Darwin’s dark matter: utter extinction

ABSTRACT

Species that died without leaving descendants Darwin called ‘utterly extinct’. They far outnumber the ancestors of all living things, so they resemble the dark matter of modern cosmology, which far outweighs visible matter. He realized in 1837 that their absence is what creates the groups in a natural classification. In his Notebook B he combined the idea that species multiply with the idea that ancestors' relatives must mostly be extinct. The fossil Megatherium was utterly extinct. The iconic branching ‘I think’ diagram shows extinction causing the origin of genera by eliminating intermediate species. Darwin’s concept of taxonomic ranks, starting with the genus, was informed by his interaction with taxonomists. Based on his familiarity with demography, Darwin reasoned that the survival of transitional forms was unlikely, which helped him decide to focus at the species level. When drafting his theory in the 1840s, he left out these speculative ideas, but they emerged again in the 1850s when he realized his theory needed a cause for branches to diverge. His ecological answer worked at the species level, but his Principle of Divergence was unconvincing at higher taxonomic levels. In the Origin, Darwin repeatedly insisted on the importance of utter extinction.

KEYWORDS:

• Charles Darwin
• history of taxonomy
• extinction
• ‘I think’ diagram
• phylogenetic tree
• principle of divergence
• demography
• history of systematics
• biological classification
• evolution

The story of how the taxonomic project of nineteenth century botanists and zoologists was connected to the emerging idea of evolution is so complex and subtle that few scholars have ventured to explore it.¹ What is certain is that what we imagine should have happened is usually very far from what, according to evidence, actually happened. Perhaps a topic full of such pitfalls is best avoided, but I believe the subject is worthy of study because it holds insights about the very nature of scientific knowledge.

All the women and men in that century who studied the resemblances that link living things deserve a mention in the history of taxonomy.² Charles Darwin, who published a four-volume monograph on living and fossil barnacles, deserves a few lines. Of course, he deserves many more in the history of evolutionary biology, and he has received millions.³ Yet with respect to the particular story of the connection between evolution and taxonomy, Darwin’s thoughts have mostly been either ignored or misunderstood. For example, the chapter on classification in the Origin of Species is sometimes read as if he were advising taxonomists on how to do their work, whereas it is clear that what he was doing was selecting from their current practice a few of their rules that his theory could explain. He adopted this strategy because he expected that it would take time for evolution, which requires a fundamental change in world view, to be accepted.

In spite of my longstanding interest in how evolution and taxonomy are connected, I had never paid attention to what Darwin himself said about the connection in the Origin, nor, as far as I can tell, has anyone else.

… the manner in which all organic beings are grouped, shows that the greater number of species of each genus, and all the species of many genera, have left no descendants but have become utterly extinct.⁴

This statement is not buried in the middle of the book. It sits just before the famous final paragraph that starts with ‘an entangled bank’ and ends with ‘grandeur in this view of life’. Darwin believed that utter extinction, the death of a species that leaves no descendants, is what carves out taxonomic groups.

Extinction is a subject that belongs to palaeontology, far outside my expertise. Only after my research dragged me into this unfamiliar territory did I discover that I had been ignoring something of central importance to Darwin. Utter extinction has nothing to do with whether an ancient species became a fossil; the point is whether it left descendants. Every evolutionist believes that some past species were the direct ancestors of today’s plants and animals. Darwin believed that, of course, but he also believed that most past species were no one’s ancestors. It was the loss of those species, much more numerous than the ancestral ones, which causes what we see as taxonomic groups. The topic of this paper is the importance of utter extinction in Darwin’s view of classification.

1. Personal narrative

Sixty years ago I began my doctoral dissertation with a simple question: since taxonomic groups are now understood to consist of species descended from a common ancestor, what did taxonomists working before Darwin think they were doing? Before 1859, the landmark year when his revolutionary book was published, taxonomic groups were already well-developed … what? Concept, topic, tradition, practice, collection of names? I was not enough of a philosopher to ask that sort of question, and I felt no need to, because I thought I already knew what taxonomy was. I had been using it for years. The tidepools near my parents’ house were home to limpets, sea slugs, periwinkles, and whelks; those, I learned, are all gastropods, members of a class within the Mollusca. I had guidebooks telling me the scientific names of the snails: Littorina littorea L. and Thais lapillus (L). The letter L means that a name traces back to the 1758 Systema naturae of Carl Linnaeus; there are parentheses around his initial for the whelk because he had put that species in another genus, naming it Buccinum lapillus. Although I liked mollusks, I chose the history of a different group for my doctoral dissertation. Radiata, one of Georges Cuvier’s four animal groups, seemed more interesting, because unlike Mollusca, Articulata (our arthropods), or Vertebrata, it did not survive close examination. The radially symmetrical animals had a rich history, because jellyfish and sea urchins had attracted the attention of several important biologists, including Thomas Henry Huxley. Darwin paid no attention to the radiates, however. When my thesis became a book, I only mentioned him at the insistence of an editor.⁵

Later in my career, I knew that plenty of first-rate scholars were deciphering Darwin’s handwriting and analysing the development of his work, so I pursued other figures in the history of evolutionary biology or the history of taxonomy: Linnaeus and Adanson in the eighteenth century, Louis Agassiz and Hugh Strickland in the 19th, and J. B. S. Haldane and J. S. L. Gilmour in the 20th. Still, there were a few problems involving Darwin that troubled me. First, I disbelieved a neat story that was being told, which goes like this: Natural classification, which was the aim of pre-Darwinian botanists and zoologists, has a group-under-group structure.⁶ Patterns in nature demand an explanation, and Darwin’s theory of branching evolution satisfied that demand. This story does not fit with what I know about the 1830s, the period when Darwin was developing his theory. At that time, many taxonomists thought that nature’s pattern of relationship is more complicated than group-under-group; they saw series, parallels, analogies, and numerical regularities. Also, many taxonomists at mid-century believed that taxonomic groups are artificial. This was the majority view, according to Agassiz.⁷ In that case, there would be no demand that the structure be explained. I worried that this story was distorting the past by suggesting that science progresses like a proof in logic.

Another source of my suspicion that fresh research was needed was a peculiar remark Darwin made in the Origin, twice. I felt it was a hint about his own encounter with the connection between taxonomy and evolution. In his chapter on classification he said:

Thus, the grand fact in natural history of the subordination of group under group, which from its familiarity does not always sufficiently strike us, is in my judgement fully explained. (my italics) (p. 413)

Here is half of that story about nature’s pattern, for he claims that his theory supplies the missing explanation. Earlier in the book, in his chapter on natural selection, Darwin said something similar:

It is a truly wonderful fact — the wonder of which we are apt to overlook from familiarity — that all animals and all plants throughout all time and space should be related to each other in group subordinate to group, in the manner which we everywhere behold — namely varieties of the same species most closely related together, species of the same genus less closely and unequally related together, forming sections and sub-genera, species of distinct genera much less closely related, and genera related in different degrees, forming sub-families, families, orders, sub-classes, and classes. (my italics) (p. 128)

Darwin wrote these sentences to finesse the skeptical claim that taxonomy is nothing more than a filing system. He achieved this by playing sleight-of-hand with the word fact. That humans put things in categories and subdivisions, so as not to be overwhelmed by chaos, is a fact, but that doesn’t make the result a fact of nature. He knew perfectly well that the ranked groups of living things, which had been labelled class, order, and genus by Linnaeus over a hundred years earlier, were considered by most botanists, and many zoologists, to be mere artifacts of our decision to classify. Darwin was implicitly aligning himself with other taxonomists, those who believed that their work was revealing nature’s own order. He was not talking about mere classification, but how organisms are ‘related to each other’.

Darwin was saying that what people often overlook is not the fact that natural classification has this group-under-group structure. What they are overlooking is how wonderful that fact is. He says the naturalness of the structure ought to arouse our curiosity. Classification is, by definition, the making of classes, sets within sets. The technique of creating categories (top down), or collecting items into groups (bottom up), had proved its usefulness for keeping track of minerals, clouds, ideas, or books, during those many centuries before people could google. When the kinds of plants and animals coming to Europe from around the globe began to number in the hundreds of thousands, classification became an indispensible tool for the study of life. Important, yes, but wonderful? I imagined that Darwin was recalling the time when he himself had failed to wonder at it. Like me, he had used such groups since childhood.

There is no evidence to suggest that during the voyage of the Beagle Darwin thought there was anything noteworthy about the group-within-group structure of classification. The names of plants and animals, both scientific names and local, were part of his competence as a naturalist, as the lines of longitude and latitude were daily tools for the ship’s officers. The general idea of evolution, however, had been identified as interesting long before the Beagle left England in 1831. Darwin knew that one of his professors in Edinburgh believed that Lamarck had been right, but at Cambridge, two of the professors to whom he was closest were sure that one species cannot change into another. During the voyage Darwin did not believe in evolution, but he did keep it in mind as a possibility.⁸

Darwin’s main interest at the time was geology. For that young science, Charles Lyell had just published a three-volume work explaining a method that Darwin adopted with enthusiasm. Geology was not the mere study of rocks; geology was the history of the earth, which included its past life. Fossils show that different plants and animals have come into existence, persisted for long periods, and then gone extinct. Lyell’s main message was that all these must be natural events. A world-destroying flood like Noah’s must not be invoked to explain extinction if the kind of floods we witness could have produced the geological effects we find. Darwin, like a graduate student with a well-chosen dissertation, worked out an explanation for coral atolls that disagreed with what Lyell had said about them while cleverly applying Lyell’s method. Darwin met Lyell very soon after the Beagle returned to England and they became fast friends.

Darwin’s conversion to evolution occurred not during the voyage but in London in March 1837, after John Gould, a respected ornithologist, identified specimens Darwin had collected in the Galapagos Islands. Darwin had assumed the mockingbirds were three varieties, but Gould pronounced them good species. Gould said that some small seed-eating birds, which Darwin imagined were species belonging to four different families, were actually closely related species for which a new genus, divided into subgenera, must be created.⁹ Thus, an expert who did not believe in evolution was responsible for Darwin becoming certain that evolution is true. This is a genuine morality tale about the nature of science. The story of Darwin meeting with a taxonomist, whose experience and collections made him a competent judge, is an improvement over the myth of an out-of-doors conversion on far-away islands. The word conversion reminds us of St. Paul, an unbeliever who suddenly saw a blinding light. Historians of science cringe at ‘eureka!’ tales, because such stories celebrate a moment of insight rather than the necessary hard work behind scientific accomplishment. There is no better example of a hard worker than Darwin. And yet, I still like the word conversion, because the element of belief is an essential part of Darwin’s story.

2. Hence genera

A very busy man in 1837, Darwin would write notes to himself in leather-covered books, small enough to be carried in a pocket. After his meeting with Gould, three months passed before Darwin found time to start writing down his ideas about evolution, in a notebook he labelled B (he was filling another, labelled A, for ideas and notes about geology). It took him about eight months to fill its 280 pages. After Darwin’s death in 1882, his son Francis inherited the notebooks; he used them in writing the Life and Letters he published in 1887. Darwin's scrawling handwriting is not easy to decipher, but after the 1959 centenary of the Origin, decades of impressive scholarly work have made these early private thoughts available to anyone.¹⁰ Like most historians of biology, I had dipped into them when preparing my undergraduate lectures. This time, though, I studied them with that remark about the ‘truly wonderful fact’ top of mind.

Very early in Notebook B (page 20), Darwin wrote ‘Hence Genera’. This page surely records a ‘eureka’ moment. He has just seen a causal connection between evolution and taxonomy. Perhaps on some other planet, life is infinitely varied, but on this planet, species come in chunks; here, life’s finite diversity can be captured by a set of categories.¹¹ Before this moment, all the known kinds of things, named and recorded and organized in books, were the commonplace foundation of natural history. Taxonomic categories had proved crucially important for his conversion to evolution, because it was their correlation to the geography of islands and continents that had convinced him that evolution was true. Now, however, the causal direction was reversed. Now, because he believed in evolution, he could see why such things as taxonomic groups existed.

Notebook B also contains several roughly-sketched trees, which I was not surprised to see, because branching diagrams would later dominate systematic biology. What I did not expect to find, however, was that those words – ‘Hence Genera’ – were surrounded by words referring to extinction. I mark them with bold face (the italics are Darwin’s).

… secondary terebratula may have propagated recent terebratula, but Megatherium nothing. We may look at Megatherium, armadillos and sloths as all offsprings of some still older type, some of the branches dying out. With this tendency to change, and to multiplications when isolated, requires deaths of species to keep numbers … equable … Organized beings represent a tree irregularly branched some branches far more branched. — Hence Genera. — as many terminal buds dying, as new ones generated. There is nothing stranger in death of species, than individuals¹² (italics Darwin’s) (B19–21)

To reconstruct what was going through Darwin’s mind in 1837, I would have to learn about his personal encounter with Megatherium, a huge extinct mammal now known as the giant sloth.¹³ Palaeontology could no longer be ignored.

3. Darwin discovers a vanished fauna

When the Beagle set sail in 1831, mainstream geologists were already convinced that the Earth is unimaginably old.¹⁴ The reading public was excited to learn about large extinct reptiles called Megalosaurus and Iguanodon, which anatomist Richard Owen would later put in a new class, Dinosauria. Cuvier had demonstrated, in a series of rigorous anatomical studies, that France had once been home to many kinds of large mammals that no longer existed. Whether extinct species had disappeared suddenly, all at once, as Cuvier argued, or had died out gradually, was an exciting research question.

While the Beagle’s officers were charting the coast of Argentina, Darwin went ashore, hoping to find fossils. He already knew about three extinct species of large mammals that had once lived in the Americas.¹⁵ One was Mastodon, common in North America and obviously related to elephants. The other two species, animals the size of a rhinoceros, were Megalonyx (meaning ‘large claw’), which had been found in what is now West Virginia, and Megatherium (‘large beast’), which had been found not far from Buenos Aires, Argentina. These two were so similar that Cuvier had put them together in the genus Megatherium. Knowing this, Darwin asked about possible collecting spots. On September 23, 1832, he pulled out of a seaside cliff fossilized shells, teeth, bones, and a huge skull he immediately guessed was from a species in the genus Megatherium.

Because he was already interested in what might cause extinction, Darwin was especially excited to find in that cliff one solitary tooth that clearly belonged to a horse. No equines existed in the Americas when Columbus arrived, yet descendants of European imports were soon thriving on grassland in wild herds, which proved that the environment suited them. The genus Equus had not gone extinct, only a portion of the species E. caballus had, or perhaps another species of Equus.¹⁶ The fate of the genus Megatherium was obviously sadder than that; such large animals could not have survived anywhere without being noticed. Whenever Darwin speculated about possible causes of extinction, the extinct fauna of Argentina was always vivid in his imagination.

Because Darwin’s ‘truly wonderful fact’ was the whole list of taxonomic ranks, I noticed that he knew the order as well as the genus that Megatherium belonged to: Edentata. The standard reference work for animal classification at the time, Cuvier’s Animal Kingdom, listed Edentata as one of the nine orders in the class Mammalia.¹⁷ The botanist John Stevens Henslow enjoyed a newsy letter from his former student in which Darwin used the word Edentata in the same casual way he used Rodentia, as a word any naturalist would know. There is no such mammalian order now, because pangolins, African anteaters, and platypuses have been reclassified, which is an instance of the kind of progress in knowledge that broke up Cuvier’s Radiata. The loss of name does not affect our story, though, because the genera relevant to Darwin – Bradypus (tree sloths), Dasypus (armadillos) and Megatherium – remain today securely grouped together (in Xenarthra, along with hundreds of other extinct South American species).¹⁸ Among Darwin’s fossils were ‘osseous polygonal plates,’ many-sided bony tiles. ‘Immediately I saw them’, he wrote Henslow, ‘I thought they must belong to an enormous Armadillo, living species of which genus are so abundant here’.¹⁹ Many decades later, when a German admirer asked how he had come upon his great theory, Darwin replied ‘I shall never forget my astonishment when I dug out a gigantic piece of armour like that of the living Armadillo’.²⁰ It was obvious that this huge edentate, which Owen would later name Glyptodon, was just as totally extinct as Megatherium was.²¹

The connection between these extinct and living edentates signalled a deep connection from past to present. Thus the primary dimension of taxonomic relationship was linked to a second dimension: time. What especially impressed Darwin was the third dimension: space. Sloths and armadillos are native to South America, and so are Glyptodon and Megatherium. All this Darwin would later compress into the very first sentence of the Origin:

When on board H.M.S. ‘Beagle,’ as naturalist, I was much struck by certain facts in the distribution of the inhabitants of South America, and in the geologic relations of the present to the past inhabitants of that continent. (p. 1)

4. Gaps in a continuous series

In 1837, Lamarck’s 1809 theory of evolution loomed large for Darwin. Having read during the voyage what Lyell said about it, Darwin on his return bought his own copy of Philosophie zoologique and filled its pages with pencilled notes.²² Lamarck repeatedly asserted that living things, when all are known and arranged by their similarities, will form two continuous series, one for plants and another for animals. Continuity means that any groups sliced out by a taxonomist can only be artificial. There were plenty of obvious breaks in the series, but Lamarck insisted that the cause of such gaps must be that our census of the living world is far from finished. When Cuvier proved that several large mammals, including Megatherium and Mastodon, have disappeared, Lamarck said humans must have killed them off; their absence is not part of nature’s order. As our knowledge progresses, Lamarck insisted, gaps between kinds will be filled in by newly-discovered transitional forms.

Lyell, writing two decades after the appearance of Lamarck’s book, complained that Lamarck failed to account for the lack of transitional forms. Those years had seen a dramatic increase in palaeontology. Any naturalist who kept up with the news wondered how extinct forms would fit into the taxonomic system. For the most part, they seemed to fit within, rather than between, existing groups. Lyell wrote,

Why, moreover, has the process of development acted with such unequal and irregular force on those classes of beings which have been greatly perfected, so that there are wide chasms in the series; gaps so enormous, that Lamarck fairly admits we can never expect to fill them up by future discoveries?²³

Lamarck had not in fact made this admission, but Lyell’s misrepresentation is beside the point, because Darwin was familiar with Lyell’s book.

Notebook B suggests that Darwin was asking the London taxonomists with whom he spoke whether their experience matched Lamarck’s prediction about gaps being filled in. They told him that as more specimens accumulated, the boundaries defining species are sometimes blurred, but the divisions between higher groups remained clear.

Species according to Lamarck disappear as collection made perfect — truer even than in Lamarck’s time. Gray’s remark, best known species (as some common land shells) most difficult to separate … .(B9)²⁴

Waterhouse says there is no TRUE connection between great groups.— … ..(B71)

Mr Don remarked to me, that he though[t] species became obscurer as knowledge increased, but genera stronger.— Mr Waterhouse says no real passage between good genera. (B79)

John Edward Gray was curator at the British Museum, and David Don, a respected botanist, was librarian of the Linnean Society. George Robert Waterhouse was curator of the Zoological Society’s museum and was describing the living mammals Darwin had collected.

The foundation of Lamarck’s ideas was that when a fossil looks distinct from living species, but is so similar that we put them in the same genus, this is not evidence that the ancient form went extinct. To Lamarck it made no sense that extinction could be part of an orderly world, so he claimed such fossils show that a species has changed. This linear sort of transformation is reflected in Darwin’s words ‘secondary terebratula may have propagated recent terebratula … ’. Terebratula is a genus that contained dozens of species (now many more) of small marine shelled animals (brachiopods), some living but also found as fossils, others known only as fossils, and still others known only as living. Darwin’s note suggests that he accepted that an ancient species could have become a different modern one (today we call this anagenesis, evolution without splitting), but he certainly disagreed with Lamarck’s denial that extinction could happen naturally. Darwin wrote in his copy of Philosophie zoologique: ‘Therfor every fossil species direct father of existing analogues & no extinction except through man !— [Hence cause of innumerable errors in Lamarck]’. (the brackets are Darwin’s)²⁵

Long before Darwin opened Notebook B, he was thinking about the origin of all living things. He was letting his imagination jump, here and there, recalling various animals and plants he had collected or read about. He speculated about their relatedness with the old metaphor of a tree, whose spreading branches represent an increase in diversity, the wide differences between kinds of living things. ‘Would there not be a triple branching in the tree of life,’ he wrote, and he wondered about how birds could be connected to fish. He drew a few diverging lines and dots. He quickly zoomed in, though, leaving aside such grand views and returning to the theme that dominated the notebooks, the mystery of reproduction, the continuity of life from individual to individual, up to the level of species. He considered and rejected the idea that a species might have a natural life span, as individuals do. He recalled the fact that armadillos and sloths live in the same region where he had found remains of the extinct giants they resemble. This would be explained, he said to himself, if they were ‘springing from one branch.’ (B35) But why, he wrote, were there ‘gaps in the series of connection’? (B35)

5. The iconic ‘I think’ diagram

At this point in his ruminations Darwin turned the page, wrote ‘I think’, and drew a picture that is now famous (Figure 1). Copies of this drawing are now common, in formats ranging from textbooks to tattoos, in celebration of Darwin as the founder of our modern understanding of branching evolution. This crude sketch shows one ancestral form dividing into several descendants, which in turn divide again, producing an array of related forms. We call it a tree, and we take it to mean that all living things are related, like members of a family. The same idea appears as a fold-out chart in the Origin, but the simpler ‘I think’ image is more striking. It has become an icon, probably rightly so. However, for my project of reconstructing how Darwin’s view of classification developed, it is a serious handicap for us to already know beforehand what this image represents. Proper historical method warns us to pay attention to relevant contemporary evidence, starting with language.

Figure 1. The diagram Charles Darwin drew in 1837 in his Notebook B. Darwin marked the living species with a short T-junction. The unmarked ends of other lines represent extinct species. In 1859 Darwin would call such species, which had left no descendants, ‘utterly extinct’. The three species marked A form a distinct genus. Six intermediate species, which would have linked them to C, are extinct.

Darwin never called the ‘I think’ drawing a tree. The old idea of the tree of life acquired a deeper meaning after the Origin was published, and diagrammatic trees became much more important in the twentieth century, when systematists did a great deal of work to clarify the relationship between taxonomic groups and evolution. Most of that work involved the use of branching lines to represent historical, comparative, or logical relationships. Today tree is no longer a metaphor, but a technical tool in biology.²⁶ Our rule book is not common sense, though, and Darwin had not attended our school. His words tell us plainly why, in 1837, he rejected tree as a metaphor for the new view he was developing. A dead tree, silouetted against the sky, its branches dividing and spreading wide, might have worked, but to Darwin the word tree meant a living plant. What makes this a poor metaphor for the history of life is that a tree’s leaves are nourished by flowing sap, connected to living roots. ‘The tree of life should perhaps be called the coral of life,’ he wrote, ‘base of branches dead so that passages cannot be seen’. (B25) All past life, both ancestors and the utterly extinct, is no longer alive. Rather than switching to a coral or coral reef, Darwin decided that metaphors do not help. He called the image under ‘I think’ a diagram (B39). In 1842 Darwin wrote out a summary of his theory, which he enlarged in 1844, leaving an instruction to his wife to publish it if he should die before doing so himself. Those two sketches were written for the public eye. In neither text do we find a diagram, nor the word tree, not even branch. In 1843, he scribbled a note to himself, ‘a tree not good simile’.²⁷ We ought to remember why not: ‘base of branches dead’.

The words Darwin wrote under the ‘I think’ diagram and on the following pages are direct evidence for what was in his mind when he drew it. The lines stand for single species, some extinct and others living. He wrote

if each species [inserted: an ancient (1)] is capable of making 13 recent forms. — Twelve of the contemporarys must have left no offspring at all, so as to keep number of species constant. With respect to extinction we can easily see that variety of ostrich, Petise may not be well adapted, & thus perish out, or on other hand like Orpheus. Being favourable many might be produced. (B37–38)

‘Orpheus’ refers to the several species of mockingbirds he had seen in South America and on the Galapagos Islands, and ‘ostrich, Petise’ refers to the smaller rhea, a new species, which Darwin had collected in Patagonia. He was continually aware, during his travels, that he could only make a guess at whether some plant or animal he collected would be considered by the experts to be a variety of a known species, or a ‘good’ species, and if good, whether it had already been named, and if not, whether it belonged in an existing genus or deserved its own new genus. Until judgement had been passed, the noncommital word form was useful. It remained useful after Darwin came to believe that a variety could be an incipient species, which explains why the species Gould named Rhea darwinii remained, in Darwin’s mind, ‘a variety of ostrich.’

Immediately beneath the branching diagram Darwin wrote:

Thus between A. & B. immense gap of relation. C and B. the finest gradation, B & D rather greater distinction Thus genera would be formed … (B36) [my boldface]

Here again, evolution is the cause, taxonomic groups the consequence, but this time more sharply focussed. The first time he was thinking of the Edentata in South America, branching out in the distant past. Now he was thinking only of species. He drew one species branching out to become several species, and this would remain his focus for the rest of his life. His thoughts are clear: it was the size of the gaps between species that cause genera.

Because the word genera is plural, we know that Darwin saw more than one genus in his drawing, but do we really know how many? Four, or three, or only two? I believe that if we could ask him, his answer would be to laugh at the question, because the uncertainty was what he meant to show.

Certainly there are two genera, because he says ‘between A and B immense gap’, but there our certainty should stop. He had not been taught our rules about phylogenetic trees. He was thinking about the decisions he had recently seen Gould and other taxonomists make.²⁸ Clearly the four species near the letter B are recent decendants from a common ancestor, which he spread apart to show they are no longer mere varieties but distinct species. The one on the right is as close to the topmost of the C species as it is to the three on its left, which is why he wrote ‘B and C the finest gradation’. Our rules about reading trees insist that B and C are distinct, but those rules say that only the branching point matters, which would make B, C, and D equally related.²⁹ His words ‘B and D rather greater distinction’ suggest that he was thinking of how easy or hard it is to tell them apart. A skilful taxonomist would detect a difference between B and C, but he might be accused of splitting hairs if he pronounced them different genera. Darwin had learned, first hand, that naturalists have no firm rules to answer a question of that kind, and he has drawn this diagram to show the sort of thing that a genus is: somewhat subjective, and yet not arbitrary, because the genus expresses real past events.

If the ‘I think’ diagram only represented two ideas: that evolution proceeds by branching, and that genera are formed by descent from a common ancestor, then all Darwin needed was one extinct ancestor and its 13 living descendants. That is not what Darwin drew. His one extinct ancestor produced 25 others, of which 13 are living. The remaining 12 are extinct, and he specified that they ‘must have left no offspring at all.’ (B37) [my italics] He was using this diagram to explore the idea that he would call, in the Origin decades later, utter extinction. That idea had come to him when thinking about Edentata. Here is the passage I already quoted, this time with new emphasis, and with some omitted words restored:

We may look at Megatherium, armadillos and sloths as all offsprings of some still older type, some of the branches dying out. With this tendency to change, and to multiplications when isolated, requires deaths of species to keep numbers of forms equable: — but is there any reason for supposing number of forms equable; this being due to subdivision & amount of differences, so forms would be about equally numerous.’ … Organized beings represent a tree irregularly branched some branches far more branched. — Hence Genera. — as many terminal buds dying, as new ones generated.³⁰ (B20–21) [italics Darwin’s, boldface mine, underlined Darwin’s insertions]

At that point he was thinking of several genera in the order Edentata, some living and some extinct, plus their more distant forebear; the word form suggests he was unsure of what entity was doing the branching. By the time he drew the ‘I think’ diagram, he had become sure that the operative unit was the species. In his ‘Hence genera’ passage, two linked ideas were already present: that the number of species should stay constant and that the addition of new species must be balanced by the subtraction of others. Those linked ideas are crystal clear in his description of his ‘I think’ diagram: ‘Twelve of the contemporarys must have left no offspring at all, so as to keep number of species constant’. (B37) No one else’s images of evolution have ever carried this heavy, gloomy load of the utterly extinct. We have Megatherium to thank for that.

Why did Darwin assume the number of species stays constant (presumably over geological time)? He certainly knew there was scant evidence for how many species lived in various past ages. There may be two reasons. Certainly, he had embraced the approach Lyell announced in the subtitle to his book: an attempt to explain the former changes of the earth’s surface by reference to causes now in operation. As a matter of principle, it was poor reasoning for geologists to imagine great and unique forces at work in past eras, without first exhausting the possibility that forces at work now could be responsible. The geologist must measure how rain, rivers, and waves are eroding land now, and how much new land volcanic lava creates. The label uniformitarian does not capture this approach, for Lyell knew the earth’s surface has often undergone large changes locally. Yet an uplift of land in one place was balanced by sinking elsewhere, so that in the long run, Lyell maintained, there is no progressive change overall. Darwin had already been using Lyell’s approach when he first unearthed those mammal fossils in Argentina and asked himself how such giant animals could have found enough to eat. For an answer he turned to information about the living animals of Africa, where huge herds of herbivores are today supported by apparently sparse plains. Allowing himself to speculate about the long history of life, Darwin was inclined to believe that the theatre would not change when new actors come on stage and others depart.

The other half of the answer may be a kind of thought experiment, as in ‘let us assume for the sake of argument’. We postulate that some species can multiply; what are the consequences? We will have many more species, and when this is repeated, the world must soon get full. That world, the one we live in, is exceedingly old, so we must presume it has been full for most of the history of life. At any point in this long, full history of life, the total number of species stays constant, yet species can multiply.³¹ This forces the question, what removes the excess? The answer must be utter extinction, from whatever cause.³²

Darwin has given some of his extinct species a major part to play in his imagined scenario. He chose to draw seven utterly extinct species in the space between C and A. If they had survived, their transitional or intermediate character would have prevented anyone saying there was an ‘immense gap of relation’ between C and A; they would have bridged over, filled in, the differences. Those of us well-schooled in phylogenetic trees may be tempted to dismiss this, because we see that A’s ancestor departed at the start from the ancestor of all the others, plus A’s ancestors continued to turn southward while the others were moving north; we could erase the extinct species without changing the successful lineages. Yet Darwin wanted those extinct species on his page.

In the Origin of Species, Darwin discussed divergence, which meant the way species become ever more different from one another as they evolve, but he did not use the words diverge or divergence in that sense until the 1850s. Looking back in 1876, he recalled that at this early period he had ‘overlooked one problem of great importance … the tendency in organic beings descended from the same stock to diverge in character as they become modified’ (italics mine).³³ His memory that he had overlooked the cause of divergence should warn us not to impose too much of our own understanding on the 1837 diagram. He did draw lines that moved apart, but he also showed utter extinction as being responsible for the gap that forms genus A.

Although species are the lines on Darwin’s ‘I think’ diagram, with genera emerging from their past separation, higher taxonomic groups were not far from his thoughts. His words at the bottom of the diagram continue onto the next page: ‘Thus genera would be formed. — bearing relation to ancient types.’ [my italics] (B36–37). Like form, the word type was indeterminate, referring to no particular taxonomic group, but taxonomists often used it to suggest that there was some model or example to which members of a group should be compared.³⁴ He had said ‘We may look at Megatherium, armadillos and sloths as all offsprings of some still older type’. (B20) (my italics) A few pages after the ‘I think’ diagram he would consider ‘the Mammalian type of organization’. (B40)

6. The analogy from demography

To focus our attention on his lines and letters, I erased a messy scribble he squeezed alongside the diagram, after turning his notebook 90 degrees. Each sentence is in its own bubble. (Figure 2)

Case must be that one generation then should be as many living as now. To do this and to have many species in same genus (as is) requires extinction. (double underlining Darwin’s, italics mine) (B36)

This repeats two ideas we had already seen: that the number of forms stays constant, and that extinction must therefore happen. Now he has added a new twist. Previously he had allowed particular genera to teach him that related species were descended from a common ancestor. Now he realizes that every genus that contains more than a few species proclaims that process. Darwin knew that taxonomists were often faced with genera containing many dozens of species (the genus Antilope had 55, and Mus, which then held rats as well as mice, had hundreds), and he knew taxonomists felt free to chop a large genus into several smaller genera for convenience, so his ‘many species in same genus (as is)’ is a comment on the multiplying power of evolution. A few pages after the drawing, the fact that there are plenty of large genera triggers a powerful new jumble of ideas.

Figure 2. Page 36 of Darwin’s Notebook B, CUL-DAR121. Reproduced by kind permission of the Syndics of Cambridge University Library. Beneath the diagram we can read ‘Thus between A and B immense gap of relation, C & B. The finest gradation, B & D rather greater distinction Thus genera would be formed. Bearing relation’.

Look, he told himself: ‘Vide two pages back. Diagram.’ (B39) His novel reasoning, its many elements tightly compressed, will require patient unpacking.

The largeness of present genera renders it probable that many contemporary would have left scarcely any type of their existence in the present world, or we may suppose only each species in each generation only breeds, like individuals in a country not rapidly increasing.

If we thus go very far back to look to the source of the Mammalian type of organization, it is extremely improbable that any of the successors of his relatives shall now exist. In same manner, if we take a man from any large family of 12 brothers and sisters in a state which does not increase, it will be chances against any one of them having progeny living ten thousand years hence; because at present day many are relatives, so that by tracing back, the fathers would be reduced to small percentage. Therefore the chances are excessively great against any two of the 12 having progeny after that distant period. (B39–41)

His analogy compares a human family of several siblings to a genus with many species.³⁵ Individual people (man, father, brother, sister) are members of a family, and those families are part of a population, filled with other people who are members of other families.

The phrases ‘individuals in a country not rapidly increasing’ and ‘in a state which does not increase’ reflect Darwin’s awareness of the subject we now call demography (then called political economy). Decades of debates had followed the 1798 publication of Malthus’s Essay on the Principle of Population, leading to the New Poor Law passed by Parliament in 1834. Darwin’s reading of a later edition, in 1838, has become a famous moment in the history of biology, because it triggered his idea of natural selection.³⁶ Long before that, however, he had been well aware of elementary demographic concepts, such as what causes a population to grow, decline, or remain constant. During the Beagle voyage, he followed Lyell’s lead in thinking that extinction would follow a slow decline in population from natural causes. In 1837, Darwin was living in London quite near his brother Erasmus, whose closest friend was the writer Harriet Martineau, who was already famous for her popularizations of political economy. With such a background, Darwin could not compare species in a genus to members of a human family without knowing that his assumption that the number of species stays roughly constant demands explanation. That was the essence of the Malthusian argument. Since human reproduction has the potential to make a population double in one generation, when the population is not growing, something must be at work to restrain it. There are two ways a theoretical population can avoid growing: either every couple has about two children, or if some couples have a dozen, others must offset this by remaining childless. Darwin was acknowledging the first option, equivalent to Lamarck’s anagenesis, when he wrote ‘we may suppose only each species in each generation only breeds’, but he was sure this is not what really mostly happens, because the existence of large genera shows that some past species multiplied. In order to leave room for the many offspring of those prolific species, their contemporaries must have left no offspring. If a human population is staying constant, though the population includes large families of 12 brothers and sisters, some people must not be reproducing. The same thing must go on with species. Since large genera exist, which are evidence of multiplication, there must have been an offsetting number of utterly extinct species.

His reasoning may be clearer in a simplified version. Let us imagine a nation that takes a regular census of young men and finds that over many centuries, the number stays around 12,000. (The analogy works better if women are left out, because a single species can generate several new ones, whereas producing a new human being requires a pair of humans. Darwin seemed to realize this, for later in the notebook he wrote, ‘Exclude mothers and then try this as simile.’ (B148)) Let us take Darwin’s ‘at present day many are relatives’ to the extreme: in our imaginary country, every person has close relatives: six brothers and six first cousins. These 12 related men all have the same surname, because being a cousin means sharing the same grandfather. In this nation, there are only 1,000 surnames. When we look back at their grandfather’s day, we can identify by their surname the men destined to leave heirs. Because the population then was 12,000, there were 11,000 men who would die without issue (or their sons were childless). Although everyone has ancestors, not everyone leaves descendants. These were not exactly Darwin’s thoughts, because his version did not postulate all people having close relatives, just many, and he supposed he might have to go back ten thousand years, not just two generations, to see the effect. The gist of his argument was the same, however.

Equipped with this model, Darwin confronted the problem that Lyell had seen as a flaw in Lamarck’s theory: the awful gap between classes, ‘wide chasms in the series’. Darwin decided that far from a problem, those enormous gaps, those apparently unbridgeable differences, are exactly what should be expected, over vast periods of time, if species are multiplying while extinction keeps the number of species stable. Darwin began his thought experiment with one man from a family of 12, but he ended it with ‘any two of the 12.’ This was not a mistake, this was his point. To expect to find a transitional form connecting mammals to birds is like expecting two members of the same family, or two species in the same genus, to both leave descendants. My arithmetic showed that not many people become ancestors, and so, for two siblings from the same family to manage to do so is even less likely. One species, long, long ago, was the ancestor of all mammals. To ask for an intermediate form linking mammals to birds is like asking that a close relative of that lucky ancestor also left a descendant, and the chances against that are excessively great.

Darwin’s metaphor from human genealogy helped him keep his speculations grounded at the species level rather than dissolving into vagueness, because a person’s ancestor, however distant, is always a person, not an entire race or type. The source of the ‘Mammalian type’ was a single long-lost species. Its relatives were other species whose similarities would have caused a taxonomist, had one been working at the time, to arrange them in genera, orders, and classes. He was imagining a severely winnowed history of life. Not only are the ancestors extinct, so too are almost all the relatives of those ancestors. The natural groups we see today are remnants from the distant past. The face of nature has been sculpted by utter extinction.

7. The greater the groups, the greater the gaps

Right after ‘chances are excessively great against any two of the 12 having progeny after that distant period’, Darwin wrote,

Hence if this is true, that the greater the groups the greater the gaps (or solutions of continuous structure) <<between them.>>. — for instance, there would be great gap between birds and mammalia, still greater between Vertebrate and Articulata, Still greater between animals & Plants (italics Darwin’s; <<his insertion>>) (B42–43)

The phrase solution of continuity was commonly used at that time to mean a break or interruption in a series.³⁷ The term greater group sometimes referred to the size of a group, meaning how many species it contains, but the examples immediately following tell us that here he was thinking of taxonomic rank; he moved from class (mammals and birds), to Cuvier’s main divisions (Vertebrata and Articulata), up to kingdom (animals and plants). Darwin was saying that groups of higher rank are separated from each other by bigger gaps than are groups of lower rank; kingdom is separated from kingdom by a bigger gap than divisions within a kingdom are, and that gap is bigger than the one that separates classes from one another.³⁸

Darwin is now convinced that in the series of living forms, the gaps are real; they will not get filled in by collectors on the far side of the world. Because he believes that the amount of difference between species is caused by the loss of ancient relatives, and the ranks used by taxonomists reflect how long ago the ancestor of various groups lived, he now infers that there should be a pattern in the natural system, a pattern beyond the group-under-group pattern that the act of classifying creates. Darwin now recalls another zoologist who had theorized about groups, transitional forms, and patterns. William Sharp Macleay’s quinarian system required five members per group, their affinities forming a circle, the circles in parallel, linked by analogies, with some circles connected (‘inosculating’) by transitional forms. Such ideas seem outlandish now, but in the 1830s, many naturalists, including Waterhouse and Darwin, felt that Macleay’s system contained valuable insights. It seemed possible that natural groups might form a repeating pattern.

Turning the page, Darwin warned himself to be careful, using the word his Spanish guides in South America would call out when a wrong step could prove fatal. He wrote, ‘Heaven know[s] whether this agrees with Nature: Cuidado’. (B44) Although it is unclear whether the word ‘this’ referred to his thoughts about Macleay, or to his greater-group-greater-gap postulate, he was certainly wondering whether the patterns reported by taxonomists could be explained by his new theory of the multiplication and extinction of species.

8. Dark matter as metaphor for utter extinction

The concept of utter extinction, which is the idea that most species in the past were nobody’s ancestors, may be usefully compared to a concept now being explored by cosmologists, called dark matter. This matter emits no light, but that is true of planets and moons too. What makes this material quite invisible is that besides sending out no electromagnetic waves, it cannot reflect them. Thus its existence must be inferred, indirectly. There is supposed to be more of this unseen stuff than all visible matter. Dark matter is a good metaphor for utterly extinct species because they too are plentiful, yet invisible. They cannot be seen, for two reasons. First, most past life simply vanished without a trace. Second, when a fossil resembling a living species is found, it is impossible to know whether it is the direct ancestor, or only a close cousin of the ancestor. Darwin was convinced that utterly extinct species outnumber the ancestors (may we call those the gently extinct?). The quantity of the utterly extinct follows logically from combining the belief that species in a genus descend from a common ancestor with the fact that genera consisting of several species are more common than genera consisting of only a few species. The ancestor, like the grandfather in Darwin’s thought experiment, was one of the minority in its generation that did leave descendants.

Extinction can befall genera, families, orders, and even classes, if we choose to use the term that way, but we may wish to be cautious. The Linnaean system of group-under-group naming was developed with respect to plants and animals in the present era. Watching the movie Jurassic Park, we enjoyed seeing brought to life members of utterly extinct families and orders, yet now taxonomists tell us that dinosaurs are not extinct. Birds are really dinosaurs. While the survival of the birds rescues the entire class, this is because of how we named the class. It is true that the particular species of Dinosauria that were the direct ancestors of modern birds are only gently extinct, but they are far outnumbered by the utterly extinct other dinosaurs. If we think about groups in terms of gaps, as Darwin was doing, we would see that the utter extinction of almost all dinosaurs explains why living birds are so different from their closest living cousins, the crocodilians.

Another way dark matter resembles utter extinction is that its existence is inferred rather than directly observed. Darwin knew of a few animals that he was sure had left no descendants, including Glyptodon and Megatherium, but the plentifulness of the unseen others emerged from his imagining their cousins and ancestors, with the help of his demographic thought experiment.

Darwin’s ‘Cuidado’ may have expressed not only his worry about whether his ideas about nature were correct, but also whether he could convince the appropriate audience. Before his return to England, Darwin had been a passive user of taxonomic information. Within a few months after his return, he had come to understand that such information is not handed to us directly from nature, but indirectly, through the work of individual zoologists and botanists, who are people of various backgrounds and personalities. Naturalists, the people entitled to name new species and propose higher groups, were just then embroiled in contentious debates.³⁹ At a meeting of the Zoological Society of London, which Darwin attended soon after the Beagle landed, ‘the speakers were snarling at each other, in a manner anything but like that of gentlemen’.⁴⁰ In 1838, Darwin wrote, in another notebook, ‘I fear [<<great evil>> inserted] from vast opposition in opinion on all subjects of classification’ (C202).

Some weeks or months after his demographic analogy, Darwin returned to the question of the number of people, in a constant population, who may be expected to leave descendants. Once again he concluded that they will be the minority. Thinking of two aristocratic families, one of which ceases to exist, he listed a variety of causes, including murder and pure accident. (B148) He seemed to be trying to make demography more concrete by adding numbers, but his calculation was riddled with confusion (see my Appendix). He must have realized he was in over his head. Yet he remained firmly convinced of the implications of his thought experiment. He noted, a year later, ‘as genera are large probably only few of extinct forms have generated species. & of 100 extinct species the greater number probably have no descendants on earth. —’ (C168–169)

The trouble with imagining fauna and flora in the distant past, populated by unrecorded species, indeed the trouble with drawing lines on a page, was that such things, however useful for brainstorming, are very far from a scientific hypothesis. More fossils were being described every year, but Darwin agreed with Lyell that the preservation of a shell or skeleton was such a rare event that nothing remotely like a full history of life could be expected. It was hard to see how the existence of a vast number of utterly extinct species could be anything but idle speculation. Darwin deliberately chose to concentrate on existing varieties and species.

People will argue & fortify their minds with such sentences as “oh turn a Buccinum [whelk] into a Tiger.” — but perhaps I feel the impossibility of this more than anyone.— no turn the Zebra into the Quagga … & then all that I want is granted. — (C145)

Darwin’s terse remark referred to Equus quagga, a South African wild horse that was mostly brown, striped on its neck; it was classified as a species distinct from the familiar black-and-white zebra E. burchelli.⁴¹ The idea that life had developed, rather than being created, had always assumed a progression from low to high. Although Cuvier insisted that the scale was wrong, because Mollusca is neither lower nor higher than Articulata, which was welcomed as a refutation of Lamarck, snails like the whelk were still obviously inferior creatures. With these few words, Darwin firmly set aside the problem of the differences between the great groups of taxonomy.

9. Utter extinction goes underground

Five years later, in the summer of 1842, having concentrated his work on evolution at the level of species, Darwin wrote out a sketch of his argument. The ideas he had played with earlier – about the number of extinct species balancing new species, about utter extinction carving out groups, and about the relatives of an ancestor being unlikely to leave descendants – are not part of his 1842 sketch. On the back of one sheet, however, there is a telltale remnant. While considering whether new species are more likely to form, and be fossilized, during a period of uplift or sinking of land, Darwin wrote,

I believe this from numbers that have lived, — mere chance of fewness. Moreover from very existence of genera and species only few at one time will leave progeny, under form of new species, to distant ages; and the more distant the ages the fewer the progenitors.⁴²

It is hard to imagine that a reader, lacking auxiliary stipulations about species multiplying while their overall number stays constant, could comprehend this claim, but he was writing this note to himself, not within his argument. In September he and his wife left London and moved to a small village named Down.

Darwin’s personal relationship with several taxonomists must have been positive, or Hugh Strickland would not have invited him, in 1842, to serve on a committee whose purpose was to draft rules for naming that zoologists could agree upon. The goal was not biological but social: to make the names of species less open to change. The committee learned that taxonomists had no agreement on the difficult question of what a genus or species really is, so it settled on the eminently practical concept that these things are whatever a competent zoologist deems worthy of naming. This pragmatic approach is what Darwin would use later in the Origin.

In 1843 Waterhouse wrote two letters to Darwin asking his opinion about whether it was all right for a taxonomist to create a higher group, such as an order, to contain just a few species, even though other orders contain many hundreds. Waterhouse’s example was the monotremes, consisting of two odd Australian egg-laying mammals, the playpus and echidna, which were clearly as distinct from the kangaroos as those marsupials are distinct from placental mammals like ourselves. Stylops, an anomalous insect that was given an order all to itself, was another example both men knew. Waterhouse’s two letters have not been found, but the frank and cordial exchange that followed has survived. Reading this correspondence tells us how important extinction still was to Darwin, while at the same time showing that he felt himself powerless to convince someone else.

According to my opinion, (which I give every one leave to hoot at, like I should have, six years since, hooted at them, for holding like views) classification consists in grouping beings according to their actual relationship, ie their consanguinity, or descent from common stocks … To me, of course, the difficulty of ascertaining true relationship ie a natural classification remains just the same … .

There is one caution, which should not be overlooked, namely the great doubt whether the groups, which are now small, may not have been at some former time abundant: and you will admit fossil & recent beings all come into one system.— In fish, it would appear, that some of the main divisions, which are now least abundant in species, appear formerly to have been most so. It w[oul]d take a Chapter to argue, how probable it is that Geology has never revealed & never will reveal, more than one out of a million forms, which have existed.

I believe (though why I should trouble you with my belief, which must & ought to appear the merest trash & hypothesis?) that if every organism, which ever had lived or does live, were collected together (which is impossible as only a few can have been preserved in a fossil state) a perfect series would be presented, linking all, say the Mammals, into one great, quite indivisible group — and I believe all the orders, families & genera amongst the Mammals are merely artificial terms highly useful to show the relationship of those members of the series, which have not become extinct —

But it is no use my going on this way — … .

… classification is almost independent of the characters of the groups, but is governed by the breaks or chasms in the series.— which is the view above given hypothetically by me with respect to the Mammals.—⁴³

When we read ‘descent from common stocks’ we may find ourselves thinking of the lineages, filled with extinct species, tracing back from living mammals to their distant ancestors, but none of those species is utterly extinct. In fact Darwin was not thinking only of ancestors, but of all extinct mammals, because the challenge Waterhouse had given him was how unbalanced it seemed to have small groups given as high a rank as large one. The groups Waterhouse was concerned with contain living species, but in reply, Darwin suggests that what was once a large group may have only left a few remnants.

When Darwin enlarged his sketch of his theory of evolution in 1844, he omitted utter extinction entirely. He did discuss taxonomy, reviewing ideas that were current: affinity, analogy, and unity of type. All these concepts, he said, branching kinship would explain. He did not mention extinction as the cause of groups.

Even though the ideas he explored in 1837 were not part of his theory in 1844, they stayed with him and remained useful. In the first place, they assured him that his theory, unlike Lamarck’s, did not need living transitional forms, nor did he need the extinct transitional forms to be found. Darwin’s theory proposed they had existed, but since his theory also said that even more numerous utterly extinct ones had also existed, discovering ancestors was not likely. He said in Notebook B,

Cuvier objects to tran propagation of species, by saying, why not have some intermediate forms been discovered. between palaeotherium, megalonyx mastadon, & the species now living.— Now according to my view. in S. America parent of all armadilloes might be brother to Megatherium.— uncle now dead. (B53–54)

The lack of intermediate forms was, and remains, the most obvious and frequent complaint against evolution, from naturalists as well as lay people, some expecting to find living missing links, others demanding that rocks should supply them. As to fossils, Darwin accepted Lyell’s argument that preservation was a rare event, but this early and novel vision about extinction assured him that uncles and cousins would always have been more numerous than ancestors.

10. The principle of divergence

In an autobiography written for his family in 1876, Darwin recalled that when he wrote out the two sketches of his theory,

I overlooked one problem of great importance; and it is astonishing to me … how I could have overlooked it and its solution.⁴⁴ The problem is the tendency in organic beings descended from the same stock to diverge in character as they become modified. That they have diverged greatly is obvious from the manner in which species of all kinds can be classed under genera, genera under families, families under sub-orders, and so forth; and I can remember the very spot in the road, whilst in my carriage, when to my joy the solution occurred to me; and this was long after I had come to Down.⁴⁵

The solution he was referring to, which he called the Principle of Divergence, is set out in great detail in the Origin. It offered an ecological explanation for the differential extinction that creates diversity.⁴⁶ Assuming that a range of variation is available within a species, the forms at the extremes are more likely to be the surviving ones, because they stand a greater chance of discovering new ways to use the environment, somewhat like the twentieth century concept of a new ecological niche.⁴⁷ Because he saw this principle as an extension of his concept of natural selection, Darwin was very pleased with it, but few of his readers paid it any attention.⁴⁸ Historians have shown that he had developed the Principle of Divergence gradually between November 1854 and March 1857.⁴⁹

It may seem obvious to us that Darwin had not overlooked the fact that species diverge as they evolve, because we cannot avoid seeing divergence in his ‘I think’ diagram. Yet his memory was perfectly accurate, because he certainly had overlooked their tendency to diverge, the cause of divergence. When he drew those southward-bound, gently extinct, ancestors of genus A, he had not speculated about why they grew away from its cousins. Nor had he asked why the six species between genus A and the other ten living species had become utterly extinct, thereby carving out the gap. This is the problem he first saw, and addressed, in the 1850s.

The Origin of Species has one illustration (Figure 3), which is so large it has to be folded; it vividly displayed the branching character of his theory. Following the offspring of species A over time, we find it has given birth to eight new species, from a¹⁰ at the far left, to m¹⁰ near the centre. Species in a large genus ‘will generally go on multiplying in number as well as diverging in character,’ he claimed; ‘Thus, as I believe, species are multiplied and genera are formed.’ (pp. 119–120). Darwin placed this diagram early in the book, in his exposition of Natural Selection in Chapter 4, not in his discussion of classification in Chapter 13, although he also needed it there and told his readers to turn back to it.⁵⁰ Each little node, like a palm with several fingers fanning out, represents varieties in a varying species. The diagram also includes other species that persist without varying or evolving at all. The fans at each node show a few varieties that die out, leaving only one or two surviving. Those little fans display his Principle of Divergence; they cause the branches to move apart. The result is our familiar tree-like shape, although Darwin always called it a diagram.

But during the process of modification, represented in the diagram, another of our principles, namely that of extinction, will have played an important part … .Hence all the intermediate forms between the earlier and later states, that is between the less and more improved state of a species, as well as the orginal parent-species itself, will generally tend to become extinct. So it probably will be with many whole collateral lines of descent, which will be conquered by later and improved lines of descent. (p. 121)

The presence of extinction in this diagram makes it quite unlike the many trees of life drawn by later biologists.

Figure 3. The fold-out diagram in Charles Darwin’s 1859 Origin of Species. Besides picturing the multiplication of species, this illustrates the idea he called the Principle of Divergence. The chance of a form persisting is greater the more it differs from its relatives. Out of the original genus consisting of eleven species, A through L, only F survives the passage of time intact. A and I are extinct, but they have left descendants; the other eight species are utterly extinct.

At the end of the chapter, Darwin accepted other people’s uses of the tree metaphor, but it seems an awkward fit.

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 … . 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 … .Of the many twigs which florished when the tree was a mere bush, only two or three, now grown into great branches, yet survive and bear all the other branches … many a limb and branch has decayed and dropped off … . (p. 129)

He began by referring to nameless others who had made the comparison, but then grafts onto it his vision of the amount of extinction his theory requires: ‘species and groups of species have tried to overmaster other species in the great battle for life.’ What woody plant grows like this?

Ancestral species A and I belonged to the same genus as eight other utterly extinct species: B, C, D, E, G, H, K, and L. Those eight, Darwin supposed, met their demise because the younger species descended from A and I won out over them in the struggle for existence.⁵¹

The intermediate species, also (and this is a very important consideration), which connected the original species (A) and (I), have all become, excepting (F), extinct, and have left no descendants. Hence the six new species descended from (I), and the eight descended from (A), will have to be ranked as very distinct genera, or even as distinct sub-families. (p. 123)

Darwin allowed himself to extend his vision beyond families and orders, up to classes, but he did so as a matter of faith, since at higher taxonomic levels he gave up appealing to any ecological factors.

Looking still more remotely to the future, we may predict that, owing to the continued and steady increase of the larger groups, a multitude of smaller groups will become utterly extinct, and leave no modified descendants; and consequently that of the species living at any one period, extremely few will transmit descendants to a remote futurity … . on this view of extremely few of the more ancient species having transmitted descendants, and on the view of all the descendants of the same species making a class, we can understand how it is that there exist but very few classes in each main division of the animal and vegetable kingdoms. Although extremely few of the most ancient species may now have living and modified descendants, yet at the most remote geological period, the earth may have been as well peopled with many species of many genera, families, orders, and classes, as at the present day. (p. 126)

Darwin had glimpsed a fragment of this vision in Argentina in 1832, five years before his conversion to evolution. He embraced it fully in 1837, when he thought about a few utterly extinct Edentata, animals that were not ancestors of living armadillos and sloths but shared with them a more distant ancestor.

Throughout the Origin, numerous times, Darwin insisted that extinction was a very important part of his theory, but in relation to taxonomy, at one point he seemed to draw back.

Extinction has only separated groups; it has by no means made them; for if every form which has ever lived on this earth were suddenly to reappear, though it would be quite impossible to give definitions by which each group could be distinguished from other groups, as all would blend together by steps as fine as those between the finest existing varieties, nevertheless a natural classification, or at least a natural arrangement, would be possible. (p. 432)

This depended upon his belief that nature makes no leaps. To get from a whelk to a tiger requires a very long walk, back in time and then forward, taking only the kind of baby steps that separate the quagga from the plains zebra. The groups are made by reproduction with multiplication; extinction makes the gaps between groups.

Conjuring into simultaneous existence ‘every form which has ever lived on this earth’ is pure fantasy, as Darwin knew. In reality, taxonomists look for similarities and find that species fall into groups separated by gaps.

Extinction, as we have seen in the fourth chapter, has played an important part in defining and widening the intervals between the several groups in each class. We may thus account even for the distinctness of whole classes from each other — for instance, of birds from all other vertebrate animals — by the belief that many ancient forms of life have been utterly lost, through which the early progenitors of birds were formerly connected with the early progenitors of the other vertebrate classes. (p. 431)

Yet how plants and animals that had vanished without being fossilized and without leaving descendants could be subject to scientific study, Darwin never explained.

11. Conclusion

As I warned at the start, the link between evolution and taxonomy is not simple. Those words are shorthand for things that exist in two parallel realms: the reality of the world, which includes its past as well as present, and the beliefs and actions of scientists who study that world. Thus there is, on the one hand, the way branching evolution, over unimaginable depths of time, has produced the variety of life we see on the planet today, variety which is enormous but not formless, while on the other hand, there are facts about scientists who study the world. The variety of snails and slugs and other mollusks, catalogued in an old museum by a variety of people, started me wondering, how is it possible for us humans, the same species that invents fables, tells jokes, and practices deceit, to uncover truth about the world?

I had long been intrigued by an awkward and odd statement of Darwin’s in the Origin. He said ‘the grand fact in natural history of the subordination of group under group … from its familiarity does not always sufficiently strike us.’ (p. 413) Surely, I thought, there must have been a time when Darwin overlooked it himself; I wonder when that grand fact first struck him. No one else seems to have asked this question, which is very easy to answer. I found the answer where I expected to find it, early in the notebook he had opened, soon after his conversion to evolution. On two pages, not far apart, Darwin told himself that branching evolution explains what a genus is: ‘Hence genera’, he wrote, ‘Thus genera are formed’. It was evolution that transformed the familiar tool of classification into something interesting. What he called a grand fact is not exactly a fact about nature but about our catalogue of nature; it is a ‘grand fact in natural history’.

When I looked into Darwin’s notebooks with the group-under-group structure of classification in mind, I was surprised to see how much he thought about extinction. Throughout the Origin, whose text I had read many times, both sorts of extinction, the loss of ancestors and the loss of their relatives, are prominent, but I had taken no notice. It was Notebook B’s dark matter, those countless childless uncles, which surround and infuse his eureka moments and his tree-like diagram, that forced me to pay attention. The absence of utter extinction from his sketch of 1844, combined with his moment of joy in his carriage, made me wonder, was I wrong about what Darwin was thinking in 1837, or did he simply forget, and then reinvent it in the 1850s? This led me to take a closer look at the diagram in the Origin and its surrounding argument about divergence. In the ‘I think’ diagram, we can see both divergence and extinction, but divergence is not named, and no cause is suggested for either. In 1859, extinction is the cause of divergence and he suggests causes of extinction.

Utterly essential to Darwin’s success in turning the idea of evolution into a scientific fact was his early and deep understanding that scientific knowledge requires a community. Because Darwin was familiar with taxonomy from childhood, and worked closely with taxonomists after the Beagle’s return, he understood their viewpoint well. His respect for their efforts, and exasperation at their shortcomings, only increased when he joined their ranks with his monograph on barnacles. To the community of taxonomists, his theory had nothing substantial to offer. When he explained his belief in evolution, including vast extinction, to his friend Waterhouse, he said ‘the difficulty of ascertaining true relationship, i.e. a natural classification, remains just the same’. At the end of the Origin, Darwin looked towards a future when evolution will have been accepted, but he said ‘systematists will be able to pursue their labours as at present’. (p. 484)

Historians are supposed to stick to the job of figuring out what happened in the past, but there are two twentieth century developments that are so relevant to this story that they must be mentioned. One began with the publication of Willi Hennig’s Phylogenetic Systematics in 1966.⁵² Thanks to him, systematists today are careful to define characters precisely and to spell out exactly how they are making comparisons. For someone trained in this modern science, the very questions early taxonomists asked, such as whether a continuous series is interrupted by a gap, large or small, must seem hopelessly subjective. The other relevant twentieth century development is palaeontologists’ discovery of mass extinction.⁵³ Darwin never strayed far from the view of geology he formed under Lyell’s influence, which made sudden, world-wide, simultaneous extinctions of many species unthinkable, but now we know that they did happen. As the case of birds makes obvious, if a mass extinction spares even one species out of a great group, its multiple descendants will be widely separated from their nearest relatives by a long list of differences.

The benefit of hindsight is both useful and dangerous to a historian whose aim is to recapture and explain what went on in the past. Everyone who has looked at his ‘I think’ diagram before me brought their own understanding of evolution to their interpretation, which in most cases meant treating the extinct species as unimportant. In many cases it also meant seeing it as a tree, each branching point producing a genus, as if a taxonomist could read ancestry directly. For years I had done the same. I looked at the diagram differently only after I connected the words on that page, ‘Thus genera are formed’, back to his thoughts about Megatherium. And only after I pondered his moment in the carriage did I notice that the very word divergence was not in his mind in the 1840s.

Everyone who has noticed the mentions of demography in Notebook B, starting with his son Francis, was already aware of Darwin’s reading of Malthus in 1838. Several writers have suggested that the 1837 paragraph was a foreshadowing of natural selection. When I was an undergraduate, the Malthus story was so interesting to me that I looked into the source of Malthus’s ideas on the growth of human populations.⁵⁴ I believe this gave me an advantage in recognizing the weight of Darwin’s private insight. It left him convinced that ‘of 100 extinct species the greater number probably have no descendants on earth. —’ (C169) This early thought experiment helps explain his confidence that ‘the greater number of species of each genus, and all the species of many genera, have left no descendants but have become utterly extinct’. (p. 489)

It has become commonplace to think of Darwin’s theory entirely in terms of species, branching evolution, and natural selection. There is abundant evidence, however, that utter extinction was of central importance to Darwin, not only in the Origin of Species, but when he developed his ideas in 1837.

Acknowledgements

For the past two years, as I worked on my research and writing, I have made unreasonable demands on many people and I have not yet thanked them adequately. I am indebted to Bill Allison, Mark Adams, Paul Brinkman, Andrew Brower, Sandra Herbert, Jon Hodge, Sharon Kingsland, Gordon McOuat, Aleta Quinn, Trevor Levere, Jordan Mursinna, Kevin Padian, Frank Sulloway, Frank Zachos, and others, who will forgive me, I hope, for not mentioning them.

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Notes

1 Two notable exceptions are Henri Daudin, De Linné à Jussieu: Méthodes de la classification et idée de série en botanique et en zoologie: (1740–1790) and Cuvier et Lamarck: Les classes zoologique et l’idée de série animal: (1790–1830) (Paris: Félix Alcan, 1926) and Peter F. Stevens, The Development of Biological Systematics: Antoine-Laurent de Jussieu, Nature, and the Natural System (New York: Columbia University Press, 1994).

2 In keeping with recent practice, I use taxonomy to refer to the identification and naming of kinds of living things. It is now treated as a sub-category within the broader discipline of systematics, although in the past the meaning of these words has shifted, sometimes even reversed.

3 A good introduction to the vast literature on Charles Darwin is Janet Browne’s ‘Reflections on Darwin Historiography’, Journal of the History of Biology, 55.2 (2022), 381–393. Darwin’s writings are accessible through John van Wyhe’s site Darwin-online.org.uk and his letters through the Darwin Correspondence Project darwinproject.ac.uk. My work is totally indebted to the creators of these monumental sites, as well as to scholars who transcribed Darwin’s handwriting: Paul H. Barrett, Gavin de Beer, Sandra Herbert, and David Kohn. I give no citations for facts repeated in multiple sources. Particularly relevant and insightful are Dov Ospovat’s The Devlopment of Darwin’s Theory: Natural History, Natural Theology and Natural Selection 1838–1859 (Cambridge University Press, 1981) and Sandra Herbert’s Charles Darwin, Geologist (Cornell University Press, 2005).

4 Charles Darwin, On the Origin of Species (London: John Murray, 1859), p. 489.

5 Mary P. Winsor, Issues in the Classification of Radiates 1830–1860 (Yale University dissertation, 1971); Starfish Jellyfish, and the Order of Life (Yale University Press, 1976).

6 I am avoiding the term Linnaean hierarchy, which was invented in the twentieth century. The adjective is misleading, because by the nineteenth century, naturalists added thousands of new species, as well as extra ranks, to the actual classifications of Linnaeus. The noun can also mislead, because the word hierarchy in other contexts implies power: generals over sergeants or bishops over priests.

7 Published in 1857, Agassiz’s ‘Essay on classification’ argued that the ranks of taxonomy reveal the Creator’s intentions, which he presented as a new idea. He wrote ‘And as to families, order, classes, or any kind of higher divisions, they seem to be universally considered as convenient devices … .’ Essay on Classification, ed. by E. Lurie (Harvard University Press 1962), p. 5.

8 Niles Eldredge shows that Darwin often considered transmutation throughout the trip, in Eternal Ephemera: Adaptation and the Origin of Species from the Nineteenth Century through Punctuated Equilibrium and Beyond (Columbia University Press, 2015).

9 Frank Sulloway, ‘Darwin’s Conversion: The Beagle Voyage and its Aftermath’, Journal of the History of Biology, 15 (1982), 325–396 and ‘Darwin and the Galapagos’, Biological Journal of the Linnean Society, 21 (1984), 29–59.

10 The centenary of the publication of the Origin stimulated fresh interest in Darwin’s unpublished papers, resulting in several transcriptions: Gavin De Beer, ‘Darwin’s Notebooks on Transmutation of Species Part 1. First Notebook (July 1837–February 1838)’, Bulletin of the British Museum (Natural History) Historical Series, 2.2 (1960), 27–73; Paul H. Barrett, ‘A Transcription of Darwin’s First Notebook on the “Transmutation of species”’, Bulletin of the Museum of Comparative Zoology, 122 (1960), [245]–296; Paul H. Barrett, Peter J. Gautrey, Sandra Herbert, David Kohn, and Sydney Smith, Charles Darwin’s Notebooks, 1836–1844 (Cambridge University Press, 1987). Those transcriptions have now been double-checked and are available online as both images and text, thanks to John van Wyhe, ed., 2002. The Complete Work of Charles Darwin Online (http://darwin-online.org.uk/).

11 I am speaking only of multicellular organisms. For variability that threatens to erase history, at least enough to frustrate classification, we need not leave our planet, just our human scale.

12 My citations use the pagination within the notebooks, in this case, Notebook B, pp. 19–21. In Barrett et al. 1987 Darwin’s Notebooks, p. 175, David Kohn transcribed the second Megatherium as Megatheria, but John van Wyhe reads them both as Megatherium.

13 Darwin seems not to have used the term. Cuvier noted that it had similarities to armadillos as well as to tree sloths.

14 Martin Rudwick, Bursting the Limits of Time: The Reconstruction of Geohistory in the Age of Revolution (Chicago: University of Chicago Press, 2005) and Earth’s Deep History: How It Was Discovered and Why It Matters (Chicago: University of Chicago Press, 2014).

15 George Gaylord Simpson, Discoverers of the Lost World: An Account of Some of those who Brought Back to Life South American Mammals Long Buried in the Abyss of Time (Yale University Press, 1984); Adrian Lister, Darwin’s Fossils: Discoveries that Shaped the Theory of Evolution (CSIRO Publishing, 2018).

16 Richard Owen was at first not sure whether this horse was a different species from domestic horses, but he later decided it was; modern mammalogists think so too.

17 The Beagle carried an impressive library, including all 16 volumes of Georges Cuvier, The Animal Kingdom Arranged in Conformity with its Organization: With Additional Descriptions of All the Species hitherto Named, and of Many Not before Noticed, ed. by Edward Griffith and others (London: Geo. B. Whittaker, 1827–35). Remarkably, the Beagle’s whole library has been reconstructed and is available online: http://darwin-online.org.uk/BeagleLibrary/Beagle_Library_Introduction.htm.

18 The so-called three-toed sloths retain the name Bradypus, but two-toed sloths are now Choloepus.

19 The Correspondence of Charles Darwin: 1831–1836, ed. by Frederick Burkhardt and Sydney Smith (Cambridge University Press, 1985), vol. 1, p. 280.

20 The German admirer was Ernst Haeckel, whom Darwin wrote to in 1864. Darwin Correspondence Project, Letter no. 4631. https://www.darwinproject.ac.uk/letter/?docId=letters/DCP-LETT-4631.xml

21 For several years there was confusion as to whether Megatherium might be the bearer of these bony plates, but that did not undermine Darwin’s vision of an extinct fauna of large edentates related to living sloths and armadillos. The confusion is untangled by Herbert, Charles Darwin, Geologist and by Adrian Lister, Darwin’s Fossils: Discoveries that shaped the theory of evolution (CSIRO Publishing, 2018).

22 David Kohn, ‘Theories to Work By: Rejected Theories, Reproduction and Darwin’s Path to Natural Selection’, Studies in History of Biology, 4 (1980), 67–170, pp. 156, 166–167, showed that Darwin purchased in 1837 a copy of the 1830 edition of Philosophie zoologique. Mario A. Di Gregorio transcribed Darwin’s marginal note that Lamarck’s claim that divisions are artificial is a ‘fallacy’: Charles Darwin’s Marginalia (Garland Reference Library of the Humanities, 1990) p. 478.

23 Charles Lyell, Principles of Geology, vol. 2, 1832, p. 12.

24 I agree with David Kohn (Barrett et al. p. 173n) that this was ‘probably personal communication’, with J. E. Gray, but it could just refer to Gray’s publications. In either case, I think Darwin may have misunderstood him, because Gray believed that species are distinct. His articles on naturalists’ difficulties in distinguishing species were meant to make naturalists more careful. I am grateful to Gordon McOuat for alerting me to the problem.

25 Di Gregorio, Darwin’s Marginalia, p. 478.

26 David A. Baum and Stacey D. Smith, Tree Thinking: An Introduction to Phylogenetic Biology (Roberts and Company, 2013).

27 J. David Archibald, Aristotle’s Ladder, Darwin’s Tree: The Evolution of Visual Metaphors for Biological Order (Columbia University Press, 2014), p. 85.

28 Besides the Galapagos birds and rhea being named by Gould, an armadillo Darwin had collected (not a new species) was described by William Martin, and his mice were being looked at by George Waterhouse. Meanwhile Owen reported to Lyell that Darwin’s fossil mammals belonged to five new species.

29 It seems likely he first drew the diagram, and then wrote the letters. If he meant to portray four genera of living species, would he not have written A, B, C, and D, in order? Where he placed them suggests that his first interest was the great gap between A and all the others, which he labelled B. This agrees with the sequence of his words.

30 Darwin’s insertion seems to mean that he is replying to his own doubt about whether it makes sense to assume a constant number of species. If the world is full of life, then any observer who decides to break it up into groups will probably arrive at the same number of groups, The words I still omit are ‘changes not result of will of animal but law of adaptation as much as acid and alkali’. (B21)

31 He addressed the question in Notebook C a year or so later: ‘The quantity of life on planet at different periods, depends, – on relations of desert, open ocean, &c this probably on long average, equal quantity, 2nd on relations of heat & cold. therefore probably fewer now than formerly. – The number of forms depends on the external relations (a fixed quantity) & on subdivision of stations & diversity –. – this perhaps on long average equal. – (C147e)

32 The idea of multiplying species in an already full world resembles the Malthusian principle of population (cf. fn 35).

33 Nora Barlow, ed. The Autobiography of Charles Darwin 1809–1882 (London: Collins, 1958), pp. 120–121.

34 Stevens, Development, p. 137ff; Joeri Witteveen, ‘Suppressing synonymy with a homonym: The emergence of the nomenclatural type concept in Nineteenth Century natural history’, Journal of the History of Biology, 49.1 (2016), 135–189.

35 We must not confuse this with two unrelated twentieth century terms: ‘sibling species’ and ‘sister species.’

36 Malthus had argued that utopian visions of universal happiness were unrealistic because the number of people could quickly double, thereby exceeding the food supply, if all checks to increase, like disease, war, or prudent avoidance of marriage, were removed. Giving money to the poor would not cure poverty, but separating husbands from wives in a workhouse would be a check to their increase. William Godwin contradicted Malthus, saying that because nature had been wisely arranged, fertility varies appropriately; he said we can trust that populations achieve their best size. In 1838 Darwin would derive from Malthus the realization that the struggle for existence operates not just between predator and prey, organism and environment, but most strongly between members of the same species. There is no hint of those issues in 1837.

37 For example, John Tyndall in 1863 wrote of ‘magnificent gradations of color, one fading into another without solution of continuity,’ quoted in the Oxford English Dictionary, Solution III, 9. Being unfamiliar with that meaning, I was puzzled by David Kohn’s transcription of Darwin’s handwriting, but Jonathan Hodge, John van Wyhe, and Kees Rookmaaker kindly checked and confirmed that reading. Google’s Ngram reveals plentiful use of the phrase ‘solution of continuity’ throughout the nineteenth century, disappearing in the twentieth century.

38 Students of current systematics may find it hard to sympathize with the very notion of gaps, because after exhaustive debate in the twentieth century, using a spatial metaphor for amount of similarity has been exposed as problematic. I suspect that rather than pure deduction from his speculations, the postulate was a rule of thumb he has learned from conversations with taxonomists, but I have not done a proper search for it in their writings. A little later, Hugh Strickland constructed a chart of the affinities among birds, and his linear scale of affinity separated genera as two degrees apart, while the affinity between two families was five degrees in length. Mary P. Winsor, ‘Considering Affinity: An Ethereal Conversation (Part Two of Three)’, Endeavour, 39.2 (2015), 116–126, p. 120.

39 A valuable introduction to this topic is Gordon McOuat, ‘Species, Rules and Meaning: The Politics of Language and the Ends of Definitions in 19th Century Natural History’, Studies in the History and Philosophy of Science, 27.4 (1996), 473–519. Jordan Mursinna’s doctoral work at Berkeley promises new insights.

40 Darwin, Correspondence vol. 1, p. 514. Jordan Mursinna tells me that the attendance list for that date, October 25, 1836, includes, besides Darwin, Richard Owen, William S. Macleay, and Hugh Strickland.

41 The quagga was already in decline from overhunting; it was extinct before the end of the century. Taxonomists today lump them as varieties. Because the quagga was given a scientific name earlier than the plains zebra was, their names are now Equus quagga quagga and E. quagga burchellii, so in this case, the dead trumps the living.

42 Francis Darwin, ed., The Foundations of the Origin of Species: Two Essays written in 1842 and 1844 (Cambridge University Press, 1909), p. 35, from John van Wyhe, ed. 2002. The Complete Work of Charles Darwin Online (http://darwin-online.org.uk/).

43 Darwin, Correspondence, vol. 2, pp. 375, 376, 378.

44 I omit the story of Columbus and his egg, which Stephen Jay Gould explained in The Structure of Evolutionary Theory (Cambridge: Harvard University Press, 2002), p. 225n.

45 Barlow, Autobiography of Darwin, pp. 120–121.

46 What Darwin called diversity is now divided into two kinds, the amount of morphological and functional difference being called disparity, while diversity counts number of species.

47 The best analysis of Darwin’s Principle of Divergence is Wolf-Ernst Reif, ‘Problematic issues of cladistics: 20, Darwin’s “Principle of Divergence” and the levels of selection’, Neues Jahrbuch für Geologie und Palaeontologie, 241.1 (2006), 25–66.

48 Gould argued (Structure pp. 224–250) that Darwin may have realized that his principle required higher-level selection, but that Darwin then retreated from dealing with it.

49 Ospovat, Development of Darwin’s Theory, pp. 184–200; Janet Browne, The Secular Ark: Studies in the History of Biogeography (New Haven: Yale University Press, 1983), pp. 210–216; David Kohn, ‘Darwin’s Principle of Divergence as Internal Dialogue’, in The Darwinian Heritage, ed. by D. Kohn (Princeton University Press, 1985), pp. 245–257 and ‘Darwin’s keystone: the principle of divergence’, in Cambridge Companion to the “Origin of Species”, ed. by M. Ruse and R. Richards (Cambridge University Press, 2008).

50 Classification is in Chapter 13 of the 1859 edition, but a whole new chapter is inserted into the 6th edition, so the classification chapter becomes 14.

51 Darwin says that while species A and I were producing variants, the other nine capital-letter species ‘may for a long period continue transmitting unaltered descendants; and this is shown in the diagram by the dotted lines not prolonged far upwards from want of spece.’ On the next page, however, he says

But we may go further than this … .[The modified descendants] will have taken the places of, and thus exterminated, not only their parents (A) and (I), but likewise some of the original species which were most nearly related to their parents. Hence very few of the original species will have transmitted offspring … . (p. 121)

52 Michael Schmitt, ed., From Taxonomy to Phylogenetics: The Life and Work of Willi Hennig (Brill, 2013); Andrew Hamilton, ed., The Evolution of Phylogenetic Systematics (University of California Press, 2014).

53 David Sepkoski, Rereading the Fossil Record: The Growth of Paleobiology as an Evolutionary Discipline (University of Chicago press, 2012).

54 Mary P. Winsor, ‘Robert Wallace: Predecessor of Malthus and Pioneering Actuary’, Acta Historica Scientiarum Naturalium et Medicinalium, 39 (1987), 215–224, based upon bachelor’s thesis, Harvard University, 1965.

55 In a population of 2000, if every ‘ten souls’ are close relatives, this means that 200 people in the past were their ancestors, which leaves 1800 people back then who left no successors. However, for close relatives there is no need to go 200 years into the past, and degrees does not help. Degree of consanguinuity is an old measure of relationship, used to regulate marriage. (Darwin married his first cousin, who was a daughter of his uncle.) People are related to their grandparents by the third degree, to their great-grandparents by the fourth degree, and so on. Degree of kinship to a contemporary distant cousin is counted by how many generations ago, not years ago, their common ancestor lived.

56 Lustrum was the five-year census period in ancient Rome. Malthus did not use this word, but it is found in William Godwin, Of Population: An Enquiry Concerning the Power of Increase in the Numbers of Mankind in Answer to Mr. Malthus’s Essay on that Subject (London, 1820), p. 87.

57 Darwin seems to be wondering if giving up his assumption of constant population numbers would undermine his reasoning.

58 ‘Great groups’ here seems to mean groups containing a large number of families, genera, and species. The examples he had in mind may have been the monotremes (echidna and platypus), of which only two species were known; because they lay eggs, they were seen as intermediates between mammals and birds.

Appendix

Appendix. Excerpt from Darwin’s Notebook B, pages 146–149.

Darwin’s insertions are noted by << >>. All footnotes by M. P. Winsor.

If population of place be constant <<say 2000 >> and at present day, every ten living souls on average are related to the (200dth year) degree. Then 200 years ago, there were 200 people living who now have successors. – Then the chance of 200 people [open-strick][open-strick][close-strick][close-strick] being related within 200 years backward might be calculated & this number eliminated say 150 people four hundred years since were progenitors of present people, and so on backwards to one progenitor, who might have continued breeding from eternity <<backwards.—>>⁵⁵

If population was increasing between each lustrum,⁵⁶ the number related at the first start must be greater, & this number would vary at each lustrum, & the calculation of chance of the relationship of the progenitors would have different formula for each lustrum. –⁵⁷

We may conclude that there will be a period though long distant, when of the present men (of all races) not more than a few will have successors at present day. In looking at two fine families one with successors <<for>> centuries, the other will become extinct. – Who can analyse causes, dislike to marriage, heredetary disease, effects of contagions & accidents: yet some causes are evident, as for instance one man killing another. – So is it with varying races of man: these races may be overlooked; mere variations consequent on climate &c – the whole races act towards each other, and are acted on, just like the two fine families <<no doubt a different set of causes must act in the two case,>> May this not be extended to all animals first consider species of cats. – [open-strick][open-strick][close-strick][close-strick]. – &c, &c Exclude mothers and then try this as simile

In a decreasing population at any one moment fewer closely related: (few species of genera) ultimately few genera (for otherwise the relationship would converge sooner) & lastly perhaps some one single one. –

Will not this account for the odd genera with few species which stand between great groups, which we are bound to consider the increasing ones. –⁵⁸