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After the words "On the Origin of Species" on page i, page ii shows quotations. The first, by William Whewell from his Bridgewater Treatise, sets out the idea that in natural theology events in the material world are brought about "by the establishment of general laws" rather than by individual miracles. The second by Francis Bacon from his Advancement of Learning argues that we should study both the word of God in the Bible and the works of God in nature together, so that the works of God teach us how to interpret the word of God. From the second to sixth editions, a third quotation is included, from the Analogy of Revealed Religion by the eighteenth century bishop Joseph Butler. This describes natural as meaning "stated, fixed or settled" by "an intelligent agent" who can equally carry out single supernatural miracles.

These quotations relate theology to nature, and in the book Darwin includes various comments aiming to harmonise science and religion, in line with Isaac Newton's belief in the glory of a rational God who established a law-abiding cosmos rather than a capricious deity. The quotations are followed by the title page then the index. The book then begins with the Introduction, though from the 3rd edition onwards this is preceded by An Historical Sketch giving credit to his predecessors in ideas of evolution and natural selection.

Introduction

WHEN on board H.M.S. 'Beagle,' as naturalist, I was much struck with certain facts in the distribution of the inhabitants of South America, and in the geological relations of the present to the past inhabitants of that continent. These facts seemed to me to throw some light on the origin of species—that mystery of mysteries, as it has been called by one of our greatest philosophers.

Darwin starts with a reference to the distribution of rheas, Galapagos tortoises and mockingbirds inspiring doubts in species being fixed, and the close relationship of fossils he found in South America to animals currently living on the same continent. He then cites the question which John Herschel had raised in correspondence with Charles Lyell shortly before Darwin met Herschel in South Africa, “that mystery of mysteries, the replacement of extinct species by others” as “a natural in contradistinction to a miraculous process”. Darwin mentions his years of work on his theory, and Wallace arriving at the same conclusion leading him to "publish this Abstract" of his incomplete work. He then outlines his ideas, and sets out its essence of his theory:

As many more individuals of each species are born than can possibly survive; and as, consequently, there is a frequently recurring struggle for existence, it follows that any being, if it vary however slightly in any manner profitable to itself, under the complex and sometimes varying conditions of life, will have a better chance of surviving, and thus be naturally selected. From the strong principle of inheritance, any selected variety will tend to propagate its new and modified form.

Variation under domestication and under nature

Chapter I discusses the considerable amount of variation of plants and animals in conditions of domestication. Darwin partly attributes this to different conditions of life, and (incorrectly) to domestication itself as well as to changed habits producing an inherited effect. He discusses how domestication has been going on since the neolithic period, then turns in detail to his studies of domestic pigeons. "The diversity of the breeds is something astonishing", yet all show evidence of being descendants of the same species of rock pigeons. He describes breeding methods and introduces the term artificial selection (though environmental changes, such as more food and protection from predators, were also factors).

In chapter II Darwin considers variation under nature. He wrote that the nineteenth-century definition of species was chiefly a matter of opinion, since the discovery of new linking forms often degraded species to varieties, and in many cases experts were unable to agree whether different forms represented different varieties of the same species or different species of the same genus. He then points out that in large genera with many species the species also tend to have numerous varieties. Darwin goes on to state "I believe a well-marked variety may be justly called an incipient species" and "that species are only strongly marked and permanent varieties". Historians have pointed out that these two chapters present one of the most important of the new ideas in Origin. Naturalists had long known that the individuals of a species differed from one another in many ways, but for the most part had considered such variations to be limited and unimportant with the basic character of each species representing an unchanging ideal in the mind of God. The ideas of Darwin and Wallace elevated variations among individuals within a species from being trivial details to being central to understanding the way the natural world worked.

Struggle for existence, natural selection, and divergence

At the start of chapter III on struggle for existence, Darwin reiterates how this results in varieties, "which I have called incipient species", becoming distinct species, grouped into genera.

Owing to this struggle for life, any variation, however slight and from whatever cause proceeding, if it be in any degree profitable to an individual of any species, in its infinitely complex relations to other organic beings and to external nature, will tend to the preservation of that individual, and will generally be inherited by its offspring.... I have called this principle, by which each slight variation, if useful, is preserved, by the term of Natural Selection, in order to mark its relation to man's power of selection.

In the 5th and 6th editions he added "But the expression often used by Mr. Herbert Spencer, of the Survival of the Fittest, is more accurate, and is sometimes equally convenient." He discusses the universal struggle for existence as shown by A. P. de Candolle and Charles Lyell, emphasising that he uses the term "in a large and metaphorical sense, including dependence of one being on another". The rate of increase in population which would follow if all offspring survived leads to a Malthusian struggle: "It is the doctrine of Malthus applied with manifold force to the whole animal and vegetable kingdoms". In reviewing checks to such increase he discusses the complex interdependencies which we now term ecology. He notes that competition is most severe between closely related forms, "which fill nearly the same place in the economy of nature".

Chapter IV details natural selection under the "infinitely complex and close-fitting.. mutual relations of all organic beings to each other and to their physical conditions of life". Darwin takes as an example a country where a change in conditions leads to extinction of some species, possibly immigration of others more suited and, where suitable variations occur, descendants of species becoming increasingly adapted to the changed conditions. Darwin points out that the artificial selection practiced by animal breeders frequently produces a sharp divergence in character between different breeds, and he suggests natural selection might do the same. He says:

But how, it may be asked, can any analogous principle apply in nature? I believe it can and does apply most efficiently, from the simple circumstance that the more diversified the descendants from any one species become in structure, constitution, and habits, by so much will they be better enabled to seize on many and widely diversified places in the polity of nature, and so be enabled to increase in numbers.

Historians have pointed out that in this passage Darwin has anticipated the modern concept of an ecological niche and the role such niches play in supporting biological diversity. He does not suggest that every individual with a favourable variation must be selected, or that the selected or favoured animals are better or higher, but merely that they are more adapted to their surroundings. Having no knowledge of Mendelian genetics, he tries to deal with anticipated blending of inherited characteristics.

The tree diagram used to show the divergence of species. It is the only illustration in the Origin of Species.

Darwin then introduces what he calls sexual selection to explain seemingly non-functional differences between sexes, as in beautiful plumage of birds. He draws attention to cross-breeding between varieties giving "vigour and fertility to the offspring", with close interbreeding or self fertilization having the opposite effect, explaining features found in flowers which avoid self-fertilisation and attract insects to cross-pollinate. He thinks that natural selection leading to new species is most favoured by isolation of a population, or by open areas with large populations leading to increased numbers of variations. The effect of natural selection in forming species is expected to be very slow, and often intermittent, but given the effectiveness of artificial selection, he "can see no limit to the amount of change, to the beauty and infinite complexity of the coadaptations between all organic beings, one with another and with their physical conditions of life, which may be effected in the long course of time by nature's power of selection." With the aid of a tree diagram and calculations he indicates the "divergence of character" from original species into multiple new species and genera, branches stopping or falling off as extinction occurs, while fresh buds form new branches in "the great Tree of life... with its ever branching and beautiful ramifications."

The first four chapters lay out the case for natural selection as an agent of evolution analogous to the artificial selection practiced by animal breeders. Historians believe that Darwin chose to start his argument with the case for natural selection rather than with evidence that evolution had occurred because he was aware that most of his readers would already have been familiar with earlier arguments for the transmutation of species. He was also aware that these earlier arguments had failed to find wide acceptance among leading scientists in large part because they lacked any plausible mechanism for evolutionary change. Therefore Darwin wanted to begin his argument by convincing his readers that his theory had a viable scientific explanation for how evolutionary change occurred before he discussed the evidence that it had.

Variation and heredity

One of the chief difficulties for Darwin and other naturalists in his time was that there was no agreed-upon model of heredity; early in chapter one Darwin states "The laws governing inheritance are quite unknown". He accepted a version of the inheritance of acquired characteristics (which after Darwin's death came to be called Lamarckism), and chapter 5 (of the first edition) discusses what he calls the effects of use and disuse, writing that he thought "there can be little doubt that use in our domestic animals strengthens and enlarges certain parts, and disuse diminishes them; and that such modifications are inherited" and that this also applied in nature. Besides changes he attributes to the use and disuse of organs (such as the loss of eyes in cave dwelling species) Darwin discusses acclimatization to environmental conditions and correlations in the growth of different parts of an organism, where variations in certain characteristics of some organisms seemed to be correlated with variations in other characteristics, as factors that could produce inheritable variation. Darwin did state that some changes that were commonly attributed to use and disuse, such as the loss of functional wings in some island dwelling insects, might well be a product of natural selection instead. In later additions of Origin Darwin expands the role attributed to the inheritance of acquired characteristics.

It was not until the early 20th century, with the advent of the modern evolutionary synthesis, that a model of heredity became completely integrated with a model of variation. It is a common theme in the history of evolution and genetics written by scientists, rather than historians, to claim that Darwin's lack of an adequate model of heredity was the source of suspicion about his idea of natural selection, but later historians of science have adequately documented the fact that this was not the source of most objections to Darwin, and that later scientists, such as Karl Pearson and the biometric school, could develop compelling models of evolution by natural selection with even a relatively simple "blending" model of heredity such as that used by Darwin.

Difficulties for the theory

In chapters VI – VIII (of the first edition) Darwin addresses possible difficulties for the theory. Darwin starts with the question of why often there are no intermediate forms between closely related species found in nature. He attributes this to the fact that competition between different forms, combined with the relatively small number of individuals of intermediate forms, result in such forms frequently becoming extinct, leaving only well differentiated and distinct forms to be found. The rest of chapter VI is concerned with whether natural selection could produce complex specialized structures, and the habits to make use of them, in cases where it would be difficult to imagine how transitional intermediate forms could be functional. Darwin says:

Secondly, is it possible that an animal having, for instance, the structure and habits of a bat, could have been formed by the modification of some animal with wholly different habits? Can we believe that natural selection could produce, on the one hand, organs of trifling importance, such as the tail of a giraffe, which serves as a fly-flapper, and, on the other hand, organs of such wonderful structure, as the eye, of which we hardly as yet fully understand the inimitable perfection?

His answer was that in many cases animals exist with intermediate habits and structures that are fully functional and adaptive for their life styles. He discusses flying squirrels, which are a relatively straight forward modification of ordinary squirrels, and flying lemurs as examples of how bats might possibly have evolved from non-flying ancestors. He discusses various simple eyes found in invertebrates, starting with nothing more than an optic nerve coated with pigment, as examples of how the vertebrate eye could have evolved in steps from much simpler structures. Darwin concludes: "If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down. But I can find out no such case."

Darwin addresses the issue of the evolution of complex instincts in chapter VII. He examines a number of examples. Among them are two that he had investigated with experiments: slave making ants and the construction of hexagonal cells by honey bees. In the case of slave making ants Darwin points out that there is a range of behaviour between different species, with some slave making species far more dependant on slave workers than others, and he observes that many ant species will collect the pupae of other species to store as food; he sees no problem with species with an extreme dependency on slave workers, having evolved in incremental steps from non slave making ancestors. He discusses in detail how bees making hexagonal cells could have evolved in incremental steps from bees that made round cells to minimize wax use. Darwin concludes the chapter by saying: "Finally, it may not be a logical deduction, but to my imagination it is far more satisfactory to look at such instincts as the young cuckoo ejecting its foster-brothers,—ants making slaves,—the larvæ of ichneumonidæ feeding within the live bodies of caterpillars,—not as specially endowed or created instincts, but as small consequences of one general law, leading to the advancement of all organic beings, namely, multiply, vary, let the strongest live and the weakest die."

In chapter VIII (of the first edition) Darwin launches into a very detailed discussion about the hybridization of plant and animal species. He addresses the idea that species had some how been imbued with some special characteristic that prevented viable and fertile hybrids from occurring in order to permanently preserve species as separate specially created entities. Darwin argues that far from being universally constant, the difficulty in producing hybrids of closely related species, and the viability and fertility of the hybrids produced, varied greatly from species to species, especially among plants. In a few cases what were nearly universally considered to be separate species produced viable fertile hybrid offspring freely, and in a few other cases what were generally considered to be mere varieties of the same species could only be crossed with great difficulty. Darwin concludes: "Finally, then, the facts briefly given in this chapter do not seem to me opposed to, but even rather to support the view, that there is no fundamental distinction between species and varieties."

Geologic record

In chapters IX and X of the first edition Darwin discusses evidence from the geological record. In chapter IX, On The Imperfection of the Geological Record, he addresses the issue of whether or not there had been enough time for the slow process of evolution by natural selection. He cites Charles Lyell's work Principles of Geology as well as his own geological observations to argue "how incomprehensibly vast have been the past periods of time". Darwin also addresses the concern that the fossil record didn't contain innumerable intermediate forms. Darwin points out that geological formations are intermittent with gaps of unknown (at the time of his writing) length between periods when sedimentary layers are deposited at any one location, and that every geologic formation is missing layers corresponding to periods known from other formations. He also states that fossils are only rarely preserved, and that 19th century fossil collections were extremely fragmentary. Darwin says: "That our palæontological collections are very imperfect, is admitted by every one... Only a small portion of the surface of the earth has been geologically explored, and no part with sufficient care, as the important discoveries made every year in Europe prove".

In chapter X, On the Geological Succession of Organic Beings, Darwin argues that despite the imperfections discussed in the previous chapter the fossil record shows certain broad patterns that are better explained by his theory of branching divergence caused by natural selection than by the idea that species are individually created and remain largely unchanged. Darwin points out that once a group of related species appears and then disappears from the fossil record, members of that group do not suddenly reappear in a much later epoch. Also, usually, only a few members of such a group appear at first, with the number of member species increasing over time until the group reaches its maximum diversity at some later point. He also states that the fossil record, especially of marine organisms, shows an overall pattern of successive change that is consistent across widely separated formations. Furthermore within a group, for example mammals, extinct species that have lived more recently tend to be much more similar to species still existing today than species that lived much longer ago, and frequently extinct species can be found that have characteristics intermediate between two more recent groups. He says: "With respect to the Vertebrata, whole pages could be filled with striking illustrations from our great palæontologist, Owen, showing how extinct animals fall in between existing groups." Darwin then discusses the fact, that at least in the most recent geological periods, extinct organism tend to resemble those organisms still living in the area. He says: "Mr. Clift many years ago showed that the fossil mammals from the Australian caves were closely allied to the living marsupials of that continent. In South America, a similar relationship is manifest, even to an uneducated eye..."

Geographic distribution

In chapters XI and XII of the first edition Darwin discusses evidence from the geographical distribution of animals and plants, what would later come to be called biogeography. He starts by pointing out that the differences in flora and fauna between different regions can not be explained by environmental differences such as climates. For example South America, Africa, and Australia all have regions with similar climates at similar latitudes but those regions have dramatically different plants and animals. The species found in one area of any of the continents are much more closely allied with species found in other regions of the same continent even if those other regions have dramatically different climates. Darwin's next point is that barriers to migration play an important role in the differences between the species of different regions. For example the sea life off the Atlantic and Pacific coasts of Central America had almost no species in common even though the isthmus of Panama was only a few miles wide. His explanation for these facts is a combination of migration and descent with modification. He goes on to say: "On this principle of inheritance with modification, we can understand how it is that sections of genera, whole genera, and even families are confined to the same areas, as is so commonly and notoriously the case." Darwin then goes on to compare the then current idea that each species had its own separate center of creation with his idea of dispersal followed by descent with modification. He discusses how a volcanic island formed a few hundred miles from a continent might be colonized over time by a few species from the continent, which would then be modified over time but which would still be related to species found on the continent, a common pattern. Darwin discusses possible mechanisms of dispersal across oceans in great detail; he had investigated many such possible mechanisms himself experimentally. He also speculates at some length about how the recent ice age might have effected the geographic distribution of some species.

In chapter XII Darwin discusses the distribution of fresh water species. He returns to the topic of oceanic islands and describes their many peculiarities, such as the fact that on many such islands the roles played by mammals on continents are played by other kinds of organisms such as flightless birds or reptiles. In the chapter summary he says:

I think all the grand leading facts of geographical distribution are explicable on the theory of migration (generally of the more dominant forms of life), together with subsequent modification and the multiplication of new forms. We can thus understand the high importance of barriers, whether of land or water, which separate our several zoological and botanical provinces. We can thus understand the localisation of sub-genera, genera, and families; and how it is that under different latitudes, for instance in South America, the inhabitants of the plains and mountains, of the forests, marshes, and deserts, are in so mysterious a manner linked together by affinity, and are likewise linked to the extinct beings which formerly inhabited the same continent... On these same principles, we can understand, as I have endeavoured to show, why oceanic islands should have few inhabitants, but of these a great number should be endemic or peculiar;

Classification, morphology, embryology, rudimentary organs

Darwin starts chapter XIII by discussing the classification of living things. He points out that classification is based on the fact that species resemble one another to varying degrees and that they can be grouped together in a multilevel system with groups such as families that contain subordinate groups such as genera. He discusses classification issues in some detail and concludes:

All the foregoing rules and aids and difficulties in classification are explained, if I do not greatly deceive myself, on the view that the natural system is founded on descent with modification; that the characters which naturalists consider as showing true affinity between any two or more species, are those which have been inherited from a common parent, and, in so far, all true classification is genealogical; that community of descent is the hidden bond which naturalists have been unconsciously seeking,...

After more detailed discussion of classification Darwin goes on to talk about morphology including the importance of homologous structures. He says "What can be more curious than that the hand of a man, formed for grasping, that of a mole for digging, the leg of the horse, the paddle of the porpoise, and the wing of the bat, should all be constructed on the same pattern, and should include the same bones, in the same relative positions?". Then he turns to embryology discussing the fact that animals of the same class often have extremely similar embryos. He cites the example of a leading naturalist who having failed to label an early stage vertebrate embryo was unable to determine later whether it was a mammal, bird, or reptile. Finally Darwin discusses evidence from rudimentary organs such as the wings of flightless birds, and the rudiments of pelvis and leg bones found in some snakes. He points out that some such rudimentary organs, such as teeth in baleen whales, are found only in embryos not in adults.

Concluding remarks

In the final chapter Darwin recapitulates major points from all the earlier chapters and concludes by hoping that his theory may produce revolutionary changes in many fields of natural history. He ends the book with the following paragraph:

It is interesting to contemplate an entangled bank, clothed with many plants of many kinds, with birds singing on the bushes, with various insects flitting about, and with worms crawling through the damp earth, and to reflect that these elaborately constructed forms, so different from each other, and dependent on each other in so complex a manner, have all been produced by laws acting around us. These laws, taken in the largest sense, being Growth with Reproduction; Inheritance which is almost implied by reproduction; Variability from the indirect and direct action of the external conditions of life, and from use and disuse; a Ratio of Increase so high as to lead to a Struggle for Life, and as a consequence to Natural Selection, entailing Divergence of Character and the Extinction of less-improved forms. Thus, from the war of nature, from famine and death, the most exalted object which we are capable of conceiving, namely, the production of the higher animals, directly follows. There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved.

Historians say that Darwin was at his best, piling on supporting fact after fact from different disciplines, in the last few chapters of the book. They point out that he never claimed to be able to directly prove that new species arose through a process of branching evolution driven by natural selection. Instead Darwin's argument was based on showing that his theory could explain a myriad of observations from many different fields of natural history that were inexplicable under alternate theories, such as species being individually created.