Design: The Origin of Biological Information and the Higher Taxonomic Categories
Proceedings of the Biological Society of Washington
August 20, 2005
On August 4th, 2004 an extensive review essay by Dr. Stephen
C. Meyer, Director of Discovery Institute's Center for Science & Culture appeared in the Proceedings
of the Biological Society of Washington (volume 117, no. 2, pp. 213-239). The Proceedings
is a peer-reviewed biology journal published at the National Museum of Natural History at the
Smithsonian Institution in Washington D.C.
In the article, entitled “The Origin of Biological Information and the Higher Taxonomic
Categories”, Dr. Meyer argues that no current materialistic theory of evolution can account for
the origin of the information necessary to build novel animal forms. He proposes intelligent
design as an alternative explanation for the origin of biological information and the higher taxa.
Due to an unusual number of inquiries about the article, Dr. Meyer, the copyright holder, has
decided to make the article available now in HTML format on this website. (Off prints are also
available from Discovery Institute by writing to Keith Pennock at Kpennock@discovery.org. Please
provide your mailing address and we will dispatch a copy).
PROCEEDINGS OF THE BIOLOGICAL SOCIETY OF WASHINGTON
The origin of biological information and the higher taxonomic categories
In a recent volume of the Vienna Series in a Theoretical Biology (2003), Gerd B. Muller and Stuart
Newman argue that what they call the “origination of organismal form” remains an unsolved
problem. In making this claim, Muller and Newman (2003:3-10) distinguish two distinct issues,
namely, (1) the causes of form generation in the individual organism during embryological
development and (2) the causes responsible for the production of novel organismal forms in the
first place during the history of life. To distinguish the latter case (phylogeny) from the former
(ontogeny), Muller and Newman use the term “origination” to designate the causal processes by
which biological form first arose during the evolution of life. They insist that “the molecular
mechanisms that bring about biological form in modern day embryos should not be confused” with
the causes responsible for the origin (or “origination”) of novel biological forms during the
history of life (p.3). They further argue that we know more about the causes of ontogenesis, due
to advances in molecular biology, molecular genetics and developmental biology, than we do about
the causes of phylogenesis--the ultimate origination of new biological forms during the remote
In making this claim, Muller and Newman are careful to affirm that evolutionary biology has
succeeded in explaining how preexisting forms diversify under the twin influences of natural
selection and variation of genetic traits. Sophisticated mathematically-based models of population
genetics have proven adequate for mapping and understanding quantitative variability and
populational changes in organisms. Yet Muller and Newman insist that population genetics, and thus
evolutionary biology, has not identified a specifically causal explanation for the origin of true
morphological novelty during the history of life. Central to their concern is what they see as the
inadequacy of the variation of genetic traits as a source of new form and structure. They note,
following Darwin himself, that the sources of new form and structure must precede the action of
natural selection (2003:3)--that selection must act on what already exists. Yet, in their view,
the “genocentricity” and “incrementalism” of the neo-Darwinian mechanism has meant that an
adequate source of new form and structure has yet to be identified by theoretical biologists.
Instead, Muller and Newman see the need to identify epigenetic sources of morphological innovation
during the evolution of life. In the meantime, however, they insist neo-Darwinism lacks any “theory
of the generative” (p. 7).
As it happens, Muller and Newman are not alone in this judgment. In the last decade or so a host
of scientific essays and books have questioned the efficacy of selection and mutation as a
mechanism for generating morphological novelty, as even a brief literature survey will establish.
Thomson (1992:107) expressed doubt that large-scale morphological changes could accumulate via
minor phenotypic changes at the population genetic level. Miklos (1993:29) argued that
neo-Darwinism fails to provide a mechanism that can produce large-scale innovations in form and
complexity. Gilbert et al. (1996) attempted to develop a new theory of evolutionary mechanisms to
supplement classical neo-Darwinism, which, they argued, could not adequately explain
macroevolution. As they put it in a memorable summary of the situation: “starting in the 1970s,
many biologists began questioning its (neo-Darwinism's) adequacy in explaining evolution. Genetics
might be adequate for explaining microevolution, but microevolutionary changes in gene frequency
were not seen as able to turn a reptile into a mammal or to convert a fish into an amphibian.
Microevolution looks at adaptations that concern the survival of the fittest, not the arrival of
the fittest. As Goodwin (1995) points out, 'the origin of species--Darwin's problem--remains
unsolved'“ (p. 361). Though Gilbert et al. (1996) attempted to solve the problem of the origin
of form by proposing a greater role for developmental genetics within an otherwise neo-Darwinian
numerous recent authors have continued to raise questions about the adequacy of that framework
itself or about the problem of the origination of form generally (Webster & Goodwin 1996;
Shubin & Marshall 2000; Erwin 2000; Conway Morris 2000, 2003b; Carroll 2000; Wagner 2001;
Becker & Lonnig 2001; Stadler et al. 2001; Lonnig & Saedler 2002; Wagner & Stadler
2003; Valentine 2004:189-194).
What lies behind this skepticism? Is it warranted? Is a new and specifically causal theory needed
to explain the origination of biological form?
This review will address these questions. It will do so by analyzing the problem of the
origination of organismal form (and the corresponding emergence of higher taxa) from a particular
theoretical standpoint. Specifically, it will treat the problem of the origination of the higher
taxonomic groups as a manifestation of a deeper problem, namely, the problem of the origin of the
information (whether genetic or epigenetic) that, as it will be argued, is necessary to generate
In order to perform this analysis, and to make it relevant and tractable to systematists and
paleontologists, this paper will examine a paradigmatic example of the origin of biological form
and information during the history of life: the Cambrian explosion. During the Cambrian, many
novel animal forms and body plans (representing new phyla, subphyla and classes) arose in a
geologically brief period of time. The following information-based analysis of the Cambrian
explosion will support the claim of recent authors such as Muller and Newman that the mechanism of
selection and genetic mutation does not constitute an adequate causal explanation of the
origination of biological form in the higher taxonomic groups. It will also suggest the need to
explore other possible causal factors for the origin of form and information during the evolution
of life and will examine some other possibilities that have been proposed.
The Cambrian Explosion
The “Cambrian explosion” refers to the geologically sudden appearance of many new animal body
plans about 530 million years ago. At this time, at least nineteen, and perhaps as many as
thirty-five phyla of forty total (Meyer et al. 2003), made their first appearance on earth within
a narrow five- to ten-million-year window of geologic time (Bowring et al. 1993, 1998a:1,
1998b:40; Kerr 1993; Monastersky 1993; Aris-Brosou & Yang 2003). Many new subphyla, between 32
and 48 of 56 total (Meyer et al. 2003), and classes of animals also arose at this time with
representatives of these new higher taxa manifesting significant morphological innovations. The
Cambrian explosion thus marked a major episode of morphogenesis in which many new and disparate
organismal forms arose in a geologically brief period of time.
To say that the fauna of the Cambrian period appeared in a geologically sudden manner also implies
the absence of clear transitional intermediate forms connecting Cambrian animals with simpler
pre-Cambrian forms. And, indeed, in almost all cases, the Cambrian animals have no clear
morphological antecedents in earlier Vendian or Precambrian fauna (Miklos 1993, Erwin et al.
1997:132, Steiner & Reitner 2001, Conway Morris 2003b:510, Valentine et al. 2003:519-520).
Further, several recent discoveries and analyses suggest that these morphological gaps may not be
merely an artifact of incomplete sampling of the fossil record (Foote 1997, Foote et al. 1999,
Benton & Ayala 2003, Meyer et al. 2003), suggesting that the fossil record is at least
approximately reliable (Conway Morris 2003b:505).
As a result, debate now exists about the extent to which this pattern of evidence comports with a
strictly monophyletic view of evolution (Conway Morris 1998a, 2003a, 2003b:510; Willmer 1990,
2003). Further, among those who accept a monophyletic view of the history of life, debate exists
about whether to privilege fossil or molecular data and analyses. Those who think the fossil data
provide a more reliable picture of the origin of the Metazoan tend to think these animals arose
relatively quickly--that the Cambrian explosion had a “short fuse.” (Conway Morris
2003b:505-506, Valentine & Jablonski 2003). Some (Wray et al. 1996), but not all (Ayala et al.
1998), who think that molecular phylogenies establish reliable divergence times from pre-Cambrian
ancestors think that the Cambrian animals evolved over a very long period of time--that the
Cambrian explosion had a “long fuse.” This review will not address these questions of
historical pattern. Instead, it will analyze whether the neo-Darwinian process of mutation and
selection, or other processes of evolutionary change, can generate the form and information
necessary to produce the animals that arise in the Cambrian. This analysis will, for the most
therefore, not depend upon assumptions of either a long or short fuse for the Cambrian explosion,
or upon a monophyletic or polyphyletic view of the early history of life.
Defining Biological Form and Information
Form, like life itself, is easy to recognize but often hard to define precisely. Yet, a reasonable
working definition of form will suffice for our present purposes. Form can be defined as the
four-dimensional topological relations of anatomical parts. This means that one can understand
form as a unified arrangement of body parts or material components in a distinct shape or pattern
(topology)--one that exists in three spatial dimensions and which arises in time during ontogeny.
Insofar as any particular biological form constitutes something like a distinct arrangement of
constituent body parts, form can be seen as arising from constraints that limit the possible
arrangements of matter. Specifically, organismal form arises (both in phylogeny and ontogeny) as
possible arrangements of material parts are constrained to establish a specific or particular
arrangement with an identifiable three dimensional topography--one that we would recognize as a
particular protein, cell type, organ, body plan or organism. A particular “form,” therefore,
represents a highly specific and constrained arrangement of material components (among a much
larger set of possible arrangements).
Understanding form in this way suggests a connection to the notion of information in its most
theoretically general sense. When Shannon (1948) first developed a mathematical theory of
information he equated the amount of information transmitted with the amount of uncertainty
reduced or eliminated in a series of symbols or characters. Information, in Shannon's theory, is
thus imparted as some options are excluded and others are actualized. The greater the number of
options excluded, the greater the amount of information conveyed. Further, constraining a set of
possible material arrangements by whatever process or means involves excluding some options and
actualizing others. Thus, to constrain a set of possible material states is to generate
information in Shannon's sense. It follows that the constraints that produce biological form also
imparted information. Or conversely, one might say that producing organismal form by
definition requires the generation of information.
In classical Shannon information theory, the amount of information in a system is also inversely
related to the probability of the arrangement of constituents in a system or the characters along
a communication channel (Shannon 1948). The more improbable (or complex) the arrangement, the more
Shannon information, or information-carrying capacity, a string or system possesses.
Since the 1960s, mathematical biologists have realized that Shannon's theory could be applied to
the analysis of DNA and proteins to measure the information-carrying capacity of these
macromolecules. Since DNA contains the assembly instructions for building proteins, the
information-processing system in the cell represents a kind of communication channel (Yockey
1992:110). Further, DNA conveys information via specifically arranged sequences of nucleotide
bases. Since each of the four bases has a roughly equal chance of occurring at each site along the
spine of the DNA molecule, biologists can calculate the probability, and thus the
information-carrying capacity, of any particular sequence n bases long.
The ease with which information theory applies to molecular biology has created confusion about
the type of information that DNA and proteins possess. Sequences of nucleotide bases in DNA, or
amino acids in a protein, are highly improbable and thus have large information-carrying
capacities. But, like meaningful sentences or lines of computer code, genes and proteins are also specified
with respect to function. Just as the meaning of a sentence depends upon the specific arrangement
of the letters in a sentence, so too does the function of a gene sequence depend upon the specific
arrangement of the nucleotide bases in a gene. Thus, molecular biologists beginning with Crick
equated information not only with complexity but also with “specificity,” where “specificity”
or “specified” has meant “necessary to function” (Crick 1958:144, 153; Sarkar, 1996:191).3
Molecular biologists such as Monod and Crick understood biological information--the information
stored in DNA and proteins--as something more than mere complexity (or improbability). Their
notion of information associated both biochemical contingency and combinatorial complexity with
DNA sequences (allowing DNA's carrying capacity to be calculated), but it also affirmed that
sequences of nucleotides and amino acids in functioning macromolecules possessed a high degree of specificity
relative to the maintenance of cellular function.
The ease with which information theory applies to molecular biology has also created confusion
about the location of information in organisms. Perhaps because the information carrying capacity
of the gene could be so easily measured, it has been easy to treat DNA, RNA and proteins as the
sole repositories of biological information. Neo-Darwinists in particular have assumed that the
origination of biological form could be explained by recourse to processes of genetic variation
and mutation alone (Levinton 1988:485). Yet if one understands organismal form as resulting from
constraints on the possible arrangements of matter at many levels in the biological
hierarchy--from genes and proteins to cell types and tissues to organs and body plans--then
clearly biological organisms exhibit many levels of information-rich structure.
Thus, we can pose a question, not only about the origin of genetic information, but also about the
origin of the information necessary to generate form and structure at levels higher than that
present in individual proteins. We must also ask about the origin of the “specified complexity,”
as opposed to mere complexity, that characterizes the new genes, proteins, cell types and body
plans that arose in the Cambrian explosion. Dembski (2002) has used the term “complex specified
information” (CSI) as a synonym for “specified complexity” to help distinguish functional
biological information from mere Shannon information--that is, specified complexity from mere
complexity. This review will use this term as well.
The Cambrian Information Explosion
The Cambrian explosion represents a remarkable jump in the specified complexity or “complex
specified information” (CSI) of the biological world. For over three billions years, the
biological realm included little more than bacteria and algae (Brocks et al. 1999). Then,
beginning about 570-565 million years ago (mya), the first complex multicellular organisms
appeared in the rock strata, including sponges, cnidarians, and the peculiar Ediacaran biota
(Grotzinger et al. 1995). Forty million years later, the Cambrian explosion occurred (Bowring et
al. 1993). The emergence of the Ediacaran biota (570 mya), and then to a much greater extent the
Cambrian explosion (530 mya), represented steep climbs up the biological complexity gradient.
One way to estimate the amount of new CSI that appeared with the Cambrian animals is to count the
number of new cell types that emerged with them (Valentine 1995:91-93). Studies of modern animals
suggest that the sponges that appeared in the late Precambrian, for example, would have required
five cell types, whereas the more complex animals that appeared in the Cambrian (e.g., arthropods)
would have required fifty or more cell types. Functionally more complex animals require more cell
types to perform their more diverse functions. New cell types require many new and specialized
proteins. New proteins, in turn, require new genetic information. Thus an increase in the number
of cell types implies (at a minimum) a considerable increase in the amount of specified genetic
information. Molecular biologists have recently estimated that a minimally complex single-celled
organism would require between 318 and 562 kilobase pairs of DNA to produce the proteins necessary
to maintain life (Koonin 2000). More complex single cells might require upward of a million base
pairs. Yet to build the proteins necessary to sustain a complex arthropod such as a trilobite
would require orders of magnitude more coding instructions. The genome size of a modern arthropod,
the fruitfly Drosophila melanogaster, is approximately 180 million base pairs (Gerhart
& Kirschner 1997:121, Adams et al. 2000). Transitions from a single cell to colonies of cells
to complex animals represent significant (and, in principle, measurable) increases in CSI.
Building a new animal from a single-celled organism requires a vast amount of new genetic
information. It also requires a way of arranging gene products--proteins--into higher levels of
organization. New proteins are required to service new cell types. But new proteins must be
organized into new systems within the cell; new cell types must be organized into new tissues,
organs, and body parts. These, in turn, must be organized to form body plans. New animals,
therefore, embody hierarchically organized systems of lower-level parts within a functional whole.
Such hierarchical organization itself represents a type of information, since body plans comprise
both highly improbable and functionally specified arrangements of lower-level parts. The specified
complexity of new body plans requires explanation in any account of the Cambrian explosion.
Can neo-Darwinism explain the discontinuous increase in CSI that appears in the Cambrian
explosion--either in the form of new genetic information or in the form of hierarchically
organized systems of parts? We will now examine the two parts of this question.
Novel Genes and Proteins
Many scientists and mathematicians have questioned the ability of mutation and selection to
generate information in the form of novel genes and proteins. Such skepticism often derives from
consideration of the extreme improbability (and specificity) of functional genes and proteins.
A typical gene contains over one thousand precisely arranged bases. For any specific arrangement
of four nucleotide bases of length n, there is a corresponding number of possible
arrangements of bases, 4n. For any protein, there are 20n
possible arrangements of protein-forming amino acids. A gene 999 bases in length represents one of
4999 possible nucleotide sequences; a protein of 333 amino acids is one of 20333
Since the 1960s, some biologists have thought functional proteins to be rare among the set of
possible amino acid sequences. Some have used an analogy with human language to illustrate why
this should be the case. Denton (1986, 309-311), for example, has shown that meaningful words and
sentences are extremely rare among the set of possible combinations of English letters, especially
as sequence length grows. (The ratio of meaningful 12-letter words to 12-letter sequences is 1/1014,
the ratio of 100-letter sentences to possible 100-letter strings is 1/10100.) Further,
Denton shows that most meaningful sentences are highly isolated from one another in the
space of possible combinations, so that random substitutions of letters will, after a very few
changes, inevitably degrade meaning. Apart from a few closely clustered sentences accessible by
random substitution, the overwhelming majority of meaningful sentences lie, probabilistically
speaking, beyond the reach of random search.
Denton (1986:301-324) and others have argued that similar constraints apply to genes and proteins.
They have questioned whether an undirected search via mutation and selection would have a
reasonable chance of locating new islands of function--representing fundamentally new genes or
proteins--within the time available (Eden 1967, Shutzenberger 1967, Lovtrup 1979). Some have also
argued that alterations in sequencing would likely result in loss of protein function before
fundamentally new function could arise (Eden 1967, Denton 1986). Nevertheless, neither the extent
to which genes and proteins are sensitive to functional loss as a result of sequence change, nor
the extent to which functional proteins are isolated within sequence space, has been fully known.
Recently, experiments in molecular biology have shed light on these questions. A variety of
mutagenesis techniques have shown that proteins (and thus the genes that produce them) are indeed
highly specified relative to biological function (Bowie & Sauer 1989, Reidhaar-Olson &
Sauer 1990, Taylor et al. 2001). Mutagenesis research tests the sensitivity of proteins (and, by
implication, DNA) to functional loss as a result of alterations in sequencing. Studies of proteins
have long shown that amino acid residues at many active positions cannot vary without functional
loss (Perutz & Lehmann 1968). More recent protein studies (often using mutagenesis
experiments) have shown that functional requirements place significant constraints on sequencing
even at non-active site positions (Bowie & Sauer 1989, Reidhaar-Olson & Sauer 1990,
Chothia et al. 1998, Axe 2000, Taylor et al. 2001). In particular, Axe (2000) has shown that
multiple as opposed to single position amino acid substitutions inevitably result in loss of
protein function, even when these changes occur at sites that allow variation when altered in
isolation. Cumulatively, these constraints imply that proteins are highly sensitive to functional
loss as a result of alterations in sequencing, and that functional proteins represent highly
isolated and improbable arrangements of amino acids -arrangements that are far more improbable, in
fact, than would be likely to arise by chance alone in the time available (Reidhaar-Olson &
Sauer 1990; Behe 1992; Kauffman 1995:44; Dembski 1998:175-223; Axe 2000, 2004). (See below the
discussion of the neutral theory of evolution for a precise quantitative assessment.)
Of course, neo-Darwinists do not envision a completely random search through the set of all
possible nucleotide sequences--so-called “sequence space.” They envision natural selection
acting to preserve small advantageous variations in genetic sequences and their corresponding
protein products. Dawkins (1996), for example, likens an organism to a high mountain peak. He
compares climbing the sheer precipice up the front side of the mountain to building a new organism
by chance. He acknowledges that his approach up “Mount Improbable” will not succeed.
Nevertheless, he suggests that there is a gradual slope up the backside of the mountain that could
be climbed in small incremental steps. In his analogy, the backside climb up “Mount Improbable”
corresponds to the process of natural selection acting on random changes in the genetic text. What
chance alone cannot accomplish blindly or in one leap, selection (acting on mutations) can
accomplish through the cumulative effect of many slight successive steps.
Yet the extreme specificity and complexity of proteins presents a difficulty, not only for the
chance origin of specified biological information (i.e., for random mutations acting alone), but
also for selection and mutation acting in concert. Indeed, mutagenesis experiments cast doubt on
each of the two scenarios by which neo-Darwinists envisioned new information arising from the
mutation/selection mechanism (for review, see Lonnig 2001). For neo-Darwinism, new functional
genes either arise from non-coding sections in the genome or from preexisting genes. Both
scenarios are problematic.
In the first scenario, neo-Darwinists envision new genetic information arising from those sections
of the genetic text that can presumably vary freely without consequence to the organism. According
to this scenario, non-coding sections of the genome, or duplicated sections of coding regions, can
experience a protracted period of “neutral evolution” (Kimura 1983) during which alterations
in nucleotide sequences have no discernible effect on the function of the organism. Eventually,
however, a new gene sequence will arise that can code for a novel protein. At that point, natural
selection can favor the new gene and its functional protein product, thus securing the
preservation and heritability of both.
This scenario has the advantage of allowing the genome to vary through many generations, as
mutations “search” the space of possible base sequences. The scenario has an overriding
problem, however: the size of the combinatorial space (i.e., the number of possible amino acid
sequences) and the extreme rarity and isolation of the functional sequences within that space of
possibilities. Since natural selection can do nothing to help generate new functional
sequences, but rather can only preserve such sequences once they have arisen, chance alone--random
variation--must do the work of information generation--that is, of finding the exceedingly rare
functional sequences within the set of combinatorial possibilities. Yet the probability of
randomly assembling (or “finding,” in the previous sense) a functional sequence is extremely
Cassette mutagenesis experiments performed during the early 1990s suggest that the probability of
attaining (at random) the correct sequencing for a short protein 100 amino acids long is about 1
in 1065 (Reidhaar-Olson & Sauer 1990, Behe 1992:65-69). This result agreed closely
with earlier calculations that Yockey (1978) had performed based upon the known sequence
variability of cytochrome c in different species and other theoretical considerations. More recent
mutagenesis research has provided additional support for the conclusion that functional proteins
are exceedingly rare among possible amino acid sequences (Axe 2000, 2004). Axe (2004) has
performed site directed mutagenesis experiments on a 150-residue protein-folding domain within a
B-lactamase enzyme. His experimental method improves upon earlier mutagenesis techniques and
corrects for several sources of possible estimation error inherent in them. On the basis of these
experiments, Axe has estimated the ratio of (a) proteins of typical size (150 residues) that
perform a specified function via any folded structure to (b) the whole set of possible amino acids
sequences of that size. Based on his experiments, Axe has estimated his ratio to be 1 to 1077.
Thus, the probability of finding a functional protein among the possible amino acid sequences
corresponding to a 150-residue protein is similarly 1 in 1077.
Other considerations imply additional improbabilities. First, new Cambrian animals would require
proteins much longer than 100 residues to perform many necessary specialized functions. Ohno
(1996) has noted that Cambrian animals would have required complex proteins such as lysyl oxidase
in order to support their stout body structures. Lysyl oxidase molecules in extant organisms
comprise over 400 amino acids. These molecules are both highly complex (non-repetitive) and
functionally specified. Reasonable extrapolation from mutagenesis experiments done on shorter
protein molecules suggests that the probability of producing functionally sequenced proteins of
this length at random is so small as to make appeals to chance absurd, even granting the duration
of the entire universe. (See Dembski 1998:175-223 for a rigorous calculation of this “Universal
Probability Bound”; See also Axe 2004.) Yet, second, fossil data (Bowring et al. 1993, 1998a:1,
1998b:40; Kerr 1993; Monatersky 1993), and even molecular analyses supporting deep divergence
(Wray et al. 1996), suggest that the duration of the Cambrian explosion (between 5-10 x 106
and, at most, 7 x 107 years) is far smaller than that of the entire universe (1.3-2 x
1010 years). Third, DNA mutation rates are far too low to generate the novel genes and
proteins necessary to building the Cambrian animals, given the most probable duration of the
explosion as determined by fossil studies (Conway Morris 1998b). As Ohno (1996:8475) notes, even a
mutation rate of 10-9 per base pair per year results in only a 1% change in the
sequence of a given section of DNA in 10 million years. Thus, he argues that mutational divergence
of preexisting genes cannot explain the origin of the Cambrian forms in that time.4
The selection/mutation mechanism faces another probabilistic obstacle. The animals that arise in
the Cambrian exhibit structures that would have required many new types of cells, each of
which would have required many novel proteins to perform their specialized functions. Further, new
cell types require Asystems of proteins that must, as a condition of functioning, act in
close coordination with one another. The unit of selection in such systems ascends to the system
as a whole. Natural selection selects for functional advantage. But new cell types require whole
systems of proteins to perform their distinctive functions. In such cases, natural selection
cannot contribute to the process of information generation until after the information
necessary to build the requisite system of proteins has arisen. Thus random variations
must, again, do the work of information generation--and now not simply for one protein, but for
many proteins arising at nearly the same time. Yet the odds of this occurring by chance alone are,
of course, far smaller than the odds of the chance origin of a single gene or protein--so small in
fact as to render the chance origin of the genetic information necessary to build a new cell type
(a necessary but not sufficient condition of building a new body plan) problematic given even the
most optimistic estimates for the duration of the Cambrian explosion.
Dawkins (1986:139) has noted that scientific theories can rely on only so much “luck” before
they cease to be credible. The neutral theory of evolution, which, by its own logic, prevents
natural selection from playing a role in generating genetic information until after the fact,
relies on entirely too much luck. The sensitivity of proteins to functional loss, the need for
long proteins to build new cell types and animals, the need for whole new systems of
proteins to service new cell types, the probable brevity of the Cambrian explosion relative to
mutation rates--all suggest the immense improbability (and implausibility) of any scenario for the
origination of Cambrian genetic information that relies upon random variation alone unassisted by
Yet the neutral theory requires novel genes and proteins to arise--essentially--by random mutation
alone. Adaptive advantage accrues after the generation of new functional genes and
proteins. Thus, natural selection cannot play a role until new information-bearing
molecules have independently arisen. Thus neutral theorists envisioned the need to scale the steep
face of a Dawkins-style precipice of which there is no gradually sloping backside--a
situation that, by Dawkins' own logic, is probabilistically untenable.
In the second scenario, neo-Darwinists envisioned novel genes and proteins arising by numerous
successive mutations in the preexisting genetic text that codes for proteins. To adapt Dawkins's
metaphor, this scenario envisions gradually climbing down one functional peak and then ascending
another. Yet mutagenesis experiments again suggest a difficulty. Recent experiments show that,
even when exploring a region of sequence space populated by proteins of a single fold and
function, most multiple-position changes quickly lead to loss of function (Axe 2000). Yet to turn
one protein into another with a completely novel structure and function requires specified changes
at many sites. Indeed, the number of changes necessary to produce a new protein greatly exceeds
the number of changes that will typically produce functional losses. Given this, the probability
of escaping total functional loss during a random search for the changes needed to produce a new
function is extremely small--and this probability diminishes exponentially with each additional
requisite change (Axe 2000). Thus, Axe's results imply that, in all probability, random searches
for novel proteins (through sequence space) will result in functional loss long before any novel
functional protein will emerge.
Blanco et al. have come to a similar conclusion. Using directed mutagenesis, they have determined
that residues in both the hydrophobic core and on the surface of the protein play essential roles
in determining protein structure. By sampling intermediate sequences between two naturally
occurring sequences that adopt different folds, they found that the intermediate sequences “lack
a well defined three-dimensional structure.” Thus, they conclude that it is unlikely that a new
protein fold via a series of folded intermediates sequences (Blanco et al. 1999:741).
Thus, although this second neo-Darwinian scenario has the advantage of starting with functional
genes and proteins, it also has a lethal disadvantage: any process of random mutation or
rearrangement in the genome would in all probability generate nonfunctional intermediate sequences
before fundamentally new functional genes or proteins would arise. Clearly, nonfunctional
intermediate sequences confer no survival advantage on their host organisms. Natural selection
favors only functional advantage. It cannot select or favor nucleotide sequences or
polypeptide chains that do not yet perform biological functions, and still less will it favor
sequences that efface or destroy preexisting function.
Evolving genes and proteins will range through a series of nonfunctional intermediate sequences
that natural selection will not favor or preserve but will, in all probability, eliminate (Blanco
et al. 1999, Axe 2000). When this happens, selection-driven evolution will cease. At this point,
neutral evolution of the genome (unhinged from selective pressure) may ensue, but, as we have
seen, such a process must overcome immense probabilistic hurdles, even granting cosmic time.
Thus, whether one envisions the evolutionary process beginning with a noncoding region of the
genome or a preexisting functional gene, the functional specificity and complexity of proteins
impose very stringent limitations on the efficacy of mutation and selection. In the first case,
function must arise first, before natural selection can act to favor a novel variation. In the
second case, function must be continuously maintained in order to prevent deleterious (or lethal)
consequences to the organism and to allow further evolution. Yet the complexity and functional
specificity of proteins implies that both these conditions will be extremely difficult to meet.
Therefore, the neo-Darwinian mechanism appears to be inadequate to generate the new information
present in the novel genes and proteins that arise with the Cambrian animals.
Novel Body Plans
The problems with the neo-Darwinian mechanism run deeper still. In order to explain the origin of
the Cambrian animals, one must account not only for new proteins and cell types, but also for the
origin of new body plans. Within the past decade, developmental biology has dramatically advanced
our understanding of how body plans are built during ontogeny. In the process, it has also
uncovered a profound difficulty for neo-Darwinism.
Significant morphological change in organisms requires attention to timing. Mutations in genes
that are expressed late in the development of an organism will not affect the body plan. Mutations
expressed early in development, however, could conceivably produce significant morphological
change (Arthur 1997:21). Thus, events expressed early in the development of organisms have the
only realistic chance of producing large-scale macroevolutionary change (Thomson 1992). As John
and Miklos (1988:309) explain, macroevolutionary change requires alterations in the very early
stages of ontogenesis.
Yet recent studies in developmental biology make clear that mutations expressed early in
development typically have deleterious effects (Arthur 1997:21). For example, when early-acting
body plan molecules, or morphogens such as bicoid (which helps to set up the
anterior-posterior head-to-tail axis in Drosophila), are perturbed, development shuts down
(Nusslein-Volhard & Wieschaus 1980, Lawrence & Struhl 1996, Muller & Newman 2003).5
The resulting embryos die. Moreover, there is a good reason for this. If an engineer modifies the
length of the piston rods in an internal combustion engine without modifying the crankshaft
accordingly, the engine won't start. Similarly, processes of development are tightly integrated
spatially and temporally such that changes early in development will require a host of other
coordinated changes in separate but functionally interrelated developmental processes downstream.
For this reason, mutations will be much more likely to be deadly if they disrupt a functionally
deeply-embedded structure such as a spinal column than if they affect more isolated anatomical
features such as fingers (Kauffman 1995:200).
This problem has led to what McDonald (1983) has called “a great Darwinian paradox” (p. 93).
McDonald notes that genes that are observed to vary within natural populations do not lead to
major adaptive changes, while genes that could cause major changes--the very stuff of
macroevolution--apparently do not vary. In other words, mutations of the kind that macroevolution
doesn't need (namely, viable genetic mutations in DNA expressed late in development) do occur, but
those that it does need (namely, beneficial body plan mutations expressed early in development)
apparently don't occur.6
According to Darwin (1859:108) natural selection cannot act until favorable variations arise in a
population. Yet there is no evidence from developmental genetics that the kind of variations
required by neo-Darwinism--namely, favorable body plan mutations--ever occur.
Developmental biology has raised another formidable problem for the mutation/selection mechanism.
Embryological evidence has long shown that DNA does not wholly determine morphological form
(Goodwin 1985, NiJnout 1990, Sapp 1987, Muller & Newman 2003), suggesting that mutations in
DNA alone cannot account for the morphological changes required to build a new body plan.
DNA helps direct protein synthesis.7
It also helps to regulate the timing and expression of the synthesis of various proteins within
cells. Yet, DNA alone does not determine how individual proteins assemble themselves into larger
systems of proteins; still less does it solely determine how cell types, tissue types, and organs
arrange themselves into body plans (Harold 1995:2774, Moss 2004). Instead, other factors--such as
the three-dimensional structure and organization of the cell membrane and cytoskeleton and the
spatial architecture of the fertilized egg--play important roles in determining body plan
formation during embryogenesis.
For example, the structure and location of the cytoskeleton influence the patterning of embryos.
Arrays of microtubules help to distribute the essential proteins used during development to their
correct locations in the cell. Of course, microtubules themselves are made of many protein
subunits. Nevertheless, like bricks that can be used to assemble many different structures, the
tubulin subunits in the cell's microtubules are identical to one another. Thus, neither the
tubulin subunits nor the genes that produce them account for the different shape of microtubule
arrays that distinguish different kinds of embryos and developmental pathways. Instead, the
structure of the microtubule array itself is determined by the location and arrangement of its
subunits, not the properties of the subunits themselves. For this reason, it is not possible to
predict the structure of the cytoskeleton of the cell from the characteristics of the protein
constituents that form that structure (Harold 2001:125).
Two analogies may help further clarify the point. At a building site, builders will make use of
many materials: lumber, wires, nails, drywall, piping, and windows. Yet building materials do not
determine the floor plan of the house, or the arrangement of houses in a neighborhood. Similarly,
electronic circuits are composed of many components, such as resistors, capacitors, and
transistors. But such lower-level components do not determine their own arrangement in an
integrated circuit. Biological symptoms also depend on hierarchical arrangements of parts. Genes
and proteins are made from simple building blocks--nucleotide bases and amino acids--arranged in
specific ways. Cell types are made of, among other things, systems of specialized proteins. Organs
are made of specialized arrangements of cell types and tissues. And body plans comprise specific
arrangements of specialized organs. Yet, clearly, the properties of individual proteins (or,
indeed, the lower-level parts in the hierarchy generally) do not fully determine the organization
of the higher-level structures and organizational patterns (Harold 2001:125). It follows that the
genetic information that codes for proteins does not determine these higher-level structures
These considerations pose another challenge to the sufficiency of the neo-Darwinian mechanism.
Neo-Darwinism seeks to explain the origin of new information, form, and structure as a result of
selection acting on randomly arising variation at a very low level within the biological
hierarchy, namely, within the genetic text. Yet major morphological innovations depend on a
specificity of arrangement at a much higher level of the organizational hierarchy, a level that
DNA alone does not determine. Yet if DNA is not wholly responsible for body plan morphogenesis,
then DNA sequences can mutate indefinitely, without regard to realistic probabilistic limits, and
still not produce a new body plan. Thus, the mechanism of natural selection acting on random
mutations in DNA cannot in principle generate novel body plans, including those that first
arose in the Cambrian explosion.
Of course, it could be argued that, while many single proteins do not by themselves determine
cellular structures and/or body plans, proteins acting in concert with other proteins or suites of
proteins could determine such higher-level form. For example, it might be pointed out that the
tubulin subunits (cited above) are assembled by other helper proteins--gene products--called
Microtubule Associated Proteins (MAPS). This might seem to suggest that genes and gene products
alone do suffice to determine the development of the three-dimensional structure of the
Yet MAPS, and indeed many other necessary proteins, are only part of the story. The location of
specified target sites on the interior of the cell membrane also helps to determine the shape of
the cytoskeleton. Similarly, so does the position and structure of the centrosome which nucleates
the microtubules that form the cytoskeleton. While both the membrane targets and the centrosomes
are made of proteins, the location and form of these structures is not wholly determined by the
proteins that form them. Indeed, centrosome structure and membrane patterns as a whole
convey three-dimensional structural information that helps determine the structure of the
cytoskeleton and the location of its subunits (McNiven & Porter 1992:313-329). Moreover, the
centrioles that compose the centrosomes replicate independently of DNA replication (Lange et al.
2000:235-249, Marshall & Rosenbaum 2000:187-205). The daughter centriole receives its form
from the overall structure of the mother centriole, not from the individual gene products that
constitute it (Lange et al. 2000). In ciliates, microsurgery on cell membranes can produce
heritable changes in membrane patterns, even though the DNA of the ciliates has not been altered
(Sonneborn 1970:1-13, Frankel 1980:607-623; Nanney 1983:163-170). This suggests that membrane
patterns (as opposed to membrane constituents) are impressed directly on daughter cells. In both
cases, form is transmitted from parent three-dimensional structures to daughter three-dimensional
structures directly and is not wholly contained in constituent proteins or genetic information
Thus, in each new generation, the form and structure of the cell arises as the result of both
gene products and preexisting three-dimensional structure and organization. Cellular structures
are built from proteins, but proteins find their way to correct locations in part because of
preexisting three-dimensional patterns and organization inherent in cellular structures.
Preexisting three-dimensional form present in the preceding generation (whether inherent in the
cell membrane, the centrosomes, the cytoskeleton or other features of the fertilized egg)
contributes to the production of form in the next generation. Neither structural proteins alone,
nor the genes that code for them, are sufficient to determine the three-dimensional shape and
structure of the entities they form. Gene products provide necessary, but not sufficient
conditions, for the development of three-dimensional structure within cells, organs and body plans
(Harold 1995:2767). But if this is so, then natural selection acting on genetic variation alone
cannot produce the new forms that arise in history of life.
Of course, neo-Darwinism is not the only evolutionary theory for explaining the origin of novel
biological form. Kauffman (1995) doubts the efficacy of the mutation/selection mechanism.
Nevertheless, he has advanced a self-organizational theory to account for the emergence of new
form, and presumably the information necessary to generate it. Whereas neo-Darwinism attempts to
explain new form as the consequence of selection acting on random mutation, Kauffman suggests that
selection acts, not mainly on random variations, but on emergent patterns of order that
self-organize via the laws of nature.
Kauffman (1995:47-92) illustrates how this might work with various model systems in a computer
environment. In one, he conceives a system of buttons connected by strings. Buttons represent
novel genes or gene products; strings represent the law-like forces of interaction that obtain
between gene products-i.e., proteins. Kauffman suggests that when the complexity of the system (as
represented by the number of buttons and strings) reaches a critical threshold, new modes of
organization can arise in the system “for free”--that is, naturally and spontaneously--after
the manner of a phase transition in chemistry.
Another model that Kauffman develops is a system of interconnected lights. Each light can flash in
a variety of states--on, off, twinkling, etc. Since there is more than one possible state for each
light, and many lights, there are a vast number of possible states that the system can adopt.
Further, in his system, rules determine how past states will influence future states. Kauffman
asserts that, as a result of these rules, the system will, if properly tuned, eventually produce a
kind of order in which a few basic patterns of light activity recur with greater-than-random
frequency. Since these actual patterns of light activity represent a small portion of the total
number of possible states in which the system can reside, Kauffman seems to imply that
self-organizational laws might similarly result in highly improbable biological outcomes--perhaps
even sequences (of bases or amino acids) within a much larger sequence space of possibilities.
Do these simulations of self-organizational processes accurately model the origin of novel genetic
information? It is hard to think so.
First, in both examples, Kauffman presupposes but does not explain significant sources of
preexisting information. In his buttons-and-strings system, the buttons represent proteins,
themselves packets of CSI, and the result of preexisting genetic information. Where does this
information come from? Kauffman (1995) doesn't say, but the origin of such information is an
essential part of what needs to be explained in the history of life. Similarly, in his light
system, the order that allegedly arises for “for free” actually arises only if the programmer
of the model system “tunes” it in such a way as to keep it from either (a) generating an
excessively rigid order or (b) developing into chaos (pp. 86-88). Yet this necessary tuning
involves an intelligent programmer selecting certain parameters and excluding others--that is,
Second, Kauffman's model systems are not constrained by functional considerations and thus are not
analogous to biological systems. A system of interconnected lights governed by pre-programmed
rules may well settle into a small number of patterns within a much larger space of possibilities.
But because these patterns have no function, and need not meet any functional requirements, they
have no specificity analogous to that present in actual organisms. Instead, examination of
Kauffman's (1995) model systems shows that they do not produce sequences or systems characterized
by specified complexity, but instead by large amounts of symmetrical order or internal
redundancy interspersed with aperiodicity or (mere) complexity (pp. 53, 89, 102). Getting a
law-governed system to generate repetitive patterns of flashing lights, even with a certain amount
of variation, is clearly interesting, but not biologically relevant. On the other hand, a system
of lights flashing the title of a Broadway play would model a biologically relevant
self-organizational process, at least if such a meaningful or functionally specified sequence
arose without intelligent agents previously programming the system with equivalent amounts of CSI.
In any case, Kauffman's systems do not produce specified complexity, and thus do not offer
promising models for explaining the new genes and proteins that arose in the Cambrian.
Even so, Kauffman suggests that his self-organizational models can specifically elucidate aspects
of the Cambrian explosion. According to Kauffman (1995:199-201), new Cambrian animals emerged as
the result of “long jump” mutations that established new body plans in a discrete rather than
gradual fashion. He also recognizes that mutations affecting early development are almost
inevitably harmful. Thus, he concludes that body plans, once established, will not change, and
that any subsequent evolution must occur within an established body plan (Kauffman 1995:201). And
indeed, the fossil record does show a curious (from a neo-Darwinian point of view) top-down
pattern of appearance, in which higher taxa (and the body plans they represent) appear first, only
later to be followed by the multiplication of lower taxa representing variations within those
original body designs (Erwin et al. 1987, Lewin 1988, Valentine & Jablonski 2003:518).
Further, as Kauffman expects, body plans appear suddenly and persist without significant
modification over time.
But here, again, Kauffman begs the most important question, which is: what produces the new
Cambrian body plans in the first place? Granted, he invokes “long jump mutations” to explain
this, but he identifies no specific self-organizational process that can produce such mutations.
Moreover, he concedes a principle that undermines the plausibility of his own proposal. Kauffman
acknowledges that mutations that occur early in development are almost inevitably deleterious. Yet
developmental biologists know that these are the only kind of mutations that have a realistic
chance of producing large-scale evolutionary change--i.e., the big jumps that Kauffman invokes.
Though Kauffman repudiates the neo-Darwinian reliance upon random mutations in favor of
self-organizing order, in the end, he must invoke the most implausible kind of random mutation in
order to provide a self-organizational account of the new Cambrian body plans. Clearly, his model
is not sufficient.
Of course, still other causal explanations have been proposed. During the 1970s, the
paleontologists Eldredge and Gould (1972) proposed the theory of evolution by punctuated
equilibrium in order to account for a pervasive pattern of “sudden appearance” and “stasis”
in the fossil record. Though advocates of punctuated equilibrium were mainly seeking to describe
the fossil record more accurately than earlier gradualist neo-Darwinian models had done, they did
also propose a mechanism--known as species selection--by which the large morphological jumps
evident in fossil record might have been produced. According to punctuationalists, natural
selection functions more as a mechanism for selecting the fittest species rather than the most-fit
individual among a species. Accordingly, on this model, morphological change should occur in
larger, more discrete intervals than it would given a traditional neo-Darwinian understanding.
Despite its virtues as a descriptive model of the history of life, punctuated equilibrium has been
widely criticized for failing to provide a mechanism sufficient to produce the novel form
characteristic of higher taxonomic groups. For one thing, critics have noted that the proposed
mechanism of punctuated evolutionary change simply lacked the raw material upon which to work. As
Valentine and Erwin (1987) note, the fossil record fails to document a large pool of species prior
to the Cambrian. Yet the proposed mechanism of species selection requires just such a pool of
species upon which to act. Thus, they conclude that the mechanism of species selection probably
does not resolve the problem of the origin of the higher taxonomic groups (p. 96).8
Further, punctuated equilibrium has not addressed the more specific and fundamental problem of
explaining the origin of the new biological information (whether genetic or epigenetic) necessary
to produce novel biological form. Advocates of punctuated equilibrium might assume that the new
species (upon which natural selection acts) arise by known microevolutionary processes of
speciation (such as founder effect, genetic drift or bottleneck effect) that do not necessarily
depend upon mutations to produce adaptive changes. But, in that case, the theory lacks an account
of how the specifically higher taxa arise. Species selection will only produce more fit
species. On the other hand, if punctuationalists assume that processes of genetic mutation can
produce more fundamental morphological changes and variations, then their model becomes subject to
the same problems as neo-Darwinism (see above). This dilemma is evident in Gould (2002:710)
insofar as his attempts to explain adaptive complexity inevitably employ classical neo-Darwinian
modes of explanation.9
Another attempt to explain the origin of form has been proposed by the structuralists such as
Gerry Webster and Brian Goodwin (1984, 1996). These biologists, drawing on the earlier work of
D'Arcy Thompson (1942), view biological form as the result of structural constraints imposed upon
matter by morphogenetic rules or laws. For reasons similar to those discussed above, the
structuralists have insisted that these generative or morphogenetic rules do not reside in the
lower level building materials of organisms, whether in genes or proteins. Webster and Goodwin
(1984:510-511) further envisioned morphogenetic rules or laws operating ahistorically, similar to
the way in which gravitational or electromagnetic laws operate. For this reason, structuralists
see phylogeny as of secondary importance in understanding the origin of the higher taxa, though
they think that transformations of form can occur. For structuralists, constraints on the
arrangement of matter arise not mainly as the result of historical contingencies--such as
environmental changes or genetic mutations--but instead because of the continuous ahistorical
operation of fundamental laws of form--laws that organize or inform matter.
While this approach avoids many of the difficulties currently afflicting neo-Darwinism (in
particular those associated with its “genocentricity”), critics (such as Maynard Smith 1986)
of structuralism have argued that the structuralist explanation of form lacks specificity. They
note that structuralists have been unable to say just where laws of form reside--whether in the
universe, or in every possible world, or in organisms as a whole, or in just some part of
organisms. Further, according to structuralists, morphogenetic laws are mathematical in character.
Yet, structuralists have yet to specify the mathematical formulae that determine biological forms.
Others (Yockey 1992; Polanyi 1967, 1968; Meyer 2003) have questioned whether physical laws could
in principle generate the kind of complexity that characterizes biological systems. Structuralists
envision the existence of biological laws that produce form in much the same way that physical
laws produce form. Yet the forms that physicists regard as manifestations of underlying laws are
characterized by large amounts of symmetric or redundant order, by relatively simple patterns such
as vortices or gravitational fields or magnetic lines of force. Indeed, physical laws are
typically expressed as differential equations (or algorithms) that almost by definition describe
recurring phenomena--patterns of compressible “order” not “complexity” as defined by
algorithmic information theory (Yockey 1992:77-83). Biological forms, by contrast, manifest
greater complexity and derive in ontogeny from highly complex initial conditions--i.e.,
non-redundant sequences of nucleotide bases in the genome and other forms of information expressed
in the complex and irregular three-dimensional topography of the organism or the fertilized egg.
Thus, the kind of form that physical laws produce is not analogous to biological form--at least
not when compared from the standpoint of (algorithmic) complexity. Further, physical laws lack the
information content to specify biology systems. As Polyanyi (1967, 1968) and Yockey (1992:290)
have shown, the laws of physics and chemistry allow, but do not determine, distinctively
biological modes of organization. In other words, living systems are consistent with, but not
deducible, from physical-chemical laws (1992:290).
Of course, biological systems do manifest some reoccurring patterns, processes and behaviors. The
same type of organism develops repeatedly from similar ontogenetic processes in the same species.
Similar processes of cell division reoccur in many organisms. Thus, one might describe certain
biological processes as law-governed. Even so, the existence of such biological regularities does
not solve the problem of the origin of form and information, since the recurring processes
described by such biological laws (if there be such laws) only occur as the result of preexisting
stores of (genetic and/or epigenetic) information and these information-rich initial conditions
impose the constraints that produce the recurring behavior in biological systems. (For example,
processes of cell division recur with great frequency in organisms, but depend upon
information-rich DNA and proteins molecules.) In other words, distinctively biological
regularities depend upon preexisting biological information. Thus, appeals to higher-level
biological laws presuppose, but do not explain, the origination of the information necessary to
Thus, structuralism faces a difficult in principle dilemma. On the one hand, physical laws produce
very simple redundant patterns that lack the complexity characteristic of biological systems. On
the other hand, distinctively biological laws--if there are such laws--depend upon preexisting
information-rich structures. In either case, laws are not good candidates for explaining the
origination of biological form or the information necessary to produce it.
Cladism: An Artifact of Classification?
Some cladists have advanced another approach to the problem of the origin of form, specifically as
it arises in the Cambrian. They have argued that the problem of the origin of the phyla is an
artifact of the classification system, and therefore, does not require explanation. Budd and
Jensen (2000), for example, argue that the problem of the Cambrian explosion resolves itself if
one keeps in mind the cladistic distinction between “stem” and “crown” groups. Since crown
groups arise whenever new characters are added to simpler more ancestral stem groups during the
evolutionary process, new phyla will inevitably arise once a new stem group has arisen. Thus, for
Budd and Jensen what requires explanation is not the crown groups corresponding to the new
Cambrian phyla, but the earlier more primitive stem groups that presumably arose deep in the
Proterozoic. Yet since these earlier stem groups are by definition less derived, explaining them
will be considerably easier than explaining the origin of the Cambrian animals de novo. In
any case, for Budd and Jensen the explosion of new phyla in the Cambrian does not require
explanation. As they put it, “given that the early branching points of major clades is an
inevitable result of clade diversification, the alleged phenomenon of the phyla appearing early
and remaining morphologically static is not seen to require particular explanation” (Budd &
While superficially plausible, perhaps, Budd and Jensen's attempt to explain away the Cambrian
explosion begs crucial questions. Granted, as new characters are added to existing forms, novels
morphology and greater morphological disparity will likely result. But what causes new characters
to arise? And how does the information necessary to produce new characters originate? Budd and
Jensen do not specify. Nor can they say how derived the ancestral forms are likely to have been,
and what processes, might have been sufficient to produce them. Instead, they simply assume the
sufficiency of known neo-Darwinian mechanisms (Budd & Jensen 2000:288). Yet, as shown above,
this assumption is now problematic. In any case, Budd and Jensen do not explain what causes the
origination of biological form and information.
Convergence and Teleological Evolution
More recently, Conway Morris (2000, 2003c) has suggested another possible explanation based on the
tendency for evolution to converge on the same structural forms during the history of life. Conway
Morris cites numerous examples of organisms that possess very similar forms and structures, even
though such structures are often built from different material substrates and arise (in ontogeny)
by the expression of very different genes. Given the extreme improbability of the same structures
arising by random mutation and selection in disparate phylogenies, Conway Morris argues that the
pervasiveness of convergent structures suggests that evolution may be in some way “channeled”
toward similar functional and/or structural endpoints. Such an end-directed understanding of
evolution, he admits, raises the controversial prospect of a teleological or purposive element in
the history of life. For this reason, he argues that the phenomenon of convergence has received
less attention than it might have otherwise. Nevertheless, he argues that just as physicists have
reopened the question of design in their discussions of anthropic fine-tuning, the ubiquity of
convergent structures in the history of life has led some biologists (Denton 1998) to consider
extending teleological thinking to biology. And, indeed, Conway Morris himself intimates that the
evolutionary process might be “underpinned by a purpose” (2000:8, 2003b:511).
Conway Morris, of course, considers this possibility in relation to a very specific aspect of the
problem of organismal form, namely, the problem of explaining why the same forms arise repeatedly
in so many disparate lines of decent. But this raises a question. Could a similar approach shed
explanatory light on the more general causal question that has been addressed in this review?
Could the notion of purposive design help provide a more adequate explanation for the origin of
organismal form generally? Are there reasons to consider design as an explanation for the origin
of the biological information necessary to produce the higher taxa and their corresponding
The remainder of this review will suggest that there are such reasons. In so doing, it may also
help explain why the issue of teleology or design has reemerged within the scientific discussion
of biological origins (Denton 1986, 1998; Thaxton et al. 1992; Kenyon & Mills 1996: Behe 1996,
2004; Dembski 1998, 2002, 2004; Conway Morris 2000, 2003a, 2003b, Lonnig 2001; Lonnig &
Saedler 2002; Nelson & Wells 2003; Meyer 2003, 2004; Bradley 2004) and why some scientists and
philosophers of science have considered teleological explanations for the origin of form and
information despite strong methodological prohibitions against design as a scientific hypothesis
(Gillespie 1979, Lenior 1982:4).
First, the possibility of design as an explanation follows logically from a consideration of the
deficiencies of neo-Darwinism and other current theories as explanations for some of the more
striking “appearances of design” in biological systems. Neo-Darwinists such as Ayala (1994:5),
Dawkins (1986:1), Mayr (1982:xi-xii) and Lewontin (1978) have long acknowledged that organisms
appear to have been designed. Of course, neo-Darwinists assert that what Ayala (1994:5) calls the
“obvious design” of living things is only apparent since the selection/mutation mechanism can
explain the origin of complex form and organization in living systems without an appeal to a
designing agent. Indeed, neo-Darwinists affirm that mutation and selection--and perhaps other
similarly undirected mechanisms--are fully sufficient to explain the appearance of design in
biology. Self-organizational theorists and punctuationalists modify this claim, but affirm its
essential tenet. Self-organization theorists argue that natural selection acting on self
organizing order can explain the complexity of living things--again, without any appeal to design.
Punctuationalists similarly envision natural selection acting on newly arising species with no
actual design involved.
And clearly, the neo-Darwinian mechanism does explain many appearances of design, such as the
adaptation of organisms to specialized environments that attracted the interest of 19th century
biologists. More specifically, known microevolutionary processes appear quite sufficient to
account for changes in the size of Galapagos finch beaks that have occurred in response to
variations in annual rainfall and available food supplies (Weiner 1994, Grant 1999).
But does neo-Darwinism, or any other fully materialistic model, explain all appearances of design
in biology, including the body plans and information that characterize living systems? Arguably,
biological forms--such as the structure of a chambered nautilus, the organization of a trilobite,
the functional integration of parts in an eye or molecular machine--attract our attention in part
because the organized complexity of such systems seems reminiscent of our own designs. Yet, this
review has argued that neo-Darwinism does not adequately account for the origin of all appearances
of design, especially if one considers animal body plans, and the information necessary to
construct them, as especially striking examples of the appearance of design in living systems.
Indeed, Dawkins (1995:11) and Gates (1996:228) have noted that genetic information bears an
uncanny resemblance to computer software or machine code. For this reason, the presence of CSI in
living organisms, and the discontinuous increases of CSI that occurred during events such as the
Cambrian explosion, appears at least suggestive of design.
Does neo-Darwinism or any other purely materialistic model of morphogenesis account for the origin
of the genetic and other forms of CSI necessary to produce novel organismal form? If not, as this
review has argued, could the emergence of novel information-rich genes, proteins, cell types and
body plans have resulted from actual design, rather than a purposeless process that merely mimics
the powers of a designing intelligence? The logic of neo-Darwinism, with its specific claim to
have accounted for the appearance of design, would itself seem to open the door to this
possibility. Indeed, the historical formulation of Darwinism in dialectical opposition to the
design hypothesis (Gillespie 1979), coupled with the neo-Darwinism's inability to account for many
salient appearances of design including the emergence of form and information, would seem
logically to reopen the possibility of actual (as opposed to apparent) design in the history of
A second reason for considering design as an explanation for these phenomena follows from the
importance of explanatory power to scientific theory evaluation and from a consideration of the
potential explanatory power of the design hypothesis. Studies in the methodology and philosophy of
science have shown that many scientific theories, particularly in the historical sciences, are
formulated and justified as inferences to the best explanation (Lipton 1991:32-88, Brush
1989:1124-1129, Sober 2000:44). Historical scientists, in particular, assess or test competing
hypotheses by evaluating which hypothesis would, if true, provide the best explanation for some
set of relevant data (Meyer 1991, 2002; Cleland 2001:987-989, 2002:474-496).10
Those with greater explanatory power are typically judged to be better, more probably true,
theories. Darwin (1896:437) used this method of reasoning in defending his theory of universal
common descent. Moreover, contemporary studies on the method of “inference to the best
explanation” have shown that determining which among a set of competing possible explanations
constitutes the best depends upon judgments about the causal adequacy, or “causal powers,” of
competing explanatory entities (Lipton 1991:32-88). In the historical sciences, uniformitarian
and/or actualistic (Gould 1965, Simpson 1970, Rutten 1971, Hooykaas 1975) canons of method suggest
that judgments about causal adequacy should derive from our present knowledge of cause and effect
relationships. For historical scientists, “the present is the key to the past” means that
present experience-based knowledge of cause and effect relationships typically guides the
assessment of the plausibility of proposed causes of past events.
Yet it is precisely for this reason that current advocates of the design hypothesis want to
reconsider design as an explanation for the origin of biological form and information. This
review, and much of the literature it has surveyed, suggests that four of the most prominent
models for explaining the origin of biological form fail to provide adequate causal explanations
for the discontinuous increases of CSI that are required to produce novel morphologies. Yet, we
have repeated experience of rational and conscious agents--in particular ourselves--generating or
causing increases in complex specified information, both in the form of sequence-specific lines of
code and in the form of hierarchically arranged systems of parts.
In the first place, intelligent human agents--in virtue of their rationality and
consciousness--have demonstrated the power to produce information in the form of linear
sequence-specific arrangements of characters. Indeed, experience affirms that information of this
type routinely arises from the activity of intelligent agents. A computer user who traces the
information on a screen back to its source invariably comes to a mind--that of a software
engineer or programmer. The information in a book or inscriptions ultimately derives from a writer
or scribe--from a mental, rather than a strictly material, cause. Our experience-based knowledge
of information-flow confirms that systems with large amounts of specified complexity (especially
codes and languages) invariably originate from an intelligent source from a mind or personal
agent. As Quastler (1964) put it, the “creation of new information is habitually associated with
conscious activity” (p. 16). Experience teaches this obvious truth.
Further, the highly specified hierarchical arrangements of parts in animal body plans also suggest
design, again because of our experience of the kinds of features and systems that designers
can and do produce. At every level of the biological hierarchy, organisms require specified and
highly improbable arrangements of lower-level constituents in order to maintain their form and
function. Genes require specified arrangements of nucleotide bases; proteins require specified
arrangements of amino acids; new cell types require specified arrangements of systems of proteins;
body plans require specialized arrangements of cell types and organs. Organisms not only contain
information-rich components (such as proteins and genes), but they comprise information-rich
arrangements of those components and the systems that comprise them. Yet we know, based on our
present experience of cause and effect relationships, that design engineers--possessing purposive
intelligence and rationality--have the ability to produce information-rich hierarchies in which
both individual modules and the arrangements of those modules exhibit complexity and
specificity--information so defined. Individual transistors, resistors, and capacitors exhibit
considerable complexity and specificity of design; at a higher level of organization, their
specific arrangement within an integrated circuit represents additional information and reflects
further design. Conscious and rational agents have, as part of their powers of purposive
intelligence, the capacity to design information-rich parts and to organize those parts into
functional information-rich systems and hierarchies. Further, we know of no other causal entity or
process that has this capacity. Clearly, we have good reason to doubt that mutation and selection,
self-organizational processes or laws of nature, can produce the information-rich components,
systems, and body plans necessary to explain the origination of morphological novelty such as that
which arises in the Cambrian period.
There is a third reason to consider purpose or design as an explanation for the origin of
biological form and information: purposive agents have just those necessary powers that natural
selection lacks as a condition of its causal adequacy. At several points in the previous analysis,
we saw that natural selection lacked the ability to generate novel information precisely because
it can only act after new functional CSI has arisen. Natural selection can favor new
proteins, and genes, but only after they perform some function. The job of generating new
functional genes, proteins and systems of proteins therefore falls entirely to random mutations.
Yet without functional criteria to guide a search through the space of possible sequences, random
variation is probabilistically doomed. What is needed is not just a source of variation (i.e., the
freedom to search a space of possibilities) or a mode of selection that can operate after the fact
of a successful search, but instead a means of selection that (a) operates during a search--before
success--and that (b) is guided by information about, or knowledge of, a functional target.
Demonstration of this requirement has come from an unlikely quarter: genetic algorithms. Genetic
algorithms are programs that allegedly simulate the creative power of mutation and selection.
Dawkins and Kuppers, for example, have developed computer programs that putatively simulate the
production of genetic information by mutation and natural selection (Dawkins 1986:47-49, Kuppers
1987:355-369). Nevertheless, as shown elsewhere (Meyer 1998:127-128, 2003:247-248), these programs
only succeed by the illicit expedient of providing the computer with a “target sequence” and
then treating relatively greater proximity to future function (i.e., the target sequence),
not actual present function, as a selection criterion. As Berlinski (2000) has argued, genetic
algorithms need something akin to a “forward looking memory” in order to succeed. Yet such
foresighted selection has no analogue in nature. In biology, where differential survival depends
upon maintaining function, selection cannot occur before new functional sequences arise. Natural
selection lacks foresight.
What natural selection lacks, intelligent selection--purposive or goal-directed design--provides.
Rational agents can arrange both matter and symbols with distant goals in mind. In using language,
the human mind routinely “finds” or generates highly improbable linguistic sequences to convey
an intended or preconceived idea. In the process of thought, functional objectives precede
and constrain the selection of words, sounds and symbols to generate functional (and indeed
meaningful) sequences from among a vast ensemble of meaningless alternative combinations of sound
or symbol (Denton 1986:309-311). Similarly, the construction of complex technological objects and
products, such as bridges, circuit boards, engines and software, result from the application of
goal-directed constraints (Polanyi 1967, 1968). Indeed, in all functionally integrated complex
systems where the cause is known by experience or observation, design engineers or other
intelligent agents applied boundary constraints to limit possibilities in order to produce
improbable forms, sequences or structures. Rational agents have repeatedly demonstrated the
capacity to constrain the possible to actualize improbable but initially unrealized future
functions. Repeated experience affirms that intelligent agents (minds) uniquely possess such
Analysis of the problem of the origin of biological information, therefore, exposes a deficiency
in the causal powers of natural selection that corresponds precisely to powers that agents are
uniquely known to possess. Intelligent agents have foresight. Such agents can select functional
goals before they exist. They can devise or select material means to accomplish those ends
from among an array of possibilities and then actualize those goals in accord with a preconceived
design plan or set of functional requirements. Rational agents can constrain combinatorial space
with distant outcomes in mind. The causal powers that natural selection lacks--almost by
definition--are associated with the attributes of consciousness and rationality--with purposive
intelligence. Thus, by invoking design to explain the origin of new biological information,
contemporary design theorists are not positing an arbitrary explanatory element unmotivated by a
consideration of the evidence. Instead, they are positing an entity possessing precisely the
attributes and causal powers that the phenomenon in question requires as a condition of its
production and explanation.
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1 Specifically, Gilbert et al. (1996) argued that changes in
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ultimately, body plans of organisms. Yet they offered no evidence that such fields--if indeed they
exist--can be altered to produce advantageous variations in body plan, though this is a necessary
condition of any successful causal theory of macroevolution.
2 If one takes the fossil record at face value and assumes that
the Cambrian explosion took place within a relatively narrow 5-10 million year window, explaining
the origin of the information necessary to produce new proteins, for example, becomes more acute
in part because mutation rates would not have been sufficient to generate the number of changes in
the genome necessary to build the new proteins for more complex Cambrian animals (Ohno
1996:8475-8478). This review will argue that, even if one allows several hundred million years for
the origin of the metazoan, significant probabilistic and other difficulties remain with the
neo-Darwinian explanation of the origin of form and information.
3 As Crick put it, “information means here the precise
determination of sequence, either of bases in the nucleic acid or on amino acid residues in the
protein” (Crick 1958:144, 153).
4 To solve this problem Ohno himself proposes the existence of
a hypothetical ancestral form that possessed virtually all the genetic information necessary to
produce the new body plans of the Cambrian animals. He asserts that this ancestor and its “pananimalian
genome” might have arisen several hundred million years before the Cambrian explosion. On this
view, each of the different Cambrian animals would have possessed virtually identical genomes,
albeit with considerable latent and unexpressed capacity in the case of each individual form (Ohno
1996:8475-8478). While this proposal might help explain the origin of the Cambrian animal forms by
reference to preexisting genetic information, it does not solve, but instead merely displaces, the
problem of the origin of the genetic information necessary to produce these new forms.
5 Some have suggested that mutations in “master regulator”
Hox genes might provide the raw material for body plan morphogenesis. Yet there are two problems
with this proposal. First, Hox gene expression begins only after the foundation of the body plan
has been established in early embryogenesis. (Davidson 2001:66). Second, Hox genes are highly
conserved across many disparate phyla and so cannot account for the morphological differences that
exist between the phyla (Valentine 2004:88).
6 Notable differences in the developmental pathways of similar
organisms have been observed. For example, congeneric species of sea urchins (from genus Heliocidaris)
exhibit striking differences in their developmental pathways (Raff 1999:110-121). Thus, it might
be argued that such differences show that early developmental programs can in fact be mutated to
produce new forms. Nevertheless, there are two problems with this claim. First, there is no direct
evidence that existing differences in sea urchin development arose by mutation. Second, the
observed differences in the developmental programs of different species of sea urchins do not
result in new body plans, but instead in highly conserved structures. Despite differences in
developmental patterns, the endpoints are the same. Thus, even if it can be assumed that mutations
produced the differences in developmental pathways, it must be acknowledged that such changes did
not result in novel form.
7 Of course, many post-translation processes of modification
also play a role in producing a functional protein. Such processes make it impossible to predict a
protein's final sequencing from its corresponding gene sequence alone (Sarkar 1996:199-202).
8 Erwin (2004:21), although friendly to the possibility of
species selection, argues that Gould provides little evidence for its existence. “The difficulty”
writes Erwin of species selection, “...is that we must rely on Gould's arguments for theoretical
plausibility and sufficient relative frequency. Rarely is a mass of data presented to justify and
support Gould's conclusion.” Indeed, Gould (2002) himself admitted that species selection
remains largely a hypothetical construct: “I freely admit that well-documented cases of species
selection do not permeate the literature” (p. 710).
9”I do not deny either the wonder, or the powerful
importance, of organized adaptive complexity. I recognize that we know no mechanism for the origin
of such organismal features other than conventional natural selection at the organismic level--for
the sheer intricacy and elaboration of good biomechanical design surely precludes either random
production, or incidental origin as a side consequence of active processes at other levels”
(Gould 2002:710). “Thus, we do not challenge the efficacy or the cardinal importance of
organismal selection. As previously discussed, I fully agree with Dawkins (1986) and others that
one cannot invoke a higher-level force like species selection to explain 'things that organisms
do'--in particular, the stunning panoply of organismic adaptations that has always motivated our
sense of wonder about the natural world, and that Darwin (1859) described, in one of his most
famous lines (3), as 'that perfection of structure and coadaptation which most justly excites our
admiration'“ (Gould 2002:886).
10 Theories in the historical sciences typically make claims
about what happened in the past, or what happened in the past to cause particular events to occur
(Meyer 1991:57-72). For this reason, historical scientific theories are rarely tested by making
predictions about what will occur under controlled laboratory conditions (Cleland 2001:987,
2002:474-496). Instead, such theories are usually tested by comparing their explanatory power
against that of their competitors with respect to already known facts. Even in the case in which
historical theories make claims about past causes they usually do so on the basis of preexisting
knowledge of cause and effect relationships. Nevertheless, prediction may play a limited role in
testing historical scientific theories since such theories may have implications as to what kind
of evidence is likely to emerge in the future. For example, neo-Darwinism affirms that new
functional sections of the genome arise by trial and error process of mutation and subsequent
selection. For this reason, historically many neo-Darwinists expected or predicted that the large
non-coding regions of the genome--so-called “junk DNA”--would lack function altogether (Orgel
& Crick 1980). On this line of thinking, the nonfunctional sections of the genome represent
nature's failed experiments that remain in the genome as a kind of artifact of the past activity
of the mutation and selection process. Advocates of the design hypotheses on the other hand, would
have predicted that non-coding regions of the genome might well reveal hidden functions, not only
because design theorists do not think that new genetic information arises by a trial and error
process of mutation and selection, but also because designed systems are often functionally
polyvalent. Even so, as new studies reveal more about the functions performed by the non-coding
regions of the genome (Gibbs 2003), the design hypothesis can no longer be said to make this claim
in the form of a specifically future-oriented prediction. Instead, the design hypothesis might be
said to gain confirmation or support from its ability to explain this now known evidence, albeit
after the fact. Of course, neo Darwinists might also amend their original prediction using various
auxiliary hypotheses to explain away the presence of newly discovered functions in the non-coding
regions of DNA. In both cases, considerations of ex post facto explanatory power reemerge
as central to assessing and testing competing historical theories.
(See also discourse 81: “Intelligent
design or evolution?”)