Natural Selection & Mutation

Mutation is a crucial component of evolution, as is natural selection. In focusing exclusively on those two mechanisms, Explore Evolution ignores other critical evolutionary mechanisms. Despite those omissions, the book's coverage of mutation is woefully inadequate. "Mutation" itself is misdefined, ways in which mutations influence morphology are omitted, and the effects of mutations on fitness are mischaracterized. Scientists views are described inaccurately, creationists are passed off as legitimate sources and even plagiarized.

In its discussion of developmental biology, the chapter carries out the predictions of biologist Rudolf Raff: "we will see more slick books of bogus science produced to influence the teaching of biology … Evo-devo data have become a part of the creationist rhetorical weaponry, and as evo-devo grows in prominence, the problem will grow in severity." Again, baic knowledge is misrepresented, scientists are misquoted, and students are left without the resources necessary to conduct their own inquiry into one of the most exciting new fields in biology.

p. 98: "Mutations can occur when genes are exposed to heat, chemicals, or radiation"

This is not an exhaustive list of causes of mutation. Errors in DNA copying and chromosomal crossing-over are more significant causes.

p. 101: "structural mutations" are mutations which "ultimately affect an animal's shape or structure"

Evolution of hindwings: Mutations in regulatory genes change the shapes of insect hindwingsEvolution of hindwings: Mutations in regulatory genes change the shapes of insect hindwings

Structural mutations are those which change the structure of a protein, not which change an organism's morphology. This is a trivial misdefinition.

p. 109: "no experimental mutations in hox genes … have proven helpful"

This is a young field, and the absence of evidence would not be evidence that no such mutations exist.

p. 103: Antibiotic resistance "mutation … impairs [bacterial] ability to perform … vital functions"

Compensatory mutations reverse such impairments, and they do not always occur.

p. 103: "The cell cannot endure an unlimited number of mutations"

Many mutations can be tolerated by a cell, and an infinite number is not necessary.

p. 103: "multiple mutations at active sites inevitably do more harm than good"

Compensatory mutations can and do increase fitness.

p. 107: "a reptile laid an egg from which a bird was hatched … two-legged sheep or two-headed turtles"

These odd phrases, and many others on this page, are plagiarized from creationist David Menton.

p. 109: "temperature changes" cause "a whole new fitness cost"

Fitness is always relative to an environment. Changing temperature changes fitness, and may either increase or decrease an organism's fitness.

p. 110: "DNA does not direct how the overall body plan gets built"

This is contrary to the best current research, and is unsupported by the evidence offered.

p. 111: "many scientists doubt that [higher-level assembly instructions] are stored in DNA alone"

The authors cited to support this claim actually dispute it. Alternatives offered are still producedstructured by DNA sequences.

p. 110: "Critics say it's a little like building a CD player."

This analogy makes no sense, and has only ever been offered by creationist sources.

p. 111: "you can mutate DNA 'til the cows come home and you still wouldn't get a new body plan"

The citation offered to support the claim actually rejects this conclusion.

p. 106: "Major mutations &hellip are always harmful or outright lethal"

The authors cited supporting this claim actually reject it. The results may be "tiny, moderate, or large."

p. 104: "In every case … resistance results from small changes to a single protein molecule"

This is not always true.

p. 105: "there is no evidence that one species of bacteria has changed into another"

This is false. New bacterial species have been produced in the lab.

Major Flaws:

Mutations: Mutation is misdefined, major types of mutation are omitted, and the effects of mutation on fitness are mischaracterized. For a chapter about mutation, these basic failures are fairly significant.

DNA: The role of DNA in development is described incorrectly throughout. It has been clear for decades that DNA ultimately controls morphology and development. Explore Evolution wrongly obscures this basic truth.

Morphology: The study of evolutionary changes in morphology – evolutionary developmental biology – is an exciting and rapidly-changing field. Explore Evolution confuses this field, giving students too little background to understand this new field, and misinformiag them about the basics of this dynamic field.

Mutations

Mutation is the raw material of evolution. Understanding what evolution is, what its sources are, and how different forms of mutation operate is crucial for students. Instead of offering that information – information crucial to the inquiry Explore Evolution purports to encourage – the book misdefines and mischaracterizes mutation and ignores basic concepts in mutation.

After providing an inaccurate definition of mutation, and misdefining "structural mutation," the book then fails to describe the most common causes of mutation. Mutation can be caused by crossing-over during production of gametes, by errors in DNA replication, as well as the environmental factors which Explore Evolution describes as the sole causes of mutation. Mutations do not just occur in genes, the description in Explore Evolution notwithstanding.

The book errs in treating mutations as principally altering protein forms, rather than also considering the ways that mutations change the regulation of other genes, including protein-coding genes and other regulatory genes. The ways that genes are regulated is a key concept in modern biology, but these issues are simply ignored by the authors. The book focuses on antibiotic resistance, but even mangles that example, mischaracterizing the way antibiotic resistance evolves and the side-effects of mutations that generate such resistance.

Mutation Definition

Unfortunately, Explore Evolution makes a confusing definition of "structural mutations" which significantly differs from normal scientific usage. Also, Explore Evolution remarkably fails to mention the major cause of mutations, errors in copying DNA.

A straightforward definition of mutation can be found in any genetics or evolution textbook. For example, the recently published Evolution textbook by Nick Barton and colleagues explains:

Mutation, formally defined as a heritable change in the genetic material (DNA or RNA) of an organism, is the ultimate source of all variation. Without mutation, there would be no evolution.
Barton, et al., (2007) Evolution, p. 325

Unfortunately, Explore Evolution takes this straightforward concept and manages to make it incomprehensible:

As we have seen, there are scientists who doubt that natural selection can produce major evolutionary change. Specifically, they question whether there is a source of new information that can produce new genetic traits – the variations needed to produce lasting biological change.

Defenders of the neo-Darwinian position dispute this critique by offering another argument for the creative power of natural selection. they say that the critics have underestimated the power of another type of variation, unknown in Darwin's time, called mutation.

Explore Evolution, p. 98

How are mutations produced?

Mutations can occur when genes are exposed to heat, chemicals, or radiation.
Explore Evolution, p. 98

Remarkably, Explore Evolution fails to mention that errors in copying DNA are a major source of mutations.

Explore Evolution's definitions of mutations are arbitrary and result in outright confusion. "Genetic mutations" are defined by Explore Evolution as:

a change in the sequential arrangement of the information-bearing bases – the "letters" in the genetic text – of the DNA molecule.
Explore Evolution, p. 98

Explore Evolution explains that there are several types of "genetic" mutations including point mutations, gene duplications, and chromosomal inversions. Presumably, chromosomal translocations and insertions would also be "genetic" mutations, although they are not mentioned. In fact, Explore Evolution's definition of "genetic mutations" encompasses every type of mutation.

Why produce an arbitrary and unnecessary definition of "genetic mutation"? Explore Evolution seems to be distinguishing "genetic mutations" from something they define as "structural mutations":

For major changes to occur in more complex, multi-cellular animals, mutations must ultimately affect an animals shape or structure. Are there examples of such structural mutations? Evolutionary biologists say they are, and point to another striking example of the novel variation that mutation can produce: the four-winged fruit fly.
Explore Evolution, p. 101

This distinction between "genetic" and "structural" mutations is found nowhere else in evolutionary biology, it misappropriates the legitimate term of "structural mutation," and it will generate considerable confusion among students. The long-standing legitimate definition of a "structural mutation" refers to a mutation in the protein coding portions of a gene that results in a change in amino acid sequence. An example of a structural mutation in the human serum cholinesterase gene that is a result of a mutation in the protein-coding region is described below.

A point mutation in the gene for human serum cholinesterase was identified that changes Asp-70 to Gly in the atypical form of serum cholinesterase. The mutation in nucleotide 209, which changes codon 70 from GAT to GGT, was found by sequencing a genomic clone and sequencing selected regions of DNA amplified by the polymerase chain reaction.
McGuire et al., (1989), "Identification of the structural mutation responsible for the dibucaine-resistant (atypical) variant form of human serum cholinesterase," PNAS 86, p. 953

According to Explore Evolution, structural mutations "ultimately affect an animal's shape or structure", but this correctly labeled "structural mutation" in human serum cholinesterase does not result in a change in organismal structure. Instead, human serum cholinesterase is involved in controlling the stability of neurotransmitters.

What Explore Evolution refers to as "structural mutations" would be recognized by most biologists as mutations in genes that are used to build animal embryos, the genetic toolkit. For example, the four-winged fruit fly referred to by Explore Evolution is due to mutations of the Hox gene, Ultrabithorax. Are mutations in the protein-coding region of Ultrabithorax responsible for the four-winged fruit fly? No, the mutations are in non-coding regions of Ultrabithorax. Explore Evolution's own example of a "structural mutation" is the opposite of what biologists consider structural mutations.

If the intent of Explore Evolution was to prevent a clear understanding of mutations and their relationship to evolution, they succeed grandly. For teachers and students, however, this treatment of mutations promises headaches.

Protein Coding

Explore Evolution ignores mutations in non-protein-coding cis-regulatory sequences (CREs). Furthermore, research has shown that mutations in the coding regions and in CREs of the genetic toolkit are both responsible for evolutionary change.

Evolutionary developmental biologists argue that mutations in members of the genetic toolkit will be most important for driving morphological change during the evolution of animals. Many genetic toolkit genes, such as Ultrabithorax, a member of Hox gene family, regulate developmental pathways by turning other genes on or off. Hox proteins bind to specific DNA sequences in CREs and control whether or not RNA is synthesized from the adjacent gene.

Explore Evolution claims:

Because hox genes are so important for coordinating the activities of the cell, some researchers think that mutations in these genes can cause large-scale changes in the structure of an organism. Many neo-Darwinists think that influencing the "coach" (hox genes) through mutation can provide a new source of beneficial variation. Critics aren't so sure. They note that, precisely because hox genes are so influential, no experimental mutations in hox genes (so far) have proven helpful to the organism.
Explore Evolution, p. 109

Explore Evolution latches onto the current circumstance that experimental mutations in the Hox genome have yet to result in an advantage to an organism. Then they invoke anonymous "critics" and suggest that evolution does not involve Hox gene mutations. This is the typical creationist ploy of identifying an experimental shortcoming to generate "doubts" about evolution. This time, they raise the bar rather high for evolutionary developmental biologists. Given the hundreds of millions of years in which evolution has been optimizing morphology, Explore Evolution injects "doubt" because researchers have yet to make a further structural improvement in a decade or so of research.

However, we can investigate whether natural mutations in the protein-coding regions of Hox genes have been responsible for changes in body plans. To understand how the changes a Hox gene could result in evolutionary change, evolutionary developmental biologists compare the functions of Hox genes in different organisms. For example, Ultrabithorax is known to repress limb formation in insects, such as fruit flies. However, the abdominal segments of crustaceans, such as brine shrimp, express Ultrabithorax and also have limbs. So, Ultrabithorax is able to repress limb formation in insect embryos but not in crustacean embryos. Notably, a major feature of the insect body plan is their lack of abdominal limbs, unlike crustaceans. Thus the difference between crustacean and insect Ultrabithorax function in repressing limbs could play an important role in arthropod evolution.

Ultrabithorax in Insect and Crustacean LimbsUltrabithorax in Insect and Crustacean Limbs

The comparison of a genetic toolkit gene, Ultrabithorax in insects, crustaceans and velvet worms has established why insects lack abdominal limbs (Galant et al., 2002; Ronshaugen et al., 2002). Changes in sequence at the tail end of Ultrabithorax protein have enabled Ultrabithorax to repress abdominal limbs in insects.

UltrabithoraxUltrabithorax

Genetic experiments in fruit flies has shown that crustacean Ultrabithorax does not repress embryonic limbs, unlike fruit fly Ultrabithorax. An important reason for the difference in Ultrabithorax function is that all modern insects have a "QA motif" - a short 15 amino acid sequence (QAQAKAAAAAAAAAA)at the tail of Ultrabithorax protein. Arthropods, such as millipedes and crustaceans, have a different type of sequence at the tail of Ultrabithorax which has a number of serines (S) and threonines (T). In a functional analysis in fruit flies, Ronshaugen et al. show that the replacement of a few of the serines (indicated by * in diagram below) in the tail of a crustacean Ultrabithorax renders it capable of repressing limbs.

As McGinnis and colleagues explain:

Previous studies led us to propose that gain and loss of transcriptional activation and repression functions in Hox proteins was a plausible mechanism to diversify morphology during animal evolution(12). Here we show that naturally selected alteration of the Ubx protein is linked to the evolutionary transition to hexapod limb pattern.
Ronshaugen et al., "Hox protein mutation and macroevolution of the insect body plan." (2002) Nature 415, p. 914

The evidence for the importance of Hox gene mutations in morphological evolution certainly extends beyond creating a four-winged fruit fly.

Normal Protein

Mutations can improve normal protein function resulting in increased fitness relative to the environment. Many mutations work by generating more effective enzymes or through novel catalytic mechanisms. Explore Evolution is wrong to claim that mutations must impair a protein's normal functioning and impose a fitness cost. Explore Evolution does not even discuss mutations in cis-regulatory elements (CREs), which have minimal fitness costs and are considered by many evolutionary biologists to have the greatest potential for generating evolutionary change (Prud'homme et al., 2007). Explore Evolution also misrepresents the basic notion of fitness, by failing to note that fitness depends on the environment.

After saying that a "resistance gene" does not develop through mutation, Explore Evolution then says mutations do confer resistance but with a "fitness cost."

… [A] mutation [changes] the shape of the active site on the "target" protein so that the antibiotic no longer recognizes the site. … However, that very same mutation also impairs that strain's ability to perform other vital functions like information processing. … Microbiologists refer to this as the "fitness cost" of a mutation.
Explore Evolution, p. 103
… Experiments show that once antibiotics are removed from the environment, the original (non-resistant) strain "out-competes" the resistant strain, which dies off within a few generations.
Explore Evolution, p. 103

Explore Evolution significantly misrepresents how antibiotic resistance arises in this description. For example, methicillin resistance is due to generation of a new binding site for penicillin-like drugs on a protein that previously did not have this activity (Wu et al., 1996, 2001). Vancomycin resistance is due to the generation of a novel enzyme that bypasses the vancomycin-susceptible step. Resistance to extended-spectrum antibiotics is due to the evolution of beta-lactamases with increased catalytic efficiency (Sideraki et al., 2001).

Increased fitness cost is not necessarily related to enzyme "impairment." Consider the example of the methicillin resistance gene. It produces a new protein which binds methicillin, preventing methicillin from acting. However, producing this protein costs energy and resources. In the absence of methicillin, making the protein diverts resources way from growth, and so the methicillin resistant bacteria will grow more slowly than a methicillin sensitive bacteria in the absence of the antibiotic. This slower growth decreases fitness.

One of the best studied examples of antibiotic resistance is the case of resistance to the antibiotic streptomycin. Streptomycin kills bacteria by interfering with protein assembly on the ribosome, turning out garbage proteins, by binding to the S12 subunit of the 30S ribosomal particle in bacteria. The 30S ribosomal particle is a multi-subunit structure which in turn forms part of the protein synthesizing ribosomal particle. The S12 subunit together with 16S RNA forms part of the proof reading centre of the transfer RNA (tRNA) acceptor binding site. A mutation that results in the substitution of threonine or asparagine for lysine at position 42 in the rspL gene results in streptomycin failing to bind to S12, with resulting resistance of the bacteria to the antibiotic streptomycin. This mutant version is actually more accurate, i.e. more specific, than the wild type. The wild-type proof reading center makes a few mistakes even in the absence of streptomycin, and the mutant forms make even fewer mistakes than the wild type, roughly 85% fewer (Bjorkman et al., 1999). This is a classic example of a beneficial mutation. Furthermore it was work on this mutation that determined that mutations were random.

Thus we can see that the mutation that produces streptomycin resistance doesn't impair information processing, it makes it more accurate. However, this increased accuracy slows protein synthesis so overall growth is slower. When you put the threonine or asparagine rspL 42 mutant streptomycin resistant bacteria and wild type streptomycin sensitive bacteria together in head to head competition in the absence of streptomycin, the wild type will out compete-them. It's a classic trade off, make your proteins carefully and grow slowly, or grow quickly and have some messed up proteins.

Importantly, not all mutations produce fitness costs. There are several examples of mutations that produce no fitness cost, or are even fitter than the wild-type antibiotic sensitive bacteria (Andersson, 1996; Zhang 2006).

Equally importantly, compensatory mutations occur that restore the fitness of the bacteria to wild type levels. There are multiple examples of this for streptomycin (Bjorkmann, 1996, 2000; Anderson, 2006) and other antibiotics (Anderson, 2006; Maisnier-Patin, 2002; Zhang 2006). This is a major issue in clinical treatment, as it means that withdrawing use of an antibiotic does not mean that the antibiotic resistant bacteria will go away.

Finally, as discussed elsewhere, mutations in the regions of non-coding DNA that act as genetic switches, CREs, have significantly lower fitness penalties than mutations in protein-coding regions of developmental regulatory genes.

References:

Andersson DI. The biological cost of mutational antibiotic resistance: any practical conclusions?Curr Opin Microbiol. 2006 Oct;9(5):461-5. Epub 2006 Aug 4.

Bjorkman J, Hughes D, Andersson DI. Virulence of antibiotic-resistant Salmonella typhimurium. Proc Natl Acad Sci U S A. 1998 Mar 31;95(7):3949-53

Bjorkman J, et al., Novel ribosomal mutations affecting translational accuracy, antibiotic resistance and virulence of Salmonella typhimurium. Mol Microbiol. 1999 Jan;31(1):53-8

Bjorkman J, Nagaev I, Berg OG, Hughes D, Andersson DI. Effects of environment on compensatory mutations to ameliorate costs of antibiotic resistance. Science. 2000 Feb 25;287(5457):1479-82

Maisnier-Patin S, Berg OG, Liljas L, Andersson DI. Compensatory adaptation to the deleterious effect of antibiotic resistance in Salmonella typhimurium. Mol Microbiol. 2002 Oct;46(2):355-66

Sideraki V, Huang W, Palzkill T, Gilbert HF. A secondary drug resistance mutation of TEM-1 beta-lactamase that suppresses misfolding and aggregation. Proc Natl Acad Sci U S A. 2001 Jan 2;98(1):283-8.

Wu S, Piscitelli C, de Lencastre H, Tomasz A. "Tracking the evolutionary origin of the methicillin resistance gene: cloning and sequencing of a homologue of mecA from a methicillin susceptible strain of Staphylococcus sciuri." Microb Drug Resist. 1996 2(4):435-4

Wu SW, de Lencastre H, Tomasz A. "Recruitment of the mecA gene homologue of Staphylococcus sciuri into a resistance determinant and expression of the resistant phenotype in Staphylococcus aureus." J Bacteriol. 2001 Apr;183(8):2417-24

Zhang Q, Sahin O, McDermott PF, Payot S. "Fitness of antimicrobial-resistant Campylobacter and Salmonella." Microbes Infect. 2006 Jun;8(7):1972-8. Epub 2006 Mar 31.

Mutation Accumulation

Evolutionary biology does not require that organisms be able to accumulate unlimited mutations. Organisms can and do accumulate large numbers of mutations. Explore Evolution is deeply misleading about the role of mutations and adaptations.

Explore Evolution claims that

The cell cannot endure an unlimited number of mutation-induced changes at these critical active sites. At some point, the cell's information processing system will be damaged so badly that it stops functioning altogether. For this reason, multiple mutations at active sites inevitably do more harm than good.
Explore Evolution, p. 103

There are a number of problems with this claim. First, not all mutations are associated with a fitness cost relative to the wild type in the original environment, and in those mutations that do reduce fitness with respect to the wild type, subsequent compensatory mutations often restore fitness, sometimes to above wild type levels. Therefore, a large number of mutations can be tolerated.

This "loss of fitness" is always in relation to the wild-type organism in the original environment. In an environment with antibiotics, the wild-type organism's fitness is very low, and the antibiotic resistant mutant is much fitter. Accumulation of mutations may indeed mean that an organism is restricted to the new environment, and cannot survive in the old environment. This is irrelevant. Penguins and polar bears have adapted to cold environments, and cannot survive in the environments their ancestors came from. Our ancestors came from the sea, but we are remarkably unfit in the sense of being able to breath underwater. There are many examples like this. Explore Evolution implies there is some universal standard of fitness, but fitness is always relative to the environment the organism is in.

Compensatory Mutations

Compensatory mutations are mutations that correct a loss of fitness due to earlier mutations. In some cases, such mutations bring their own fitness costs, but often they do not. Even when they do, it is irrelevant to the power of mutation and selection to produce novelty.

Explore Evolution claims:

the effectiveness of the second [compensatory] mutation is a limited-time offer, a coupon only good for the exact environment in which it was issued. If the temperature changes in the environment,* or if the salinity changes, a whole new fitness cost comes to light. The compensatory mutation now "codes for" a protein that doesn't fold properly under the new conditions. And if it doesn't fold properly, it doesn't work properly. Or, it may not work at all.

* This is what happens when your body "runs a temperature" when you have a cold. Your body is changing the temperature of the environment, trying to make it less hospitable to the invading bacteria or virus.

Explore Evolution, p. 108-109

In contrast to the claims of Explore Evolution many compensatory mutations do not have hidden fitness costs. Their "example" is a bacterium which has a compensatory mutation that makes it more temperature sensitive, and therefore unable to cope with the increased temperature seen in animals when they have fever. This appears to be an imaginary example, and the compensatory mutations seen in Staphylococcus aureus allow them to infect mice as easily, if not more easily, than the wild type.

But even if there were hidden fitness costs, the main issue is that the mutant is fitter in the altered environment. It does not matter if the mutant is less in the wild type environment unless it is returned to that ancestral environment. Penguins and polar bears are fitter than normal seabirds and brown bears in polar regions, but unfit in temperate and tropical regions. This hardly means that polar species are less fit than their ancestors in more temperate regions.

An inquiry-based textbook could readily present a real example from the scientific literature, and encourage students to predict how compensatory mutations would affect a species' ability to adapt to other environments. Instead, it presents a made-up example with too little detail for students or a teacher to practice inquiry-based learning.

Pre-Existing Resistance

All antibiotic resistance that develops in bacteria can be traced back to mutations in bacteria that were originally susceptible to antibiotics. Explore Evolution is rather incoherent in its discussion of antibiotic resistance. It incorrectly presents antibiotic resistance as due to pre-existing coding in the bacterial population for different varieties of beta-lactamase (an enzyme that breaks down penicillin).

Explore Evolution claims:

In the case of penicillin resistance, critics agree that when penicillin is present in the bloodstream, a bacterial strain that already has a gene coding for penicillinase will have a significant survival advantage over a strain that doesn't. … They do not develop such a gene when penicillin is introduced.
Explore Evolution, p. 102

Before discussing the origin of antibiotic resistance further, a little background is required. Antibiotics revolutionised medicine. For example, prior to antibiotics, 82% of people infected with the bacteria Staphylococcus aureus died. After the introduction of penicillin in 1944, most people infected with this bacterium survived. However, by 1947 the first clinical case of S. aureus resistant to penicillin was described. By 1952, over 75% of S. aureus was resistant to penicillin. A similar history is seen with other antibiotics. Methicillin, an antibiotic developed to be resistant to beta-lactamases (the bacterial enzymes that break down penicillin), was introduced in the 1960’s, by the 1970’s the first reports of resistance to methicillin were coming in. Vancomycin, the antibiotic of last resort for organisms like S. aureus, was introduced in the mid-1950’s but bacterial resistance to vancomycin was first seen in the 1980's and in 2002 vancomycin resistant S. aureus were reported. As can be seen, antibiotic resistance in populations of bacteria develop after a lag phase of some years, which would not happen if antibiotic resistance was just selection of pre-existing variability.

Antibiotic resistance occurs in many ways (Patostini et al, 2007), some bacteria are resistant because they develop enzymes that break down antibiotics, such as the beta-lactamases that break down penicillin, others develop proteins that bind the antibiotics and prevent them acting on their targets, such as the penicillin-binding-proteins that inactivate methicillin, still others develop enzymes that bypass the biological process that the antibiotic targets, such as the alternative cell wall synthesis enzymes that evade vancomycin.

Still other mechanisms involve altering the ability of enzymes to bind the antibiotic, decreasing the antibiotics entry into the cell, or increasing the activity of cell membrane pumps which remove the antibiotic from the cell. Antibiotic resistant bacteria may utilise one or more of these mechanisms.

Antibiotic resistant bacteria gain these mechanisms in one of two ways. They may develop by mutation of one or more genes in previously antibiotic sensitive bacteria, or bacteria may gain resistance genes via horizontal gene transfer from bacteria that are already resistant.

However, the genes that have been transferred were originally the products of mutation. The methicillin resistance gene is a mutant duplicate of a gene that did not originally bind penicillin found in the widely distributed bacteria S. sciuri that was transferred to S. aureus (Wu et al., 1996, 2001). The vancomycin resistance gene is a mutant version of the D-ala-D-ala ligase cell wall synthesis enzyme that has been transfered from Enterococcus faecium to S. aureus. Only a single mutation is required to change the cell wall synthesis enzyme D-Ala-D-Ala ligase to the D-Ala-D-Lac ligase that is the vancomycin resistance gene product (Park et al., 1996).

Explore Evolution treats the variants of beta-lactamase as if they were always present and could not have been produced through mutations, whereas research shows that beta-lactamases are mutant versions of a variety of enzymes (one group are mutant D-ala-D-ala ligases, Knox et al., 1996). As these enzymes originated very early on, their evolutionary history is more obscure than that of the vancomycin or methicillin resistance genes. However, in the continuing “arms race” of humans versus bacteria, new beta-lactamase resistant antibiotics have been introduced, and new beta-lactamases have evolved that can break down these antibiotics. Generally, as newer variants of beta-lactam antibiotics have been introduced, beta lactamase variants active against those beta-lactams have appeared within 2 to 3 years. The study of these mutations is a classic in evolution research (Petrosino et al., 1998).

References:

Knox JR, Moews PC, and Frere JM, Molecular evolution of bacterial beta-lactam resistance, Chemistry & Biology 3, 1996, p. 937-947.

Park IS, Lin CH, Walsh CT. Gain of D-alanyl-D-lactate or D-lactyl-D-alanine synthetase activities in three active-site mutants of the Escherichia coli D-alanyl-D-alanine ligase B. Biochemistry. 1996 Aug 13;35(32):10464-71.

Pantosti A, Sanchini A, Monaco M. Mechanisms of antibiotic resistance in Staphylococcus aureus. Future Microbiol. 2007 Jun;2:323-34.

Petrosino J, Cantu C 3rd, Palzkill T. beta-Lactamases: protein evolution in real time. Trends Microbiol. 1998 Aug;6(8):323-7.

Wu S, Piscitelli C, de Lencastre H, Tomasz A. Tracking the evolutionary origin of the methicillin resistance gene: cloning and sequencing of a homologue of mecA from a methicillin susceptible strain of Staphylococcus sciuri. Microb Drug Resist. 1996 2(4):435-41

Wu SW, de Lencastre H, Tomasz A. Recruitment of the mecA gene homologue of Staphylococcus sciuri into a resistance determinant and expression of the resistant phenotype in Staphylococcus aureus. J Bacteriol. 2001 Apr;183(8):2417-24.

Protein Changes

Antibiotic resistance comes from a variety of mechanisms, including changes in gene regulation, production of new genes with novel activities, as well as simple point mutations. All these mechanisms are representative of the kinds of mutation involved in the sorts of morphological change that Explore Evolution thinks are important. Explore Evolution misrepresents the basic biology of mutations and their significance in antibiotic resistance in claiming:

In every case where mutations lead to antibiotic resistance, resistance results from small changes to a single protein molecule.
Explore Evolution, p. 104

Explore Evolution tries several times to make distinctions between different kinds of mutations. These distinctions are incorrect. In the case of antibiotic resistance, while the most intensively studied mutations are simple point mutations, such as those responsible for resistance to streptomycin, there are many other mutations that are involved. For example, resistance to some antibiotics is due to mutations that change the expression of drug transporters. Changes in gene expression are important in the evolution of many organismal traits.

Another example is gene duplication. Methicillin resistance originated with the duplication of a gene, which subsequently mutated, gaining a new function, penicillin binding. The first step was duplication of the cell wall synthesis enzyme D-Ala-D-Ala ligase. A single mutation then resulted in a novel cell wall synthesis enzyme D-Ala-D-Lac ligase, which confers vancomycin resistance.

Gene duplication, with duplicates gaining new functions though mutation, is a major source of gene gain in evolution. For example, the expansion of cell signaling systems in evolution is almost entirely through gene duplication and function gain via mutation. Most of what Explore Evolution later refers to as "molecular machines" are aggregates of duplicated genes. By failing to provide students with this background, they hinder any inquiry those students might choose to undertake into these issues.

DNA

A great shame of creationism and intelligent design is their appropriation and mischaracterization of genuine scientific concerns about whether we currently possess a complete explanation for the unity and diversity of life. Explore Evolution thoroughly mixes up scientific issues of gene-centric vs. epigenetic phenomena with much broader unsupported anti-evolutionary claims that genes do not control development and that new body plans need new sets of non-genetic instructions.

The success of developmental genetics in identifying an evolutionarily conserved set of genes that are used to construct organisms can lead to the temptation of restricting explanation of morphological evolution to genes alone. The question of whether nuclear genes were responsible for embryonic development has a long history. In the first half of the 20th century, proponents of nuclear inheritance battled with advocates of cytoplasmic inheritance. More recent authors argue that the metaphor of a genetic program does not take into consideration environmental affects upon development. Some argue that genes alone cannot explain cellular organization in microbes; that self-organizing properties of sub-cellular structures operating in physically constrained environments are also important. Others suggest that physical forces acting upon the earliest multi-cellular organisms played a major role in morphological evolution. A growing body of research indicates that the emergent properties of gene networks and cellular behaviors are also important for explaining morphological evolution. Other research suggests that development does not have the goal of producing an adult form and that the role of genes in regulating animal development is presently overemphasized.

Explore Evolution caricatures the nature of these scientific critiques of a gene-centric biology. Explore Evolution concludes that “something else – some other source of information” besides DNA is necessary to construct an organism and therefore evolution of body plans could not have resulted from mutations. Explore Evolution hints that the something else is still a mystery. They should have described to students how non-genetic processes (such as biomechanical forces and exploratory behavior of cells) contribute to morphological evolution.

Neil DeGrasse Tyson, the Director of the Hayden Planetarium at the American Museum of Natural History has described intelligent design as "a philosophy of ignorance" and his description is exemplified in this section of Explore Evolution.

Information

Explore Evolution is part of a longstanding effort by creationists, many of them authors of Explore Evolution, to mischaracterize and obscure scientific critiques of a gene-centric view of biology. In 1994, an argument was put forth by Jonathan Wells, a Senior Fellow at the Discovery Institute whose discredited arguments are repeated throughout Explore Evolution, in a publication of the Unification Church, often called "Moonies", that genes do not determine the "floor plan" - morphological development - of organisms.

So DNA does not program the development of the embryo… In a developing organism, the DNA contains templates for producing proteins-the building materials.To a very limited extent, it also contains information about the order in which those proteins should be produced-assembly instructions. But it does not contain the basic floor plan. The floor plan and many of the assembly instructions reside elsewhere (nobody yet knows where).
Jonathan Wells (1994) Why I Went for a Second Ph.D

The next year, the Nobel Prizes in Physiology or Medicine was awarded to scientists studying the genetic regulation of fruit fly development and another was awarded in 2002 to scientists studying the genetic regulation of nematode development. Nonetheless, Explore Evolution repeats Wells-like denials of the scientific consensus that genes carry instructions for embryonic development.

From Explore Evolution:

Also, on the cutting edge of research is the noteworthy claim that genes may not do as much as scientists previously thought.
Explore Evolution, p. 109
But some scientists contend that while the genes in DNA carry assembly instructions for building proteins out of amino acids, they do not carry the assembly instructions for building organs out of proteins or for building whole creatures out of organs or other body parts.
Explore Evolution, p. 110
many biologists (embryologists in particular) are beginning to think that genes do not (by themselves) carry the instructions for building a whole organism or animal.
Explore Evolution, p. 110
Scientist are not entirely sure where these higher-level assembly instructions are stored. However, these instructions are clearly necessary, and many scientists doubt that they are stored in DNA alone.
Explore Evolution, p. 111

Explore Evolution ignores the fact that DNA does significantly more than code for proteins, it has regulatory information (such as cis-regulatory elements) that controls when and where genes are expressed. More seriously, Explore Evolution ignores the fundamental unit of life, the cell, when it claims that genes "do not carry the assembly instructions for building organs out of proteins". In order to raise questions about the plausibility of morphological evolution, Explore Evolution must shield students from the uncomfortable fact that critics of a gene-centric view of biology propose viable alternative scientific explanations that are fully compatible with evolutionary biology.

References in the quotations above cite the Origination of Organismal Form, edited by Gerd Muller and Stuart Newman, to assert that DNA: "does not carry out the assembly instructions for … building whole creatures." Muller and Stuart's essay is an introduction, giving an overview of the various issues that the research published in the rest of the book will address. Muller and Newman write:

Organismal evolution is nowadays almost exclusively discussed in terms of genetics. But are genes determinants of form? … The chapters of part III [Relationships between Genes and Form] provide viewpoints on several of the problems that will have to be taken into account in future modeling approaches.
G. Muller and S. A. Newman (2003) The Origination of Organismal Form pp. 5-6

Explore Evolution asserts that the "mutation argument" has serious problems since DNA (alone) does not carry assembly instructions and "scientist are not entirely sure where the higher level assembly instructions are stored," therefore calling into question whether morphological evolution is possible. However, these claims are not supported by Origination of Organismal Form. As the book's back cover explains, the goal is not to remove gene sequences and gene expression from biological consideration, but to introduce another set of factors into biology's toolkit.

By placing epigenetic processes, rather than gene sequence and gene expression changes, at the center of morphological origination, this book points the way to a more comprehensive theory of evolution.
The Origination of Organismal Form, Back Cover

Each paper in Part III of Origination of Organismal Form discusses other factors besides genes which are important for generating form. Mina Bissell and colleagues argue that the 3-D organization of a tissue in the extracellular matrix is important for cellular differentiation. Roy Britten argues that molecular interactions as opposed to "global control mechanisms" are responsible for embryonic development. Scott Gilbert explains that genomes have been selected to respond to environmental cues during embryonic development. Finally, Ellen Larson summarizes how changes in cellular behaviors in development facilitates morphological evolution. Larson explains:

1. Rates of morphological evolution depend upon changes in the coordination of developmental processes

2. The hierarchical organization of biological systems facilitates relatively rapid evolution and change because developmental systems are modular.

3. At the molecular level, surprisingly few genetic changes may lead to change in coupling between genes and their regulatory signal.

4. Genes affect morphogenesis by affecting cell behaviors, including cell behaviors that modify morphogenetic fields.

5. At the tissue level, cell-autonomous genetic behavior in two-dimensional sheets may permit large and evolutionarily rapid changes in morphogenesis, compared to changes in interacting tissues that probably require complementary changes in both interacting tissues to achieve change.

6. Because there are alternative routes to achieve a morphology using different cellular behaviors, the likelihood of having sufficient genetic variation for selection is increased.

E. Larson, (2003), "Genes, Cells and Form" in The Origination of Organismal Form p. 126

Far from denying the importance of DNA, this is an acknowledgment of the importance of genes, and an exploration of the ways that genes vary. Explore Evolution is wrong to offer this book as evidence that biologists do not thing DNA is crucial in establishing morphology. The same passages in Explore Evolution mischaracterize teh views of Alessandro Minelli. Minelli also acknowledges that embryonic development is influenced by genes, but argues that there is too much an emphasis placed upon morphological changes in embryos as a means to generate adults. As with Stuart Newman, Minelli does not think that his arguments are anti-evolutionary.

Development, even in its simplest forms … is the complex networking of cellular behaviors and mechanisms influenced by the expression of all these genes …All of these behaviors, mechanisms, and genes are not there to ensure the deployment of wonderfully complex shapes of living beings. Much more modestly, they are simply there and consequently affect other behaviors, mechanisms or genes and set in place those forms of self-regulation that are the key to avoid developmental bankruptcy.
Alessandro Minelli (2003) The Development of Animal Form pp. 4-5
The non-adultocentric view of development I am advocating here is perfectly compatible with most views of development and evolutionary biology – for example, with the concept of the developmental module, a local cell population with its own developmental dynamics, but also interacting with other modules in a kind of metapopulation of cells (the biological individual or colony).
Alessandro Minelli (2003) The Development of Animal Form, p. 6

In claiming compatibility with "most views of development and evolutionary biology," Minelli is surely not supporting the anti-evolution arguments of Explore Evolution, nor its particular claim that Minelli claims DNA is not crucial to "building whole creatures out of organs and other body parts."

Explore Evolution also wrongly claims support from a paper by Brian Hall, a developmental biologist with a long-standing interest in evolution who thinks that cellular behaviors play an important role in morphogenesis. Is "DNA demoted" according to Brian Hall?

By emphasizing the role of cells, I want to be very explicit and not misunderstood. I am not downgrading the role of genes, either in development or in evolution.
B. Hall (2003) "Unlocking the Black Box between Genotype and Phenotype: Cell Condensations as Morphogenetic (modular) Units." Biology and Philosophy, 18, p. 219

The diagram below, based upon Figure 8 of Hall (2003), shows how Brian Hall views the relationship between genes (genotype) and organismal structure (phenotype). Notably, these "higher-level assembly instructions" consist of interactions of genes as networks and cascades, and the interactions of cells in aggregation and communication which are fully able to "translate the effects of mutations into phenotypic change."

Genotype to Phenotype: Figure 8 from B. Hall (2003) "Unlocking the Black Box between Genotype and Phenotype: Cell Condensations as Morphogenetic (modular) Units." Biology and Philosophy, 18, p. 219Genotype to Phenotype: Figure 8 from B. Hall (2003) "Unlocking the Black Box between Genotype and Phenotype: Cell Condensations as Morphogenetic (modular) Units." Biology and Philosophy, 18, p. 219
This modular and hierarchical cellular organization allows like cells to receive the intra- and extra-organismal environmental and epigenetic signals that allow organisms to develop, adapt to their environment, modify their development and translate the effects of mutations into phenotypic change on both developmental (including regeneration) and evolutionary (including asexual reproduction) time scales.
B. Hall (2003) "Unlocking the Black Box between Genotype and Phenotype: Cell Condensations as Morphogenetic (modular) Units."Biology and Philosophy, 18, p. 219

Another reference in the quotations above cites a 1990 essay by Fred Nijhout as an example of a scientist who now doubts that "higher-level assembly instructions" are stored in DNA alone. Undoubtedly, Nijhout expresses clear reservations about a gene-centric approach to biology.

The reason that pattern and form exhibit heritability is that they develop under a specific and restricted set of physical circumstances. When these circumstances are altered whether by changes in gene products or by changes in the environment a different pattern, equally heritable, develops. Changes in the heritable phenotype that are cause by changes in the environment are referred to as norm of reaction and have occasionally have been studied from the evolutionary perspective. Since gene do not 'code' for form, but form emerges out of an interaction of gene product and environment, it is clear that the norm of reaction deserves more wide spread study.
F. Nijhout (1990) "Metaphors and the Role of Genes in Development," Bioessays 12, p. 445

Despite this, Nijhout's research can hardly be said to reject DNA's role in morphology. In a recent Science paper, Suzuki and Nijhout show how a mutation in a gene affecting the hormonal regulatory pathway increases the environmental sensitivity to moth larval coloration and the origination of an new adaptive phenotype.

Polyphenisms are adaptations in which a genome is associated with discrete alternative phenotypes in different environments. Little is known about the mechanism by which polyphenisms originate. We show that a mutation in the juvenile hormone-regulatory pathway in Manduca sexta enables heat stress to reveal a hidden reaction norm of larval coloration. Selection for increased color change in response to heat stress resulted in the evolution of a larval color polyphenism and a corresponding change in hormonal titers through genetic accommodation. Evidently, mechanisms that regulate developmental hormones can mask genetic variation and act as evolutionary capacitors, facilitating the origin of novel adaptive phenotypes.
Y. Suzuki and F. Nijhout (2006) "Evolution of a Polyphenism by Genetic Accommodation," Science, 311, p. 650

Science journalist Elizabeth Pennisi explains how the study of reaction norms supports role of mutations in evolution, contrary to the claim Explore Evolution advances.

The study demonstrates how species can mask effects of genetic mutations until an environmental trigger reveals them, an adaptive mechanism that may help organisms survive changing conditions. The work "is a tour de force of experimental evolutionary biology," says Mary Jane West-Eberhard, an evolutionary biologist at the University of Costa Rica. "It [begins] to answer a question of fundamental importance: How does a novel, environmentally sensitive trait originate?"
E. Pennisi (2006) "Hidden Genetic Variation Yields Caterpillar of a Different Color,"Science, 311, p. 591

Explore Evolution also cites a book by Lenny Moss, entitled What Genes Can't Do, published in the MIT Press's Basic Bioethics Series. Moss promotes the ideas of two embryologists, John Gerhart and Marc Kirschner, to explain the formation of multicellular organisms. Gerhart and Kirchner's explanation emphasizes the ways that modular processes can be linked together to generate novelty in evolution.

The evolution of complex, internally differentiated, and yet globally coordinated life forms, including Homo sapiens, was not achieved by the elaboration of a master code or script, but by the fragmentation of functional resources of the cell into many modular units whose linkages to one another have become contingent (Gerhart & Kirschner, 1997). The more contingently uncoupled the molecular and multimolecular constituents of the cell become, the greater becomes the subset of potential specializations that can be achieved.
Lenny Moss (2004) What Genes Can't Do., pp. 188-189

The critique by Gehart and Kirschner provides no support for Explore Evolution's claim that mutations are insufficient to produce morphological change, simply showing that a full understanding of the evolution of morphology will require other levels of explanation beyond stating that a gene was mutated.

Most anatomical and physiological traits that have evolved since the Cambrian are, we propose, the result of regulatory changes in the usage of various members of a large set of conserved core components that function in development and physiology. Genetic change of the DNA sequences for regulatory elements of DNA, RNAs, and proteins leads to heritable regulatory change, which specifies new combinations of core components, operating in new amounts and states at new times and places in the animal. These new configurations of components comprise new traits.
J. Gerhart and M. Kirschner (2007) "The Theory of Facilitated Variation," PNAS 104, p. 8582
Although recent insights in developmental biology and physiology deepen the understanding of variation, they do not undermine evolutionary theory. Laws of variation begin to emerge, such as regulatory change as the main target of genetic change, the means to minimize the number and complexity of regulatory changes, and the regulatory redeployment of conserved components and processes to give phenotypic variations and selected traits.
J. Gerhart and M. Kirschner (2007) "The Theory of Facilitated Variation," PNAS 104, p. 8588
This is a new and active field of research, and an inquiry-based textbook could take advantage of the field's new results to encourage student exploration. Instead, as elsewhere in Explore Evolution, students are encouraged to treat unanswered questions as unanswerable, as chances to stop investigating. Students are given neither the conceptual background nor the scientific resources to engage with the ideas introduced here, and the book's approach is to encourage intellectual surrender, giving up whenever scientists seem to disagree or scientific questions are unresolved. This is not "inquiry-based," and is not good science.

Other sources

Explore Evolution asserts:

Something else – some other source of information – must orchestrate the assembly of the component proteins into unique cell types and direct the organization of cell types into various tissues and organs, and controls the arrangements of organs and body parts into an overall body plan (18).
Explore Evolution, p. 110

As to the nature of this "other source of information" that is not DNA, Explore Evolution cites a study in the history of science by Jan Sapp, Beyond the Gene: Cytoplasmic Inheritance and the Struggle for Authority in Genetics. In one section, Sapp describes how embryologists at the start of the 20th century thought the cytoplasm played the most prominent role in directing development and heredity. A more contemporary topic that Sapp examines is cortical inheritance in ciliates, single celled organisms such as paramecium. Ciliates divide by fission and the two daughter cells are able to inherit the pattern of cilia at their cell cortex. This inheritance of ciliary patterns is an example of cytoplasmic inheritance and appears to be largely independent of direct control by nuclear genes.

As Sapp noted in 1987,

Even some leading neo-Darwinian evolutionists have admitted their concern about the significance of the "the phenomenon of cortical inheritance in ciliates." At a symposium on Development and Evolution held at the University of Sussex in 1982, the centenary year of Darwin's death, John Maynard Smith (1983) p. 39) stated "Neo-Darwinists should not be allowed to forget these cases, because they constitute the only significant threat to our views."
Jan Sapp (1987) Beyond the Gene: Cytoplasmic Inheritance and the Struggle for Authority in Genetics, p. 219-220

However, to date, cortical inheritance has failed to displace nuclear genes as the most important player in regulating embryonic development in the ensuing 25 years after John Maynard Smith's warning to fellow evolutionists. Indeed, in this period there have been two sets of Nobel Prizes for scientists who have been leaders in the genetic analysis of animal development.

As Alessandro Milenni – also cited by Explore Evolution notes:

From the point of animal evo-devo, the question is whether these aspects of cytoplasmic information (cytotaxis sensu, Sonneborn, 1964) are limited to ciliates or are a general property of cells. I am not aware of the inheritance of intracellular patterns in animals, but it is certain that very few biologists have thought it a rewarding topic be investigated.
Alessandro Minelli (2003) The Growth of Animal Form, p. 29

Far from supporting the claim that modern biologists cytoplasmic factors as an alternative to DNA, the citations offered by Explore Evolution actually show that science has rejected various alternatives and all evidence points to DNA as the repository of "instructions" for biological development.

DNA and CD players

According to Explore Evolution:

Critics say it's a little like building a CD player. Even if you have all the information you need to build all the individual electrical components – resistors, capacitors, jumper switches and laser unit – you will still need additional information to arrange all the components and circuit boards. You'll need even more information to coordinate the circuit boards with the mechanical components. Remarkably, many scientists say the same concept is true in biological systems. An organism needs genetic information to build proteins. It also needs higher-level assembly instructions to arrange tissues and organs into body plans.
Explore Evolution, p. 110-111

Arguments from analogy are only as good as the strength of the analogy and this is a terribly wrong analogy. Biologists know that building a multicellular organism has no similarity to the assembly of a CD player. Unlike multicellular organisms, CD players do not grow from a single cell, they are constructed in factories. CD players do not reproduce, and thus have no system of inheritance, no way to pass variation from generation to generation.

While attributed to "many scientists," this technology-based analogy has almost exclusively been used by Stephen Meyer, an Explore Evolution author, to argue that "a purposive intelligence" designed organisms:

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.
S. Meyer (2004) "Origins of Biological Information and the Higher Taxonomic Categories," Proceedings of the Biological Society of Washington 117(2):213-239.

However, this paper was later disavowed by the of Biological Society of Washington.

The paper by Stephen C. Meyer in the Proceedings (“The origin of biological information and the higher taxonomic categories,” vol. 117, no. 2, pp. 213-239) represents a significant departure from the nearly purely taxonomic content for which this journal has been known throughout its 124-year history. It was published without the prior knowledge of the Council, which includes officers, elected councilors, and past presidents, or the associate editors. We have met and determined that all of us would have deemed this paper inappropriate for the pages of the Proceedings.
Biological Society of Washington, 9/7/2004

A critique of Meyer's paper by Alan Gishlick, Nick Matzke and Wes Elsberry of the National Center for Science Education can be found at Panda's Thumb. The paper has enjoyed no support in the scientific community, as revealed by examining papers citing it. Almost all are social, political, or theological critiques or defenses of intelligent design creationism. This argument has made no significant impact on scientific research, and the claim that "many scientists" agree to the analogy simply does not hold up. The analogy is uninformative and will only mislead students reading it.

"Genomic equivalence"

Explore Evolution quotes Jonathan Wells, a senior fellow of the creationist Discovery Institute, in support the claim that "assembly instructions" are not solely in DNA. Inaccurately citing Wells as a "developmental biologist," the footnote quotes from Wells' creationist work Icons of Evolution, critiqued elsewhere on NCSE's website:

Developmental biologist Jonathan Wells has noted: "A skin cell is different from a muscle cell, which in turn is different from a nerve cell and so on. Yet with a few exceptions, all these cell types contain same genes as the fertilized egg. The presence of identical genes in cells that are radically different from each other is known as "genomic equivalence. According to Wells, this equivalence presents us with a paradox. "If genes control development, and the genes in every are the same, why are the cells so different?" Genes, says Wells, "are being turned on or off by factors outside themselves … [C]ontrol rests with something beyond the genes…". Icons of Evolution (Washington, D.C., Regnery Press, 2000):191.
Explore Evolution, p. 112

One could note that Zeno's paradox is not discussed in physics as a major problem in the study of motion, since the calculus of Newton and Leibniz solved the paradox. Likewise, this supposed paradox of "genomic equivalence" is not discussed as a major problem in developmental biology courses since it has been solved by the last 40 years of research in developmental biology.

If the genome is the same in all somatic cells within an organism (with the exception of lymphocytes; see Sidelights and Speculations), how do cells become different from one another?… Based upon the embryological evidence for genomic equivalence (as well as bacterial models of regulation), a consensus emerged in the 1960's that cells differentiate through differential gene expression.
Scott Gilbert (2003) Developmental Biology 7th ed., p. 92

This consensus view of development has been overwhelmingly supported by the discovery of genes such as Ultrabithorax which regulate other genes involved in developmental pathways. The claim by Jonathan Wells that genomic equivalence remains a paradox is another demonstration of how the anti-evolutionary arguments of the intelligent design movement embrace ignorance.

Morphology

Evolutionary developmental biology – evo-devo – is one of the most dynamic fields in modern biology, and is often poorly covered by introductory textbooks. Rather than providing students with background that would let them conduct scientific inquiry into this field, Explore Evolution provides an account that is too brief and deeply misleading. Perhaps the greatest failing of the book is its misrepresentation of authors, citing them in support of claims that they directly disagree with.

The only thing that exceeds this consistent misrepresenting of scientists' views is this chapter's plagiarism of a creationist source. In discussing the views of Richard Goldschmidt, a biologist of the 1940s, Explore Evolution borrows text from a letter to the editor by young earth creationist David Menton. Menton is not credited as the author of the text. Oddly, the plagiarized text adds little to the chapter, as Goldschmidt has no impact on 21st century biology. The plagiarism demonstrates the authors' lack of academic rigor and the book's deep ties to creationism.

In addition to misappropriating the words of a creationist to revive long-forgotten ideas, Explore Evolution mischaracterizes the views of modern scientists. The authors claim that scientists do not think mutations in DNA can explain new morphology, but the sources cited in support of this argument actually support the role of DNA as the repository of instructions for embryological development. This approach to the scientific literature is inaccurate and misleading, and ultimately contradictory to the principles of inquiry-based learning that Explore Evolution purports to exemplify.

The Four-Winged Fly

The four-winged fruit fly is a classic example of how creationists misinterpret the genetic analysis of development. Developmental geneticists try to understand the role of a gene by modifying a gene and analyzing the consequences, so it is of little consequence that four winged flies would not survive in the wild. The importance of the four-winged fruit fly is that it demonstrated that a few mutations in a single gene were able to transform an entire structure. This work by Ed Lewis led to the discovery of Hox genes and other members of the genetic toolkit (genes which play roles in constructing animal embryos) as well as to a Nobel Prize in 1996. An inquiry-based textbook might well use Nobel-winning research as a way to encourage inquiry, rather than as a way to obscure critical scientific concepts.

Explore Evolution explains the importance of the four-winged fruit fly by focusing upon the importance of mutations as opposed to the importance of the function of a gene:

These experiments show that mutations can induce dramatic changes in the anatomical structure of organisms. And, for many evolutionary biologists, they provide a powerful confirmation of the neo-Darwinian claim that mutations provide the novel variations that natural selection needs to build new anatomical architectures and animals.
Explore Evolution, p. 101

However, as Explore Evolution correctly claims, one cannot assume that natural selection in the wild will operate on the same type of mutations that were artificially selected for in the laboratory:

The neo-Darwinian scenario says that new structures are produced by natural selection acting upon purely undirected and random mutations. Yet, the mutants that produce four-winged fruit flies survive only in a carefully controlled environment and only when skilled researchers meticulously guide their subjects through one non-functional stage after another. This carefully controlled experiment does not tell us much about what undirected mutations can produce in the wild.
Explore Evolution, p. 105

No evolutionary biologist would dispute this point.

Have evolutionary biologists been able to actually identify mutations from the wild that cause morphological differences between related species? This work has only recently been undertaken and has already found clear cases in which mutations result in morphological differences between species.

  • Mutations in Pitx1 gene affect pelvic hindlimb structure in sticklebacks (Shapiro et al., 2004, Shapiro et al., 2006).
  • Mutations in the Ectodysplasin gene affecting armor plates in sticklebacks (Colosimo et al., 2005).
  • Mutations in yellow gene affect formation of wing spots in fruit flies (Prud'homme et al., 2006).
  • Mutations in shavenbaby affect trichome pattern in fruit flies (Mcgregor et al.,2007).
  • Mutations in BMP4 affecting beak morphology in “Darwin’s finches" (Abzhanov et al. 2004).
  • Mutations in the KNOT gene in the mustard plant, Arabidopsis, affecting leaf structure(Hay and Tsiantis, 2006).
  • Mutations in the Scute gene in fruit flies affecting sensory bristle formation (Marcellini and Simpson, 2006).

These experiments are not meant to show the exact mechanism by which today's biological structures evolution. Laboratory experiments will not perfectly replicate wild conditions, but by considering simpler circumstances, researchers can gain insights into big questions. Lab work like the work described above allows researchers to refine their understanding and move the research to ever-more complex situations, balancing a desire for greater realism for decreased ability to focus on a single factor. Explore Evolution misinforms students about what the research they are describing was meant to show, and misinforms them about the methods of inquiry employed by scientists. This is the opposite of what an inquiry-based textbook should do.

Survival

Explore Evolution claims that some current evolutionary biologists think that mutations that result in major changes in morphology (such as the mutations in the Hox gene Ultrabithorax, which produce the four-winged fruit fly) are necessary to explain morphological evolution. Modern evolutionary biologists do not suggest mutations in the genetic toolkit must have dramatic effects (as discussed elsewhere in this critique). Explore Evolution falsely asserts that evolutionary developmental biologists doubt the role of mutation in development.

The "mutation argument," according to Explore Evolution is:

even if the existing gene pool doesn't supply enough information to build a fundamentally new organism, new mutations can.
Explore Evolution, p. 98

Explore Evolution finds significant problems with this straw man "mutation argument" and implies that "small, limited mutations" are restricted to genes which do not regulate morphology:

Critics of the mutation argument say these textbook examples point to a kind of Catch-22. Small, limited mutations (like those that produce antibiotic resistance) can be beneficial in certain environments but they don't produce enough change to produce fundamentally new forms of life. Major mutations can fundamentally alter an animal's anatomy and structure, but these mutations are always harmful or outright lethal (12) …. That is why critics say mutations have not turned out to be the information-rich super-variations that neo-Darwinian biologists had hoped for.
Explore Evolution, p. 106

To support their case, Explore Evolution cites four papers in reference 11 as critical of the "mutation argument":

Wallace Arthur, "The effect of development on the direction of evolution: toward a twenty-first century consensus." Evolution and Development 6 (2004) 282-288.

K.S.W. Campbell and C.R. Marshall "Rates of evolution among paleozoic echinoderms," in Rates of Evolution, K.S.W. Campbell and M.F. Day eds. (London, Allen and Unwin, 1987).

Eric H. Davidson, Genomic Regulatory Systems, Development and Evolution (San Diego Academic Press, 2001).

Scott F. Gilbert, John M. Opitz, and Rudolf A. Raff "Resynthesizing evolution and developmental biology," Developmental Biology 173 (1996): 357-372.
Explore Evolution, p. 112

Notably, all of the more recent citations (after 1987) are evolutionary developmental biologists and, as we shall see, the citations of their work by Explore Evolution is another example of "creationist abuse of evo-devo."

As Rudolf Raff, a critic of the "mutation argument" (according to Explore Evolution) notes:

There is a whole stable of intelligent design creationist writers associated with the Discovery Institute, and we will see more slick books of bogus science produced to influence the teaching of biology, and even federal funding of research. Evo-devo data have become a part of the creationist rhetorical weaponry, and as evo-devo grows in prominence, the problem will grow in severity
Rudolf Raff, "The Creationist Abuse of Evo-Devo," (2001), Evolution and Development, 3:6, p. 374

Explore Evolution asserts that mutations in the genes regulating development will only produce major mutations that will be harmful. Does Wallace Arthur actually think about mutations that affect development (ontogeny)? Is Arthur a "critic of the mutation argument"?

Subsequent to the modification of a developmental gene (e.g., a Hox gene) by mutation, the ontogenetic trajectory will in many (but not all) cases be reprogrammed so that it follows a different route. The difference may be tiny, moderate, or large.
Wallace Arthur, (2004) "The effect of development on the direction of evolution: toward a twenty-first century consensus." Evolution and Development 6, p. 282

In other words, not all mutations in a developmental gene (a genetic toolkit gene) need have major affects, such as the four-winged fruit fly. Indeed, evolutionary developmental biologists think that relatively modest changes in genes of the genetic toolkit are more likely to prove useful to organisms.

Scott Gilbert is also cited as a "critic of the mutation theory" according Explore Evolution. Gilbert has explained about his view of evolution, (available at National Center for Science Education) in response to misrepresentations of his work by the Discovery Institute in 2002 in their testimony to the Ohio Board of Education.

My research on turtles and my research into evolutionary developmental biology is fully within Darwinian parameters. My gripe has been that neo-Darwinism has supposed that population genetics was the only genetics needed to explain Darwinian evolution. I claim that developmental genetics is also needed. So my research has been to include developmental genetics into the Darwinian mix.
National Center for Science Education (2002), Analysis of the Discovery Institute’s “Bibliography of Supplementary Resources for Ohio Science Instruction”

In contrast to Explore Evolution's misrepresentation, Eric Davidson actually argues that mutations in the "regulatory genome" (CREs and proteins encoded by the genetic toolkit genes) play important roles in animal evolution.

Since the morphological features of an animal are the product of its developmental process, and since the developmental process in each animal is encoded in it's species-specific regulatory genome, then change in animal form during evolution is the consequence of change in genomic regulatory programs for development.
Eric Davidson, in The Regulatory Genome: gene regulatory networks in development and evolution, (2006), p. 27

None of the recent research cited actually undermines what Explore Evolution refers to as "the mutation argument." They all argue that mutations can and do change developmental trajectories, and that these changes are important in our understanding of evolutionary developmental biology. Explore Evolution misleads students by suggesting otherwise.

"Hopeful Monsters"

The discussion of Richard Goldschmidt and his saltational model of evolution is largely copied (without credit) from an essay by "creationist anatomist" David Menton. Goldschmidt's ideas were widely criticized when first publicized, and their reputation has not improved with time. There's no particular reason to cover them in a modern biology textbook at all.

It is difficult to be sure why Explore Evolution invests a full page in a discussion of Richard Goldschmidt's ideas. His work was rejected by biologists of his own day, and age has not improved his reputation. A recent assessment of his influence on modern biology concluded:

Richard Goldschmidt's research on homeotic mutants is not significant because it was right or paradigmatic. It is significant because it represents one of the first serious efforts to integrate genetics, development, and evolution. As such, Goldschmidt's research reveals the great difficulty of balancing the different contributors to a developmental evolutionary genetics. Consider the major flaws with his different models of macroevolution. Evolution by systemic mutations placed too much emphasis on a model of genetic structure which could not be confirmed or fully integrated with a model of gene action (not every inversion or chromosomal repatterning produces a phenotypic effect). Evolution by developmental macromutations placed too much faith in the ability of developmental processes to create functioning new species from major genetic changes. Goldschmidt needed [Sewall] Wright's counsel to provide a reasonable evolutionary dynamics for major mutations, which in turn made speciation by macromutation a possibility.
Michael R. Dietrich (2000) "From Hopeful Monsters to Homeotic Effects: Richard Goldschmidt's Integration of Development, Evolution, and Genetics" American Zoologist 40(5):738–747

In short, Goldschmidt's erroneous ideas spurred other scientists to consider ideas which did ultimately improve our understanding of evolution. The insight that mutations could have both large and small effects influenced Sewall Wright's "shifting balance" evolutionary model — a major component of modern population genetics. Similarly, evolutionary biologist Stephen Jay Gould wrote an essay on the "Return of the Hopeful Monster," in which he rejected most of Goldschmidt's actual argument, but identified useful insights which could guide modern researchers:

I disagree fundamentally with his claim that abrupt macroevolution discredits Darwinism. For Goldschmidt also failed to heed Huxley's warning that the essence of Darwinism – the control of evolution by natural selection – does not require a belief in gradual change. …

[A]ll theories of discontinuous change are not anti-Darwinian, as Huxley pointed out nearly 120 years ago. Suppose that a discontinuous change in adult form arises from a small genetic alteration. Problems of discordance with other members of the species do not arise, and the large, favorable variant can spread through a population in Darwinian fashion. Suppose also that this large change does not produce a perfected form all at once, but rather serves as a "key" adaptation to shift its possessor toward a new mode of life. Continued success in this new mode may require a large set of collateral alterations, morphological and behavioral; these may arise by a more traditional, gradual route once the key adaptation forces a profound shift in selective pressures …

In my own, strongly biased opinion, the problem of reconciling evident discontinuity in macroevolution with Darwinism is largely solved by the observation that small changes early in embryology accumulate through growth to yield profound differences among adults. Prolong the high prenatal rate of brain growth into early childhood and a monkey's brain moves toward human size. Delay the onset of metamorphosis and the axolotl of Lake Xochimilco reproduces as a tadpole with gills and never transforms into a salamander.

The element that Gould borrowed from Goldschmidt was not the erroneous view of genetics, nor Goldschmidt's model of how large morphological changes could be produced in that bogus genetic scheme. The connection between the sort of developmental biology research Gould describes and Goldschmidt's work is negligible. Hence Dietrich's observation above that the significance of Goldschmidt's work not being that "it was right or paradigmatic."

Neither Goldschmidt nor "hopeful monsters" is mentioned in the index to any of the most common college or high school biology textbooks. Evolutionary biology textbooks mention him only in passing, to note that his ideas were not and are not generally accepted. Ridley's Evolution merely observes that Ernst Mayr's arguments in favor of the Modern Synthesis won out against Goldschmidt's suggestions, and Futuyma rightly noting that Goldschmidt's genetic ideas "have been entirely repudiated by modern geneticists" and that his "saltationism was rejected in favor of gradual change" (even the changes Gould discusses above would be gradual in this sense). The lesson Futuyma draws from the coalescence of the Modern Synthesis, and the consequent rejection of ideas like Goldschmidt's, is that "the rejection of false ideas is an important part of the progress in science" (Futuyma, D., 1998, Evolutionary Biology, Sinauer Associates, Inc.:Sunderland, MA. p. 25).

In the perverted view of science promulgated by Explore Evolution, bad ideas never die. While there might be pedagogical value in leading students on a discussion of the flaws in Goldschmidt's ideas and the advantages of the Modern Synthesis, there is no value in the approach Explore Evolution takes. Simply tossing out a bad idea as if it were generally accepted today is unethical. Presenting an incomplete account of Goldschmidt, and leaving the impression that biologists today rely on his work, simply leaves students with the wrong impression.

An even worse impression will be left if students realize that the first paragraphs of Explore Evolution's page about Goldschmidt are copied without credit from another author. David Menton wrote those words for a young earth creationist group called the Missouri Association for Creation. Menton wrote:

In the 1930s, paleontologist Otto Schindewolf concluded that the missing links in the fossil record were not really missing at all, but rather were never there in the first place! Schindewolf proposed that all the major evolutionary transformations must have occurred in single large steps. He proposed, for example, that at some point in evolutionary history, a reptile laid an egg from which a bird was hatched! This bizarre notion was championed in 1940 by the geneticist Richard Goldschmidt of the University of California at Berkeley. Like Schindewolf, Goldschmidt resigned himself to the fact that true transitional forms were not found despite over a hundred years of searching for them, and that evolutionary theory would simply have to accommodate this fact.

Goldschmidt sought to advance Schindewolf's notion of evolution through single large steps by trying to imagine a plausible mechanism for it. He suggested that the answer might lie in what are known as embryological monsters, such as the occasional birth of a two-legged sheep or a two-headed turtle. Goldschmidt conceded that such monsters rarely survived very long in nature, but he hoped that over a long period of time some monsters might actually be better suited to survive and reproduce than their normal siblings. Goldschmidt named this monstrously hopeless speculation the "hopeful monster theory." Since there was not even the slightest shred of evidence to support the hopeful monster theory, it was dismissed with derision by almost all evolutionists of his time.

Compare this to the material in Explore Evolution (identical passages bolded, paraphrases in italics):

In the 1930s, paleontologist Otto Schindewolf proposed that all the major evolutionary transformations must have occurred in single, large steps. (He proposed, for example, that at some point in evolutionary history, a reptile laid an egg from which a bird was hatched.) In 1940, geneticist Richard Goldschmidt took Schindewolf's idea one step further, suggesting that true evolutionary change takes place in the rare successes of large-scale mutations, not by the accumulation of small changes (as Darwin predicted).

Goldschmidt conceded that the vast majority of large-scale mutations produce hopelessly maladapted freaks like two-legged sheep or two-headed turtles. However, he suggested that on rare occasions a lucky accident might produce a fundamentally new form of life — an organism that was actually better suited to survive and reproduce than its "normal" siblings.

Explore Evolution, p. 107

Teachers know that it is not appropriate to quote so much material from a source without proper credit. Paraphrasing a few passages and correcting some grammatical errors does not excuse the failure to identify the source. Not only does this passage misinform students about the current state of the science, distract from real science, and repeat creationist canards, it is also built on a serious ethical lapse. Students should not be sent the message that plagiarism is appropriate.

Hox & Development

In claiming that developmental processes are too integrated to allow change, Explore Evolution ignores over 10 years of research in evo-devo on the modularity of development. Evolutionary developmental biologists who study Hox genes think that mutations in the CREs of target genes for Hox genes are more likely to be more important for morphological evolution than mutations in Hox genes themselves.

Developmental biologists are investigating another kind of mutation - mutations in "hox genes" - that many neo-Darwinists think can provide a signficant source of major variation in living forms. Hox genes are "master regulator" genes that turn other genes in the cell on and off during the developmental process…Because hox genes are so important for coordinating the activities of the cell, some researchers think that mutations in these genes can cause large-scale changes in the structure of an organism.
Explore Evolution, p. 109

Explore Evolution disregards research on Hox genes that strongly suggest that instead of soley acting at the top of a hierarchy as a "master regulator", they work at many sites in a developmental pathway as "micromanagers".

We still have little idea how the differential expression of one 'master' gene can control the morphology of complex structures, but recent studies suggest that the Drosophila Hox gene Ultrabithorax micromanages segment development by manipulating a large number of different targets at many developmental stages.
Michael Akam (1998) "Hox genes: from master genes to micromanagers," Current Biology 8:676

Explore Evolution gestures towards accuracy in suggesting that there is a challenge in mutating the protein-coding regions of Hox genes. As Sean Carroll and colleagues explain below, developmental regulatory genes, such as Hox genes are pleitropic - they control many different developmental processes, making it more difficult to mutate their protein-coding region without harmful consequences (although the case of the evolution of Ultrabithorax function in limb repression in insects appears to be a notable exception). In contrast to most mutations in the protein-coding regions of developmental regulatory genes, mutations in CRE's minimize the fitness penalty - an important issue which is completely ignored by Explore Evolution.

A clear principle is emerging from the increasing number of case studies: pleiotropy imposes a genetic constraint on the type of changes that can be accommodated in morphological evolution. Highly pleiotropic genes (including most developmentally regulated genes) are more likely to contribute to morphological evolution through cis-regulatory changes than through coding sequence alterations. In contrast, known examples of pigmentation evolution resulting from the alteration of coding sequences affect genes involved in a single process, such as the overall body color in fish, mammals, or birds. Coding sequence changes appear to be better tolerated in minimally pleiotropic genes. This principle of minimizing fitness penalties delimits the scope of what changes are permissible under natural selection and explains why CRE evolution is a pervasive mechanism underlying morphological diversification.
Prud'homme et al., (2007) "Emergining Principles of Regulatory Evolution," PNAS 104:8609

To understand how Hox genes, such as Ultrabithorax, act to regulate developmental pathways, we must consider how CREs act as genetic switches. Recall that the four-winged fruit fly is generated by mutations in Ultrabithorax, (Ubx) that turn the gene off in hindwings (halteres).

A Four-Winged FlyA Four-Winged Fly

The diagram below shows the basic gene network involved in patterning the forewing along the anterior-posterior and dorsal-ventral axes. If Ubx was working as a "master regulator" in the hindwing, Ubx would be predicted to only affect genes at the top of the hierachy, such as selector or short-range signals. Instead, it has been shown by Sean Carroll and colleagues (Weatherbee et al., 1998, Hersh et. al, 2005) that Ubx may directly regulate many wing patterning genes at all levels of the hierarchy, including the primary target genes, demonstrating that Ubx is acting as a micromanager.

Wing PatterningWing PatterningUbx 10Ubx 10

How can Ubx regulate multiple genes involved in wing patterning? Ubx binds to CREs that contain the specific DNA sequence as shown in the diagram below.

This short sequence is present in many different CREs throughout the genome. CREs also have different binding sites for other proteins that can turn genes on or off. In the figure below, future wing cells lack the Ultrabithorax protein, Ubx (U), while future haltere cells contain Ubx. Additionally, there are other proteins (A,B,C,D,E,F) which bind to the CRE to regulate the nearby target gene.

Note that whether or not Ubx can bind to a CRE depends upon whether Ubx is present and if the CRE has a binding site on it for Ubx. For example, Omb does not have a Ubx binding site and is not regulated by Ubx. In contrast, sal and CG13222 have Ubx binding sites and are respectively turned off or on in halteres.

Is there direct evidence that Ultrabithorax binds to CREs of target genes involved in wing patterning? So far Sean Carroll's lab has identified four such genes (Galant et al., 2002; Hersh and Carroll, 2005; and Hersh et al, 2007).

Since the proteins which bind to CREs generally bind to different sites on the CRE, a mutation in a CRE which abolished the binding of Ubx would not affect the binding of A,B,C etc. to their sites on the CRE. This independence of binding sites on CREs means that these binding sites can evolve independently.

Ubx and CREUbx and CRE
As we have seen with four-winged fruit flies, it requires a great many coordinated changes to transform one system into another without losing function in the "in-between" steps. The more the individual parts of a system depend on each other, the harder it is to change any one part without destroying the function of the organism as a whole. Since Hox genes affect so many genes and systems, it seems unlikely that they could be mutated without damaging the way some of the genes are switched 'on or 'off.'
Explore Evolution, p. 109

How is a hindwing transformed into a forewing? In this case, "a great many coordinated changes" are actually mutations in three CREs controlling in which part of the hindwing the Hox gene Ultrabithrox is normally expressed. These three mutations result in the absence of Ultrabithorax in all of hindwing and the conversion of a hindwing into a forewing. As we shall see, mutations of CREs, even in genes that are involved in highly complex networks, such as Hox genes, are very capable of evolving.

Can protein-coding regions of Hox genes be changed? Elsewhere, we examine the case of how Ultrabithorax evolved the ability to repress limbs in insects by the replacement of the amino acids serine or threonine with the amino acid alanine at the tail of Ultrabithorax. In that example, "a great many changes" may involve as much as five such replacements, hardly an insurmountable barrier.

Modularity in Hox genes

To buttress the false claim that developmental pathways regulated by Hox genes cannot evolve Explore Evolution engages in a major error of omission by failing to address the issue of modularity. This is concept is not obscure - a PubMed search of "modularity and evolution" yields over 140 publications in the last ten years. Modularity describes the independent control of hierarchical levels in development and evolution ranging from anatomical structures to signaling pathways to genetic switches.

In 1996, modularity in development and evolution was fully discussed in the influential book on evolutionary developmental biology, The Shape of Life by Rudolf Raff. As a book review of the Shape of Life in the journal Bioscience notes:

Raff defines modules as units "…that are distinct in genetic specification, autonomous features, hierarchical organization, interactions with other modules, location, time of occurrence, and dynamic properties" … Modularity permits change because developmental processes are free to dissociate, duplicate, diverge, and be co-opted to new uses. Although developmental modules themselves are complex, Raff argues that they may often be activated by single or few regulatory genes acting as switches, such as Pax-6 in eye development. The mostly likely changes in ontogeny are those that alter the relative timing, number, or location of preexisting modules rather than those that produce wholly novel modules or structures. This feature of development also helps to explain the essential conservation of body plan.
Terri Williams, "The Modularity of Development" (1998), Bioscience 48 p. 60

As Eric Davidson notes in 2006, the modularity of cis-regulatory elements (CREs) is now well-established.

When cis-regulatory sequences were first proposed to be generally modular in organization (Kirchamer et al. 1996), there were on ly a modest number of examples from work in Drosophila and sea urchins, and the idea was largely inferential. Now there are literally scores of genes for which detailed experimental analyses have demonstrated sharply modular cis-regulatory elements, such that given non-overlapping regions of the genomic DNA each control a specific subcomponent of the overall expression pattern.
Eric Davidson, The Regulatory Genome: gene regulatory networks in development and evolution (2006) p. 33

How does the modularity of CRE's relate to whether the integrated networks regulated by Hox genes can evolve? Consider how Ubx regulates the target genes Sal and CG13222 by binding to their CREs. A mutation that disabled Ubx binding to CG13222 would prevent it from being from turned on in the hindwing, but would not affect Ubx turning off Sal in the hindwing. Similarly, a mutation in Omb that caused it to turned off in the hindwing would not affect how Ubx controls Sal or CG13222.

Hindwing EvolutionHindwing Evolution

Thus Ubx binding sites on CREs of different genes can be gained or lost independently of binding sites for other proteins genes. Although these genes can be involved in a complicated gene network, the modularity of CREs allow specific genes to be independently changed without affecting the rest of the network. Ubx is known to regulate hindwing development in all insects, from beetles to fruitflies, even though the morphology of their greatly differs. These major changes in morphology are easily explained when considering how Ubx binding sites on CREs can evolve.

Body Plans

Explore Evolution completely ignores studies showing that mutations in both protein coding sequences and in non-coding cis-regulatory element sequences (CREs) are responsible for changes in morphology. Explore Evolution muddies the distinction between mutations which affect protein structure and function, and mutations which affect when and where genes are turned on or off.

In its discussion of DNA and mutations, Explore Evolution asserts:

DNA is actually closer to the bottom of the organizational ladder. Yes, it directs the building of proteins, and yes, proteins are important. But DNA does not direct how the overall body plan gets built.
p. 110

In making this claim, Explore Evolution fails to acknowledge the extensive research on mutations in DNA sequences that do not encode proteins, but which have important morphological effects. Explore Evolution thereby misses out on the opportunity to present the genuinely relevant and interesting scientific debate in evolutionary morphology concerning the relative importance of mutations in protein-coding sequences versus mutations in non-coding sequences.

An important tenet of evolutionary developmental biology ("evo devo") is that adaptive mutations affecting morphology are more likely to occur in the cis-regulatory regions than in the protein-coding regions of genes… Although this claim may be true, it is at best premature. Adaptation and speciation probably proceed through a combination of cis-regulatory and structural mutations, with a substantial contribution of the latter.
Hoekstra et al., (2007) "The locus of evolution: Evo devo and the genetics of adaptation," Evolution 61:005

Non-coding regions of DNA contain genetic switches called cis-regulatory elements (CREs). CREs control when and where a gene is turned on (expressed). Mutations in the CREs of Ultrabithorax are responsible for that gene being turned off in fly hindwing resulting in the four-winged fruit fly. As Sean Carroll and colleagues argue, recent analyses have shown that mutations in CREs play an important role in morphological evolution.

A growing number of case studies exploring the mechanisms of morphological changes have provided direct evidence that CRE evolution plays a major role. From these examples, we have identified general rules regarding regulatory evolution, namely how regulatory evolution exploits available genetic components, irrespective of their hierarchical position in gene networks to generate novelty, and minimizes fitness penalties. These rules offer a rationale explaining why regulatory changes are more commonly favored over other kinds of genetic changes in the process of morphological evolution, from the simplest traits diverging within or among species to body-plan differences at higher taxonomic levels.
Prud'homme et al., (2007), "Emerging Principles of Regulatory Evolution", PNAS 104:8611

An example of the Pitx1 gene in the marine stickleback fish is shown below. Genetic studies of sticklebacks by David Kingsley and colleagues have established the mutations in Pitx1 have played an important role in the evolution of sticklebacks. There two important CREs controlling Pitx1 expression. One CRE is postulated to control Pitx1 expression in the mouth and jaw while another CRE is postulated to control Pitx1 expression in the pelvic hindlimb.

Mutations in the protein-coding region can affect the sequence and the function of a protein. On the other hand, mutations in the CRE can affect when and where a gene is turned on. Have mutations in CREs or in protein-coding regions of genes been involved in morphological evolution? This question has been addressed in a number of different studies described below.

David Kingsley and colleagues (Shapiro et al., 2003) have studied the evolution of sticklebacks. Over the last 10,000 years, marine sticklebacks have invaded freshwater lakes and have undergone an extensive adaptive radiation. One important adaptation in freshwater stickleback has been the reduction of pelvic spines that helps to reduce predation from arthropods. To address what gene(s) are responsible for pelvic spine reduction, Kingsley and colleagues conducted genetic experiments on sticklebacks and showed that mutation in the Pitx1 gene was responsible.

Recall that Pitx1 is expressed in development of the pelvic spine and of the mouth and jaws in marine sticklebacks. However, in freshwater sticklebacks with reduced pelvic spines, Pitx1 is expressed only in the mouth and jaws. So, although they have not yet identified the precise mutation(s), a technically demanding job of finding a needle in a haystack, this observation strongly suggests that mutations in the CRE controlling pelvic spine expression of Pitx1 are responsible for this reduction. Note that a mutation in the protein-coding region of Pitx1 would affect Pitx1 function in both the mouth, jaw and pelvic spines. This type of mutation is fatal in mice. However, because mutations in one CRE do not affect the function of a different CRE, Pitx1 function can be lost in the pelvic spine and retained in the mouth and jaw of freshwater sticklebacks.

As Kingsley and colleagues show, the mutations in a CRE can cause the loss of Pitx1 function in pelvic spines, but can mutations generate new CREs? Sean Carroll and colleagues (Prud'homme et al., 2006) have addressed this question by focusing upon how wing spots have evolved in fruit flies. Wing spots play an important role in mating behaviors of fruit flies and would be predicted to be under strong natural selection. By a functional analysis of wingspot CREs of different fruit fly species, Prud'homme et al. show that CREs responsible for wing spots in fruit flies have been independently gained as shown below. Interestingly, these new CREs have been generated by the modification of pre-existing CREs.

David Stern and colleagues have examined a different type of morphological evolution in fruit flies, trichome formation on limbs. They have recently discovered that multiple mutations in the CREs controlling the genetic toolkit gene, shavenbaby, are responsible for the evolution of this morphological feature.

Here we examine the genetic basis of a trichome pattern difference between Drosophila species, previously shown to result from the evolution of a single gene, shavenbaby (svb), probably through cis-regulatory changes(6),,, Our results demonstrate that the accumulation of multiple small-effect changes at a single locus underlies the evolution of a morphological difference between species. These data support the view that alleles of large effect that distinguish species may sometimes reflect the accumulation of multiple mutations of small effect at select genes.
McGregor et al., "Morphological evolution through multiple cis-regulatory mutations at a single gene," (2007), Nature 448:487

Mutations in CREs in fruit flies and sticklebacks have been shown to play important roles in their morphological evolution. Do mutations in CREs play any role in the evolution of humans? To address this question, Greg Wray and colleagues examined the PDYN gene which is involved in the synthesis of endogenous brain opiates. Through comparing the genomes of chimps and humans, population genetics and experimental analyses, they demonstrate that a 68 base-pair element is important for turning the PDYN gene on at higher levels in human brains and that this element has been under positive natural selection.

Changes in the cis-regulation of neural genes likely contributed to the evolution of our species' unique attributes, but evidence of a role for natural selection has been lacking. We found that positive natural selection altered the cis-regulation of human prodynorphin, the precursor molecule for a suite of endogenous opioids and neuropeptides with critical roles in regulating perception, behavior, and memory.
Rockman et al., "Ancient and Recent Positive Selection Transformed Opioid cis-Regulation in Humans," (2005), PLOS Biology 3, p. 387

This is an important and active field of evolutionary research, and if Explore Evolution aimed to live up to its title, it is a field that could have generated the basis for genuine inquiry. Instead, unsolved questions are offered as unsolvable obstacles, and ongoing scientific research is ignored or obscured to serve the authors' misconceptions.

Mutations & New Body Plans

Explore Evolution claims:

According to Neo-Darwinism, new biological form arises when natural selection acts on randomly occurring mutations and variations in DNA. But new research seeems to say that mutations in DNA assembly instructions will produce, at best, a new protein. Higher-level instructions – for building tissues, organs and body types – are not stored only in DNA. This means that you can mutate DNA 'til the cows come home and you still wouldn't get a new body plan.
Explore Evolution, p. 111

It is outright baffling that Explore Evolution cites Franklin Harold's book, The Way of the Cell, to support the claim that mutations are insufficient to change body plans. Franklin Harold is a microbiologist, and a proponent of the role of self-organization and structural constraints in the spatial organization of cells and does not remotely address the issue of body plans in his book. He's interested in microbes, not higher organisms.

This book celebrates microorganisms, and that requires explanation because with most folks the word "life" does not conjure up the image of a bacteria or protozoa … Microorganisms, the bacteria and protists, can make a biosphere all by themselves, and did so for billions of years when the earth was young. Higher organisms hold mysteries that are of special concern to us humans; the genetic basis of disease, the immune response, embryonic development and the nature of mind are now at the forefront of the research effort. But for the purposes of an inquiry into the nature of life, these are peripheral issues. They represent potentialities inherent in living matter, but they are not required for its existence.
Franklin Harold (2001) The Way of the Cell, Preface, p. xi

Nor is Franklin Harold sympathetic to the special pleading that a mysterious "something else" is needed to explain cellular morphology.

Spatial organization is not written out in the genetic blueprint; it emerges from the interplay of genetically specified molecules, by way of a hierarchy of self-organizing processes, constrained by heritable structures, membranes in particular.
Franklin Harold (2005) Molecules into Cells: Specifying Spatial Architecture, Microbiology and Molecular Biology Reviews, 69 p. 545

Perhaps Explore Evolution meant to include reference 21, Stephen Meyer's paper, "The origin of biological information and the higher taxonomic categories," which was later retracted by the Proceedings of the Biological Society of Washington.

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.
S. Meyer (2004) "Origins of Biological Information and the Higher Taxonomic Categories," Proceedings of the Biological Society of Washington 117(2):213-239

As in Explore Evolution, Meyer refers to Origination of Organismal Form for support. But, as described elsewhere in this critique, Muller and Newman are not addressing the origin of higher taxonomic categories per se, they are concerned with the origin of the forms of the earliest multi-cellular life and of their embryos.

However, Simon Conway Morris, a paleontoloist who studies Cambrian and pre-Cambrian fossils, does address the issue of body plans in the Origination of Organismal Form:

Despite the seeming welter of body plans emerging in the Cambrian, it is difficult to escape the conclusion that the process and products, far from requiring a radical revision of existing theory, fit comfortably into the neo-Darwinian framework.
S.C. Morris (2003) "Metazoan Phylogeny," in Origination of Organismal Form,, p. 21

The vibrant field of evolutionary developmental biology has generated significant insights into the mechanisms by which mutations in DNA would have generated the morphological novelty that produces tissues, organs, and body types. The only citation the authors offer to support their beliefs to the contrary turns out not to support the claim by Explore Evolution.

Developmental Controls

Explore Evolution insists, contrary to the consensus of developmental biologists, that we don't really know what controls development or whether that mystery force could mutate:

Some developmental biologists now think that two other cellular features – the cytoskeleton and the cell membrane – store structural information that affecdts how the embryo develops, but there is much we do not know yet.

What we do know is that if DNA doesn't control development, something else must. Identifying the "something else" is one of the next great areas of research. Another question, of course, is whether the "something else" can be altered by mutation, which would provide a whole new vista of variations on which natural selection could act. Is this what research will reveal? Or will it reveal even deeper questions? Stay tuned.

Explore Evolution, p. 111

Explore Evolution is not clear whom they are referring to in this passage. If this is truly "the next great area of research," an "inquiry-based" textbook would do well to lead students through the leading hypotheses and the evidence researchers in the field are considering, so that students could engage in their own inquiry. Unfortunately, the citations offered earlier in this chapter are uninformative. Franklin Harold, cited earlier and quoted in this critique observing that "[s]patial organization … emerges from the interplay of genetically specified molecules," takes this position:

I do not mean to imply that eukaryotic cells are the product of intelligent purposeful design, the supposition is that the adaptive evolution of a cytoskeleton and intracellular membranes made possible the proliferation of larger cells displaying varied and elaborate morphologies.
Franklin Harold (2001) The Way of the Cell, p. 121

Another possibility is the creationist pseudoscience of Jonathan Wells:

Jonathan Wells, a molecular biologist with the Discovery Institute, argues that genes, environment, and cell structure all affect development. DNA controls the production of proteins that affect development, but the cytoskeleton (a network of microscopic fibers) and certain features in the cell membrane determine what happens to these proteins after they are made…

"The notion that genes control development is a fallout from neo–Darwinian evolutionary theory," Mr. Wells added. Evolutionists use genetic mutations to explain how organisms could change gradually over time. But if development involves the entire egg, then its complexity is much stronger evidence that a Creator designed life.

Setting aside the absurd implication that evolutionary biologists think that development does not involve the "entire egg," could genes affect how the egg is produced? Indeed they can and do. Fruit fly geneticists have searched for "maternal effect mutations" in such genes and have identified genes necessary for the proper construction of the oocyte, the future egg. One such gene encodes Protein Kinase A (PKA) that has a direct effect upon the organization of microtubules through mediating a external signal from nearby follicle cells.

Microtubule polarity has been implicated as the basis for polarized localization of morphogenetic determinants that specify the anteroposterior axis in Drosophila oocytes. We describe mutation affecting Protein Kinase A (PKA) that act in the germ line to disrupt both microtubule distribution and RNA localization along this axis.
M. E. Lane and D. Kalderon (1994) "RNA localization along the anteroposterior axis of the Drosophila oocyte requires PKA-mediated signal transduction to direct normal microtubule organization," Genes and Development 8, p. 2896

Unfortunately for creationists, the organization of microtubules in the oocyte is under genetic control and will be sensitive to mutation. In this case, a mutation affecting PKA function in the egg can result in an embryo which has heads at both ends, or in more subtle variations. In a similar fashion, if the "certain features of the cell membrane" are due to actions of proteins, either in the cell membrane or involved in generating the cell membrane of eggs, they will also sensitive to genetic control and mutation, since, as Harold observes, those structures are genetically specified.

Bacterial speciation

The study of evolution in the bacterial world is one of the most dynamic and exciting areas of current biological research. New analytical tools from molecular biology and the increasing wealth of data from genomics research are currently offering new insights into the nature of bacterial species and the mechanisms of speciation. These studies also promise to illuminate the early history of life on earth. Explore Evolution obscures this active area of research by claiming:

As British bacteriologist Alan Linton has noted, "Throughout 150 years of the science of bacteriology, there is no evidence that one species of bacteria has changed into another.
Explore Evolution, p. 104-5

This claim is made to imply once again that natural evolutionary mechanisms cannot account for speciation. As worded, it again misrepresents what evolutionary biology actually claims, and what research has shown. Explore Evolution ignores the hundreds of papers which address the study of speciation in bacteria. The quotation offered is from a book review by a British microbiologist affiliated with the Biblical Creation Society, hardly a credible source.

Recent research indicates that speciation in bacteria occurs when otherwise relatively frequent and genome-wide genetic recombination events become more limited.

A recent study notes that when eukaryotic organisms become reproductively isolated, their entire genomes become isolated. In bacteria, the situation is very different. Bacteria exchange pieces of DNA, not whole genomes. This study showed that "different regions of the Escherichia coli and Salmonella enterica chromosomes diverged over a ~70-million-year period. Genetic isolation first occurred at regions carrying species-specific genes, indicating that physiological distinctiveness between the nascent Escherichia and Salmonella lineages was maintained for tens of millions of years before the complete genetic isolation of their chromosomes."

Note also that the authors of this paper emphasize that their research on bacterial evolution is important for dealing with urgent practical problems. The proper identification and delineation of bacterial species plays critical roles in medical diagnosis, food safety, epidemiology, and bioterrorism mitigation.

Recent work by Richard Lenski has even shown new bacterial species evolving in the laboratory. Lenski and his student Zachary Blount note that "E. coli cells cannot grow on citrate under oxic conditions, and that inability has long been viewed as a defining characteristic of this important, diverse, and widespread species." They then exposed several identical populations of E. coli to an environment high in citrate and low in other energy sources. "For more than 30,000 generations, none of them evolved the capacity to use the citrate. … [O]ne population eventually evolved the Cit+ function [a gene that could metabolize citrate], whereas all of the others remain Cit− [unable to metabolize citrate] after more than 40,000 generations." Given that the Cit- trait is a defining feature of E. coli, the population that gained Cit+ could be considered a new species.

Bacterial evolution is an interesting and important field. There are also important questions to ask about what it even means for bacteria to speciate. Without offering a clear definition of a bacteria species, it is impossible to know whether it's true that scientists have not seen bacterial speciation, nor what significance that would hold if true. Without giving students that information, there's no way for them to pursue their own inquiry, again falsifying the claim that Explore Evolution is inquiry-based.

References:

Adam C. Retchless and Jeffrey G. Lawrence (2007) "Temporal Fragmentation of Speciation in Bacteria" Science 317(5841):1093-1096. DOI: 10.1126/science.1144876

Christophe Fraser, William P. Hanage, Brian G. Spratt (2007) "Recombination and the Nature of Bacterial Speciation" Science 315(5811):476-480 DOI: 10.1126/science.1127573

Zachary D. Blount, Christina Z. Borland, Richard E. Lenski (2008) "Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli" Proc. Nat. Acad. Sci. 105(23):7899-7906