What exactly did Lynn Margulis contribute to science?

Lynn Margulis (wiki)

In my previous blogpost I remarked that Lynn Margulis deserved a Nobel prize for her endosymbiosis theory. This triggered a comment essentially denying the scientific merits of Lynn Margulis for evolutionary biology. It was claimed that Margulis was not the first to propose a symbiosis theory for the origin of mitochondria and chloroplasts and that she did not provide the DNA evidence. Here I provide evidence that during the critical 1960s and 70s mainstream science rejected and ridiculed the endosymbiosis theory and cytoplasmic heredity, whereas Margulis was defending this. Finally, I discovered two publications proving that she did publish DNA evidence.

Priorities, predecessors and prejudices

Indeed, there were predecessors of the symbiosis theory. However, previous publications were not generally known or, when they were noticed at all, they were ridiculed. For example, American biologist Ivan Wallin published in 1927 the book 'Symbionticism and the Origin of Species' proposing his version of the symbiosis theory. Unfortunately, "The reviews were so scathing that Wallin withdrew from scientific discourse. (...) To mainstream biologists, Wallin was little better than a crank." [1]. And according to wikipedia "Wallin and his works were largely forgotten, until Lynn Margulis introduced a more complete endosymbiotic theory with better evidences in 1967." [12].

Further, the Russian biologist Merezhkovsky "proposed that the organelles [chloroplasts] are actually cyanobacteria that took up residence in an early ancestor of plant cells. (...) That scenario was ignored or flatly rejected." (...) "But in 1966 decisive evidence for the validity of his proposal about mitochondria came with the discovery that these organelles have their own DNA." [2].

Additional evidence: the website 'Understanding Evolution' states: "Biologist Lynn Margulis first made the case for endosymbiosis in the 1960s, but for many years other biologists were skeptical. (...) Why should we think that a mitochondrion used to be a free-living organism in its own right? (...) Based on decades of accumulated evidence, the scientific community supports Margulis’ ideas: endosymbiosis is the best explanation for the evolution of the eukaryotic cell." [3].

Continuing from the same website:

"When one of her [Margulis] professors saw DNA inside chloroplasts, Margulis was not surprised. After all, that’s just what you’d expect from a symbiotic partner. Margulis spent much of the rest of the 1960s honing her argument that symbiosis was an unrecognized but major force in the evolution of cells. In 1970 she published her argument in the book The Origin of Eukaryotic Cells." [4].

Three big bangs that made genetics

Next, we need to place Margulis in the context of the history of genetics. In 1900 the rediscovery of Mendel made the first big bang in the biological sciences. The second was no less important: the identification of chromosomes as the physical location of Mendel's hypothetical factors. At the time this was called the Boveri–Sutton chromosome theory or the chromosome theory of inheritance. Nobody knows those name anymore. And it isn't a theory anymore. But it is an essential and necessary step in the construction of genetics as a science because the theory 1) located the hypothetical Mendelian factors on chromosomes, 2) showed elegantly that Mendels pairs of factors corresponded with pairs of chromosomes (homologous chromosomes). Amazingly, Mendel's theory predicted that we are all diploid creatures! Mendel never knew. The third big bang happened a decade before Margulis was trained as a biologist (1960s). That was the publication of the chemical structure of DNA by Watson and Crick in 1953. With a big bang molecular genetics became the most successful theory in the biological sciences. Together these 3 big bangs made genetics the most successful discipline within the biological sciences. Don't underestimate the feeling of triumph.

What is the relevance of all this? The relevance of these three discoveries for my argument is that chromosomes are located in the nucleus of the cell. In other words: 'genetics' was synonymous with chromosomal based heredity or nuclear heredity. This was the status of biology in the 1960s. Margulis was working in the shadow of mainstream nuclear genetics. She stubbornly decided to study extra-chromosomal inheritance or 'cytoplasmic heredity'. It is called 'cytoplasmic heredity' because mitochondria and chloroplasts are located in the cytoplasma of the cell. It was opposed to mainstream genetics in no less than 3 ways: non-chromosomal, non-nuclear (outside the nucleus or extra-nuclear) and non-Mendelian heredity. Cytoplasmic heredity was considered unimportant or controversial by the majority of geneticists. For example, Margulis quotes the Drosophila geneticist and Nobel Prize winner Thomas Hunt Morgan: 

"From the point of view of heredity, the cytoplasm of a cell can safely be ignored." [5] 

Margulis commented: "I considered it an arrogant oversimplification." I agree. In general it is 'amusing' and instructive to browse through old genetics textbooks to get a feeling of the thinking at the time [14]. Everybody knew that heredity was exclusively located in the nucleus of eukaryotes. It was an established truth. It wasn't even called 'nuclear genetics' or 'nuclear genes', because everybody knew that the hereditary material was located in the nucleus! 

Illustrative for the status of science is the statement of John Jinks (1964) in his monograph Extrachromosomal inheritance: 

"There have been increasingly persistent claims that DNA is present in structures such as plastids and mitochondria." [10]. 

 Please note that 'claims' means not proven ideas.

In A History of Genetics the genetics pioneer A.H. Sturtevant (1965) wrote: 

Sturtevant 1965
A History of Genetics

"Quite recently it has been found that there is DNA in plastids and at least some mitochondria. ... It may therefore be supposed that these bodies carry genes of the same nature as those in the chromosomes" [6]. 

It must have been a disturbing discovery for those unaware of the symbiosis theory. See for example what historian of science Jan Sapp wrote:

"The symbiotic theory of eukaryotic organelles attracted criticism from many sides during the 1970s. Crucial evidence was lacking. ... Leading cell biologists also argued that theories about eukaryotic cell origins were unscientific because they could not be proven." (!) [7]. (my emphasis)

That was how biologists used to think at the time. In 1972 Tribe and Whittaker wrote in their monograph Chloroplasts and Mitochondria:

"Up until the last few years, it was generally assumed that the total information necessary for the synthesis of a cell resided in the DNA of the nucleus." [8].

Indeed! Remarkably, at the time it was uncertain whether mitochondria and chloroplasts could divide at all, or whether they were synthesized de novo (from scratch). It was also a problem how much of the DNA in mitochondria and chloroplasts was functional at all and, if functional, what role it played. Furthermore, the authors point out two major objections to the symbiotic theory [9]. So, my point is that one should not ignore the status of biology at the time Margulis was working.

DNA evidence!

The blog commenter also claimed that Margulis did not provide DNA evidence for the symbiosis theory. This is not correct. I discovered an ignored publication: 

L. Sagan (1961) Evidence for cytoplasmic DNA in Euglena gracillis [11] in the  Journal of Protozoology. 

This publication is not listed in the Lynn Margulis wikipedia page. Unfortunately, google scholar returns the title only, not the contents, not even an abstract. However, the title is revealing [12]. The most reliable and exemplary demonstration of DNA in plastids is given by S. Nass and M.K. Nass (1963) [13]. From the fact that they perform extensive control experiments, it is clear that they are aware that extraordinary claims require extraordinary evidence. They wanted to exclude any contamination with nuclear DNA or other false positives. At the time these authors were not interested in evolutionary explanations and did not interpret the DNA as evidence for symbiosis theory. They were busy unraveling the structure and function of cellular organelles. No time for speculation. This shows that the discovery of DNA in mitochondria occurred independent of the symbiosis theory. On the other hand knowledge of the symbiosis theory would be an excellent reason to search for DNA in mitochondria. Nass & Nass came incredibly close to the discovery of an evolutionary symbiosis theory with this quote : "a structure homologous with the mitochondrion is the entire bacterial cell." That statement is still not a symbiosis theory. The most far-reaching conclusion they dared to draw was:

"In any case, the presence of D N A in mitochondria appears to require modification and extension of some generally accepted hypotheses of cell function which consider the nucleus to be the exclusive site of cellular D N A and genetic information." [13].

Indeed. Clearly, the authors doubted a well established truth. It was the first step towards a symbiosis theory. Lynn Margulis devoted herself to developing a comprehensive symbiosis theory.

Principles of Population Genetics

'Symbiosis' is still a sensitive subject. A stunning demonstration is the textbook Principles of Population Genetics [15]. Many pages are devoted to describing all genetics aspects of mitochondrial DNA (mtDNA) and chloroplast DNA (cpDNA). And those aspects are without doubt useful for understanding certain aspects of evolution. However, endo-symbiosis is never mentioned. It is not that mitochondria are absent. It is not that mitochondrial DNA is absent. No. It is the word 'Symbiosis' that is absent. It doesn't occur in the index. I find that really baffling. Is symbiosis so far beyond the scope of population genetics? It seems symbiosis does not fit in the theory of population genetics. Could it be that the origin of mitochondria and chloroplasts can not even be described by the most advanced mathematical population genetic models? If true, than it clearly shows the limits of population genetics for understanding all the facts of evolution of life on earth. Symbiosis is not a rarity [19].

A second paper of DNA evidence by Lynn Margulis is:

L Sagan, Y Ben-Shaul, HT Epstein, JA Schiff (1965) 'Studies of chloroplast development in Euglena. XI. Radioautographic localization of chloroplast DNA', Plant physiology 1965 Nov;40(6):1257–1260. (pdf). (Note: at the time Lynn Margulis published under the name L. Sagan because she was married with Carl Sagan.)

This publication does not occur in wikipedia either. The authors conclude that chloroplasts (like mitochondria) contain DNA and RNA; they are self-duplicating bodies which do not arise de novo; the DNA represents a multigenic hereditary system which is not derived from the nucleus and is, in part, responsible for the biochemical properties of the organelle. In her 1967 paper On The Origin of Mitosing Cells she made the prediction that all eukaryotes should contain mitochondrial DNA and all eukaryotic plants should contain chloroplast DNA. Also in that 1967 paper she refers to  (Sagan, L., 1964, unpublished data) [16]. 

We should not be surprised that Margulis worked on DNA evidence! Her thesis was: 'An Unusual Pattern of Thymidine Incorporation in Euglena', 1965 (mentioned in wikipedia). The abstract can be found in the The Journal of Protozoology (published under the name Lynn Sagan). Although the results are confusing and inconclusive, the thesis shows that she used techniques to detect DNA in the cytoplasm. (Thymidine is a component of DNA).  Interestingly, in the References of her thesis I found 3 other publications with L. Sagan as author:

14. Sagan, L. & Scher, S. 1962. Cytoplasmic incorporation of H3-thymidine in Euglena gracilis. J. Protozool. 8, Suppl. 20.
15. Plaut, W. & Sagan, L. A.*) 1958. H3-thymidine incorporation into the cytoplasm of Amoeba. (pdf) J. Biophys. Biochem. Cytol.**) 4, 843–7.
      *)  Lynn Petra Alexander Sagan Margulis (1938-2011)
    **) "Content prior to 1962 was published under the journal name The Journal of Biophysical and Biochemical Cytology."
16. Sagan, L., Ben-Shaul, Y. & Schiff, J. A. 1964. Radiographic localization of DNA in the chloroplasts of Euglena. Abstracts of the 4th Annual Meeting of the American Society for Cell Biology, Cleveland, Ohio.

These three publications do not occur in Wikpedia.The publications prove that Margulis started working on DNA in 1958 or earlier. That is 5 years earlier than Nass & Nass (1963) [18].

Conclusion

The claim that Margulis was not the first to propose a symbiosis theory is right. However, that is not the point. The point is that the symbiosis theory was disregarded at the time when Margulis started working on the subject. The evidence presented here shows that it was risky and unpopular to study and publish about the symbiosis theory during the 1960s and 1970s. Margulis (1967,1970) elaborated the theory and provided enough initial evidence to justify further research into the theory. Furthermore, I showed that the claim that she did not come up with DNA evidence is wrong. She produced 5 - 6 publications. The symbiosis theory provided a correct evolutionary explanation for why there is DNA in mitochondria and chloroplasts.

Now we have reached this conclusion, it is useful to compare Darwin and Margulis. Darwin did not prove his theory in 1859. Neither was he the first to propose a theory of evolution. And his theory was very controversial at the time. But, Darwin provided enough reasons for his contemporaries to take the theory serious. Subsequent generations of biologists have shown that the theory was indeed worth investigating and came with abundant evidence. It is now an accepted theory. The same holds for the endosymbiosis theory.

I am not the only one with a positive assessment of the contribution of Lynn Margulis to the theory of evolution. For example Michael Ruse and Joseph Travis [17] wrote:

"But it was Margulis who took up the idea, now known as the endosymbiotic theory, offered microscopic evidence, and pushed it (in her book Origin of Eukaryotic Cells, 1970) until it became orthodoxy.".

And the architects of the Evolutionary Synthesis wrote:

"The most complete hypothesis is that of Margulis (1970), who has marshalled a great wealth of morphological, biochemical, and paleontological facts ... ". [20].

Notes

1. Lynn Margulis, Dorion Sagan (1997) Slanted Truths chapter 4, page 50.  
2. Lynn Margulis, Dorion Sagan (1997) Slanted Truths, chapter 3, page 38.
3. Website Understanding Evolution page 'Evidence for endosymbiosis' of the Berkeley museum of paleontology. (by the way, very good website!)
4. The full title: Origin of eukaryotic cells;: Evidence and research implications for a theory of the origin and evolution of microbial, plant, and animal cells on the Precambrian earth (1970) Yale University Press. (still available at amazon). See also: the website Understanding Evolution page Endosymbiosis: Lynn Margulis
5. Lynn Margulis (1998) The Symbiotic Planet. A new look at evolution, hardback, page 22.
6. A.H. Sturtevant (1965) A History of Genetics page 125 chapter 19 'Maternal Effects'. Sturtevant refers to: Gibor and Granick (1964) Science 145: 890-897. This publication is also referred to by Margulis (1967). 
7. Jan Sapp (2003) Genesis. The Evolution of Biology. page 246.
8. Michael Tribe, Peter Whittaker (1972) Chloroplasts and Mitochondria. page 54.
9. idem page 57.
10. John L. Jinks (1964) Extrachromosomal inheritance. Prentice-Hall. p.89. Dutch: John L. Jinks (1968) Extrachromosomale erfelijkheid. Het Spectrum. paperback, pagina 132. He did not refer to publications. 
11. Sagan, L, Evidence for cytoplasmic DNA in Euglena gracillis, Journal of Protozoology 8 4: 20 (1961). Euglena is a single-celled eukaryote. 
12. I found the publication via the references in Lynn Sagan (1967) On the origin of mitosing cells (her first publication. It is a large, complex, wide-ranging publication). She writes: "A plethora of recent studies elegantly reviewed by Gibor & Granick": A. Gibor and S. Granick (1964) Plastids and Mitochondria: Inheritable Systems: Do plastids and mitochondria contain a chromosome which controls their multiplication and development? Science 28 Aug 1964. Only the Abstract is available, but, amazingly, I discovered in the References of G&G: "L. Sagan (1961)" [11].  
13. S. Nass and M.K. Nass (1963) Intramitochondrial fibers with DNA characteristics. II. Enzymatic and Other Hydrolytic Treatments. J Cell Biol 1963 Dec 1;19(3):613–629. A pdf is available.
14. For example the genetics textbook Srb, Owen, Edgar (1965) General Genetics, Second edition, hardback, which I still have on my bookshelf, contains a chapter 'Extrachromosomal and Epigenetic Systems'. That is great. But browsing through the pages reveals that the most important criterion for extrachromosomal inheritance is simply that it does not obey the laws of Mendel and must be located in the cytoplasma. Mitochondria and chloroplasts are mentioned, but at the time it was impossible to prove that these organelles contain DNA. It was an open question whether extrachromosomal heredity relies on 'coded information'. "Extrachromosomal heredity has reality, and manifests itself in almost bewildering variety." (p.345). There is no mention of '(endo)symbiosis'. How amusing and useful a little time travel can be!
15. Hartl & Clark (1997) Principles of Population Genetics, third edition. Sinauer Associates. hardback. 
16. "This is quite analogous to the presence of two distinct DNA bands of nearly equal size found in CsCl density gradient runs on DNA isolated from Paramecium bursaria (Sagan, L., 1964, unpublished data). 
17. Michael Ruse, Joseph Travis (2009) Evolution. The First Four Billion Years,  Harvard University Press, hardback, 979 pages. page 712-713. This is just one example. The influential evolutionary biologist John Maynard Smith recognized her contribution to science; see my review of Lynn Margulis.
18. This paragraph was added 14 Mar 2025. See for a summary of the first attempts to demonstrate cytoplasmic DNA: William A Wells (2005) There's DNA in those organelles J Cell Biol. 2005 Mar 14.
19. Nancy A. Moran (2025) 'Symbiosis. A Very Short Introduction', Oxford University Press. 192 pages. "The majority of evolutionary biologists continue to regard symbiosis as a marginal process that can mostly be disregarded."  15 Mar 2025
20. Dobzhanksy, F.J. Ayala, G.L. Stebbins, J. Valentine (1977) 'Evolution', W H Freeman and Company. hardback. page 383–389. The book is a comprehensive overview of the theory of evolution as it was at that time. 17 Mar 2025
    

My top 20 evolution books. 12 February 2025

Darwin Day 12 February 2025

Last year population geneticist Zach Hancock made a video 10 most influential papers on evolution. His list is a personal list and reflects his areas of research: Population Genetics and Molecular Evolution. Although this covers a large part of what is called 'Evolutionary Biology' today, my own list would be significantly different. However, I hadn't made such a list yet. When a visitor of my website asked whether I could produce  my own top-20 books, I decided that after 20 years of devouring books that have 'evolution' or 'Darwin' in the title, it was about time!

Surprise: this requires some additional thinking! What are the most important books? Choices have to be made. Perhaps the biggest difference with Hancock's list and with many of the popular evolution textbooks is that I have sought to include books that place evolution in its planetary and cosmological context. Life happens on a planet, so this fact must show up in the evolution textbooks. Practically speaking, Evolutionary biology textbooks are aimed at biology students preparing for a job in biological research, mostly lab research, sometimes field work. Evolutionary biology has become a specialized field separated from related scientific disciplines such as ecology, geology, paleontology, climatology, cosmology and Earth System Science. But all these disciplinary borders are created for practical purposes only. Nature does not know these borders. They are artificial. They are created by humans [1].

An Evolution textbook should discuss questions such as: Why is the Earth a habitable planet? What are the necessary conditions? How likely is the origin of a planet suitable for life? (introducing astrobiology and Earth systems science). Does a habitable planet require a moon? Is a solar system like ours inevitable? Is a planet with oceans and continents necessary for complex life? Could complex life originate on a planet with only oceans or only continents? Does life require a geologically active planet with continental drift and vulcanism? Do we need a planet that is rotating around/on its axis? a tilted axis? an orbital period of one year? Does the earth have the right size for life or could it be significantly smaller or larger? What about the composition of the atmosphere? Assuming the Periodic Table of Elements, how many chemical elements are necessary for life? How likely is it that they are present on a planet in the right proportions? Which features of life are universal and which are earth-bound? Is the origin of life on the earth inevitable? Is life necessarily a far-from-equilibrium system? Is life necessarily cellular? Why DNA? Is DNA the only possible carrier of hereditary information? Why proteins? Is the DNA-protein system the only possible form of life? Could proteins be replaced with RNA? Why exactly this genetic code? Are there alternative genetic codes possible? Is the genetic code a 'frozen accident' or is it necessary or both? Is the genetic code earth-bound or truly universal? Is the universal genetic code the main proof of common descent of all life on earth? Is photosynthesis a necessary precondition for the evolution of animal life? Is the autotroph-heterotroph system necessary for the evolution of complex life? Is oxygen necessary for any form of life on any planet? What is the likelihood that life on earth has existed uninterrupted for 3,5 billion years without going extinct? Why did it take so long for life to invent multi-cellularity? Is multicellularity the most difficult transition in evolution? Is the soma-germline distinction (Weizmann) necessary for complex life? Must complex life necessarily be of the haploid-diploid system? Or could complex life be haploid? Is Mendelian heredity necessary for complex life? Is sex necessary? Is the prokaryote-eukaryote dichotomy necessary or could there be intermediates? Is complex life dependent on endosymbiosis? Or could evolution have developed alternatives for the energy production by our endosymbiotic mitochondria? Does the human species need exactly 46 chromosomes? Do humans require 25,000 protein-coding genes? Do we require 3.1 billion base pairs in our genome? Why do we have so much junk DNA? Are there alternatives for all these features? Combining the probability of all events in the history of the Earth, is the origin of 'intelligent life' inevitable? Does evolution need millions or billions of species in order to be able to create humans? Is natural selection, that is the differential reproduction of heritable variants, the only way to create (complex) life? Must 'intelligent life' necessarily be a warm-blooded mammal with internal fertilization and gestation?

Ideally, evolutionary biology textbooks should discuss these questions to inspire the students, to stimulate the imagination, to ask exciting new questions and to make evolution an attractive study. Furthermore, both biology students and evolution doubters alike must be confronted with the fact that 'Darwin' and 'evolution' stand for evolutionary processes lasting 4.5 billion years on planet Earth. That planet is part of a planetary system which itself has a history. And that this planetary system itself is part of a universe which itself has a history. So, Darwin-doubters and evolution-deniers should be made aware that the theory of evolution is not an isolated biological theory that could be denied or replaced without consequences for the rest of the scientific knowledge. Textbooks should not make the same error of teaching evolution in isolation.

"There is grandeur in this view of life,
with its several powers, having been originally breathed
into a few forms or into one; and that,
whilst this planet has gone cycling
on according to the fixed law of gravity,
from so simple a beginning
endless forms most beautiful and most wonderful
have been, and are being, evolved."
Charles Darwin

Surely, evolution textbooks are intended to prepare students for a research job in a biology department. Laboratory science is based on isolating organisms from the environment and from the whole earth system. But that is not a good reason for textbook authors to neglect the way in which evolution is connected with the earth as a system (geosphere, hydrosphere, atmosphere). The history of our planet shows that there were many geological disasters, resulting in several large extinctions, despite the fact that there is a continuous line of descent from the first forms of life to our own species. Students can not understand evolution if they don't understand why the earth is a habitable planet. Yes, in practice researchers have to specialize, they can't be allround scientists, but biology students should learn the essentials of the whole system. You can't have a scientifically correct worldview if it is restricted by the borders of your own scientific discipline. My choice of books is based on these criteria. A textbook that meets all these criteria doesn't exist, but taken together the following books come close to the perfect evolution textbook. They are listed here in no particular order:

1. John Maynard Smith & Eörs Szathmáry (1999) The Origins of Life. From the Birth of Life to the Origin of Language (review) is a popular version of The Major Transitions in Evolution (1995). The authors are authorities in the field of evolutionary biology and write in a logical and factual style. They focus on the central and often unsolved problems in evolutionary theory and discuss them in a way understandable for the non-professional reader. A really unique achievement.
   
2. Jerry A. Coyne (2009) Why Evolution Is True. We still need a book that focuses on the evidence for evolution without the technical details present in a standard textbook. I hope an updated edition will be published (and a separate chapter about common descent will be added).
   
3. S J Gould (2002) The Structure of Evolutionary Theory. (review). Not many people will want to read this intimidating book from page 1 to page 1433, but what he wrote about the logical structure of evolutionary theory is very useful (chapter 1,2,7).
   
4. Brian K. Hall and Benedikt Hallgrímsson (2008) Strickberger's Evolution, Fourth Edition and Fifth edition 2013. This textbook includes the planetary context and geological timescales. Compare with Stearns and Hoekstra below. Compare this with other textbooks on my Introduction page.
   
5. Mark Ridley (2000) Mendel's Demon. (review). A popular and educational account of the fact and consequences of the eukaryotic merger, uni-parental inheritance of mitochondria, Mendelian inheritance, sexual reproduction, error threshold, mutational meltdown. These are the fundamental issues in evolutionary biology. More important than Dawkins' Selfish Gene.
   
6. Nick Lane (2002) Oxygen. The Molecule that made the World. (blog). This work was an eye-opener for me. According to Lane, Oxygen made the existence of complex animals possible. More than that: he shows how life itself created a habitable planet. Absolutely crucial. Lane connects evolution, geology and biochemistry. Oxygen is a prime example of niche construction on a planetary scale. Amazingly, this fact is not reflected in the evolution textbooks. Quotes: "Viewing evolution through the prism of oxygen gives us some surprising perspectives on our lives and deaths. If water is the foundation of life, then oxygen is its engine. Without oxygen, life on Earth would never have got beyond a slime in the oceans, and the Earth would probably have ended its days in the sterility of Mars or Venus." p.340. "Oxygenic photosynthesis only ever evolved once" (p.145).
7. James Lovelock (1988) The Ages of Gaia. A Biography of our Living Earth. (review). Lovelock is important because he pointed out that the atmosphere of a planet harboring life is in a chemical disequilibrium. This is a signature of the presence of life on any planet. Again: one cannot have full understanding of evolution without its planetary context. Darwin didn't know this. Now, we do know. It's time this fact is included in the textbooks.
   
8. Lynn Margulis (2002) Acquiring Genomes. A theory of the origins of species (review). Margulis deserved the Nobel Prize for the theory of eukaryotic endosymbiosis. A revolution in biology. She is often ignored in the textbooks because of her criticism of neo-Darwinism. See my blog What exactly did Lynn Margulis contribute to science?
9. F. John Odling-Smee (2003) Niche construction. The neglected process in evolution (review). The reality of niche construction is undeniable. One can disagree about the extent, but not about its existence. Organisms do not passively adapt to their environments. Niche construction ought to be discussed in the evolution textbooks. Compare with Dawkins Extended Phenotype.
   
10. Stuart Kauffman (1995) At Home in the Universe (review). This theoretical biologist had a huge impact on my thinking. This book was published 30 years ago, but still important. Kauffman developed a theory about life and the origin of life build on first principles (auto-catalysis). He is a critic of the gene- and DNA-centered worldview of Neo-Darwinism.
    
11. Kevin W. Plaxco, Michael Gross (2006) Astrobiology: A Brief Introduction. The emphasis is on the 'biology' part of astro-biology. Putting life in its planetary and cosmic context. The best popular introduction with the proper amount of detail.
    
12. Paul Davies (1999) The Fifth Miracle. The Search for the Origin and Meaning of Life. Important chapter 'Against the tide" (chapter 2): "One of the principal ways in which life distinguishes itself from the rest of nature is its remarkable ability to go "against the tide" and create order out of chaos". Chapter 4: 'The message in the Machine' contains a superb explanation of the fundamental concepts "order", "organization", "entropy", "chance", "randomness", "information", "complexity". Particularly his insightful explanation of what it means that genomes contain information. Davies explains life in a way no biologist could have done.
    
13. Tim Lenton (2016) Earth System Science: A Very Short Introduction. Recommended introduction. Earth system science must be included in the evolution textbooks simply in order to understand why the earth has been a habitable planet for billions of years.
    
14. Stephen Stearns, Rolf Hoekstra (2005) Evolution. Second edition. I include this evolution textbook (now 20 years old) because of the treatment of 'The history of life' (83 pages) including a chapter 'Key events in evolution' and 'Major events in the geological theater'. Unfortunately no new edition has been published. Compare this with other textbooks on my Introduction page.
15. Ernst Mayr (1982) The Growth of Biological Thought. A conceptual and historical overview of Darwinism by one of the founders of neo-Darwinism. Very rich in content and complete. I learned a lot from this book. Very important is his identification of Darwin's Five Theories (page 505-510). A shorter version of this work is: One Long Argument. Charles Darwin and the Genesis of Modern Evolutionary Thought (1991).
16. Tibor Gánti (2003) The Principles of Life with commentary by James Griesemer & Eörs Szathmáry (review). His definition of life is superior. Based on first principles. Withstood the test of time. A standard by which all other definitions must be compared. It continues to have a fundamental influence on my thinking on what 'life' is and how the problem of the origin of life must be approached.
    
17. Sean Carroll (2001, 2004) From DNA to Diversity. Molecular Genetics and the Evolution of Animal Design. See also: Endless Forms Most Beautiful: The New Science of Evo Devo and the Making of the Animal Kingdom (2005). A beautifully illustrated popular exposition of evo-devo. Animal development is under genetic control, and genetic modifications create animal diversity.
    
18. Johnjoe McFadden (2021) Life Is Simple: How Occam's Razor Set Science Free and Shapes the Universe. Not about evolution. An illuminating history of science viewed from Occam's perspective. In a sense, Occam started the scientific revolution in the 14th century. Original. Very well written. A rewarding and entertaining read.
    
19. Edward Dolnick (2017) The Seeds of Life. (blog in Dutch). Evolution cannot be understood without a good understanding of sexual reproduction. The struggle to eliminate stubborn misconceptions about sex. What are the contributions of males and females to the next generation?
    
20. David Sedley (2008) Creationism and its Critics in Antiquity (review). Greek philosopher Epicurus was opposed to creationism and advanced a non-creationist explanation of adaptation. Paley argued against this Epicurean explanation. Darwin argued against Paley and strongly improved the Epicurean argument. Darwin in his historical and philosophical context.
    

Disclaimer: when a book is not on this list, it certainly doesn't mean it is unimportant! Very probably, it is on the Introduction page of my WDW website. If not, please leave a comment!

Finally, some books have wrong ideas, but nonetheless (or because of!) stimulated my thinking. Two of them are: 

Periannan Senapathy (1994) Independent Birth of Organisms. A New Theory That Distinct Organisms Arose Independently From The Primordial Pond Showing That Evolutionary Theories Are Fundamentally Incorrect. (review). This is an extreme DNA-centric view of life and the origin of life [1]. This book is wrong in unsuspected ways. Many problems are easy to find.  But, it took me many years to see the elephant in the room and formulate the most decisive argument against this theory. While unraveling the tangle of the facts and his arguments, I gained fundamental insights about the DNA-centric view of life, the origin of life and evolution in general. It showed me the best reasons why we need a theory of evolution!     

Michael Behe (1996) Darwin's Black Box. (review). Now nearly 30 years old. 'Irreducible Complexity' is an interesting potential falsifier of the theory of evolution by natural selection. According to Karl Popper, falsifiability is a requirement for a proper scientific theory. Michael Behe has been crucified over and over by the scientific community because he believes in Intelligent design. However, ID can safely be rejected without rejecting the idea of irreducible complexity as a potential falsifier. It highlights the fact the Darwinian gradualness has its challenges. It stimulated research in to seemingly irreducible complex biological systems in fruitful way.

Notes

1. "...if we want to create a synthesis, we must understand that evolution is not something that pertains exclusively to biology, but rather to all domains of reality. Nature knows nothing about disciplines." David Obon (2024) Evolution: the invention of creativity: a new unifying vision.
2. Craig Venter made in essence the same mistake as Senapathy. See also: František Baluška, Guenther Witzany (2014) Life is more than a computer running DNA software,  World J Biol Chem. (I think the authors didn't bring up the most important objection).
   

Why the standard definition of evolution fails

In a recent blog Larry Moran wrote:

"Recall that evolution is defined as a change in the frequency of alleles in a population and the main mechanisms of change are natural selection and random genetic drift."

and further:

"Symbiosis is a rare example of substantial change in the frequency of alleles in a population. It helps explain some of the changes we see in the history of life. It does not require a revision of population genetics."

The definition of evolution he uses is very restrictive and out-dated. It implies that Darwin's Origin of Species was not about evolution. Darwin simply did not know about "a change in the frequency of alleles". Poor Darwin! More importantly, the second quote above demonstrates what the consequences are of such a restricted definition: the outrageous misrepresentation of the eukaryotic endosymbiosis event. It is a gross distortion of what the Eukaryotic symbiosis entails. Endosymbiosis is the permanent incorporation of one complete genome of one species in a single cell of another species resulting in two different genomes in one cell (now called mitochondria and chloroplasts). This event has nothing to do with 'a change in allel frequencies'. This definition of evolution implies that the Eukaryotic symbiosis event is not evolution! However, the Eukaryotic merger is the single most important event in the history of life on Earth. Without it no animals and plants. Without mitochondria and chloroplasts we would not exist. They are crucial. If you stubbornly and dogmatically hold to an outdated definition, it can only result in the distortion of the facts. That is not science. 

The funny thing is the definition 'a change of gene frequencies in populations' does not occur in a textbook where one would certainly expect it, namely Principles of Population Genetics  [4]. But, no. It reads "By evolution we mean descent with modification". ! Darwin's definition.

There is more. Much more. What about speciation? That is: The Origin of Species! (the title of Darwin's breakthrough work). Speciation is certainly more than 'a change in frequency of alleles in a population'. The theory of evolution should explain why there are species at all. And how they originate. And why they don't merge into one species again ( reproductive isolation ), that is how the separateness and individuality of species is maintained. 

What about genome duplication ( polyploidy )? Polyploidy, or whole-genome duplication, is widespread in the plant kingdom, but also known in animals. Polyploidy occurs in invertebrates and vertebrates: flatworms, fish, amphibians, lizards. Polyploidy has arisen by a variety of mechanisms in a diverse array of animal taxa, covering nearly every major phylum (source). Susumu Ohno proposed that two rounds of polyploidy occurred early in vertebrate evolution (source). If anything is inappropriate to describe polyploidy than is certainly is 'the change of frequency of alleles in populations'.

What about Lateral Gene Transfer? That is:  the transfer of genetic material between organisms other than by the vertical transmission of DNA from parent to offspring. A change of gene frequency? No, it is a sudden increase of the genomic content of an organism.

What about deletions of (large) segments of DNA? What about chromosomal inversions? What about chromosomal translocations? What about chromosomal fusions? What about gene fusion? Let's focus on an important, but not well-known chromosome fusion in the human lineage. A fusion of two relatively small chromosomes in our ancestors created the human chromosome 2. This resulted in a reduction of the diploid number of chromosomes from 2n=48 to 2n=46 chromosomes. No significant loss of chromosomal material, but a significant event nonetheless. It defines the human species. It separates us from  the apes. 

The origin of chromosome 2 by fusion of two chromosomes (wikipedia)

human chromosome 2 lined up with chimpansee, gorilla, orangutan
For details see blog John Hawks

The diagram shows that the chromosome bands of two different chromosomes of chimpansee, gorilla, and orangutan precisely match human chromosome 2. Strong evidence of a fusion. This couldn't be further removed from 'a change in the frequency of alleles' [2].

What about structural variants in the human genome including cytogenetically detectable and submicroscopic deletions, duplications, large-scale copy-number variants, inversions and translocations? (source). It has been calculated that humans have more than 15,000 duplicated genes [3]. To describe each of them with 'a change of the frequency of alleles' would be a gross distortion. It ignores the creation of new genes.

What about the subject of Larry Moran's book: junk DNA? 90% of Your Genome Is Junk. Can the scandalous accumulation of so much junk DNA in the human genome be described in terms of 'a change of the frequency of alleles'? Which alleles? Anyway, can junk DNA be described in terms of alleles? Junk alleles? How do you define the begin and end of a junk allel? 

Futuyma & Kirkpatric

The definition of evolution in the most recent evolution textbook:

"Biological evolution is inherited change in the properties of groups of organisms over the course of generations". Futuyma and Kirkpatric (2023) page 9.

It's immediately clear that 'alleles' or 'genes' are not mentioned in this definition. It's all about inherited phenotypic properties of groups of organisms [1].

Let me quote the famous evolutionary biologist Ernst Mayr:

"It is simply not true that evolution can be explained as a change in gene frequencies." Mayr points out that this definition fails to explain "the multiplication of species, the origins of evolutionary novelties and higher taxa, and the occupation of new adaptive zones." (Ernst Mayr, William Provine (1998) The Evolutionary Synthesis, Prologue page 12.)

Blindness for chromosomal location of alleles

The definition of evolution as "a change in the frequency of alleles in a population" is blind for the location of an allel on a chromosome. Suppose, a gene moves from chromosome A to chromosome B without changing its sequence. So, there is no change in the frequency of the allel. A population geneticist would not note any difference. A cytogeneticist however would note a difference. This migration of genes from one chromosome to another has happened during evolution of the Y-chromosome. By one estimate, the human Y chromosome has lost 1,393 of its 1,438 original genes over the course of its existence (the wikipedia Y-chromosome page is of high quality). There is evidence that genes located on the Y-chromosome have been relocated to autosomes (source). There is also evidence that during evolution genes moved from mitochondrion to the nucleus. These migrations, although evolutionarily important, do not show up as a change in the frequency of alleles of a species. In fact any change in the chromosome complement of a population or a species (for example a reciprocal translocation) would and could not be noticed as a change in gene frequency. This idea could be further elaborated. [paragraph added 4 Feb 2025] 

Notes

1. This definition is compatible with all chromosomal rearrangements mentioned in this blog because they are inherited. For example, the fusion that created human chromosome 2 is inherited. In a sense it is the phenotype (appearance) of the karyotype. The karyotype is different from the DNA sequence. The karyotype is the way how the total of DNA is distributed over the chromosomes. [6 Feb 2025]
2. A very nice illustration of the role of chromosomes in reproductive isolation see: Rapid chromosomal evolution in island mice, Nature 13 January 2000. [7 Feb 2025]
3. Jianzhi Zhang (2003) Evolution by gene duplication: an update, TRENDS in Ecology and Evolution Vol.18 No.6 June 2003. [7 Feb 2025]
4. Daniel Hartl, Andrew Clark (1997) Principles of Population Genetics, third edition, hardback. Preface.  [10 Mar 2025]