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Evolution without accidents | Aeon
Evolution without accidents
Despite advances in molecular genetics, too many biologists think that
natural selection is driven by random mutations
Siamese fighting fish (Betta splendens) provide evidence of ‘alternative
splicing’. Photo by Anadolu Agency/Getty

James A Shapirois professor of microbiology in the Department of
Biochemistry and Molecular Biology at the University of Chicago. His
books include Bacteria as Multicellular Organisms (1997), co-edited with
Martin Dworkin, and Evolution: A View from the 21st Century, Fortified
(2nd ed, 2022).

Edited byCameron Allan McKean
5,000 words
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Since 1859, when Charles Darwin’s On the Origin of Species was first
published, the theory of natural selection has dominated our conceptions
of evolution. As Darwin understood it, natural selection is a slow and
gradual process that takes place across multiple generations through
successive random hereditary variations. In the short term, a small
variation might confer a slight advantage to an organism and its
offspring, such as a longer beak or better camouflage, allowing it to
outcompete similar organisms lacking that variation. Over longer periods
of time, Darwin postulated, an accumulation of advantageous variations
might produce more significant novel adaptations – or even the emergence
of an entirely new species.

Natural selection is not a fast process. It takes place gradually
through random variations, or ‘mutations’ as we call them today, which
accumulate over decades, centuries, or millions of years. Initially,
Darwin believed that natural selection was the only process that led to
evolution, and he made this explicit in On the Origin of Species:

If it could be demonstrated that any complex organ existed, which could
not possibly have been formed by numerous, successive, slight
modifications, my theory would absolutely break down. But I can find out
no such case.
A lot has changed since 1859. We now know that Darwin’s ‘gradualist’
view of evolution, exclusively driven by natural selection, is no longer
compatible with contemporary science. It’s not just that random
mutations are one of many evolutionary processes that produce new
species; they have nothing to do with the major evolutionary
transformations of macroevolution. Species do not emerge from an
accumulation of random genetic changes. This has been confirmed by
21st-century genome sequencing, but the idea that natural selection
inadequately explains evolutionary change goes back 151 years – to
Darwin himself. In the 6th edition of On the Origin of Species,
published in 1872, he acknowledged forms of variations that seemed to
arise spontaneously, without successive, slight modifications:

It appears that I formerly underrated the frequency and value of these
latter forms of variation, as leading to permanent modifications of
structure independently of natural selection.
– from Chapter 15, p395, emphasis added
Today, we know in exquisite detail how these larger-scale ‘spontaneous’
variations come about without the intervention of random mutations. And
yet, even in the age of genome sequencing, many evolutionary scientists
still cling stubbornly to a view of evolution fuelled by a gradual
accumulation of random mutations. They insist on the accuracy of the
mid-20th-century ‘updated’ version of Darwin’s ideas – the ‘Modern
Synthesis’ of Darwinian evolution (through natural selection) and
Mendelian genetics – and have consistently failed to integrate evidence
for other genetic processes. As Ernst Mayr, a major figure in the Modern
Synthesis, wrote in Populations, Species and Evolution (1970):

The proponents of the synthetic theory maintain that all evolution is
due to the accumulation of small genetic changes, guided by natural
selection, and that transpecific evolution [ie, the origins of new
species and taxonomic groups] is nothing but an extrapolation and
magnification of the events that take place within populations and species.
This failure to take account of alternative modes of change has been
foundational to popular and scientific misconceptions of evolution. It
continues to impact the study of antibiotic and pesticide resistance,
the breeding of new crops for agriculture, the mitigation of climate
change, and our understanding of humanity’s impacts on biodiversity.

Discoveries like hers should have inspired a radical rethinking of evolution

During the past century, discoveries that have challenged the gradualist
view of evolution have been sidelined, forgotten, and derided. This
includes the work of 20th-century geneticists such as Hugo de Vries, one
of the rediscoverers of Mendelian genetics and the man who gave us the
term ‘mutation’, or Richard Goldschmidt, who distinguished between
microevolution (change within a species) and macroevolution (changes
leading to new species). Their findings were ignored or ridiculed to
convey the message that the gradual accumulation of random mutations was
the only reasonable explanation for evolution. We can see the absence of
other perspectives in popular works by Richard Dawkins, such as The
Selfish Gene (1976), The Extended Phenotype (1982), and The Blind
Watchmaker (1986); or in textbooks used in universities across the
world, such as Evolution (2017) by Douglas Futuyma and Mark Kirkpatrick.
However, it’s an absence that’s particularly conspicuous because
alternatives to random mutation have not been difficult to find.

One of the most significant of these alternatives is symbiogenesis, the
idea that evolution can operate through symbiotic relationships rather
than through gradual, successive changes. In the early 20th century,
American and Russian scientists such as Konstantin Mereschkowsky, Ivan
Wallin and Boris Kozo-Polyansky argued that symbiotic cell fusions had
led to the deepest kinds of evolutionary change: the origins of all
cells with a nucleus. These arguments about symbiotic cell fusions,
despite being vigorously championed by the evolutionary biologist Lynn
Margulis in later years, did not find a place in evolutionary textbooks
until they were confirmed by DNA sequencing at the end of the 20th
century. And yet, even though these arguments have now been confirmed,
the underlying cellular processes of symbiotic cell fusions have still
not been incorporated into mainstream evolutionary theory.

The pioneering geneticist Barbara McClintock at work at the Cold Spring
Harbor Laboratory, 1947. Photo courtesy the Smithsonian Institution Archives

An absence that’s perhaps even harder to explain is why the pioneering
work of the cytogeneticist Barbara McClintock, one of the giants of
20th-century genetics, has not been accepted as posing a viable
alternative to dominant theories of evolution. McClintock won the Nobel
Prize in 1983 for her discovery during the 1940s of rapid genetic
changes in maize plants that were definitely not random – changes found
not only in maize but, we now know, across all forms of life. After
confirmation by molecular geneticists in the 20th century, discoveries
like hers should have inspired a radical rethinking of evolution.
Instead, these ideas were accepted only among a small circle of
geneticists. The scientists of the Modern Synthesis simply could not
imagine any other way for hereditary variation to occur besides
Darwinian gradualism. And so, for more than a century, natural selection
through random mutations has dominated public conceptions of evolution.

Ibecame embroiled in the evolution debates in the 1960s, at the
beginning of my life as a scientist. While doing my PhD research, I
isolated genetic mutations in E coli bacteria whose properties differed
from standard explanations of genetic variations at the time. According
to molecular geneticists in 1965, mutations were supposed to take place
only in two ways: through errors in DNA replication limited to just one
or two base pairs, or by deletions of longer stretches of the genome. I
eventually showed that the puzzling mutations I found in E coli were
caused by the insertion of long segments of genetic material, typically
more than 1,000 base pairs.

I wasn’t the only one to come across these long insertions. Other
bacterial geneticists had isolated unusual mutations in different
locations in the genome of bacteria, and they turned out to be DNA
insertions too. So, in 1976, two colleagues and I organised the first
meeting on DNA insertions. During this meeting, it became clear that
geneticists working on bacteria, yeast, fruit flies, plants and animals
were all studying the same phenomenon McClintock had discovered in her
maize plants 30 years earlier. This realisation would profoundly change
the way we understood evolution, and it led me to begin thinking of
insertions as important evolutionary tools, rather than supposedly
harmful ‘junk DNA’ as they were later claimed to be.

It was at this 1976 meeting that I first met McClintock. In the early
1930s, she’d discovered that X-rays broke chromosomes, and that maize
could repair the damage by joining broken ends together. If the rejoined
ends came from the same breakage event, the chromosome was restored to
its original configuration, but if those ends came from two different
breakage events, the chromosomes were restructured. As McClintock delved
deeper into chromosome breakage and repair, she uncovered processes that
led to chromosome restructurings and rapid genetic changes in her maize
plants. She had discovered biologically mediated genome change, but even
more startling results lay ahead.