The inspiration for Darwin's early work was grounded in the geological and geographical methods expounded in Alexander von Humboldt's Personal Narrative of Travels in the Equinoctial Regions of the New Continent (1821) and Charles Lyell's Principles of Geology (1831).  Darwin had read and re-read Humboldt's explorations,  finding both romantic inspiration to explore but also a sense of how to use extensive geographical information for comparison, revealing the necessary interconnectedness of all phenomena.  Likewise, Lyell's treatise drew on multiple disciplines for deciphering geology, through mapping guided by the search for uniform and gradual geological actions.   The book became a guide for Darwin's early explorations of geology.

In the following extracts from The Voyage of the Beagle [2nd ed., 1845], Darwin writes about his observations in Patagonia, on immensity of geological changes, and the inferences one can draw from geological formations. In discussing a fossil discovery, he reasons about the taxonomic relationships between extinct and current animals, and the ecological complexities that control populations and extinctions. He concludes with a defense of interpreting the cause of changes to be ordinary processes, rather than cataclysmic events (pp. 162-68).

 Geology of Patagonia

       The geology of Patagonia is interesting. Differently from Europe, where the tertiary formations appear to have accumulated in bays, here along hundreds of miles of coast we have one great deposit, including many tertiary shells, all apparently extinct. The most common shell is a massive gigantic oyster, sometimes even a foot in diameter. These beds are covered by others of a peculiar soft white stone, including much gypsum, and resembling chalk, but really of a pumiceous nature. It is highly remarkable, from being composed, to at least one-tenth of its bulk, of Infusoria. Professor Ehrenberg has already ascertained in it thirty oceanic forms. This bed extends for 500 miles along the coast, and probably for a considerably greater distance. At Port St. Julian its thickness is more than 800 feet! These white beds are everywhere capped by a mass of gravel, forming probably one of the largest beds of shingle in the world: it certainly extends from near the Rio Colorado to between 600 and 700 nautical miles southward; at Santa Cruz (a river a little south of St. Julian), it reaches to the foot of the Cordillera; half way up the river, its thickness is more than 200 feet; it probably everywhere extends to this great chain, whence the well-rounded pebbles of porphyry have been derived: we may consider its average breadth as 200 miles, and its average thickness as about 50 feet. If this great bed of pebbles, without including the mud necessarily derived from their attrition, was piled into a mound, it would form a great mountain chain! When we consider that all these pebbles, countless as the grains of sand in the desert, have been derived from the slow falling of masses of rock on the old coast-lines and banks of rivers; and that these fragments have been dashed into smaller pieces, and that each of them has since been slowly rolled, rounded, and far transported, the mind is stupefied in thinking over the long, absolutely necessary, lapse of years. Yet all this gravel has been transported, and probably rounded, subsequently to the deposition of the white beds, and long subsequently to the underlying beds with the tertiary shells. 

       Everything in this southern continent has been effected on a grand scale: the land, from the Rio Plata to Tierra del Fuego, a distance of 1200 miles, has been raised in mass (and in Patagonia to a height of between 300 and 400 feet), within the period of the now existing sea-shells. The old and weathered shells left on the surface of the upraised plain still partially retain their colours. The uprising movement has been interrupted by at least eight long periods of rest, during which the sea ate deeply back into the land, forming at successive levels the long lines of cliffs, or escarpments, which separate the different plains as they rise like steps one behind the other. The elevatory movement, and the eating-back power of the sea during the periods of rest, have been equable over long lines of coast; for I was astonished to find that the step-like plains stand at nearly corresponding heights at far distant points. The lowest plain is 90 feet high; and the highest which I ascended near the coast, is 950 feet; and of this, only relics are left in the form of flat gravel-capped hills. The upper plain of Santa Cruz slopes up to a height of 3000 feet at the foot of the Cordillera. I have said that within the period of existing sea-shells, Patagonia has been upraised 300 to 400 feet: I may add, that within the period when icebergs transported boulders over the upper plain of Santa Cruz, the elevation has been at least 1500 feet. Nor has Patagonia been affected only by upward movements: the extinct tertiary shells from Port St. Julian and Santa Cruz cannot have lived, according to Professor E. Forbes, in a greater depth of water than from 40 to 250 feet; but they are now covered with sea-deposited strata from 800 to 1000 feet in thickness: hence the bed of the sea, on which these shells once lived, must have sunk downwards several hundred feet, to allow of the accumulation of the superincumbent strata. What a history of geological changes does the simply-constructed coast of Patagonia reveal!

Fossil gigantic Animal

       At Port St. Julian, I have lately heard that Capt. Sulivan, R.N., has found numerous fossil bones, embedded in regular strata, on the banks of the R. Gallegos, in lat. 51° 4'. Some of the bones are large; others are small, and appear to have belonged to an armadillo. This is a most interesting and important discovery. in some red mud capping the gravel on the 90-feet plain, I found half the skeleton of the Macrauchenia Patachonica, a remarkable quadruped, full as large as a camel. It belongs to the same division of the Pachydermata with the rhinoceros, tapir, and palæotherium; but in the structure of the bones of its long neck it shows a clear relation to the camel, or rather to the guanaco and Llama. From recent sea-shells being found on two of the higher step-formed plains, which must have been modelled and upraised before the mud was deposited in which the Macrauchenia was entombed, it is certain that this curious quadruped lived long after the sea was inhabited by its present shells. I was at first much surprised how a large quadruped could so lately have subsisted, in lat. 49° 15', on these wretched gravel plains, with their stunted vegetation; but the relationship of the Macrauchenia to the Guanaco, now an inhabitant of the most sterile parts, partly explains this difficulty.

Types of Organization constant

       The relationship, though distant, between the Macrauchenia and the Guanaco, between the Toxodon and the Capybara,-- the closer relationship between the many extinct Edentata and the living sloths, ant-eaters, and armadillos, now so eminently characteristic of South American zoology,-- and the still closer relationship between the fossil and living species of Ctenomys and Hydrochaerus, are most interesting facts. This relationship is shown wonderfully-- as wonderfully as between the fossil and extinct Marsupial animals of Australia-- by the great collection lately brought to Europe from the caves of Brazil by MM. Lund and Clausen. In this collection there are extinct species of all the thirty-two genera, excepting four, of the terrestrial quadrupeds now inhabiting the provinces in which the caves occur; and the extinct species are much more numerous than those now living: there are fossil ant-eaters, armadilloes, tapirs, peccaries, guanacos, opossums, and numerous South American gnawers and monkeys, and other animals. This wonderful relationship in the same continent between the dead and the living, will, I do not doubt, hereafter throw more light on the appearance of organic beings on our earth, and their disappearance from it, than any other class of facts.

Change in the Zoology of America

       It is impossible to reflect on the changed state of the American continent without the deepest astonishment. Formerly it must have swarmed with great monsters: now we find mere pigmies, compared with the antecedent, allied races. If Buffon had known of the gigantic sloth and armadillo-like animals, and of the lost Pachydermata, he might have said with a greater semblance of truth that the creative force in America had lost its power, rather than that it had never possessed great vigour. The greater number, if not all, of these extinct quadrupeds lived at a late period, and were the contemporaries of most of the existing sea-shells. Since they lived, no very great change in the form of the land can have taken place. What, then, has exterminated so many species and whole genera? The mind at first is irresistibly hurried into the belief of some great catastrophe; but thus to destroy animals, both large and small, in Southern Patagonia, in Brazil, on the Cordillera of Peru, in North America up to Behring's Straits, we must shake the entire framework of the globe. An examination, moreover, of the geology of La Plata and Patagonia, leads to the belief that all the features of the land result from slow and gradual changes. It appears from the character of the fossils in Europe, Asia, Australia, and in North and South America, that those conditions which favour the life of the larger quadrupeds were lately co-extensive with the world: what those conditions were, no one has yet even conjectured. It could hardly have been a change of temperature, which at about the same time destroyed the inhabitants of tropical, temperate, and arctic latitudes on both sides of the globe. In North America we positively know from Mr. Lyell, that the large quadrupeds lived subsequently to that period, when boulders were brought into latitudes at which icebergs now never arrive: from conclusive but indirect reasons we may feel sure, that in the southern hemisphere the Macrauchenia, also, lived long subsequently to the ice-transporting boulder-period. Did man, after his first inroad into South America, destroy, as has been suggested, the unwieldy Megatherium and the other Edentata? We must at least look to some other cause for the destruction of the little tucutuco at Bahia Blanca, and of the many fossil mice and other small quadrupeds in Brazil. No one will imagine that a drought, even far severer than those which cause such losses in the provinces of La Plata, could destroy every individual of every species from Southern Patagonia to Behring's Straits. What shall we say of the extinction of the horse? Did those plains fail of pasture, which have since been overrun by thousands and hundreds of thousands of the descendants of the stock introduced by the Spaniards? Can we believe that the Capybara has taken the food of the Toxodon, the Guanaco of the Macrauchenia, the existing small Edentata of their numerous gigantic prototypes? Certainly, no fact in the long history of the world is so startling as the wide and repeated exterminations of its inhabitants.

Causes of Extinction.

       Nevertheless, if we consider the subject under another point of view, it will appear less perplexing. We do not steadily bear in mind, how profoundly ignorant we are of the conditions of existence of every animal; nor do we always remember, that some check is constantly preventing the too rapid increase of every organized being left in a state of nature. The supply of food, on an average, remains constant; yet the tendency in every animal to increase by propagation is geometrical; and its surprising effects have nowhere been more astonishingly shown, than in the case of the European animals run wild during the last few centuries in America. Every animal in a state of nature regularly breeds; yet in a species long established, any great increase in numbers is obviously impossible, and must be checked by some means. We are, nevertheless, seldom able with certainty to tell in any given species, at what period of life, or at what period of the year, or whether only at long intervals, the check falls; or, again, what is the precise nature of the check. Hence probably it is, that we feel so little surprise at one, of two species closely allied in habits, being rare and the other abundant in the same district; or, again, that one should be abundant in one district, and another, filling the same place in the economy of nature, should be abundant in a neighbouring district, differing very little in its conditions. If asked how this is, one immediately replies that it is determined by some slight difference, in climate, food, or the number of enemies: yet how rarely, if ever, we can point out the precise cause and manner of action of the check! We are, therefore, driven to the conclusion, that causes generally quite inappreciable by us, determine whether a given species shall be abundant or scanty in numbers.

       In the cases where we can trace the extinction of a species through man, either wholly or in one limited district, we know that it becomes rarer and rarer, and is then lost: it would be difficult to point out any just distinction between a species destroyed by man or by the increase of its natural enemies. The evidence of rarity preceding extinction, is more striking in the successive tertiary strata, as remarked by several able observers; it has often been found that a shell very common in a tertiary stratum is now most rare, and has even long been thought to be extinct. If then, as appears probable, species first become rare and then extinct -- if the too rapid increase of every species, even the most favoured, is steadily checked, as we must admit, though how and when it is hard to say-- and if we see, without the smallest surprise, though unable to assign the precise reason, one species abundant and another closely allied species rare in the same district-- why should we feel such great astonishment at the rarity being carried a step further to extinction? An action going on, on every side of us, and yet barely appreciable, might surely be carried a little further, without exciting our observation. Who would feel any great surprise at hearing that the Magalonyx was formerly rare compared with the Megatherium, or that one of the fossil monkeys was few in number compared with one of the now living monkeys? and yet in this comparative rarity, we should have the plainest evidence of less favourable conditions for their existence. To admit that species generally become rare before they become extinct -- to feel no surprise at the comparative rarity of one species with another, and yet to call in some extraordinary agent and to marvel greatly when a species ceases to exist, appears to me much the same as to admit that sickness in the individual is the prelude to death-- to feel no surprise at sickness-- but when the sick man dies to wonder, and to believe that he died through violence.

After experiencing an earthquake in Chile, Darwin again infers the long-term geological effects of such forces of change, confirming once more his Lyellian perspective (p. 297).

Permanent elevation of the land

       The most remarkable effect of this earthquake was the permanent elevation of the land; it would probably be far more correct to speak of it as the cause. There can be no doubt that the land round the Bay of Concepcion was upraised two or three feet; but it deserves notice, that owing to the wave having obliterated the old lines of tidal action on the sloping sandy shores, I could discover no evidence of this fact, except in the united testimony of the inhabitants, that one little rocky shoal, now exposed, was formerly covered with water. At the island of S. Maria (about thirty miles distant) the elevation was greater; on one part, Captain Fitz Roy found beds of putrid mussel-shells still adhering to the rocks, ten feet above high-water mark: the inhabitants had formerly dived at lower-water spring-tides for these shells. The elevation of this province is particularly interesting, from its having been the theatre of several other violent earthquakes, and from the vast numbers of sea-shells scattered over the land, up to a height of certainly 600, and I believe, of 1000 feet. At Valparaiso, as I have remarked, similar shells are found at the height of 1300 feet: it is hardly possible to doubt that this great elevation has been effected by successive small uprisings, such as that which accompanied or caused the earthquake of this year, and likewise by an insensibly slow rise, which is certainly in progress on some parts of this coast.