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© Equinox Publishing Ltd. 2008, Unit 6, The Village, 101 Amies Street, London SW11 2JW

[Expositions 2.1 (2008) 111–128] Expositions (print) ISSN 1747-5368  
doi:10.1558/expo.v2i1.111 Expositions (online) ISSN 1747-5376 

Review ARticle

The Evolution of Evolution Theory and Its Controversies

ANdrEA d. WoLfE

The Ohio State University

Keith Thomas. Before Darwin:  Reconciling God and Nature. New 
Haven, CT: Yale University Press, 2005. 314 pp, $27.00 hc, ISBN 
9780300107937.

Michael Ruse. Darwinism and Its Discontents. New York: Cambridge 
University Press, 2006. 316 pp, $30.00 hc, ISBN 9780521829472.

Marc W. Kirschner and John C. Gerhart. The Plausibility of Life:   
Resolving Darwin’s Dilemma. New Haven, CT: Yale University 
Press, 2005. 314pp., $18.00 pb, ISBN 9780300119770.

Charles darwin’s On the Origin of Species was published in 1859. In 
the nearly 150 years since that landmark publication, evolution theory 
has been under attack from conservative religionists all over the world, 
particularly in the United States. Since the Scopes Trial in 1925, anti-
evolution movements in the form of “creation science” and “intelli-
gent design theory” have made their way into classrooms and court-
rooms across America (Numbers 1998; Pennock 2001; Humes 2007). 
In 2007 a “museum” dedicated to young earth creationism opened 
in Kentucky, complete with exhibits featuring dinosaurs and humans 
“living in harmony.” Clearly, there is a huge disconnect between sci-
ence and contemporary American society for this kind of scenario to 
continue to thrive in the twenty-first century.

Three recent books (Kirschner and Gerhart 2005; Thomas 2005; 
ruse 2006) take different approaches to explain why evolution theory 
has been so hard for some to accept, or to expand on “classical” evolu-
tion theory to put forward a new explanation for the diversity of life 

http://dx.doi.org/10.1558/expo.v2i1.111


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on earth. The context of these three tomes is set in an historical over-
view of the development of evolution theory, discussions on perceived 
conflicts between religion and science, and contemporary research that 
builds on existing ideas and pushes evolution theory forward to a more 
comprehensive explanation for the morphological variation separating 
genera, families and phyla, or, what some would call, “macroevolu-
tion.”  A parallel theme of the three authors is that the conflict between 
science and religion, as it relates to evolution theory, is very old and the 
arguments do not seem to change from one generation to another.

Thomas has written a perspective on the history of science with 
regard to the development of darwin’s ideas on natural selection as 
a driving force for speciation. Biographical sketches and the signifi-
cance of their contributions are provided for, in order of appearance, 
Charles darwin, William Paley, Nicolas Copernicus, Galileo Galilei, 
Isaac Newton, robert Hooke, rené descartes, robert Boyle, Erasmus 
darwin, John Locke, david Hume, John Toland, John ray, robert 
Plot, Edward Lhwyd, William Smith, Thomas Burnet, John Wood-
ward, William Whiston, Nicolas Steno, James Hutton, Charles Lyell, 
William Buckland, Jean Baptiste de Lamarck, Philip Henry Gosse, 
Thomas Huxley, Thomas Malthus, and Samuel Wilberforce. Some of 
these men were proponents of natural explanations for observed phe-
nomena, others were firmly in the theological camp, and some were 
torn between the two. Before Darwin begins with a section placing the 
conflict between religion and science in the context of the paradigm 
of darwin’s time, namely natural theology a la William Paley. At the 
time of writing On the Origin of Species, darwin had lost his faith as a 
Christian and thought himself a deist; he died an agnostic and, while 
we cannot be sure exactly when darwin first faced the challenges pre-
sented to conventional faith by contemporary science, we know that 
he was well aware of the issues in 1831, because we know what books 
he read (Thomas 2005, 4).

darwin, as a student at Cambridge, would have been required to 
read Paley’s Natural Theology (1803), and we’re informed in the first 
chapter that darwin enthusiastically endorsed the ideas presented 
therein. darwin’s transition from Paley’s paradigm occurred slowly, but 
surely, over the years. To be sure, he was exposed to the idea of muta-



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ble species through the writings of his grandfather, Erasmus darwin, 
and he was influenced by contemporary thinkers of the era, including 
Charles Lyell, Thomas Malthus, and a host of others who posed ques-
tions about species and diversity of life a century or more before dar-
win’s first inquiries into the nature of species. Thomas places darwin’s 
contributions in the context of prior ideas, especially those trying to 
reconcile fact with Christian dogma. In addition, Thomas discusses the 
conflicts between science and religion as they relate to the development 
of evolution theory and the problems of moving away from theological 
explanations for nature’s diversity of pattern and process.

The dilemma created by the new scientific philosophies was therefore 
the potential relegation of God from all-powerful to first power only, 
and the acknowledgement that other scientific (Second) causes drove 
the world day by day, year by year. The consequent and even greater 
dilemma was that, once one admitted Second Causes, it was only a 
simple extrapolation to all the processes of life being definable in terms 
of such causes. In the process, the need for a first Cause would simply 
fade away. There would be no room—no need—for God at all. (41)

A main theme is that natural explanations inevitably lead to atheism, 
one of the accusations often made in the contemporary criticism of 
evolution theory by creationists. Thomas weaves a narrative that builds 
on the successive steps required to move from theological to scientific 
explanations for natural phenomena, and then poses the real dilemma 
of reconciling observations with explanations.

By the mid-nineteenth century, there were really only three ways in 
which natural theologians could deal with the growing evidence that 
the earth was very old, that it was recycling inexorably beneath their 
feet, and that life on earth had constantly changed over millions of 
years. They could ignore it, they could accommodate it to the biblical 
accounts of history by more or less denying the literal truth of Genesis, 
or they could explain it all away. (223)

On the Origin of Species was a turning point for removing religion from 
the equation to explain biological diversity. As Thomas also shows, 
however, it has also been the focus of controversy, beginning with 
the famous encounter between Thomas Huxley and “Soapy” Samuel 
Wilberforce at the British Association for the Advancement of Sci-



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ence meeting in 1860 (269–279). In the years after 1859, the wa-
tershed date in evolution’s respectability, adherents to natural theol-
ogy increasingly came from more fundamentalist groups, such as the 
staunchly Calvinist palaeontologist Hugh Miller in Scotland, whose 
books reached a huge audience. The argument from design, in its  
elemental version of “irreducible complexity,” is today principally  
favoured by various groups of anti-evolutionists and modern Crea-
tionists, offshoots of fundamentalist Protestantism in the USA 
(261–262).

The societal impact of darwinism in America in the late 1800s 
through the twentieth century has been documented by ronald Num-
bers (1998). After a lag phase of modest acceptance of darwin’s ideas, 
a body of work that became modern evolution theory started to build 
at the turn of the twentieth century with the discovery of Gregor Men-
del’s studies on inheritance. Adding the mathematical framework pro-
vided by ronald fisher and Sewell Wright and the collective studies of 
Theodosius dobzhansky, J.B.S. Haldane, G. Ledyard Stebbins, George 
Gaylord Simpson, Bernhard rensch, Julian Huxley, and Ernst Mayr 
generated the neo-darwinian synthesis. Contributions to the theory 
from the 1940s onward include the discovery of dNA as the curren-
cy of inheritance, the structure of dNA, the genetic code, restriction  
enzymes and the birth of genetic engineering, plate tectonics, advances 
in systematics methods and analysis, the polymerase chain reaction, and 
developments in biotechnology. All these advances in modern science 
spawned growing fields of studies, a key feature of the scientific term 
“theory” in the robust sense of the word. Science is a heuristic process; 
queries and answers should lead to additional questions and studies. 
Unfortunately, the word “theory” is often misused and misconstrued 
in the criticism of evolution theory. “It’s only a theory” is the common 
degradation one hears in critiques of evolution. This equates “theory” 
with “wild guess,” rather than a body of knowledge that is so robust 
that it is accepted as the best possible explanation of a phenomenon.

Michael ruse addresses the misperceptions of evolution theory 
in Darwinism and Its Discontents (2006). ruse is a philosopher and  
approaches the defense of evolution theory from this perspective. He 
begins with an overview of darwin’s contributions to the scientific 



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revolution that shaped modern biology.
At the risk of damning myself in the eyes both of sound scholarship 
and of God, let me be categorical. All of the critics of darwinism are 
deeply mistaken. Charles darwin was a good scientist, the biological 
revolution of the nineteenth century led to genuine understanding, 
and today’s version of the theory is good quality science… finally, 
although, like all good science, darwinism challenges religion, Chris-
tianity specifically, it can and should provide a positive and creative 
stimulus for religious people to think about their faith and move for-
ward in a richer and deeper way. (4)

As in Thomson, ruse’s theme revolves around the conflict between 
science and religion as it relates to evolution. Evolution theory is per-
ceived as a threat to Christian ideals on creation and biblical dogma, 
especially where a literal interpretation is a key component to a denom-
ination’s beliefs. Conflicts arise with the interpretation of origins— 
origin of life, origin of species, and origin of humans. ruse sets the stage 
in chapter two (“The fact of Evolution”) with a summary of darwin’s 
arguments in On the Origin of Species. He builds on that foundation 
by bringing in examples from modern biology ranging from classical 
genetics studies to what molecular studies can tell us about evolution. 
However, the key question on origins is about the origin of life.

As we set out to look at the origin of life, at once we encounter a 
paradox. No self-respecting evolution textbook today avoids the topic, 
but the truth is that evolutionists are really not at all qualified to talk 
on the subject—one needs masses of biochemistry and like knowledge 
really to get involved, far more than that possessed by the average stu-
dent of life’s history. (53)

origin of life, of course, is not a simple topic, and ruse begins his 
discussion by asking the key question, “What is this life that we want 
to explain?” (53). After a history of science overview from Aristotle to 
ideas about hypotheses of an rNA world, the discussion turns to the 
philosophical aspects of the origin of life. ruse states that the problem 
is neither insoluble nor a “threat”: “It is rather inspiring and excit-
ing. There are Nobel prizes to be won” (71). A book such as this isn’t 
able to address origin of life issues, but ruse uses the next six chapters 
to defend evolution theory against criticisms by bringing in examples 



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from morphology through molecules, beginning with the fossil record 
(chapter four) and a discussion of the historical record of evolution 
preserved therein. He addresses the patterns observed using examples 
and then expands on the usual discussion of fossil evidence to include 
cladistics and molecular methods. ruse then moves from observed pat-
terns of evolution to discuss “The Cause of Evolution” in chapter five. 
He begins with an overview of basic genetics and the role genes play in 
selection as compared to the unit of selection, the organism. ruse dis-
cusses the definition of natural selection in a tongue-in-cheek fashion 
using biologists and philosophers as examples of organisms that may 
have different reproductive success rates.

At least part of the problem (if that is what it is) seems to stem from the 
fact that so simple a mechanism supposedly does so much. People cannot 
believe that mere differential reproduction can create the incredibly com-
plex living world that we have around us. It is just not plausible that the 
hand and the eye—let alone the brain—are the end result of something 
like selection. At the very least, the feeling is, the cause should be as com-
plex as the result, and that means that whatever it was that made the brain 
should be on a par with advanced quantum mechanics, totally opaque 
to those without a doctoral degree in the subject, and preferably rather 
more. So the sense is that selection must be simply redescribing what is 
going on, rather than providing genuine empirical insight. (110–111)

ruse then describes numerous examples of selection, starting with 
convergences among marine animals with regard to body shape and 
appendages and then examples from artificial selection. This latter 
strategy was used to good effect by darwin in Origin of Species when he 
described examples from the domestication of animals, but ruse adds 
new information from genetic research studies on the common fruit 
fly to illustrate how much farther our knowledge base has grown since 
darwin’s time. A discussion on speciation and adaptation and the role 
selection plays in these processes comes back to the fossil record with 
an example of reverse engineering a fossil to determine the function of 
a structure found in a skeleton. The reader, up to this point, of ruse’s 
book would assume that the entire volume is a celebration of natural 
selection as the primary driving force in evolutionary change.

It has always been recognized by evolutionists—certainly from the 



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Origin of Species on—that however common or ubiquitous adaptation 
may be, it is only part of the story. The living world is not—cannot 
be—totally and completely adaptive. In fact, this is one of the strong-
est points against Paley’s God. There is far too much wrong with the 
world—too many instances of malfunction—to think that a designer 
has been directly involved with making organisms. (135)

Evolution theory has gone through several periods of growth as our 
body of knowledge expands with each scientific advance. Some of the 
growth phases have been contentious as scientists argue amongst them-
selves as to mechanisms, pattern and process, and analytical method-
ology. The role of natural selection in evolution has also been a focal 
point within the field of biology, and the tempo and mode of evolution 
arguments are discussed in chapter six, “Limitations and restrictions.”  
It is interesting that critics of evolution theory spend so much time 
focusing on the arguments biologists make against this or that aspect 
of evolutionary mechanism (e.g., selection, genetic drift, mutation), 
but miss the whole picture that although the minute details may differ 
among phyla, the overall pattern of evolutionary change remains the 
same. In addition, evolution theory is blamed for many societal ills 
that have nothing to do with biology.

In recent years, darwinism has become the whipping boy of every dis-
gruntled member of society—the root cause of problems from fascism 
to sexism, from anti-Semitism to capitalism, from cross dressing (I kid 
you not) to the breakdown of the traditional family. It is argued that 
darwinism is no true scientific theory by a mere reflection of the more 
offensive elements of the society within which it finds itself, at best a 
social construction—an epiphenomenon of the culture within which 
it resides—and at worst a secular-religious rival to Christianity—a 
world picture complete with moral directives and eschatology. (194)

Perhaps it was the setting in which On the Origin of Species was pub-
lished that set up many of the conflicts we’ve seen in the past 150 
years. darwin’s era was during the industrial revolution and the rise of 
capitalism. Whereas the controversies of scientific advances vs. natural 
theology were the main themes prior to darwin (as Thomson shows), 
after publication of On the Origin of Species, the differences among 
economic classes could be put into the context of the phrase “survival 



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of the fittest,” which was coined by Herbert Spencer. Modern critics of 
evolution focus on aspects of Social darwinism, accusations of atheism, 
secular humanism, and their perceived dangers to human society (ruse 
2006, 194–196). However, it’s important to remember that evolution 
theory isn’t about any of these topics. Under the umbrella of evolution 
through natural selection, darwin brought in just about every area of 
biology—instinct, paleontology, biogeographical distribution, anato-
my, embryology, classification—and showed how they are illuminated 
by the mechanism and in turn support the mechanism (208).

Since darwin’s time, evolution theory has expanded to include  
genetics, mathematics, molecular biology, genomics, and bioinformat-
ics. The number of scientific journals dedicated to evolutionary pattern 
and process studies have increased each decade since the early 1900s. 
The contributions of evolution theory in the applied sciences with 
direct benefit to humans (e.g., medicine, agriculture, biotechnology) 
have also increased each decade since publication of On the Origin of 
Species. Thus, it is puzzling as to why evolution theory is continually 
under attack from conservative religionists.

one is tempted to let Christians—believers of any kind—fend for 
themselves. If they want to accept darwinism, then it is there to be  
accepted. If they want to reject it on religious grounds, then that is 
their option. But many are genuinely puzzled and concerned, and 
would like an answer that is not just based on the prejudice and igno-
rance of one side or the other. (276)

Is it possible to accommodate science and religion given the deep 
divide that has kept the attack on evolution theory in the news head-
lines?  It appears as if Paley’s argument from design is still the preferred 
option for those that cannot accept a scientific explanation for origins. 
ruse summarizes the modern “argument from design” here:

organisms show design-like features: the hand, the eye, the leaf, the 
fin, the funny plates on the back of stegosaurus. These “adaptations” 
function, they work, for the benefit of their possessors. They seem far 
too complex to have come about by chance. In the real world, things 
break down and go wrong, rather than build up into working units. So 
there must be an explanation. And the only reasonable explanation is 
that there is a designer, an intelligence behind adaptations. (281)



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one wonders if the proponents of this view prefer it because they per-
ceive science as being too hard to understand. Given the complex-
ity of modern research involving biochemistry and molecular biology  
together with mathematics and physics, it’s no wonder that many peo-
ple prefer an easier explanation for the diversity of life and how it came 
to be. Marc W. Kirschner and John C. Gerhart tackle this subject from 
a scientific perspective in The Plausibility of Life (2005). This book  
begins with Paley’s argument for design based on the complexity of a 
pocket watch, a common tactic for modern day creationists.

Paley compared the complexity of the watch, which he could under-
stand, with the complexity of life, which in 1802 he could not, as a 
measure of their creators. However, such comparisons look different 
today. Where he would have seen an earthworm and a skylark each as 
a unique and complex design, we now see underlying similarities; they 
have the same system of heredity, the same genetic code, the same cellu-
lar makeup, the same subcellular components, largely the same metabo-
lism, and many of the same processes of embryonic development. (2)

Kirschner and Gerhart present a new explanation for the diversity of 
life by expanding evolution theory to include “facilitated variation,” 
which deals with evolutionary development and the timing and loca-
tion of gene expression in organisms. Thus, the problem of novelty’s 
origin in evolution becomes, How could the eye be created in the first 
place, or the brain, or wing, or lungs, or limbs?  Could they have been 
plausibly assembled, small piece by small piece, each presupposing a 
selective advantage?  It is this feature of darwin’s theory, the uncertain 
accounting for novelty, that creationists seize on; meanwhile, evolu-
tionary biologists assert that variation must be sufficient, though they 
lack a general explanation for the origin of complex novel structures. 
Answers to these questions affect the plausibility of life’s arising by way 
of evolution (4).

Contemporary arguments for design as presented in “intelligent  
design theory” a la “irreducible complexity” (Behe 1996) use the  
vocabulary of molecular biology, but ignore or reject hypotheses from 
that field of research to explain the origin of biological structures. Kir-
schner and Gerhart begin with an overview of evolution theory from 
darwin through the neo-darwinian synthesis and then bring the read-



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er up-to-date on recent developments in embryology and evolutionary 
development (evo-devo). The cardinal issue in evolution is the origin 
of complex and heritable variation from a limited reservoir of com-
ponents. Although selection has preoccupied evolutionary biologists, 
the study of the origin of variation and novelty has idled. Is the organ-
ism’s capacity to generate heritable variation great enough to supply 
the succession of variants needed for natural selection to bring forth a 
circadian clock, or—more challenging—a human being from a single-
celled ancestor, all within the time span of the earth?  Heritable vari-
ation requires mutational change of the genome, but that is only the 
start of the story.

What else is required to get an adequate frequency of selectable vari-
ants? Mutation only changes what already exists. It does not create new 
anatomy, physiology, and behavior from nothing, so we need to know 
how readily one structure can be transmuted into another, particularly 
when we consider structures of intricate design and interdependent 
activities. With an understanding of how random genetic change is 
converted into useful innovation, a theory of novelty can be devised. 
darwin’s general theory of evolution can then be established at the 
most fundamental level. (Kirschner and Gerhart 2005, 8–9)

The major point made in the early chapters of  The Plausibility of Life 
is that we are only now beginning to understand the big picture of how 
life on earth diversified from unicellular organisms to the complex mul-
ticellular ones represented by animals, plants, and fungi. The emphasis, 
until recently, has been on attempts to explain the origin of lineages 
and morphological diversification (i.e., the ill-defined “macroevolu-
tion” of the creationist lexicon). A big surprise of modern biology has 
been conservation—that even distantly related organisms use similar 
processes for cellular function, development, and metabolism. When 
a process is conserved, most of its protein components are conserved. 
details of metabolism are the same in bacteria and humans; basic cell 
organization and function are similar between yeast and humans; and 
developmental strategies in fruit flies are strikingly similar to those in 
humans. The conservation of key processes in diverse organisms today 
implies, as we shall see, that we can deduce the basic physiological and 
developmental processes of organisms in the past (34).



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“facilitated phenotypic variation” expands on classical evolution 
theory by including the development of organisms in the equation. In 
addition to the requirement of genetic variation and natural selection, 
Kirschner and Gerhart argue that novelty in organisms arise “by the 
use of conserved processes in new combinations, at different times, and 
in different places and amounts rather than by the invention of new 
processes” (35).

Novelty usually comes about by the deployment of existing cell behav-
iors in new combinations and to new extents, rather than in their dras-
tic modification or the invention of completely new ones. True novelty 
in the invention of cellular processes is rare. once such novelty occurs, 
it may be carried through stably in many lineages. Hence, evolution 
is divided into epochs of invention of cellular behaviors, interspersed 
with long periods without invention. (39)

This statement is an interesting twist on the idea of punctuated equi-
librium (Eldredge and Gould 1972) where species are stable and rela-
tively unchanged in the fossil record for long periods of time followed 
by a rapid change and burst of speciation and lineage diversification. 
Kirschner and Gerhart explain that although all organisms share a large 
percentage of dNA sequences and genes, morphological and physi-
ological differences arise when cellular changes occurring during devel-
opment are fixed in lineages. rather than go through the fossil record 
to explain evolutionary divergence, the authors discuss “the history 
of the world according to genes” (45–70). “Core processes have been  
introduced at rare intervals during evolution (the punctuated part), 
then are largely unchanged until the present (an equilibrium or stasis)” 
(45). diversification is placed in the context of adaptive cell behaviors 
rather than morphological changes. This historical account of diversi-
fication is biased toward the animal kingdom and involves: 1) novel 
chemical reactions, 2) cell organization and regulation, 3) evolution of 
multicellularity, 4) origin of body plans, 5) and origin of appendages. 
Kirschner and Gerhart drive home the point that cellular processes, 
dNA sequences, gene content, and physiologies are highly conserved 
from bacteria to animals and yet diversification happens through cel-
lular processes common to all lineages.



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If we follow the path from the bacterium-like ancestor toward humans, 
we find repeated episodes of great innovation. New genes and proteins 
arose in each episode. Afterward, the components and processes settled 
into prolonged conservation. The existence of “deep conservation” is a 
surprise. To some biologists it is a contradiction of their expectations 
about the organism’s capacity to generate random phenotypic varia-
tion from random mutation. To some, it borders on paradox when 
held against the rampant diversification of anatomy and physiology in 
the evolutionary history of animals. (67–68)

In chapter three (“Physiological Adaptability and Evolution”), the 
authors discuss this paradox in terms of previous research on adapta-
tion and phenotypic plasticity (changes in morphology or physiology 
in response to environmental conditions). Such physical changes in 
response to environmental stimuli do not contribute to evolutionary 
change unless the changes are heritable. The authors introduce this 
concept by giving examples of developmental plasticity where organ-
isms have different morphological outcomes depending on environ-
mental cues. Examples include animals that have very different lar-
val morphologies compared to adult morphologies that go through a  
series of metamorphoses (insects, ascidians, amphibians), which repre-
sent sequential alternative phenotypes. When timing of development is 
affected, speciation may occur where one species resembles an alternate 
morphological stage of another species. Alternate adult phenotypes may 
also occur as a result of environmental cues. for example, the different 
castes of social insects and alternate sex determination of some reptiles 
come from temperature differences in egg incubation. Kirschner and 
Gerhart finish the chapter with a discussion of the evolution of hemo-
globins and their role in adaptation of animals to their environments.

It may seem counterintuitive that mechanisms such as oxygen regula-
tion, which function to maintain the existing phenotype by buffer-
ing the effects of variation in the environment, should simultaneously 
serve as vehicles for creating variation in evolution. This pseudopara-
dox of stability versus change stands juxtaposed to another of conser-
vation and diversity. How do highly conserved processes like oxygen 
transport in hemoglobin or determination of sex in mammals lower 
the barrier for generation of diversity? (107)



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In chapter four (“Weak regulatory Linkage”), Kirschner and Gerhart 
begin their explanation of facilitated phenotypic variation. “Let us now 
delve directly into the conserved core processes that are responsible 
for generating most of the anatomy, physiology, and behavior of the  
organism” (109). Variation arises through the multiple use of conserved 
core processes. New combinations of the core processes also occur and 
“individual core processes are constructed so that new linkages can eas-
ily be forged and broken” (110). Timing and regulation of gene expres-
sion is a key concept in terms of the evolution of variation.

Understanding embryonic development is central for explaining phe-
notypic novelty in animals. It is in the embryo that much of the phe-
notype is established with all its anatomical and physiological com-
plexity… The implications for evolution are powerful, for if complex 
development is elicited by simple signals, then changes in complex 
development may be achieved by changing the amount or the location 
of these simple signals, rather than by changing a highly integrated 
and complex process. (111–112)

Kirschner and Gerhart then explain the details of gene expression and 
regulation in bacteria, eukaryotes and multicellular organisms. This 
is a precursor to a later discussion on gene expression in embryos and 
its role in evolution of novel traits. first, however, they come back to 
one of the criticisms of evolution theory, the difficulty of explaining 
mechanisms for macroevolution.

Much of the skepticism over the years about the capacity of random 
mutation or genetic reassortment to generate phenotypic change has 
arisen from the assumption that genetic changes must create very spe-
cific, multiple, complex phenotypic changes. our view is that specifi-
city and complexity are already built into the conserved processes, as is 
the propensity for regulatory coupling. It is not necessary for genetic 
change to create those characteristics, though they are still needed for 
heritable change. (142)

Chapter five (“Exploratory Behavior”) describes a biological phenom-
enon common to the development of a cell’s cytoskeleton to the organi-
zation of the vascular system of mammals and to the behavioral ecology 
of foraging social insects. Exploratory behavior is described as a critical 
process in the evolution of novelty, especially with regard to anatomical 



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changes that are perceived as difficult to explain if they originated by a 
slow stepwise accumulation of mutations (e.g., the eye or different limb 
anatomies of vertebrates). At each stage an exploratory process could, 
even without genetic modification, adapt to changes in anatomy. Such 
highly adaptive processes facilitate the production of significant viable 
and novel variation on which selection can act (147).

The general effect of exploratory behavior at a cellular level appears to 
be a buffering one that allows for changes in anatomy without causing 
lethality. There is a lot of tolerance for variation in getting from point 
A to point B in the development of an organism as long as the criti-
cal functions of metabolic pathways, organs, and structures are intact. 
Exploratory mechanisms have a dual role in facilitating evolutionary 
change—which on the surface seems paradoxical. By being globally 
responsive and adaptive they blunt the effects of mutation and reduce 
its effect and lethality. In this way they make possible the persistence 
of novel changes by reducing collateral damage, thus increasing the 
amount of heritable variation (176).

The first five chapters of Kirschner and Gerhart set the stage for the 
big explanation of the importance of evolutionary development studies 
for expanding on classical evolution theory to include a new paradigm 
of facilitated variation. Chapter six (“Invisible Anatomy”) specifically 
deals with how the conserved core processes of cellular biology relate to  
embryology and the anatomical differences among animals. The invis-
ible anatomy referred to throughout the chapter is the anatomy of the  
embryo in terms of specific gene expression patterns and zones of activity.

When a trait of anatomy changes in evolution, it is really the develop-
ment of that trait that has changed. Anatomy itself is not inherited, but 
rather the means to generate the anatomy. The real target of heritable 
genetic change is the development by which the trait is produced… 
Therefore, in seeking to explain anatomical change in evolution,  
biologists have come to understand that what they must explain is the 
changes in developmental processes. (178)

This, then, is the heart of the subject—how evolutionary development 
studies contribute to a better understanding of evolutionary pattern 
and process. An explanation of modern embryology in terms of the 
“compartment plan” of a young embryo is given:  



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once organized in an advanced multicellular stage, but well before the 
cells have differentiated into their final cell types, the compartment plan 
gives each cell its address, its identity, and its location relative to the cells 
in the rest of the body… We call the compartment plan an “invisible 
anatomy” because the compartments are only identifiable if one can 
establish which genes are expressed there. At these early stages, compart-
ments cannot be distinguished by anatomical features. The actual dif-
ferentiation of the organism will depend not only on the compartments 
but also on the interactions of cells of one compartment with signals 
from other compartments. The compartment map is an extensible map:  
individual compartments can expand and shrink independently while 
overall neighbor relations are retained. This flexibility occurs not only 
in development, when certain regions grow relative to others, but also 
in evolution where there is disproportionate growth—for example the 
neck of the giraffe relative to the neck of the whale. (183)

The discovery of the compartment plan and the importance of this 
discovery for understanding evolution make up the bulk of this chapter. 
The discussion emphasizes the importance of genes conserved across 
phyla (e.g., Hox, transcription factors, selector genes) and their role in 
embryological development and anatomy. By comparing the invisible 
anatomy of animals from invertebrates to vertebrates it is possible to 
understand the differentiation of tissues into structures and organs. 
By small changes in timing, location, and signaling of gene expression 
during the early stages of embryo development, the mechanisms for all 
animal body plans and anatomy are explained.

A significant implication of the comparison is that compartments are 
much more stable across evolutionary history than are the anatomical 
structures developed upon them. Compartments, it seems, are uncon-
strained in the anatomical structures and differentiated cell types they 
can support. …
The molecular information is so precise and detailed that the inter-
polations are nearly unassailable. Between insects and vertebrates the 
sequence of Hox genes is conserved, the order of Hox genes on the 
chromosome is conserved, and correspondence of the chromosome 
order to the anatomical order is conserved. These similarities cannot 
be accidental or convergent from separate starting points. In combina-
tion with an increasingly detailed fossil record that shows maintenance 



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of the body plans of almost all phyla for the last 535 million years, 
the commonality of the basic anterior-posterior patterning is proven 
far beyond any demonstration possible from fossils and comparative 
anatomy alone. (197–198)

The authors pull all the information from chapters one to six  
together in chapter seven to state their theory of facilitated variation. 
The outline takes five pages of their book, but it can be summarized in 
their point number six:

Most evolutionary change in the metazoa since the Cambrian has come 
not from changes of the core processes themselves or from new proc-
esses, but from regulatory changes affecting the deployment of the core 
processes. These regulatory changes alter the time, place, circumstance 
and amount of gene expression, rNA availability, or protein synthesis 
of components of the core processes, or alter the activity and interaction 
of proteins of the processes by modifying them or by changing their sta-
bility. Because of these regulatory changes, the core processes are used in 
new combinations and amounts at new times and places. Also because 
of the regulatory changes, different parts of the adaptive ranges of per-
formance of the processes are used in new circumstances. (221–222)

The final chapter of The Plausibility of Life focuses on the topic of 
evolution and its impact on society. first there is a discussion on how 
their theory of facilitated variation dovetails with existing evolution 
theory, namely by expanding on the framework of selection, genetics, 
and the neo-darwinian synthesis to include a mechanism that explains 
phenotypic changes in organisms. Kirschner and Gerhart admit that 
the origins of the core processes remain unresolved currently.

The theory of facilitated variation opens up a new set of questions 
about the origins of the conserved core processes that, as we have  
argued, facilitate the generation of all kinds of anatomical, physiologi-
cal, and behavioral diversity. There is really no alternative but to think 
that new core processes, such as those that first arose in eukaryotic 
cells, were cobbled together from the existing process in prokaryo-
tic cells. The transformations from prokaryotes to eukaryotes or from 
single-celled to multicellular organisms are profound, and evidence 
is spare. However, as methods for identifying weakly related dNA  
sequences have improved, and as more organisms have been sequenced, 
we can glean hints about these major transitions.



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Core processes may have emerged together as a suite, for we know of 
no organism today that lacks any part of the suite. (253)

Kirschner and Gerhart express confidence that remaining and new 
questions will be resolved as research progresses. Scientists, in general, 
agree that the heuristic process of research is an important hallmark of 
what makes science a robust endeavor and differentiates it from alterna-
tive approaches such as those believed by creationists. Though modern 
scientists may have questioned the completeness of the theory of evo-
lution, few believed that the fundamental principles of variation and 
selection would not in the end explain the diversity of life. Certain 
groups, however, particularly active in the United States, have exagger-
ated and fabricated weaknesses in evolution theory in order to discredit 
it. from its beginning, the theory of evolution has caused problems 
for some traditional religious groups. By depicting human beings as  
derived from simpler animals, evolutionary theory not only under-
mined the biblical account of creation, but also seemed to debase  
human beings by suggesting that they were not of divine origin (264).

And so, we are back to my opening paragraph for this review. It 
is perfectly clear that evolution theory will continue to be controver-
sial in the United States for many years to come, despite the scientific  
advances that reinforce the robustness of evolutionary biology. Thom-
son describes the history of the conflict between science and religion 
as it relates to origins and evolution theory, ruse discusses the soci-
etal impact and disagreements among segments of society with regard 
to evolution theory, and Kirschner and Gerhart expand on evolution 
theory to add some explanation for the diversification of animal line-
ages. one wonders what scientific research, if any, would be sufficient 
to convince the masses that evolution has occurred. 

References

Behe, Michael J.

1996 Darwin’s Black Box: The Biochemical Challenge to Evolution. New York:  
The free Press.



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darwin, Charles

1859 On the Origin of the Species by Means of Natural Selection: or, The Preserva-
tion of Favoured Races in the Struggle for Life. London: John Murray.

Eldredge, N. and S.J. Gould

1972 Punctuated equilibria:  An alternative to phyletic gradualism. In Models 
in Paleobiology, ed. T.J.M. Schopf, 82–115. San francisco, CA: freeman, 
Cooper.

Humes, Edward

2007 Monkey Girl: Evolution, Education, Religion, and the Battle for America’s 
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Numbers, ronald L.

1998 Darwinism Comes to America. Cambridge, MA: Harvard University Press.

Paley, William

1803 Natural Theology; or, Evidences of the Existence and Attributes of the Deity, 
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Pennock, robert T., ed.

2001 Intelligent Design Creationism and its Critics:  Philosophical, Theological, and 
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