Just as organisms evolve, so too, do societies and iPhones evolve.  But what about the theory of evolution?

Has  Darwin’s theory of evolution evolved?

Evolution happens. We have mountains of fossils and terabytes of genomic data to prove that life evolves.

Yet what exactly happened?  Which ancient creature was the ancestor of which current species?  How do new traits appear?   To answer these questions, scientists propose  different theories to describe details about how evolution occurs.

Many people assume that the theory put forth by Darwin in Origin of Species is the final say on evolutionary theory. Biologists, however, know that the theory of evolution has evolved over time.  For example,  evolutionary theory dramatically changed when Darwin’s original ideas were merged with ideas from genetics to become the Modern Synthesis.  Evolution textbook author, Douglas Futuyma, presents a wonderful slideshow available on Youtube demonstrating the emergence of the Modern Synthesis.

Yet what most people don’t realize is the theory of evolution has progressed way beyond the Modern Synthesis.  Failure to recognize this new unfolding theory and the many recent discoveries in support of it has caused a great deal of confusion among students and non-scientists.  This confusion partly explains why so many people doubt that evolution happens (Newport, 2012).  This confusion also contributes to an outdated and less useful understanding of the world, and worse predictions about the future. 

People will see that evolution makes sense when they realize that the theory of evolution has been updated.  The updated and revised theory becomes easier to understand, appreciate and embrace.  This more integrated theory of evolution has even greater power to explain the origins of the great diversity of life on Earth.

The following table offers a brief overview of how our understanding of evolution has changed over time. This table presents three major versions of evolutionary theory: 1) Darwin’s theory 2) the Modern Synthesis and 3) the Integral Model of evolution.

Table 1. Evolution of Evolutionary Theory

Three theories of evolution have different facts to support Variation, Inheritance, Selection and Time.  Darwin’s theory is represented by the color green.  Updated information supporting the “Modern Synthesis” is highlighted in blue. Updated information supporting the “Integral Model” is highlighted in purple. 

To make sense of the confusion surrounding the theory of evolution, it helps to know that the theory of evolution is itself evolving. The table above shows three different models of evolutionary theory.  The first is Darwin’s model as described in Origin of Species.  The second model (featured in most textbooks and popular web sites) is the Modern Synthesis, a model that combined mid 20th-century genetics with Darwinian theory.  The most recent model I call the “Integral Model.” I discuss these three theories in more detail below.

Darwin’s Theory

Darwin’s theory was captured by his sketch of a Tree of Life.

Since before Darwin’s time, people have wondered how life diversified into such a vast array of forms.     Most people think Darwin’s greatest contribution was “Natural Selection.”  While Natural Selection (co-discovered by Wallace)  was indeed an important contribution, Darwin’s greatest and most enduring accomplishment was to create a powerful framework for understanding how species change over time.  Darwin suggested that descent with modification (what we today call evolution) involves several “laws.”  These include the law of variation, the law of inheritance, and the law of selection (what scientists today call “differential reproductive success”). Darwin also acknowledged that long periods of time were required.  The acronym VIST describes these necessary ingredients (Variation, Inheritance, Selection, and Time).  Over the years, many details of evolutionary theory have changed, but Darwin’s basic structure for how evolution works remains the same.

Darwin obssersved that variation, inheritance, selection, and time are important for evolution.  Yet because Darwin didn’t know about DNA, genomes, or genetics, he knew nothing about how variation occurred and he knew nothing about horizontal gene transfer.  Instead, he focused his attention on what he could observe, which was natural selection.  In his famous book, On the Origin of Species, Darwin not only outlined the general laws of how species change over time, but he also detailed the principles of natural selection.

Defining Terms

Before delving into the details of evolutionary theory, it is essential to define our terms. The phrase “Natural Selection” often causes confusion because it has two distinct meanings.  1) For some people, including Darwin, Natural Selection is one element of evolution (the other elements being Variation, Inheritance and Time.)  Today, many scientists use the term “differential reproductive success” as a more accurate description that includes natural selection and excludes the processes of variation. 2) For other people, “Natural Selection” is synonymous with the entire theory of evolution and all the processes associated with it, including Variation, Inheritance, Selection, and Time.  Because the latter definition includes a reference to itself (natural selection), this circularity tends to confuse.  Also, since scientists (including Darwin) have shown that evolution can happen by means other than natural selection, (for example via random drift, via endosymbiosis, or via hybridization)  it is confusing to equate evolution with natural selection.    Therefore, when I refer to natural selection, I mean the process that describes “differential reproductive success” and not the whole theory of evolution.

Modern Synthesis

This tree of life represents the Modern Synthesis. It does not show horizontal gene transfer.

While Darwin offered a reasonable explanation for how natural selection works,  he had little insight into another essential aspect of evolution, which is variation.  In the early 20th century, biologists were beginning to understand how variation occurs.  Geneticists clearly saw how heritable material contributed to evolution.  In 1942, Julian Huxley wrote a book entitled Evolution, The Modern Synthesis.  This book summarized and gave a name to the work of hundreds of researchers who had been elucidating the mechanisms of variation.  The Modern Synthesis united the Laws of Selection with the Laws of Variation as they were known at the time.  



Where Does Variation Come From?

Darwin had no idea about DNA and thus had no clue where variation came from.   In the early 20th century, scientists discovered that changes to DNA were responsible for genetic variation.   Changes to DNA are called “mutations.” Although scientists knew that changes to DNA were key to understanding variation, it would take another 50 years to understand how DNA changed to create useful variants. 

Mutation of a word

In Darwin’s time, the term “mutation” originally simply meant “change.” Over time, however, the meaning of “mutation” began to mutate.  Instead of simply meaning “change,” the word mutation began to take on the meaning of deleterious change or change due to error or damage.   For some people, mutation evokes images of flies with legs sprouting from their heads.  In the popular imagination, mutation evokes images of Godzilla, a mythical monster created by radiation from nuclear bombs. (Godzilla was created by Japanese artists after the nuclear bombs unleashed radioactive destruction on the people of Hiroshima and Nagasaki.)   Today, According to the Collins Thesaurus of the English Language, the term “mutant” is synonymous with freak, monster, mutation, deviant, oddity, monstrosity, freak of nature.  So, the word mutant mutated from “change” to “deviant or monster.”

By coincidence, the mechanisms of variation were discovered in the “Nuclear Age.” This was the age in the 1940s when nuclear weapons and nuclear power were being explored.  Just a nuclear power was being tested and explored, scientists exposed flies, molds, bacteria, and other organisms to radiation.  The aberrant creatures and their altered genes resulting from radiation exposure were called mutants.

Scientists observed that genetic changes happen as a result of exposure to radiation.  (Beadle and Tatum, 1941; Muller, 1946.) Later, the growing field of synthetic chemistry led scientists to discover that many chemicals damaged the structure of DNA, and hence introduce variation.  Damage from radiation and from certain chemicals produced random changes in the DNA.  These changes were called “mutations.”

Since the Modern Synthesis, many scientists and teacherss taught that variations result from random accidents due to damage or replication errors.   In classes and textbooks on evolution, professors show slides of nuclear bombs and chemical factories to illustrate the causes of variation.  For years, people assumed that these random errors and damage were responsible for the useful variation that gives rise to the tremendous diversity of life.  While biologists were learning the source of useful variation, this was not apparent to many non-scientists.


While some scientists were satisfied that errors and damage could create the variations that explain life’s diversity, many cell biologists and geneticists sought to better understanding how useful genes evolved to create the tremendous variety of life on Earth.

Thanks to the breakthroughs of many great scientists like Barbara McClintock, Lynn Margulis, James Shapiro, Lorraine Olendzenski, Peter Gogarten, Susumu Ohno and others, scientists now know about the mechanisms that contribute to useful variations.  Thanks to huge breakthroughs in genetics and genomics, we now know that the essential mechanisms for creating variation are not due to solely to random errors or damage. For more information in these diiscoveries, see below.  

Understanding this information requires a deeper understanding of cell biology and genetics.  Many of the people who could have been teaching instead continued with their exciting research, and these useful new ideas about evolutionry theory remaines obscure to members of the general public. 

While scientists were discovering how useful genes were made, many students were not yet being taught this new information.  Textbooks were a few years behind the newest discoverieiss.  And many remained unaware of these advances. 

A whole industry called “Intelligent Design” has spring up  declaring that errors and damage alone could not explain evolution, and therefore, an “Intelligent Designer” was needed to explain the useful variations.   By not understanding where  useful variations come from,  some non-scientists assumed that evolution could not explain how life came to be.  Paradoxically, just as scientists were gaining a clearer picture of how evolution happens, the public had another (false) reason to doubt evolution.

As more genetic  data became available, the  Modern Synthesis theory of evolution lost it’s explanatory ability because it relied on “errors and DNA damage” to explain genetic variation.     As a result of not understanding how variation occurs, a large number of Americans still doubts that evolution explains human origins, according to 2012 Gallup Poll (Newport, 2012.) 

Darwin’s Dilemma is the title of Stephen Meyer’s book about Intelligent Design.  This book, like others in the Intelligent Design movement, seeks to understand where useful variation comes from.  While members of the Intelligent Design movement asked imporant questions that cell biologists had asked, Intelligent Design fails to offer an evidence-bassed explanation for how useful variations are created.   

Instead, curious and clever scientists kept observing and experiementing and came up with the answer to explain where useful variations come from. 

Integral Model of Evolution

Ford Doolittle’s Web of Life replaces the Tree of Life by showing horizontal gene transfer.  This image illustrates the importance of genetic recombination as foundational for the Integral Model of Evolution.

Since the Modern Synthesis, scientists have made huge discoveries about DNA, the molecule of evolution.  Watson and Crick discovered the double-helix structure of DNA.  Barbara McClintock  discovered  “jumping genes” aka transposons and mobile DNA.  Lynn Margulis discovered the role of symbiosis in cell evolution.  Many others discovered the role of  horizontal gene transfer,  gene duplication, and chromosome rearrangements in evolution.   Sequenced genomes have shown that over 50 percent of most genomes have mobile genetic elements.  The field of Evo-Devo (evolutionary and developmental biology) has emerged showing how genetic recombination can have huge evolutionary changes. These new discoveries have changed the theory of evolution yet again. 

We now know where useful genetic variation comes from: from recombination.


Recombination is the key to understanding biological evolution. Recombination explains where functional and useful variation comes from.  Just as Darwin did not know about DNA, the pioneers of the Modern Synthesis did not understand recombination.   Today, thanks to the work of thousands of scientists, we know that recombiantion is the result of active cell processes.  Cells have evolved many active processes to rearrange their DNA.  These processes include meiosis, transposons, reverse transcription, viral integration.   Recombination is an evolved capacity.  It is not due to damage or error, although damage may instigate cell processesses that use recombination to repair the damage. This evolved capacity helps life evolve.  Survival of the most evolvable. 

Over billions of years, cells have evolved the genetic machinery to facilitate this recombination.  Various enzymes (molecular machines) have evolved to cut and paste DNA to move it about the genome and from one genome to another.   These enzymes (recombinases, ligases, transposases to name  just a few)   conferred huge fitness advantages, allowing organisms to recombine their genomes to more quickly adapt to changing environments.  Sex, the recombination of DNA, is another example of the genetic machinery that has emerged to enhance genetic variation.

I call this updated theory the “Integral Model” of biological evolution because it integrates Darwin’s ideas with the Modern Synthesis with major breakthroughs in biology over the past 50 years.

What I call the “Integral Model” is what James Shapiro talks about in his book Evolution: A View from the 21st Century.   

Some people, including James Shapiro, call this new view of evolutionary theory  The Third Way of Evolution. 

Whatever you call this new view of Evolutionary Theory, it finally explains where USEFUL variations come from. 

This information helps us understand how new viral strains evolve. It helps us more acurately undesstand the past so we ight better predict the future. 

Useful variants arise from recombination in all it’s glorious forms: transposition, sex, horizontal gene transfer, gene duplication, symbiosis, retrotransposition, transformation, conjugation, and hybridization.

This updated, integral model of evolution , based on recombiination, solves Darwin’s Dilemma without the need for an Intelligent Designer.

Recombination also helps us understand cultural evolution.  Richard Dawkins gave us a name for cultural replicons, memes, that behave much like biological replicons, genes.   The way that cultures create useful new memes is via recombination.   

Learning from biological evolution, we know that the way for cultures to evolve is through the recombination of useful memes. 



For Further Exploration

Ames, Bruce (1979). “Identifying environmental chemicals causing mutations and cancer”Science 204

Beadle George and Edward Tatum (1941). “Genetic Control of Biochemical Reactions in Neurospora”. PNAS 27 (11): 499–506.

Doolittle, Ford, W. (February 2000). “Uprooting the Tree of Life”. Scientific American. 282(2): 72–7.

Jacob, François (1977). “Evolution and Tinkering.” Science, New Series, Vol. 196, No. 4295 , pp. 1161-1166

Margulis, Lynn (1970). Origin of Eukaryotic Cells. Yale Univ. Press

Margulis, Lynn (Sagan at the time) (1967). “On the origin of mitosing cells”. J Theor Bio. 14 (3): 255–274.

McGowan, Catherine, Roberta Fulthorpe, Alice Wright and James Tiedje (1998). “Evidence for Interspecies Gene Transfer in the Evolution of 2,4-Dichlorophenoxyacetic Acid Degraders.” Appl Environ Microbiol. 1998 October; 64(10): 4089–4092. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC106609/

Muller, Herman Joseph, (1946) “For the discovery of the production of mutations by means of X-ray irradiation.” http://www.nobelprize.org/nobel_prizes/medicine/laureates/1946/muller.html?print=1

Newport, Frank (2012). “In U.S., 46% Hold Creationist View of Human Origins: Highly religious Americans most likely to believe in creationism  http://www.gallup.com/poll/155003/hold-creationist-view-human-origins.aspx

Olendzenski, Lorraine and J. Peter Gogarten (2009).  “Evolution of Genes and Organisms: The Tree/Web of Life in Light of Horizontal Gene Transfer” in Natural Genetic Engineering and Natural Genome Editing: Ann. N.Y. Acad. Sci. 1178: 137–145.

Ohno, Susumu (1970). Evolution by gene duplication. Springer Verlag.

Shapiro, James (2012). Huffington Post Blog, http://www.huffingtonpost.com/james-a-shapiro/

Shapiro, James (2011). Evolution: A View from the 21st Century. FT Press Science.

Woese, Carl (June 2004). “A New Biology for a New Century”. Microbiol. Mol. Biol. Rev. 68 (2): 173–86