About this website

updated 5 Nov 2024

Scientists who follow Charles Darwin –evolutionary biologists– have become somewhat dogmatic. Here I am investigating alternatives and extensions of the theory of evolution. However, I want to be critical of both mainstream and alternative theories. This website contains 100 reviews of books about evolution. The homepage lists all my reviews, and the Introduction page gives an overview of the Evolution literature.

About the author

    Even at the time when I was a student and attended evolutionary biology courses and did lab experiments on evolution, I had the vague idea that the theory of evolution was incomplete, although at the time I could not say why, or what exactly was missing. My university study left me ill prepared for the critics of evolution (81).

Publications and lectures

• Gert Korthof (2014) Expanding the genetic alphabet, Panda's Thumb, May 15 2014.
• Gert Korthof (2013) New Szostak protocell is closest approximation to origin of life and Darwinian evolution so far, Panda's Thumb, December 13, 2013
• Lecture at the Skepsis congres, Utrecht on 7 Nov 2009 (program).
• Lecture at Groningen University 2 April 2009 (Arts Meet Science Symposium).
• Lecture at NIBI onderwijsconferentie 9 Januari 2009 Lunteren "Is het Neo-darwinisme compleet?" (see powerpoint presentation).
• Gert Korthof (2007) Non-lokale biologie. Misleidende citaten van Pim van Lommel, Skepter, nr 2 2007.
• Gerdien de Jong and Gert Korthof (2006) 'Claim of bias against critics is refuted by publication', Nature, 7 December 2006, p.679. | Pubmed
• Martin Hafner and Gert Korthof (2006) 'Does a "500 million-year-old hormone" disprove Darwin?' FASEB J. 2006 20: 1290-1292. PubMed; pdf
• Gert Korthof (2005) "Virussen als raakvlak tussen Biologie en IT", lecture on 24 November 2005 at RIVM. This lecture has been significantly expanded as: Similarities and Dissimilarities of Computer Viruses and Biological Viruses.
• Gert Korthof (2005) "God door de voordeur. Intelligent Design over de oorsprong van Alles". Skepter, zomer 2005, pp.33-35. (boekbespreking van Schitterend ongeluk of sporen van ontwerp?) [ Dutch ].
• G. Korthof: "Common Descent: It's All or Nothing" in: Matt Young and Taner Edis (2004): Why Intelligent Design Fails: A Scientific Critique of the New Creationism, Rutgers University Press. See for more information about the book this page.
• Gert Korthof and Andrew Carothers (1991) "Tests of performance of four semi-automatic metaphase-finding and karyotyping systems", Clinical Genetics 1991:40:441-451. | PubMed | pdf (1.072 kB) | Wiley Online Library
• J. Vrolijk, G. Korthof, G. Vletter, C.R.G. van der Geest, G.W. Gerrese, P.L. Pearson (1989) "An automated System for the Cultering and Harvesting of Human Chromosome Specimens", book chapter, pp.135-148 of C. Lundsteen, J.Piper Automation of Cytogenetics, Springer-Verlag Berlin Summary: PDF (165 kB)
• J. Vrolijk, G. Korthof, G. Vletter, C.R.G. van der Geest, G.W. Gerrese and P.L. Pearson (1986) "The automation of culturing and harvesting of human chromosome specimens", Histochemistry and Cell Biology Volume 84, Numbers 4-6 July 1986 pages: 586 - 593 | Pubmed
• 
  G. Korthof (1986) "An improved fixation method for chromosome preparation of Chinese hamster, Chinese hamster-human hybrid, and mouse cell lines", Cytogenetics and Cell Genetics, 41:181-184 (1986). | PubMed | PDF (758 kB) |
  
  
  
  
  
  

• Gert Korthof (1978) Wetenschapsfilosofie en wetenschapsbeleid. Amersfoortse Stemmen, maart 1978 pag 58-61.
• Gert Korthof (1977) Locomotorische activiteit en paringsvoorkeur bij Drosophila melanogaster. Doctoraal onderzoek populatiegenetica. Rijks Universiteit Utrecht, onder leiding van Folchert van Dijken, aug 1976 – jan 1977.

The philosophy of this website

"Consensus is a dangerous thing in science. The notion that researchers can ever prove their theories is long gone – they can only wait for others to knock them down. This means that to be healthy, science needs an opposition, and when to be healthy, science needs an opposition, and when politicians ask scientists to reach a common view, it pays to be wary."

"Evidence that might refute a theory can often be unearthed only with the help of an incompatible alternative." (113)

"A scientist who wishes to maximize the empirical content of the views he holds and who wants to understand them as clearly as he possibly can, must therefore introduce other views; that is, according to Feyerabend (1993), he must adopt a pluralistic methodology. He must compare ideas with other ideas rather than discard the views that have failed in the content." (source)

"The first step in our criticism of customary concepts is to step outside the circle and either to invent a new conceptual system or import such a system from outside science, from religion, from mythology." (Paul Feyerabend, Against Method, third impr. 1976, page 68.)

"How wonderful that we have met with a paradox. Now we have some hope of making progress." (113)

"Any physicist who openly criticized or even seriously questioned these foundations ... was immediately branded as a 'quack'. Quacks naturally found it difficult to find decent jobs within the profession." 116).

Cosmologist Claudia de Rham told in an interview in Nature:

"Every day, I try out an idea and it fails. And there's something beautiful in failing, and falling. The book is about gravity, but it is also about embracing this falling, because it's how we get better – it's how we understand the world. (...)
So the [Einstein's] theory itself is telling you that you shouldn't trust it any more. And that is not something to be ashamed of. It is an opportunity to learn something more."
Nature, 2 April 2024.

Famous physicist Richard Feynman (1918–1988):

"For example, if you're doing an experiment, you should report everything that you think might make it invalid ... other causes that could possibly explain your results ... Details that could throw doubt on your interpretation must be given, if you know them. You must do the best you can–if you know anything at all wrong, or possibly wrong–to explain it. If you make a theory, for example, and advertise it, or put it out, then you must also put down all the facts that disagree with it as well as those that agree with it."

About this website

• http://www.worldaccess.nl/~gkorthof/
• http://home.planet.nl/~gkorthof/
• http://home.wxs.nl/~gkorthof/

The Evolutionary Syntheses

1. First Evolutionary Synthesis (1859–1900)
   In 1858 Charles Darwin and Alfred Russel Wallace published a joint paper containing a theory of the origin of species. In 1859, 150 years ago, Charles Darwin published On The Origin of Species which can now be called the First Evolutionary Synthesis ('Darwinism'). This was the first synthesis because Darwin was the first scientist to construct a synthesis of all biological knowledge of his time on the basis of the concept of evolution. 'Darwinism' is defined as: "Darwin's theory, that species originate by evolution from from other species and that evolution is mainly driven by natural selection" (24), (31). Some include neo-Darwinism in the period before 1900 defining it as the removal of Lamarckian inheritance from Darwinism (84).
2. Second Evolutionary Synthesis (1900–1953)
   The incorporation of the Mendelian and population genetics created the Evolutionary Synthesis or: The Modern Synthesis (Julian Huxley, 1942) or: Neo-Darwinism (31),(84) which in fact is the Second Evolutionary Synthesis. According to (26) this synthesis includes: genetics, paleontology, systematics, and cytology. Keep in mind that the second synthesis was just before the birth of molecular genetics.
3. Third Evolutionary Synthesis (1953–today)
   or 'Extended Evolutionary Synthesis' (17), (50) or Post-Modern Synthesis (53) is the Second Evolutionary Synthesis plus molecular genetics (Watson & Crick, 1953). What else to include, or even whether this synthesis deserves a new name at all is controversial: it has been defended and disputed (82). Proposed for inclusion are: evo-devo (not controversial anymore), genomics, epigenetics, ecology (23), (83), endo-symbiosis, life history, hybridization, Horizontal Gene Transfer, Systems Biology, Earth System Science (including Niche Construction and Gaia?), Origin of Life, astrobiology, sociobiology (incl. evolutionary psychology?), evolution of the brain and consciousness.

What is missing:

To give just a few examples of the importance of biogeochemistry for evolution: the 'Cambrian explosion' has long been unexplained. June 2008 geologists reported in Nature that "the Early Cambrian animal radiation may have been triggered by a major change in ocean circulation, terminating a long period during which the Proterozoic ocean was stratified, with sulphidic deep water." Few evolutionary textbooks seem to be worried about our lack of knowledge of the geochemical fossil record (fossil molecules). But, how can be understand the path of evolution and biodiversity if we don't know its environment? "Changes in the availability of bioessential elements must have shaped the evolution of life. It may be that eukaryotes emerged from ecological niches as bulk ocean chemistry shifted to favor their element requirements" (20).
Another example of a trace metal is nickel. A major decrease in the oceanic inventory of nickel (around 2.7 billion years ago) led to a cascade of events in which methanogens, who depend on nickel, would have become starved of the element and so have produced much less methane, and this could have become the driving mechanism of the Great Oxidation Event (GOE). "This marked the beginning of the most significant series of chemical changes Earth has ever experienced, setting the stage for oxidative weathering of the continents, successive changes in ocean chemistry, and the eventual rise of multicellular life" (22).
Possibly, the largest of the earth's five known mass extinctions, the end-Permian extinction, 252 million years ago, was caused by methane-producing archaea called Methanosarcina aided by a sudden influx of nickel in the oceans (76).
Also the identification of a general connection between biogeochemistry and the structure of food webs would constitute a considerable advance in understanding ecosystems (27),(28), (102) speciation and extinction. A book that tries to unite chemistry, biology and geology is: 'Echoes of Life: What Fossil Molecules Reveal about Earth History' (wiki).

Biogeography

The integration of phylogeny, evolution and earth history would be a great step towards the next evolutionary synthesis (30).

Climate

Another example is the relation between the diversification of herbivorous mammals, their gut microbes, the origin of C4-grasses, and the climate (CO₂) (15). Another recent publication highlights the importance of climate: "climate played an overarching role in promoting the unprecedented increases in biodiversity that characterized The Ordovician Period." (18). Biochemical and physical laws constrain the evolution of life, because evolution necessarily depends on them, but fall outside a biological theory of evolution. But in the New Evolutionary Synthesis every factor (maybe even cosmic rays: 21) that influences evolution must be incorporated.

Physics

An example of physical phenomena that constrain morphology of multicellular organisms is: Stuart Newman and Gerd Müller (16). A good exampe of a biologist who investigates physical constraints on the form of organisms is Steven Vogel (The life of a Leaf). But the physical aspects of evolution are hard to find in evolution textbooks.

Brainless evolution textbooks?

On the other end of the spectrum that runs from physics to psychology is the evolution of the human brain and mind. Recent contributions to the neo-Darwinistic theory of the human mind are: Gary Marcus (2004) The Birth of the Mind and Gary Lynch and Richard Granger (2008) Big Brain and more. John Allman (2000) Evolving Brains is completely devoted to the evolution of brains including the genetics of the brain. Evolutionary brain research recently produces new insights (19), (96). Clinical genetics can sometimes reveal links between cognition, brain and genes (39). Despite this research of the last 10 years, there is no trace of brain evolution in modern evolution textbooks. There is no 'brain' in the index of Barton et al (2007) Evolution; and Stearns, Hoekstra (2005) Evolution. The exceptions are: Freeman and Herron (2007) Evolutionary Analysis (a few pages: 771, 791 about skulls but not explicitly on the evolution of the brain); Monroe Strickberger (2000, 2007) Evolution. The 2008 edition of Strickberger's Evolution contains a diagram of Hox gene expression in the embryonic mouse brain (p.298) (19). We need more of this. In fact so much knowledge has been accumulated that dedicated textbooks are necessary. In 2020 the 3rd edition of Comparative Psychology: Evolution and Development of Brain and Behavior appeared (109). In my view, important questions are:

• What genes, regulators and how many mutations are needed to evolve the human brain from a vertebrate brain? from a mammalian brain? from a primate brain?
• Do humans have unique types of brain cells? How did the cerebral neocortex evolve? (43)
• How did the nervous system evolve? (25).
• How did neurons and synapses evolve? (29), (103)
• How difficult was it to evolve the human brain? A completely new area and territory has been initiated with the description of the transcriptome of the human brain (40).

Was Darwin Wrong?

updated: 26 Jun 2022

1. Was Darwin wrong about his theory of heredity?
   Darwin's Pangenesis theory as a theory of heredity was wrong because a migration of hereditary material (gemmules) from all parts of the body to the sexual organs and the subsequent inheritance to the offspring, was already refuted during Darwin's lifetime. However, recently extracellular vesicles have been discovered that are secreted from cells and carry RNA and proteins and maybe transmitted to germ cells in some cases (99). It could be argued that his gemmules were in fact circulating cell-free DNA, mobile RNAs and extracellular vesicles (100).
   
2. Was Darwin wrong about blending inheritance?
   Darwin was also wrong about blending inheritance, the second idea about inheritance to which Darwin had turned in a half-hearted attempt to complete his theory (50). Blending inheritance made it difficult to explain the origin and maintenance of variation. We now know that genetic factors do not blend (Mendelism). How does this affect other parts of his theory? "The claim that Darwin's theory was unworkable without genetics is an artifact of hindsight. It was perfectly possible to construct a theory of natural selection on the basis of blending inheritance" (13). See also: (59).
3. Was Darwin wrong about the inheritance of acquired characters?
   Darwin stated: "whereas, even in the first edition of the 'Origin of Species,' I distinctly stated that great weight must be attributed to the inherited effects of use and disuse, with respect both to the body and mind. I also attributed some amount of modification to the direct and prolonged action of changed conditions of life."(48). However, Darwin was wrong to believe that acquired characters, for example changes in organs caused by use and disuse, are heritable (Lamarckism) (5, 6, 49). But, "Both Darwinian and Lamarckian modalities of evolution appear to be important" (80).
4. Was Darwin wrong about common descent?
   The Common-descent-of-life part of evolution does not depend on a correct theory of heredity. Common descent was quickly accepted in Darwin's time and is quietly ignored by many critics because it such a powerful idea confirmed by a great diversity of facts. "Tree-like evolution is a fundamental implication of the binary replication of the genetic material, so it served Darwin well to use a tree as the single illustration of his book. Without, obviously, knowing anything of DNA replication, Darwin grasped the central principle of the evolution of life, descent with modification, and the tree pattern followed naturally." (78). Next question:
5. Was Darwin wrong about the Tree of Life (TOL)?
   "In the sixth edition of The Origin, Darwin went further and explicitly introduced the TOL. For Darwin's day, this was an incredibly bold proposition as no hard evidence supported the common origin of all life forms." (41), (60). Furthermore, Darwin's account of evolution dealt exclusively with animals and plants, not bacteria and viruses (78). Today, no one denies that evolution of animals is tree-like (41). At the beginnings of life, the period of single celled organisms, there was a lot of horizontal gene transfer (HGT), which 'violates' the pure tree of life concept. Especially for bacteria and archaea the tree of life is more like a web (37). The branches of the evolutionary tree fork, but they also fuse (56). Darwin could not know that. In the beginning of the 21st century some even argue that "tree thinking in biology" might be a sheer myth, however deeply entrenched in the textbooks and the minds of biologists (78).
6. Did Darwin produce the first tree of life?
   The only line drawing Darwin produced in the Origin of Species is an abstract schema of the principles of the origin of (sub)species, including extinction and stasis. There are no species names, and no geological-paleontological names. "Giving credit to Haeckel, his famous 'Monophyletischer Stammbaum der Organismen' (1866) is traditionally cited as the first illustration of a phylogeny or phylogenetic tree (92), (93), (94). Darwin never produced such a tree, although it is inherent in his Common Descent with Modification. The American geologist Edward Hitchcock produced in 1840 a sort of tree of life against a background of geological strata, but he was not an evolutionist! (95).
7. Was Darwin wrong about natural selection?
   "While most scientists accepted the notions of evolution and common ancestry soon after Darwin proposed them in 1859, natural selection wasn't widely accepted by biologists until about 1930." (38). In 1859 Darwin "did not have direct proof that evolution by natural selection happens nor that it causes speciation" (33). "Darwin did not present any empirical evidence for natural selection" (52). Hardly any biologist at the end of the nineteenth century conducted scientific research on natural selection in the wild (64). The success of natural selection as the main causal factor in evolution depended substantially on an adequate theory of heredity. Darwin believed that heredity blended in each generation (see above). Therefore each advantageous variation would be diluted out of existence in a few generations (4), and natural selection would be powerless. It seems that Darwin's contemporaries were slow to accept natural selection for good reasons (32). Mimicry is a good example of natural selection but was discovered in 1862 (65) and appeared only from the 4th edition of The Origin (70), (71).
8. Was Darwin wrong about sexual selection?
   The theory of sexual selection was largely discounted for 75 years, and although sexual selection is now accepted by most evolutionary biologists in some form, one scientist (Joan Roughgarden) claims there are too many problems with it and completely rejects sexual selection (11). Evidence for sexual selection is independent of evidence for common descent or natural selection.
   Bird song has historically been considered an almost exclusively male trait, an observation fundamental to the formulation of Darwin's theory of sexual selection. But recently it has been found that female song is present in 71% of surveyed species (both females and males sing), mainly in tropical regions (73), (74), (75).
   According to Lucy Cooke, Darwin was wrong in claiming that the female generally requires to be courted by the male, she is coy." (111).
   According to William G. Eberhard, Darwin failed to appreciate that male-male competition and sexual selection can continue even after copulation has begun (112). This seems an unfair criticism.
9. Was Darwin wrong about adaptation?
   "Cain makes a similar point about so-called trivial characters, criticizing Darwin for being too ready, under the at first sight surprising influence of Richard Owen, to concede functionlessness: 'No one will suppose that the stripes on the whelp of a lion, or the spots on the young blackbird, are of any use to these animals ...' Darwin's remark must sound foolhardy today even to the most extreme critic of adaptionism." (91). "The testing of Darwin's argument, that is, the resolution of whether natural selection could be as powerful as artificial selection, whether trait differences that were under selection would prove heritable, and ultimately whether populations would diverge through differences in their selective regimes, has occupied biologists for nearly a century and a half". (106). So, Darwin had the right theory, but it was impossible at his time to prove it.
10. Did Darwin explain the origin of species?
    Darwin's On the Origin of Species by Means of Natural Selection (1859) didn't really explain how new species arose. He knew evolution was branching evolution, but he never explained how one species splits in two (34). In 1867, that is 8 years after The Origin of Species, J. D. Campbell noted in his Reign of Law that Darwin had in fact not explained the origin of new species (114). Darwin never really understood that explaining species means explaining barriers to gene exchange. Ernst Mayr stated: "It is not nearly so widely recognised that Darwin failed to solve the problem indicated in the title of his work." (46). So, Darwin was not wrong, but incomplete.
    The problem of speciation was not seriously addressed until the mid-1930s (34). The reason of this that Darwin had a morphological species concept, not one based on reproductive isolation, and above that he thought that 'species' is an arbitrary man-made concept (77). However, see (67). The opposite of branching evolution is Hybrid speciation.
11. Did Darwin explain the origin of major groups and phyla?
    Darwin did not attempt to describe the origin of phyla or the major groups of animals and plants. He did not describe the evolutionary relations of animal and plant phyla. The only illustration in The Origin of Species was an abstract tree of several species labelled a-z and abstract geological periods arbitrarily labelled I - XIV. However, he defended the common descent of plants and animals (in the last chapter of the Origin), but he did not have the evidence we have today. Even today, with modern DNA techniques, the evolutionary relationships between the five major branches of animals are very hard to establish (90), so we cannot blame Darwin. Example: the origin of bats (animals with unique features such as echolocation, extreme longevity and unique immunity) is even today not definitively established (104)
12. Did Darwin explain the origin of flowering plants?
    Darwin's abominable mystery: in a letter to Hooker, July 1879, Darwin characterized the rapid rise and early diversification of flowering plants (angiosperms) in the fossil record as an "abominable mystery". However, an ancient genome duplication predated angiosperm diversification and throws light on Darwin's abominable mystery (58).
13. Was Darwin wrong about the importance of hybridization in the origin of species?
    The controversy about the role of hybridization in evolution began almost 300 years ago when the Swedish botanist Carl Linnaeus posited that new forms of plants could arise by hybridization. Darwin also expressed scepticism about the importance of hybridization. In the 20th century, the prevailing view among evolutionary biologists aligned closely with Darwin's, holding that hybridization was rare, and when it did occur, it was likely to be maladaptive and transitory, leading either to the completion of speciation or to the merging of hybridizing entities. Now there is evidence that the footprints of hybridization are a common feature of plant and animal genomes and that hybridization can provide the fuel for adaptive diversification. (101)
14. Did Darwin discover the importance of the so-called Darwin's finches?
    Darwin had remarkably little to say about how the birds that bear his name –Darwin's finches– came to have such a variety of beaks, despite their iconic status in evolutionary biology (88). Darwin omitted the 'Darwin-finches' from his Origin of Species simply because there were too many unanswered questions (107). It was left to an English schoolmaster, David Lack, on sabbatical in the late 1930s to carry out the first serious work on this question. More recently, Canadian evolutionary biologist Dolph Schluter quipped that Darwin's finches, should be known as Lack's finches (44). Only in 2015 genome sequencing revealed the evolutionary relationships of the Darwin's finches (87).
15. Was Darwin wrong about gradualism?
    Because Darwin presented his theory in opposition to the theory of special creation (instantaneous creation of species), he emphasized the gradual nature of evolution by natural selection. In 1972 Eldredge and Gould claimed that sudden appearance in the fossil record and stasis for million of years is not the result of the incompleteness of the fossil record, but is a real pattern in the fossil record. Another example is: "Myelin appears suddenly in vertebrates, animals with backbones that arose 500 million years ago. Not a trace of it is found in the ancestral line that preceded the arrival of vertebrates." (115).
16. Did Darwin ignore the primary sexual characters: the sexual organs?
    According to Menno Schilthuizen, Darwin's sexual selection theory was concerned only with secondary sexual characteristics (colorful bird plumage, etc), not with the primary sex organs (penises, vaginas). The primary sexual organs are maintained by natural selection (97).
17. Was Darwin's species concept wrong?
    Darwin's species concept as an arbitrary demarcation imposed by the human mind on an otherwise continuous process of diversification, was largely wrong (50), (77). It was replaced by Ernst Mayr's biological species concept: species boundaries are natural ('interbreeding individuals', 'reproductive isolation'). It needs further research to find out how important 'hybridism' was for Darwin to delineate species. (see CHAPTER VIII of The Origin of Species)
18. Was Darwin wrong about progress in evolution?
    "The idea of a general evolutionary trend toward increasing complexity is extremely popular among both lay public and scientists and certainly was shared by Darwin who wrote, for example, in famous quote: "as natural selection works solely by and for the good of each being, all corporeal and mental endowments will tend to progress toward perfection". (78). Indeed, "the most organizationally complex organisms with the largest genomes, animals, and plants, appear only at relatively late stages of evolution" (78). However, "There is no consistent tendency of evolution towards increased genomic complexity" (79).
19. Did Darwin explain "The Cambrian Explosion"?
    "To the question why we do not find rich fossiliferous deposits belonging to these assumed earliest periods prior to the Cambrian system, I can give no satisfactory answer." (Darwin, The Origin of Species, 5th ed., 1869, p.286). (54)
    Today, this is called the 'Cambrian Explosion': "The near-simultaneous appearance of most modern animal body plans in the Cambrian explosion suggests a brief interval of rapid phenotypic and genetic evolution, which Darwin believed were too fast to be explained by natural selection. However, the rates of genetic and phenotypic evolution were shown to be ~4 times and ~5.5 times faster, respectively, than all subsequent parts of the Phanerozoic era – consistent with natural selection during the Cambrian explosion." (55).
    "In Charles Darwin's day, no fossils had been found below the rock layers documenting the Cambrian explosion. That blank rock record troubled Darwin, who reasoned that if his theory of evolution were correct, there must have been life before the Cambrian's riches. "The case at present must remain inexplicable," he wrote in On the Origin of Species in 1859. 'Darwin's dilemma' would remain unsolved for a century." (108).
20. Did Darwin have any transitional fossil forms to support this theory?
    In On the Origin of Species by Means of Natural Selection (1859) Darwin did not have any transitional forms to prove common descent. The first fossils of Archaeopteryx lithographica were discovered in 1860 and 1861. Too late for the first 3 editions of The Origin. But Darwin, "curiously, mentioned it only briefly in the later editions of The Origin, and only then as an oddity." (34), (117). Neanderthaler fossils found in 1856 did not appear in The Origin at all (89), but it did appear in The Descent of Man. "Darwin was faced with a scant fossil record (it played almost no role in his Origin of Species)" (38), (118). "In 1859 there were still no good hominid fossils for him to point to, and this was still true when he wrote The Descent of Man in 1871" (61). Darwin worried about the abrupt appearence and fast diversification of the Angioperms (62). Although Darwin discusses some intermediate fossils in the sixth edition of The Origin, Chapter XI, page 302, he did not have the famous fossil horse series which was published in 1926 (63).
21. Was Darwin wrong about biogeography?
    Darwin had no complete explanation of biogeography and his theories of biogeography were partly wrong. That's been corrected by plate tectonics (Jerry Coyne interview). Darwin did not know about continental drift. Darwin struggles to explain why different continents have different faunas on them, and why the geological record is so intermittent in most places (35). Alfred Russel Wallace's conceptualization of evolution by natural selection had a distinctly geographical slant (47).
22. Was Darwin wrong about the age of the earth?
    Unfortunately, Darwin and his fellow geologists could not determine exactly how old a particular fossil or rock might be. They could make only rough estimates of the time it had taken for a geological formation to emerge; radiometric dating did not exist at that time (68). Darwin accepted the calculation of Sir William Thompson (later Lord Kelvin) that the earth is about 200 million years old, but confesses uneasily that "it can hardly be considered as sufficient for the development of the varied forms of life." Darwin's own calculation resulted in an estimate of 100 up to 300 million years, but he was so unsure about it that he removed it from the third edition onwards (57). Thompson was out by a factor of seven, because he had omitted the effect of radioactivity which is slowing the cooling of the earth (35). Also, Darwin did not know the antiquity of life on earth.
23. Was Darwin wrong about the continuity between humans and animals?
    "The Origin barely touched upon the most contentious evolutionary issue: If all life has evolved from "lower forms", does that include people? Darwin finally addressed the issue in The Descent of Man, and Selection in Relation to Sex (1871)." (66).
    "Over the last quarter century, the dominant tendency in comparative cognitive psychology has been to emphasize the similarities between human and non-human minds and to downplay the differences as "one of degree and not of kind" (Darwin, 1871). In the present target article, we argue that Darwin was mistaken: the profound biological continuity between human and nonhuman animals masks an equally profound discontinuity between human and nonhuman minds" (51).
24. Was Darwin wrong about universal human facial expressions?
    "In the 1960s, guided by the prevailing anthropological orthodoxy, Paul Ekman, now retired, set out to prove Darwin wrong by asking for interpretations of facial expressions from the farthest flung people he could get to. He ended up confirming that Darwin had a point. "The evidence is very strong, from studies of both recognition and expression in Western and Eastern, literate and preliterate, cultures that Darwin was indeed prescient," says Ekman. "At least six, perhaps seven, emotions have a pancultural facial expression." (Nature)
25. Was Darwin able to resolve the evolutionary relationships of barnacles? or any other group?
    "Ironically, in four monographs on living and fossil barnacles, the only taxonomic work that Darwin ever did, he was unable to resolve their genealogical relationships. He recognized why: Selective extinction over the ages had removed all the intermediate related forms" (Kevin Padian). Darwin could not resolve the evolutionary relationships between any group of organisms because he lacked DNA data (85).
26. Did Darwin explain altruistic behaviour?
    "Although Darwin did not confront the problem of altruistic behaviour directly, he was aware of the challenge posed by the development of sterile castes in some social insects and, in Chapter VIII of The Origin of Species, he describes how he thought, at first, that this was fatal to the whole theory of natural selection" (Tim Clutton-Brock in Nature).
27. Darwin did not include microbes and viruses in his theory of evolution
    "Of course, Darwin was unaware of this vast [microbial] ecology right under (and inside) his nose. At the time of Darwin's 1835 Galápagos Island expedition, the germ theory of disease had yet to be described; Jenner's smallpox vaccination was only forty years old (and no one could adequately explain how and why it worked, as viruses wouldn't be described for another sixty years); and Pasteur's most famous experiments were almost thirty years in the future. Even though Darwin was unable to bring microbial evolution into his wide-ranging ideas, modern-day evolutionary biologists are not as limited." (69). In 1876 the anthrax bacillus Bacillus anthracis was discovered by Robert Koch. In 1882 the cause of tuberculosis Mycobacterium tuberculosis was discovered also by Koch. "The phylogenomic study of microbes and viruses uncovered new biological realms which Darwin and even the authors of the Modern Synthesis could not possibly fathom." (78), (86), (105). However, Darwin used the word 'infusoria' in the 3d and later editions of The Origin.

Was Darwin Wrong?
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updated: 12 Jul 2013

About the website WAS DARWIN WRONG? (2)

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Notes

1. "Scientific explanations remain perpetually incomplete. If we learn anything from the pursuit of science, it is that even something as basic as an atom is quite difficult to understand. This alone should induce skepticism about any dogma or any claim to have achieved more than a very incomplete and metaphorical insight into any profound aspect of our existence." (interview with Sir Martin Rees in Scientific American, July 2004, p.24-25.)
2. TalkOrigins provides mainstream scientific responses to the many frequently asked questions about the evolution/creation controversy. The following website has been awarded by the Scientific Amercian: Understanding Evoluton: learning and teaching evolution.
3. Evolutionary Biology resources by the Konrad Lorenz Institute for Evolution and Cognition Research (Austria). The site contains resources of many related areas.
4. Michael Ruse (2003) Darwin and Design, p.153.
5. Ernst Mayr: The Growth of Biological Thought, 1982, page 694.
6. However Darwin's pangenesis hypothesis was partly right according to Edward Steele (review).
7. John Maynard Smith (1986) The Problems of Biology, Preface page v. Oxford University Press.
8. Massimo Pigliucci (2005) More Than You Ever Wanted To Know About Intelligent Design, Evolution: Vol. 59, No. 12, pp. 2717-2720. "Of course, it is true (though not universally acknowledged by evolutionary biologists) that the current evolutionary paradigm is incomplete."
9. Marc Kirschner & John Gerhart (2005) The Plausibility of Life - Resolving Darwin's dilemma Yale University Press.
10. Doubts Over Evolution (Discovery Institute), April 1, 2004.
11. Joan Roughgarden, Meeko Oishi, Erol Akcay (2006) "Reproductive Social Behavior: Cooperative Games to Replace Sexual Selection", Science. See also: Evolution and Christian Faith (Chapter 11: Gender and Sexuality)
12. Leonard Susskind (2005) The Cosmic Landscape, page x.
13. Peter Bowler (2003) Evolution the history of an idea, page 200 .
14. Joan Roughgarden (2006) Evolution and Christian Faith, p.66
15. Ruth E. Ley et al (2008) 'Evolution of Mammals and Their Gut Microbes', Science, 20 juni 2008. (free abstract).
16. Elizabeth Pennisi (2008) 'Modernizing the Modern Synthesis', Science 11 July 2008.
17. Massimo Pigliucci (2008) Is there fundamental scientific disagreement about evolutionary theory? (July 02, 2008). He gives a list of 16 scientists working on the Third Evolutionary Synthesis. See his Notes from Altenberg, part I, II, III. The list of subjects does overlap with my list, but there are also non-overlapping subjects on both lists. The proceedings of the Altenberg 2008 workshop will be published 2009 by MIT Press. John Whitfield wrote about the meeting in Nature 18 sep 2008: Biological theory: Postmodern evolution?
18. Julie A. Trotter et al (2008) 'Did Cooling Oceans Trigger Ordovician Biodiversification? Evidence from Conodont Thermometry', Science, 25 July 2008:
    "The temperature record of Ordovician oceans is central to understanding links between seawater chemistry, climate change, major bio-events, and thus fundamental Earth processes. The marine biosphere underwent a profound transformation during the Great Ordovician Biodiversification Event (GOBE), recognized as the longest period of sustained biodiversifications, increasing family and genus numbers three- to fourfold".
19. John Allman (2000) Evolving Brains, Scientific American Library (see a good review). More recent works are:
    • George F. Striedter (2005) Principles of Brain Evolution
    • Platek et al (2009) Foundations in Evolutionary Cognitive Neuroscience.
    • Scientific American published 'Evolutionary Origins of Your Right and Left Brain' (July 2009).
    • Textbooks: Douglas J. Futuyma (2005) Evolution has 3 pages about the hominin fossil record, but this is about skulls not brains. Interestingly, he writes "Neanderthals had brains as large as or even larger than ours (up to 1500 cc)" (page 82). Intriguingly, Neanderthals are absent from his graph 4.12 (brain volumes)! Homo sapiens is at the top! The evolution textbook Strickberger's Evolution (4th Edition) (2007) has the best coverage of brain evolution, but does not mention 'Boskop' (modern humans have the largest brain: 1350 cc). Figure 13-8c (mouse brain) of the book is excellent, but is not listed in the index under brain, which makes it difficult to find. Also figure 3-7 shows schematic brains of fish, reptile, bird, cat and human, but it is a drawing from 1888 (!) and is not in the index.
    • Recently The Genetics of Cognitive Neuroscience (edited by Terry E. Goldberg and Daniel R. Weinberger) (Info) was published, being an important step towards evolutionary cognitive neuroscience.
    • Nature News and Views article: 'Neuroscience: Genes and human brain evolution', by Daniel H. Geschwind & Genevieve Konopka, Nature 28 Jun 2012.
20. Ariel D. Anbar (2008) 'Oceans: Elements and Evolution', Science 5 December 2008 Vol. 322. no. 5907, pp. 1481 - 1483.
    See also: Susan M. Gaines (2009) Echoes of Life. What Fossil Molecules Reveal About Earth History, Oxford University Press, reviewed in Science.
    See also: Guy M. Narbonne 'Ocean Chemistry and Early Animals': "Li et al.'s geochemical studies elucidate the critical link between the Neoproterozoic chemical evolution of the oceans and atmosphere and the early evolution of animals. Animals require oxygen", Science 2 April 2010.
21. Henrik Svensmark, Nigel Calder (2008) 'The Chilling Stars. A Cosmic View of Climate Change', Icon Books, UK.
22. Mak A. Saito (2009) 'Biogeochemistry: Less nickel for more oxygen', Nature 458, 714-715 (9 April 2009)
23. "Ecosystems ecology and evolutionary biology have existed separately for more than a century, and their integration is long overdue". Ole Seehausen 'Ecology: Speciation affects ecosystems', Nature 458, 1122-1123 (30 April 2009). See also: a volume linking ecology and evolution: Speciation and Patterns of Diversity, edited by Roger Butlin (2009).
24. Mark Ridly (2004) Evolution, Glossary.
25. Greg Miller (2009) 'On the Origin of The Nervous System', Science. An interesting suggestion by Dennis Bray (2009) Wetware A Computer in Every Living Cell is the possibility that many features of conscious beings, including learning, knowledge, and awareness, are present within single cells (Science).
26. Michael R Rose, Todd H Oakley (2007) 'The new biology: beyond the Modern Synthesis', Biology Direct 2007, 2:30
27. Josep Peñuelas1 & Jordi Sardans (2009) 'Ecology: Elementary factors', Nature 460, 803-804 (13 August 2009)
28. Robert Warner Sterner, James J. Elser (2002) 'Ecological stoichiometry: the biology of elements from molecules to the biosphere', Princeton University Press, pb 584 pages. Info. There is certainly a link with astrobiology possible. See also wiki summary.
29. T. J. Ryan (2009) 'The origin and evolution of synapses', Nature Reviews Neuroscience 10, 701-712 (October 2009) is an important review. See also: 'Evolution of the neocortex: a perspective from developmental biology' (very promising!) and other articles in the special Darwin issue of Nature Reviews Neuroscience.
30. Lynne R. Parenti, Lynne R. Parenti (2009) 'Comparative Biogeography: Discovering and Classifying Biogeographical Patterns of a Dynamic Earth' (Species and Systematics) University of California Press. See also a popular account: Dennis McCarthy (2009) 'Here Be Dragons: How the Study of Animal and Plant Distributions Revolutionized Our Views of Life and Earth.
31. George Romanes defined 'neo-Darwinism' as Darwinism without the inheritance of acquired characters (in the 1890s).
32. Now we have a 'correct' theory of genetics, Lamarckism is rejected, genetics is integrated in evolutionary theory, and natural selection is accepted as an important factor in evolution. The historical question whether Darwin's theories were accepted at the time for good reasons is of course unanswered by the current status of genetics. I find it still an interesting question.
33. David Reznick (2009) The Origin Then and Now, p.401 and 403. Also: Ernst Mayr (2001) This is Biology, p.191.
34. Jerry Coyne, 2009 Why Evolution is True, p.7, p.185, p.43 (Archaeopteryx).
35. Matt Ridley, Current Biology, Volume 19, Issue 3, 10 February 2009, Pages R96-R104.
36. Carl Zimmer (2009) The Tangled Bank: An Introduction to Evolution, Chapter 14 showing evolutionary trees of brains (p.336-337).
37. See: Graham Lawton Why Darwin was wrong about the tree of life, New Scientist 21 January 2009 and: New Scientist 24 January 2009 'Darwin was Wrong' on the cover! Dutch: New Scientist: Darwin Was Wrong! Friday, January 23, 2009 (my old blog)
38. Jerry A. Coyne The Improbability Pump, The Nation, April 21, 2010. That implies one should not attack critics of evolution when they say: Darwin had no fossil evidence for transitionals in 1859, because that particular claim is right.
39. Ursula Bellugi and Marie St. George (2001) Journey from Cognition to Brain to Gene - Perspectives from Williams Syndrome, MIT Press.
40. Hyo Jung Kang, et al (2011) 'Spatio-temporal transcriptome of the human brain', Nature, 478, 483-489 (27 October 2011)
41. Eugene V. Koonin (2011) The Logic of Chance. Pearson Education, hardback, p.40. However, is it fair to accuse Darwin of this omission considering the state of microbiology at 1859? See page 165, remarkably Koonin is silent about plants and the TOL. See also his recommended further reading (p.166-167).
42. Carl Zimmer, Douglas J. Emlen (2012) Evolution: Making Sense of Life, Roberts and Company. 720 pages. hardback, paperback. Chapter 16 is about the evolution of behavior and brains. This is a step in the right direction, but more attention to the biochemical and genetic evolution of brains is possible and recommended.
43. Has Evolution Given Humans Unique Brain Structures?, Sciencedaily.
44. Ted R. Anderson (2013) The Life of David Lack: Father of Evolutionary Ecology, Oxford University Press: 2013. Reviewed in Nature 25 Jul 2013.
45. Arbitrary example: "Biologists Tell Dueling Stories of How Turtles Get Their Shells. ... Just how the developing turtle embryo builds its fortress–a feat unique among vertebrates–is unclear. But two scenarios are now vying to explain this major evolutionary puzzle. ... A clearer understanding of how turtles build their shells could illuminate another mystery: which group of reptiles turtles evolved from, and their evolutionary path from a shell-less ancestor to the armored beasts of today." Science 26 Jul 2013.
46. Ernst Mayr (1982) The Growth of Biological Thought, p.401.
47. Sandra Knapp (2013) What, Where, and When? Science, 13 Sep 2013: "every species has come into existence coincident both in space and time with a pre-existing closely allied species"; in other words, diversification has a geographical as well as time dimension." But: "There was a lot Wallace did not know." (plate tectonics).
48. Darwin wrote in the 1872 edition of The Origin: "... that species have been modified, during a long course of descent. This has been effected chiefly through the natural selection of numerous successive, slight, favourable variations; aided in an important manner by the inherited effects of the use and disuse of parts; ..." (source). See also: 'Preface To The Second Edition of The Descent of Man' (source).
49. See my review of: Fabulous Science. Fact and Fiction in the history of scientific discovery by John Waller (see: 'Darwin: a lifelong Lamarckist').
50. Massiomo Pigliucci and Gerd Müller (2010) Evolution. The Extended Synthesis, p. 5. See my short review of the book on this website.
51. Derek C. Penn et al (2008) 'Darwin's mistake: Explaining the discontinuity between human and nonhuman minds', Behavioral and Brain Sciences (2008) 31, 109-178.
52. Masatohsi Nei (2013) Mutation-Driven Evolution, Oxford University Press, p. 39.
53. Eugene V Koonin (2009) 'Evolutionary Biology 150 years after the 'Origin': is a post-modern synthesis in sight?', Biology Direct, collection of articles published: 24 April 2009. (Open Access)
54. The words "Cambrian explosion" and "Cambrian" do not occur in the first edition of The Origin. The word "Cambrian" appears first in the 5th edition.
55. Michael S.Y. Lee et all (2013) Rates of Phenotypic and Genomic Evolution during the Cambrian Explosion, Current Biology, Volume 23, Issue 19, 1889-1895, 12 September 2013. See also: Hannah Stower (2013) Resolving Darwin's dilemma, Nature Reviews Genetics, 14, 747 (2013).
56. Lynn Margulis (2002) Acquiring Genomes . A theory of the Origin of Species, p. 202.
57. Brian Hall, Benedikt Hallgrimsson (2008) Strickberger's Evolution, Fourth edition, hardback, p. 40–41.
58. Amborella Genome Project (2013) 'The Amborella Genome and the Evolution of Flowering Plants', Science, 20 December 2013. See also: William E. Friedman (2008) The meaning of Darwin's "abominable mystery", American Journal of Botany, January 2009 vol. 96 no. 1 5-21 (contains the quote in context). See for a reference to the letter here. See also: Massive Duplication Of Genes May Solve Darwin's 'Abominable Mystery' About Flowering Plants, Science Daily, May 13, 2006 (and many older publications). See also: The Origin of Flowers: DNA of Storied Plant Provides Insight Into the Evolution of Flowering Plants, Science Daily Dec. 19, 2013. 'Darwin's abominable mystery' is discussed in Strickberger's Evolution Fourth Edition page 331.
59. University of Reading (2011) DNA to Darwin website: "Charles Darwin knew almost nothing about genetics".
60. Charles Darwin (1857) "The time will come, I believe, though I shall not live to see it, when we shall have fairly true genealogical trees of each great kingdom of Nature" in a letter to T. H. Huxley, 26 Sept [1857] Darwin Correspondence Project.
61. Donald R. Prothero (2007) Evolution: What the Fossils Say and Why It Matters, hardback Columbia University Press, p. 335.
62. William E. Friedman (2009) The meaning of Darwin's "abominable mystery" American Journal of Botany January 2009 vol. 96 no. 1 5-21 (free full text)
63. W. D. Matthew (1926) 'The Evolution of the Horse: a record and its interpretation', The Quarterly Review of Biology, Vol. 1, No. 2 pp. 139-185 quoted in: see note 61.
64. "At the end of the nineteenth century, Raphael Weldon (1898) particularly should be mentioned as one who did groundbreaking experiments on marine organisms, showing how selective pressures can operate in nature. But, by and large, these were exceptions." from: Michael Ruse chapter 12 'Evolution: From Pseudoscience to Popular Science, from Popular Science to Professional Science' in: Philosophy of Pseudoscience. Reconsidering the Demarcation Problem', Edited by Massimo Pigliucci and Maarten Boudry (2013).
65. Darwin's opponents demanded inductive or experimental proof of natural selection. "Almost the only thing Darwin could offer was analogy with artificial selection. The discovery of mimicry by H. W. Bates (1862) came as a godsend." from: Ernst Mayr: The Growth of Biological Thought, 1982, p. 522.
66. Thomas Hayden (2009) What Darwin Didn't Know, Smithsonian Magazine February 2009. (journalist Thomas Hayden)
67. John S. Wilkins (2009) Myths 2: The origin of species, Evolving Thoughts, February 12, 2009
68. Carl Zimmer, Douglas Emlen (2013) Evolution. Making Sense of Life, page 52.
69. Tara C Smith (2014) Reports of the National Center for Science Education Vol 34, No 1 (2014) in a review of: Roberto Kolter, Stanley Maloy (2014) Microbes and Evolution: The World That Darwin Never Saw. Indeed the word 'microbe' does not occur in any of the works of Darwin. However, this could also be seen is unexpected confirmation of the theory of evolution.
70. "Indeed, in the years immediately after the publication of Charles Darwin's On the Origin of Species, Henry Walter Bates and Alfred Russel Wallace recognized that butterfly mimicry was an obvious adaptation that could be explained only by natural selection. For the next 150 years, however, the mechanisms that generate these striking patterns eluded biologists." David W. Loehlin, Sean B. Carroll (2014) 'Evolutionary biology: Sex, lies and butterflies', Nature 13 Mar 2014.
71. "R. A. Fisher called mimicry the 'greatest post-Darwinian application of Natural Selection'.": K. Kunte et al 'doublesex is a mimicry supergene', Nature 13 Mar 2014.
72. See for (non-)Mendelian inheritance: this review.
73. Karan J. Odom et al (2014) Female song is widespread and ancestral in songbirds, Nature Communications 5, Published 04 March 2014. However, the authors do not mention that Darwin was aware of female bird song, but he dismissed it as an aberration (Darwin, 1882. The descent of man, and selection in relation to sex).
74. ScienceDaily: Birdsong is not all about sexual selection: Female birds sing much more often than previously thought, March 5, 2014.
75. Gould and Gould (1997) Sexual Selection. Mate Choice and Courtship in Nature, Scientific American Library paperback. "Though it may seem almost intuitively obvious that females must be choosing, there is, in fact, nothing conclusieve in Darwin's argument– no single observation or experiment, for example– that excludes the possibility that females are actually responding to the results of subtle contests among the males." p. 97. On the other hand "Darwin's idea that sexual selection might allow monogamous males to gain advantage by attracting mates earlier–a hypothesis ridiculed for decades–is now known to be largely correct" (p.89).
76. Ancient whodunit may be solved: Methane-producing microbes did it! ScienceDaily, March 31, 2014
77. "Charles Darwin (9) dealt with this problem. He simply preferred not to address the issue of species concepts, stating: "But to discuss whether they are rightly called species or varieties, before any definition of these terms has been generally accepted, is vainly to beat the air". Peter de Knijff (2014) How carrion and hooded crows defeat Linnaeus's curse, Science 20 June 2014.
78. Eugene V. Koonin and Yuri I. Wolf (2012) Evolution of microbes and viruses: a paradigm shift in evolutionary biology?, Front Cell Infect Microbiol. 2012. (free) (important article)
79. Eugene V. Koonin (2009) Darwinian evolution in the light of genomics, Nucl. Acids Res. (2009) 37 (4)
80. Koonin EV, Wolf YI. (2009) Is evolution Darwinian or/and Lamarckian?, Biol Direct. 2009
81. See for example the review of one of the first 'anti-evolution' books (here). I wish I had (philosophy) courses like detecting pseudo-science, arguing with creationists, the structure of the theory of evolution and its development from Darwin to today.
82. Kevin Laland plus 14 authors (2014) 'Does evolutionary theory need a rethink?', Nature, 8 October 2014 (free)
83. David Tilman, Emilie C. Snell-Rood (2014) Ecology: Diversity breeds complementarity, Nature, 06 November 2014: "These results exemplify the emerging field of eco-evolutionary dynamics, which emphasizes that not only does ecology drive evolution, but evolutionary change feeds back to affect ecological processes". "Although the disciplines of ecosystem ecology and evolution have developed their own perspectives, if each incorporated elements of the other, both disciplines would be strengthened. It is time for a reunification of all of the branches of natural history in a renewed search for unified explanations of the patterns seen in the natural world."
84. Massimo Pigliucci (2014) The (ongoing) evolution of evolutionary theory: "The first major improvement on the original Darwinism, which came to be known as neo-Darwinism (and which to this day even practitioners of the field confuse with the later Modern Synthesis!) came at the hands of Wallace himself, together with developmental biologist August Weismann."
85. "It struck me that there's this pretty major unsolved question in avian evolutionary history, which is how do the different bird orders relate to each other?" Gilbert says. [Tom Gilbert of the Natural History Museum of Denmark in Copenhagen]. Ewen Callaway (2014) 'Flock of geneticists redraws bird family tree. Birds get fresh perches in revamped tree of life built by vast collaboration.', Nature 11 December 2014. [super-sized multi-lab projects!]
86. "We now know that microbes make up the vast diversity of the biosphere, and that animal biology was shaped by interacting with microbes," she says. "In my mind, this is the most significant revolution in biology since Darwin." (McFall-Ngai in Nature, 15-1-2015).
87. Sangeet Lamichhaney et al (2015) 'Evolution of Darwin's finches and their beaks revealed by genome sequencing', Nature 518, 19 Feb 2015.
88. John van Wyhe (2012) Where Do Darwin's Finches Come From? The Evolutionary Review, vol 3, issue 1, pp. 185-195. pdf available.
89. "From the mid-nineteenth century, the study of human origins bristled with self-appointed experts. The book's title refers to a case in point: in the late 1850s, physiologist August Franz Mayer identified Neanderthal remains from northern Germany as belonging to a Cossack soldier with rickets who had died in 1814 and somehow become buried in 2 metres of fossiliferous deposits. Other anatomists, including Thomas Henry Huxley, were happy to agree that the individual anatomical features of Neanderthals fell within the range of variation in Homo sapiens." from a Nature review of The Strange Case of the Rickety Cossack: And Other Cautionary Tales from Human Evolution by Ian Tattersall.
90. Maximilian J. Telford, Leonid L. Moroz, Kenneth M. Halanych (2016) Evolution: A sisterly dispute, Nature, 21 January 2016.
91. From the chapter 'Constraints on perfection' page 31 in Dawkins The Extended Phenotype and requoted in Brief Candle in the Dark: My Life in Science, page 344. (Quotes can be found via google books).
92. Benoît Dayrat (2003) The Roots of Phylogeny: How Did Haeckel Build His Trees? Syst. Biol. 52(4):515–527, 2003
93. Uwe Hoßfeld & Georgy S. Levit (2016) Phylogeny: 'Tree of life' took root 150 years ago, Nature, 540, 38; 2016
94. Uwe Hoßfeld, Elizabeth Watts, Georgy S. Levit (2017) The First Darwinian Phylogenetic Tree of Plants, Trends in Plant Science, Published online: January 05, 2017
95. J. David Archibald (2009) Edward Hitchcock's Pre-Darwinian (1840) Tree of Life, Journal of the History of Biology 42, 561-592; 2009
96. Evolution of the brain: Just how related are reptilian and mammalian brains? Tosches et al. used single-cell transcriptomics to study turtle, lizard, mouse, and human brain samples. Science, 25 May 2018 'Evolution of pallium, hippocampus, and cortical cell types revealed by single-cell transcriptomics in reptiles'.
97. Menno Schilthuizen (2014) 'Nature's Nether Regions: What the Sex Lives of Bugs, Birds and Beasts Tell Us about Evolution, Biodiversity, and Ourselves', Viking Press USA. Preliminaries and Chapter 1.
98. Elizabeth Pennisi (2019) Did neurons arise from an early secretory cell? Science 18 Jan 2019 finding a common developmental source for neurons in comb jellies, jellyfish, and many other animals.
99. Yongsheng Liu, Qi Chen (2018) 150 years of Darwin's theory of intercellular flow of hereditary information, Nature Reviews Molecular Cell Biology 19, 749–750 (2018)
    Comment: interesting as it may be, it is far from being a complete mechanism of inheritance. At most, it is a minor and facultative addition to the main hereditary mechanism, which is not beneficial by definition.
100. Yongsheng Liu (2019) Darwin and Nature's 150th anniversary, Nature Correspondence 1 Oct 2019.
101. Loren H. Rieseberg (2019) Mapping footprints of past genetic exchange, Science, 1 Nov 2019.
102. Rafael Marcé, Biel Obrador (2019) Reuniting biogeochemistry with ecology and evolution, Science, 15 Nov 2019.
103. A vital structure found in the neurons of all animals might have originated in a hot spring bacterium. Complexes (ion channels) that are central to nerve-cell function might predate the split between bacteria and the lineage that led to more-complex organisms. Source: Hardy microbes hint at primeval roots for a key animal protein, Nature, 6 Mar 2020.
104. "However, the phylogeny of Laurasiatheria and–in particular–the origin of bats is a long-standing and unresolved phylogenetic question, as multiple phylogenetic and systematic studies support alternative topologies." from: David Jebb et al (2020) Six reference-quality genomes reveal evolution of bat adaptations, Nature Published: 22 July 2020. Open Access.
105. The Tobacco Mosaic Virus (TMV) was discovered in the 1890s, when researchers were attempting to isolate the pathogen that was harming the plants, and found that it was too small to be a bacterium. Obviously, Darwin could not have known the origin and evolution of viruses.
106. Michael Ruse (2009) Evolution The First Four Bilion Years. page 107.
107. Frank J. Sulloway (1982) Darwin and his finches: The evolution of a legend (pdf).
108. Traci Watson (2020) These bizarre ancient species are rewriting animal evolution, Nature 28 October 2020.
109. This revised third edition provides an up to date, comprehensive overview of the field of comparative psyhology, integrating both evolutionary and developmental studies of brain and behavior. Starts with the fundamentals of biological evolution, continues with the evolution of nervous systems and brains, learning, cognition, primate evolution, humans.
110. Amélie Beaudet (2021) The enigmatic origins of the human brain, Science 9 April 2021
111. Lucy Cooke (2022) 'Bitch. On the Female of the Species', Basic books.
112. William Eberhard (2009) Postcopulary sexual selection: Darwin's omission and its consequences, PNAS June 16, 2009.
113. "How wonderful that we have met with a paradox. Now we have some hope of making progress." Quoted in R. Moore, Niels Bohr: the Man and the Scientist (1967), p. 140. Also: Stuart G. Baker (2015) A Cancer Theory Kerfuffle Can Lead to New Lines of Research. See also: Francisco J. Ayala (2009) Darwin and the scientific method.
114. Johnjoe McFadden (2021): Life Is Simple: How Occam's Razor Set Science Free and Shapes the Universe.
115. R. Douglas Fields (2024) A Random Influx of DNA from a Virus Helped Vertebrates Become So Stunningly Successful", Scientific American 12 Apr 2024. A new study in the journal Cell provides an answer to this long-standing puzzle: the genetic instructions to make myelin were slipped into our vertebrate ancestor's DNA by infection with a virus.
116. Jim Baggott (2024) 'Shut up and calculate': how Einstein lost the battle to explain quantum reality, Nature, ESSAY 25 April 2024.
117. Darwin wrote in the 4th edition of The Origin (1866): "and still more recently, that strange bird, the Archeopteryx, with a long lizard-like tail, bearing a pair of feathers on each joint, and with its wings furnished with two free claws, has been discovered in the oolitic slates of Solenhofen. Hardly any recent discovery shows more forcibly than this how little we as yet know of the former inhabitants of the world." And Darwin repeats this in the 6th en final editin (1876)! Darwin uses the name "Archeopteryx". See also: Richard G. Delisle, James Tierney (2022) Rereading Darwin. [6 Aug 2024]
118. Richard G. Delisle, James Tierney (2022) Rereading Darwin's Origin of Species: The Hesitations of an Evolutionist. They argue: "First, rather than absorbing himself in the fossil record, Darwin expends significant effort discounting it, listing numerous reasons as to why it is uninformative" (Chapter 3). "As surprising as it seems, Charles Darwin was only superficially committed to historical thinking ... the explanatory foundation of the Origin of Species is an essentially ahistorical view." (Chapter 3). [6 Aug 2024]