Darwin's Doubt: The Explosive Origin of Animal Life and the Case for Intelligent Design

EPub Edition © APRIL 2013 ISBN: 9780062071491

by Stephen C. Meyer

Illustrations © 2013 Ray Braun, Seattle, WA.

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 640 p
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 2013 by Stephen C. Meyer 

When people today hear the term “information revolution,” they typically think
of silicon chips and software code, cellular phones and supercomputers. They
rarely think of tiny one-celled organisms or the rise of animal life. But, while
writing these words in the summer of 2012, I am sitting at the end of a narrow
medieval street in Cambridge, England, where more than half a century ago a
far-reaching information revolution began in biology. This revolution was
launched by an unlikely but now immortalized pair of scientists, Francis Crick
and James Watson. Since my time as a Ph.D. student at Cambridge during the
late 1980s, I have been fascinated by the way their discovery transformed our
understanding of the nature of life. Indeed, since the 1950s, when Watson and
Crick first illuminated the chemical structure and information-bearing properties
of DNA, biologists have come to understand that living things, as much as hightech
devices, depend upon digital information—information that, in the case of
life, is stored in a four-character chemical code embedded within the twisting
figure of a double helix.

Because of the importance of information to living things, it has now become
apparent that many distinct “information revolutions” have occurred in the
history of life—not revolutions of human discovery or invention, but revolutions
involving dramatic increases in the information present within the living world
itself. Scientists now know that building a living organism requires information,
and building a fundamentally new form of life from a simpler form of life
requires an immense amount of new information. Thus, wherever the fossil
record testifies to the origin of a completely new form of animal life—a pulse of
biological innovation—it also testifies to a significant increase in the information
content of the biosphere.

In 2009, I wrote a book called Signature in the Cell about the first
“information revolution” in the history of life—the one that occurred with the
origin of the first life on earth. My book described how discoveries in molecular
biology during the 1950s and 1960s established that DNA contains information
in digital form, with its four chemical subunits (called nucleotide bases)
functioning like letters in a written language or symbols in a computer code. And
molecular biology also revealed that cells employ a complex informationprocessing
system to access and express the information stored in DNA as they
use that information to build the proteins and protein machines that they need to
stay alive. Scientists attempting to explain the origin of life must explain how
both information-rich molecules and the cell’s information-processing system arose.

The type of information present in living cells—that is, “specified”
information in which the sequence of characters matters to the function of the
sequence as a whole—has generated an acute mystery. No undirected physical or
chemical process has demonstrated the capacity to produce specified information
starting “from purely physical or chemical” precursors. For this reason, chemical
evolutionary theories have failed to solve the mystery of the origin of first life—
a claim that few mainstream evolutionary theorists now dispute.

In Signature in the Cell, I not only reported the well-known impasse in
origin-of-life studies; I also made an affirmative case for the theory of intelligent
design. Although we don’t know of a material cause that generates functioning
digital code from physical or chemical precursors, we do know—based upon our
uniform and repeated experience—of one type of cause that has demonstrated
the power to produce this type of information. That cause is intelligence or mind.
As information theorist Henry Quastler observed, “The creation of information
is habitually associated with conscious activity.”1 Whenever we find functional
information—whether embedded in a radio signal, carved in a stone monument,
etched on a magnetic disc, or produced by an origin-of-life scientist attempting
to engineer a self-replicating molecule—and we trace that information back to
its ultimate source, invariably we come to a mind, not merely a material process.
For this reason, the discovery of digital information in even the simplest living
cells indicates the prior activity of a designing intelligence at work in the origin of the first life.

My book proved controversial, but in an unexpected way. Though I clearly
stated that I was writing about the origin of the first life and about theories of
chemical evolution that attempt to explain it from simpler preexisting chemicals,
many critics responded as if I had written another book altogether. Indeed, few
attempted to refute my book’s actual thesis that intelligent design provides the
best explanation for the origin of the information necessary to produce the first
life. Instead, most criticized the book as if it had presented a critique of the
standard neo-Darwinian theories of biological evolution—theories that attempt
to account for the origin of new forms of life from simpler preexisting forms of
life. Thus, to refute my claim that no chemical evolutionary processes had
demonstrated the power to explain the ultimate origin of information in the DNA
(or RNA) necessary to produce life from simpler preexisting chemicals in the
first place, many critics cited processes at work in already living organisms—in
particular, the process of natural selection acting on random mutations in already
existing sections of information-rich DNA. In other words, these critics cited an
undirected process that acts on preexistent information-rich DNA to refute my
argument about the failure of undirected material processes to produce
information in DNA in the first place.2

For example, the eminent evolutionary biologist Francisco Ayala attempted to
refute Signature by arguing that evidence from the DNA of humans and lower
primates showed that the genomes of these organisms had arisen as the result of
an unguided, rather than intelligently designed, process—even though my book
did not address the question of human evolution or attempt to explain the origin
of the human genome, and even though the process to which Ayala alluded
clearly presupposed the existence of another information-rich genome in some
hypothetical lower primate.3

Other discussions of the book cited the mammalian immune system as an
example of the power of natural selection and mutation to generate new
biological information, even though the mammalian immune system can only
perform the marvels it does because its mammalian hosts are already alive, and
even though the mammalian immune system depends upon an elaborately
preprogrammed form of adaptive capacity rich in genetic information—one that
arose long after the origin of the first life. Another critic steadfastly maintained
that “Meyer’s main argument” concerns “the inability of random mutation and
selection to add information to [preexisting] DNA”4 and attempted to refute the
book’s presumed critique of the neo-Darwinian mechanism of biological
evolution accordingly.

I found this all a bit surreal, as if I had wandered into a lost chapter from a
Kafka novel. Signature in the Cell simply did not critique the theory of
biological evolution, nor did it ask whether mutation and selection can add new
information to preexisting information-rich DNA. To imply otherwise, as many
of my critics did, was simply to erect a straw man.

To those unfamiliar with the particular problems faced by scientists trying to
explain the origin of life, it might not seem obvious why invoking natural
selection does not help to explain the origin of the first life. After all, if natural
selection and random mutations can generate new information in living
organisms, why can it also not do so in a prebiotic environment? But the
distinction between a biological and prebiotic context was crucially important to
my argument. Natural selection assumes the existence of living organisms with a
capacity to reproduce. Yet self-replication in all extant cells depends upon
information-rich proteins and nucleic acids (DNA and RNA), and the origin of
such information-rich molecules is precisely what origin-of-life research needs
to explain. That’s why Theodosius Dobzhansky, one of the founders of the
modern neo-Darwinian synthesis, can state flatly, “Pre-biological natural
selection is a contradiction in terms.”5 Or, as Nobel Prize–winning molecular
biologist and origin-of-life researcher Christian de Duve explains, theories of
prebiotic natural selection fail because they “need information which implies
they have to presuppose what is to be explained in the first place.”6 Clearly, it is
not sufficient to invoke a process that commences only once life has begun, or
once biological information has arisen, to explain the origin of life or the origin
of the information necessary to produce it.

All this notwithstanding, I have long been aware of strong reasons for
doubting that mutation and selection can add enough new information of the
right kind to account for large-scale, or “macroevolutionary,” innovations—the
various information revolutions that have occurred after the origin of life. For
this reason, I have found it increasingly tedious to have to concede, if only for
the sake of argument, the substance of claims I think likely to be false.
And so the repeated prodding of my critics has paid off. Even though I did
not write the book or make the argument that many of my critics critiqued in
responding to Signature in the Cell, I have decided to write that book. And this is that book.

Of course, it might have seemed a safer course to leave well enough alone.
Many evolutionary biologists now grudgingly acknowledge that no chemical
evolutionary theory has offered an adequate explanation of the origin of life or
the ultimate origin of the information necessary to produce it. Why press a point
you never made in the first place?

Because despite the widespread impression to the contrary—conveyed by
textbooks, the popular media, and spokespersons for official science—the
orthodox neo-Darwinian theory of biological evolution has reached an impasse
nearly as acute as the one faced by chemical evolutionary theory. Leading
figures in several subdisciplines of biology—cell biology, developmental
biology, molecular biology, paleontology, and even evolutionary biology—now
openly criticize key tenets of the modern version of Darwinian theory in the
peer-reviewed technical literature. Since 1980, when Harvard paleontologist
Stephen Jay Gould declared that neo-Darwinism “is effectively dead, despite its
persistence as textbook orthodoxy,”7 the weight of critical opinion in biology has
grown steadily with each passing year.

A steady stream of technical articles and books have cast new doubt on the
creative power of the mutation and selection mechanism.8 So well established
are these doubts that prominent evolutionary theorists must now periodically
assure the public, as biologist Douglas Futuyma has done, that “just because we
don’t know how evolution occurred, does not justify doubt about whether it
occurred.”9 Some leading evolutionary biologists, particularly those associated
with a group of scientists known as the “Altenberg 16,” are openly calling for a
new theory of evolution because they doubt the creative power of the mutation
and natural selection mechanism.10

The fundamental problem confronting neo-Darwinism, as with chemical
evolutionary theory, is the problem of the origin of new biological information.
Though neo-Darwinists often dismiss the problem of the origin of life as an
isolated anomaly, leading theoreticians acknowledge that neo-Darwinism has
also failed to explain the source of novel variation without which natural
selection can do nothing—a problem equivalent to the problem of the origin of
biological information. Indeed, the problem of the origin of information lies at
the root of a host of other acknowledged problems in contemporary Darwinian
theory—from the origin of new body plans to the origin of complex structures
and systems such as wings, feathers, eyes, echolocation, blood clotting,
molecular machines, the amniotic egg, skin, nervous systems, and
multicellularity, to name just a few.

At the same time, classical examples illustrating the prowess of natural
selection and random mutations do not involve the creation of novel genetic
information. Many biology texts tell, for example, about the famous finches in
the Galápagos Islands, whose beaks have varied in shape and length over time.
They also recall how moth populations in England darkened and then lightened
in response to varying levels of industrial pollution. Such episodes are often
presented as conclusive evidence for the power of evolution. And indeed they
are, depending on how one defines “evolution.” That term has many meanings,
and few biology textbooks distinguish between them. “Evolution” can refer to
anything from trivial cyclical change within the limits of a preexisting gene pool
to the creation of entirely novel genetic information and structure as the result of
natural selection acting on random mutations. As a host of distinguished
biologists have explained in recent technical papers, small-scale, or
“microevolutionary,” change cannot be extrapolated to explain large-scale, or
“macroevolutionary,” innovation.11 For the most part, microevolutionary
changes (such as variation in color or shape) merely utilize or express existing
genetic information, while the macroevolutionary change necessary to assemble
new organs or whole body plans requires the creation of entirely new
information. As an increasing number of evolutionary biologists have noted,
natural selection explains “only the survival of the fittest, not the arrival of the
fittest.”12 The technical literature in biology is now replete with world-class
biologists13 routinely expressing doubts about various aspects of neo-Darwinian
theory, and especially about its central tenet, namely, the alleged creative power
of the natural selection and mutation mechanism.

Nevertheless, popular defenses of the theory continue apace, rarely if ever
acknowledging the growing body of critical scientific opinion about the standing
of the theory. Rarely has there been such a great disparity between the popular
perception of a theory and its actual standing in the relevant peer-reviewed
scientific literature. Today modern neo-Darwinism seems to enjoy almost
universal acclaim among science journalists and bloggers, biology textbook
writers, and other popular spokespersons for science as the great unifying theory
of all biology. High-school and college textbooks present its tenets without
qualification and do not acknowledge the existence of any significant scientific
criticism of it. At the same time, official scientific organizations—such as the
National Academy of Sciences (NAS), the American Association for the
Advancement of Sciences (AAAS), and the National Association of Biology
Teachers (NABT)—routinely assure the public that the contemporary version of
Darwinian theory enjoys unequivocal support among qualified scientists and that
the evidence of biology overwhelmingly supports the theory. For example, in
2006 the AAAS declared, “There is no significant controversy within the
scientific community about the validity of the theory of evolution.”14 The media
dutifully echo these pronouncements. As New York Times science writer
Cornelia Dean asserted in 2007, “There is no credible scientific challenge to the
theory of evolution as an explanation for the complexity and diversity of life on earth.”15

The extent of the disparity between popular representations of the status of
the theory and its actual status, as indicated in the peer-reviewed technical
journals, came home to me with particular poignancy as I was preparing to
testify before the Texas State Board of Education in 2009. At the time the board
was considering the adoption of a provision in its science education standards
that would encourage teachers to inform students of both the strengths and
weaknesses of scientific theories. This provision had become a political hot
potato after several groups asserted that “teaching strengths and weaknesses”
were code words for biblical creationism or for removing the teaching of the
theory of evolution from the curriculum. Nevertheless, after defenders of the
provision insisted that it neither sanctioned teaching creationism nor censored
evolutionary theory, opponents of the provision shifted their ground. They
attacked the provision by insisting that there was no need to consider weaknesses
in modern evolutionary theory because, as Eugenie Scott, spokeswoman for the
National Center for Science Education, insisted in The Dallas Morning News,
“There are no weaknesses in the theory of evolution.”16

At the same time, I was preparing a binder of one hundred peer-reviewed
scientific articles in which biologists described significant problems with the
theory—a binder later presented to the board during my testimony. So I knew—
unequivocally—that Dr. Scott was misrepresenting the status of scientific
opinion about the theory in the relevant scientific literature. I also knew that her
attempts to prevent students from hearing about significant problems with
evolutionary theory would have likely made Charles Darwin himself
uncomfortable. In On the Origin of Species, Darwin openly acknowledged
important weaknesses in his theory and professed his own doubts about key
aspects of it. Yet today’s public defenders of a Darwin-only science curriculum
apparently do not want these, or any other scientific doubts about contemporary
Darwinian theory, reported to students.

This book addresses Darwin’s most significant doubt and what has become of
it. It examines an event during a remote period of geological history in which
numerous animal forms appear to have arisen suddenly and without evolutionary
precursors in the fossil record, a mysterious event commonly referred to as the
“Cambrian explosion.” As he acknowledged in the Origin, Darwin viewed this
event as a troubling anomaly—one that he hoped future fossil discoveries would
eventually eliminate.

The book is divided into three main parts. Part One, “The Mystery of the
Missing Fossils,” describes the problem that first generated Darwin’s doubt—the
missing ancestors of the Cambrian animals in the earlier Precambrian fossil
record—and then tells the story of the successive, but unsuccessful, attempts that
biologists and paleontologists have made to resolve that mystery.
Part Two, “How to Build an Animal,” explains why the discovery of the
importance of information to living systems has made the mystery of the
Cambrian explosion more acute. Biologists now know that the Cambrian
explosion not only represents an explosion of new animal form and structure but
also an explosion of information—that it was, indeed, one of the most significant
“information revolutions” in the history of life. Part Two examines the problem
of explaining how the unguided mechanism of natural selection and random
mutations could have produced the biological information necessary to build the
Cambrian animal forms. This group of chapters explains why so many leading
biologists now doubt the creative power of the neo-Darwinian mechanism and it
presents four rigorous critiques of the mechanism based on recent biological research.

Part Three, “After Darwin, What?” evaluates more current evolutionary
theories to see if any of them explain the origin of form and information more
satisfactorily than standard neo-Darwinism does. Part Three also presents and
assesses the theory of intelligent design as a possible solution to the Cambrian
mystery. A concluding chapter discusses the implications of the debate about
design in biology for the larger philosophical questions that animate human
existence. As the story of the book unfolds, it will become apparent that a
seemingly isolated anomaly that Darwin acknowledged almost in passing has
grown to become illustrative of a fundamental problem for all of evolutionary
biology: the problem of the origin of biological form and information.
To see where that problem came from and why it has generated a crisis in
evolutionary biology, we need to begin at the beginning: with Darwin’s own
doubt, with the fossil evidence that elicited it, and with a clash between a pair of
celebrated Victorian naturalists—the famed Harvard paleontologist Louis
Agassiz and Charles Darwin himself.

Table of Contents

Part One: The Mystery of the Missing Fossils
1 - Darwin’s Nemesis
2 - The Burgess Bestiary
3 - Soft Bodies and Hard Facts
4 - The Not Missing Fossils?
5 - The Genes Tell the Story?
6 - The Animal Tree of Life
7 - Punk Eek!
Part Two: How to Build an Animal
8 - The Cambrian Information Explosion
9 - Combinatorial Inflation
10 - The Origin of Genes and Proteins
11 - Assume a Gene
12 - Complex Adaptations and the Neo-Darwinian Math
13 - The Origin of Body Plans
14 - The Epigenetic Revolution
Part Three: After Darwin, What?
15 - The Post-Darwinian World and Self-Organization
16 - Other Post-Neo-Darwinian Models
17 - The Possibility of Intelligent Design
18 - Signs of Design in the Cambrian Explosion
19 - The Rules of Science
20 - What’s at Stake
Credits and Permissions
Photographic Insert
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