iDarwin AS 0020 (2020 AD)

Introduction of published bookiDarwin volume 0, pp. 24-29
Published on September 4, AS 0020 (2020 AD)
Darwin: An Introduction– Prospects for Modern Evolutionary Studies –Saitou Naruya
Population Genetics Laboratory, National Institute of Genetics (Main appointment)
School of Medicine, University of the Ryukyus
Department of Biological Sciences, Graduate School of Science, University to Tokyo
Department of Genetics, School of Life Science, Graduate University for Advanced Studies
1111 Yata, Mishima, 411-8540, Japan
Email: saitounr@nig.ac.jp
I published one book on Charles Darwin in 2011 in Japanese (Saitou, 2011; see Figure 1). Many books on Charles Darwin were published in 2009, inJapan too, to celebrate his 200th year anniversary. Chikuma Shobo editors approached me sometime in late 2008 and they asked me to write aboutDarwin. I published one booklet on Japanese three years before (Saitou, 2005) and it was sold well. I also published one textbook on genome evolution
one year before (Saitou 2007). Editors probably thought that I was appropriate to write about Darwin. I think they were right. I respect Darwin, and I
like history of sciences. However, I was so busy in those days, and could not complete my writing in 2009, and eventually my book on Darwin was
published two years later, in 2011. Darwin bicentennial fever was already over, and my book did not sell well. Three years later, in 2014, publisher
decided to cease distribution of printed book, though this book is still on sale as electric book.
My book about Darwin consists of eight chapters. In English, they are as follows:
Chapter 1: Darwin and his age
Chapter 2: Biology before Darwin
Chapter 3: Darwin’s evolutionary theory
Chapter 4: Other area studied by Darwin
Chapter 5: World view of Darwin
Chapter 6: Up and downs of Darwinism
Chapter 7: From selection theory to neutral theory24

iDarwin AS 0020 (2020 AD)
Chapter 8: Darwin in modern biology
Appendix: Explanation of basic concepts regarding organismal evolution
I will brie y explain contents of each chapter. Charles Darwin was born on February 12th,1809, and died on April 19th, 1882. He thus lived most of the 19th century. Therefore Chapter 1 starts
with sketch of that century. As mentioned in Saitou (2020), Abraham Lincoln was born on the same
day when Charles Darwin was born. Darwin published “On the Origin of species” in 1859 (Darwin,1859), however, most popular book in British Empire at that year was “Notes on nursing” written by
Florence Nightingale, founder of modern nursing. Section 2 of Chapter 1 is about Darwin’s relatives,
particularly Erasmus Darwin, paternal grandfather of Charles. Charles Darwin is now much morefamous than his grandfather Erasmus, however, Charles was only known to be one grandson of thatfamous Erasmus Darwin when Charles was young. In fact, this was major reason that Robert
FitzRoy, Captain of H.M.S. Beagle, invited Charles for dinner every day on that ship. JosiahWedgwood, founder of pottery company Wedgwood, was maternal grandfather of Charles. RobertDarwin, father of Charles, was medical doctor. Robert was taller than Charles with 185cm and waspretty heavy, often more than 150kg. Francis Galton, who invented correlation concept and manyother statistical analyses, was also grandson of Erasmus Darwin, though his paternal grandmotherwas different from that of Charles Darwin. Section 3 of this chapter is titled “Dropout of schooleducation”, followed by “Voyage of Beagle” in section 4, and “Returning to England until death” insection 5. Life of Charles Darwin is well known, and I do not go into detail.
Chapter 2, titled “Biology before Darwin” has following seven sections; Until Renaissance,
Natural History and Taxonomy, Developments of other areas of biology, Geology, Evolutionary
thoughts before Lamarck, Evolutionary thoughts after Lamarck and before Darwin, and Evolutionary
thoughts in Japan during Edo Period. Development of biology is also well studied and many books
were published in English, so I only introduce three Japanese mentioned in section 7. First one isFigure 1. Cover of Saitou (2011)
Kamata Ryuou (1754-1821), medical doctor and philosopher. In his book published in 1822, after he died,he clearly mentioned both organismal evolution and evolution of universe. Second one is Ninomiya
Takanori (1787-1856), who is famous as social reformist. Third one is Matsumori Takeyasu (1825-1892), who worked as high rank samurai in
Yamagata Prefecture, but also was naturalist. It is not clear how these three individuals reached evolution concept. But at least it is clear that in Japan,
organismal evolution was naturally accepted by some naturalists.
Chapter 3, titled “Darwin’s evolutionary theory”, is explanation of his “Origin of Species”. This book is pretty well known for many people, soI only mention my comment on epigraphs. In rst edition, Darwin cited sentences from works of two famous English writers, his contemporary W.
Whewell (1794-1866) and Francis Bacon (1561-1626), probably most famous philosopher in 17th Century England.

fifl25

iDarwin AS 0020 (2020 AD)"But with regard to the material world, we can at least go so far as this—we can perceive thatevents are brought about not by insulated interpositions of Divine power, exerted in eachparticular case, but by the establishment of general laws."
W. Whewell: Bridgewater Treatise.
"To conclude, therefore, let no man out of a weak conceit of sobriety, or an ill-appliedmoderation, think or maintain, that a man can search too far or be too well studied in the bookof God's word, or in the book of God's works; divinity or philosophy; but rather let men
endeavour an endless progress or pro cience in both."Bacon: Advancement of Learning.
Second edition was published in January 1860, less than three months later after publication of rst edition. Darwin now added one more epitaph by
Joseph Butler (1692-1752).
"The only distinct meaning of the word 'natural' is stated, xed, or settled; since what isnatural as much requires and presupposes an intelligent agent to render it so, i.e. to effect it
continually or at stated times, as what is supernatural or miraculous does to effect it for once."
Butler: Analogy of Revealed Religion.
All these three sentences are from natural theology thinkings. Thus some people argued that Darwin believed or tried to behave to believe in naturaltheology. I doubt it. In contrast, he found some logic, even in natural theology, that he can agree with. Addition of sentences by Butler, who wereactive in 18th century, can be considered to be inserted between 17th century Bacon and 19th century Whewell. I guess Darwin wanted to show
gradual deepening or even “evolution” of human’s philosophical thoughts during three centuries, and he implicitly suggested that he is following thistrend.
Chapter 4, titled “Other area studied by Darwin” rst list 19 books he published during his life. I mentioned his books related to Voyage ofBeagle, classi cation of Barnacles, and study of plants. I skip them and would like to brie y mention about his trial for searching principles of heredity.
In his “The different forms of owers on plants of the same species” published in 1877, Darwin used primrose and focused on discrete characters suchas length of styles. Unfortunately, Darwin did not have clear hypothesis on principles of heredity unlike Mendel, and he also did not understand law oflarge numbers. He produced only less than 300 primrose seeds, and did not reach that famous 3:1 ratio discovered by Mendel.
Chapter 5, titled “World view of Darwin”, starts from world views before Darwin or Darwinian revolution. In Europe, it was simply based onChristianity. However, there were already some preludes to non-Christian thinking, such as Immanuel Kant (1724-1804), who proposed origin of Solarsystem from interstellar clouds and Georges-Louis Buffon (1707-1788) who published “Histoire Naturelle”. In this sense, Darwin showed up inappropriate timing. Second section of this chapter is “In uence from surrounding people”. Charles contended in his autobiography (Darwin, 1958) that
he was not in uenced from “Zoonomia” written by Erasmus Darwin, paternal grand father of Charles. However, Charles also became atheist asErasmus was, as well as Elder brother of Charles, Erasmus. In contrast, Emma, wife of Charles, was devout Christian. She did not like Charles notattending Church. Last section of this chapter was “Incomplete Darwinian revolution”. Darwin was great for clearly showing evidence of organismal

fi

flfi

fi

flfi

flflfi26

iDarwin AS 0020 (2020 AD)
evolution, including human evolution. However, he was stuck in main evolutionary mechanism, for he pushed his favorite “natural selection”. Bothnatural theology and his natural selection assume that organisms are so adapted to this world. This view is now known to be wrong, as we will see inlater chapters of this book.
Chapter 6, titled “Up and downs of Darwinism” is now dealing with developments of evolutionary studies mainly after Darwin. Moritz Wagner(1813-1887), contemporary of Darwin, pointed out importance of geographical isolation as cause of speciation. This idea is now well established, but
surprisingly, speciation was assumed to be driven by natural selection for many years. August Weismann (1834-1914) was proponent of germ-line
theory that rejects inheritance of acquired characters. He also proposed “Neo-Darwinism” in which only natural selection is mechanism for evolution.
Genetics was established after “rediscovery” of Mendel’s laws of heredity in 1900. DNA was discovered as material basis of heredity in 1940s, anddouble-helix structure of DNA was proposed in 1953. Importance of mutations in evolution was rst clearly demonstrated by Hugo de Vries(1848-1935), and Thomas Morgan (1866-1945) also supported this idea with combination of elimination of detrimental mutations through negative
selection. Therefore, Darwin’s natural (positive) selection theory was almost rejected in early 20th Century. Unfortunately, natural (positive) selection
was resurrected by emergence of population genetics theory established by J. B. S. Haldane (1892-1964), R. A. Fisher (1890-1962), and Sewall Wright(1889-1988) during 1920s and 1930s. But new data emerged from biochemistry; amino acid sequences of proteins. Emile Zuckerkandl (1922-2013)
and Linus Pauling (1901-1994) discovered approximate constancy of amino acid changes, and they nicknamed this phenomenon as “molecularclock” (Zuckerkandl and Pauling, 1965). This and other new molecular data brought molecular evolution as mainstream of modern evolutionary
studies from 1960s.
Chapter 7, titled “From selection theory to neutral theory”, describes paradigm shift from Darwin’s natural selection theory to Kimura’s neutraltheory. Motoo Kimura (1924-1994) was already famous for his theoretical studies on population genetics. He was Neo-Darwinist until he faced aminoacid sequence data. He realized that substitution rates of protein amino acids are too high if we assume these changes are solely governed by Darwinian(positive) natural selection (Kimura, 1968). It was Kimura (1983) who coined “positive selection” (Darwinian selection) and “negativeselection” (purifying selection). Kimura’s neural theory was supported by DNA sequence data too. Interested readers may read Saitou (2018) on neutralevolution at DNA and genome levels. Kimura in uenced many Japanese researchers who were interested in evolutionary studies. Yasuda Norikazu,
Ohta Tomoko, Maruyama Takeo (1936-1987), Takahata Naoyuki, Yamazaki Tsuneyuki, Aoki Ken-ichi, Tajima Fumio, Tachida Hidenori, and Takano
Toshiyuki once belonged to Division of Population Genetics at National Institute of Genetics. This laboratory was renamed as Population Genetics
Laboratory in January 2020, and I (Saitou) is professor there. Masatoshi Nei was also in uenced by Kimura, and became one of most well-known
neutralist. NEI produced many Japanese Ph.D.s including Tateno Yoshio, Tajima Fumio, Ota Tatsuya, Takezaki Naoko, and myself. Many Japanese
researchers also worked at Nei laboratory as postdoctoral fellows. They include Gojobori Takashi, Takahata Naoyuki, Goto Osamu, Tamura Koichiro,Suzuki Yoshiyuki, Ito Tsuyoshi, Nozawa Masafumi, Misawa Kazuharu, and Katsura Yukako.
Chapter 8, titled “Darwin in modern biology” is nal chapter of this book. There are eight sections in this chapter. Section 1 is “Naturalselection under evolution of organisms cultivated by human”. This section discusses arti cial selection, in which positive Darwinian selection isexpected to occur. This is because humans carefully choose organisms for their own purposes; humans are gods for these organisms, and both positive
and negative selection occur under this situation. I mentioned about genetic changes in rice and silkworm. Section 2 is “Darwinian natural selection
really observed in nature”. Molecular evidences of positive Darwinian selection was explained for in uenza virus spike proteins reported by Gojobori
Takashi’s group and for one portion of HLA proteins whose function is to grasp foreign antigens such as corona virus spike proteins reported byfi

flfi

flfi

fl27

iDarwin AS 0020 (2020 AD)
Masatoshi Nei’s group. However, relationship between host immune system and infectious disease is special case of evolution, and any change is
acceptable in extreme case. Therefore, there is no “improvement” in this circular system. In contrast, optimum pH changes of stomach lysozymes invarious mammalian species may be considered to be “improvement” or adaptation to new environment for this enzyme, when this enzyme started to be
expressed in stomach where HCl, strong acid, is extracted. After publication of this book in 2011, our group found that common ancestral sequences oflineage speci c conserved noncoding sequences seem to experience nucleotide substitutions whose rates were higher than mutation rate (Saber et al.
2016; Saber and Saitou 2017). This suggests that evolutionary conservation started after lineage speci c nucleotide sequences emerged throughDarwinian positive selection.
Sections 3-7 of Chapter 8 was “Geology and paleontology”, “Sociobiology”, “Molecular phylogeny”, “Origin of Life”, and “Humanevolution”. Last section 8 was “In uence of <Darwin>”, and Darwinian medicine was mentioned here. This section ends with comparison of twowords in Google; Darwin and Beatles. “Darwin” appeared 60 million and more times, while “Beatles” appeared 90 million and more times. I justchecked again these two words. Now, as of September 1, 2020, “Darwin” appeared ~165 million times, while “Beatles” appeared ~214 million times.
Darwin is now much closer to Beatles! I am very happy to know this result, for we started new journal iDarwin this year (Saitou 2020).
References
Charles Darwin (1859) On the origin of species by means of natural selection, or the preservation of favoured races in the struggle for life. London: John Murray. Web: http://darwinonline.org.uk/content/frameset?itemID=F373&viewtype=text&pageseq=1
Charles Darwin (1958) The Autobiography of Charles Darwin 1809-1882 (Nora Barlow ed.). Collins, London. Web: http://darwin-online.org.uk/content/frameset?
pageseq=1&itemID=F1497&viewtype=side
Kimura Motoo (1968) Evolutionary rate at the molecular level. Nature 217, 624–626.
Kimura Motoo (1983) The neutral theory of molecular evolution. Cambridge University Press, Cambridge.
Florence Nightingale (1859) Notes on nursing: what it is, and what it is not. London: Harrison.
Morteza Mahmoudi Saber, Isaac A. Babarinde, Nilmini Hettiarachchi, and Saitou Naruya (2016) Emergence and evolution of Hominidae-speci c coding and noncoding genomicsequences. Genome Biology and Evolution, vol. 8, pp. 2076-2092.
Morteza Mahmoudi Saber and Saitou Naruya (2017) Silencing effect of Hominoid highly conserved non-coding sequences on embryonic brain development. Genome Biology andEvolution, vol. 9, no. 8, pp. 2037-2048.
Saitou Naruya (2005) Japanese viewed from DNA. Chikuma Shobo, Tokyo (written in Japanese).｛斎藤成也 (2005)『DNAから見た日本人』. ちくま新書525. 筑摩書房.
Web = https://www.chikumashobo.co.jp/product/9784480062253/.｝
Saitou Naruya (2007) Introduction to Evolutionary Genomics. Kyoritsu Shuppan, Tokyo (written in Japanese).｛斎藤成也 (2007)『ゲノム進化学入門』. 共立出版.｝
Saitou Naruya (2011) Darwin: An Introduction – prospects for modern evolutionary studies –. Chikuma Shobo, Tokyo (written in Japanese).｛斎藤成也 (2011)『ダーウィン入門‒‒現代進化学への展望』. ちくま新書892. 筑摩書房. Web = https://www.chikumashobo.co.jp/product/9784480065971/｝
Saitou Naruya (2018) Introduction to Evolutionary Genomics Second Edition. Springer.
Saitou Naruya (2020) iDarwin: Quixotic idea? iDarwin, volume 0, pp. 1-6.
Emile Zuckerkandl and Linus Pauling (1965) Evolutionary divergence and convergence in proteins. In V. Tyson and H. J. Vogel eds. “Evolving Genes and Proteins”, pp. 97-166.
Academic Press, New York.

fifi

flfi

28

iDarwin AS 0020 (2020 AD)===========================================================================================================Publication history of this article
September 4, AS 0020: this article was published in iDarwin.
May 14, AS 0022: Following revision of the publication style of iDarwin (see Saitou [0022]), last names were no longer capitalized. Some additional
editorial changes were also made.

29