasionally see an animal like the Ornithorhynchus or Lepidosiren, which in some small degree connects by its affinities two large branches of life, and which has apparently been saved from fatal competition by having inhabited a protected station. As buds give rise by growth to fresh buds, and these, if vigorous, branch out and overtop on all sides many a feebler branch, so by generation I believe it has been with the great Tree of Life, which fills with its dead and broken branches the crust of the earth, and covers the surface with its ever-branching and beautiful ramifications.
...Whilst on board the Beagle I was quite orthodox, and I remember being heartily laughed at by several of the officers... for quoting the Bible as an unanswerable authority on some point of morality... But I had gradually come by this time, i.e., 1836 to 1839, to see that the Old Testament from its manifestly false history of the world, with the Tower of Babel, the rainbow at sign, &c., &c., and from its attributing to God the feelings of a revengeful tyrant, was no more to be trusted than the sacred books of the Hindoos, or the beliefs of any barbarian....By further reflecting that the clearest evidence would be requisite to make any sane man believe in the miracles by which Christianity is supported, (and that the more we know of the fixed laws of nature the more incredible do miracles become), that the men at that time were ignorant and credulous to a degree almost uncomprehensible by us, that the Gospels cannot be proved to have been written simultaneously with the events, that they differ in many important details, far too important, as it seemed to me, to be admitted as the usual inaccuracies of eyewitnesses; by such reflections as these, which I give not as having the least novelty or value, but as they influenced me, I gradually came to disbelieve in Christianity as a divine revelation. The fact that many false religions have spread over large portions of the earth like wild-fire had some weight with me. Beautiful as is the morality of the New Testament, it can be hardly denied that its perfection depends in part on the interpretation which we now put on metaphors and allegories.But I was very unwilling to give up my belief... Thus disbelief crept over me at a very slow rate, but was at last complete. The rate was so slow that I felt no distress, and have never since doubted even for a single second that my conclusion was correct. I can indeed hardly see how anyone ought to wish Christianity to be true; for if so the plain language of the text seems to show that the men who do not believe, and this would include my Father, Brother and almost all of my friends, will be everlastingly punished. And this is a damnable doctrine.