Natural Selection

Natural selection is one of the major mechanisms of evolution, but where most evolution textbooks discuss several such mechanisms, often devoting separate chapters to each, Explore Evolution ignores nearly all of them, devoting a chapter and a half to misrepresenting natural selection. The chapter devoted to this concept inaccurately describes natural selection, mischaracterizes several widely-known examples of natural selection at work, misconstruing howthe significance of those examples.

Students need to understand natural selection, and there are many inquiry-based techniques for teaching about it. Explore Evolution fails to offer any new additions to this literature. Worse yet, it neglects to even draw on that literature to help students deepen their understanding of this basic aspect of evolutionary biology.

p. 95: "changes in the sub-population take place as genetic information is lost to that population"

Ongoing research by geneticists and evolutionary biologists shows that evolutionary processes (including natural selection) do increase information, including through the evolution of new genes, and of genes that are better able to operate under novel conditions. Explore Evolution fails to confront this ongoing research, preferring to criticize decades-old experiments.

Field data vs. Explore Evolution: An illustration of the evolution of finch beaks from Explore Evolution shows no relationship with actual data from the field.  The former restricts its period of analysis to exclude periods of intense change, adding a line of "extrapolation" with no relatField data vs. Explore Evolution: An illustration of the evolution of finch beaks from Explore Evolution shows no relationship with actual data from the field. The former restricts its period of analysis to exclude periods of intense change, adding a line of "extrapolation" with no relationship to anything predicted by working scientists. Explore Evolution uses these inaccuracies to argue for a fallacious extrapolation: limits on the variation possible through natural selection.

p. 94: "not only does the experiment [on peppered moths] not show what the story says it's supposed to, the experiment itself is highly questionable"

While Explore Evolution was being written, a researcher re-ran Kettlewell's classic experiment on peppered moths, correcting various criticisms offered of the original. The new research confirmed the original findings, and those findings affirm the importance of natural selection as an evolutionary mechanism.

p. 90: "definite, discoverable limits on what artificial [and therefore natural] selection can do"

Shortly before decrying extrapolation from short periods to long-term trends, Explore Evolution claims that limits on what animal breeders can accomplish over a century or two demonstrate that evolution could not produce the diversity of life we see over life's 4 billion year history. In fact, intensive selective breeding over a few hundred years has produced a range of sizes and morphologies among domestic dogs that exceeds the diversity of all other members of the family Carnivora. Whatever limits evolution reaches after intense selection, they are much smaller than what the diversity of life requires us to explain.

p. 87: "Is it possible that something like [artificial selection] occurs in nature – only without any intelligence to guide it?"

Explore Evolution plays a slight of hand here, treating "intelligence" interchangeably with the practices of animal breeders, when the difference between artificial and natural selection lies not in the application of intellect, but the application of selective pressures other than those which would occur naturally. Natural selection will tend to be messier than artificial selection, zigging and zagging to match changing environmental conditions, but the practical aspects of each are identical. Explore Evolution wrongly treats artificial selection as an analogy for natural selection, when natural selection is just a more general process.

Major Flaws:

Natural and Artificial Selection: The nature of natural selection is obscured, confusing natural selection's use in evolutionary explanations, the relationship between natural selection and artificial selection, and the way in which evolution from generation to generation produces new genes and new anatomical structures.

Experiments: It is true that many textbooks describe classic experiments on the evolution of beak size in Galápagos finches and peppered moths in England, they also discuss many other examples. Rather than further supplementing textbooks with new knowledge, Explore Evolution devotes itself to factually misleading accounts of those classic experiments, confusing students rather than deepening their understanding.

Extrapolation: Explore Evolution criticizes scientists for extrapolating from evolutionary changes over short timespans to long-term processes like speciation. Instead, the book encourages students to extrapolate from apparent limits to artificial selection to the existence of absolute limits to evolution. While the book's extrapolation is unjustified, the scientific study of evolution is not rooted in extrapolation but in detailed experimentation, mathematical modeling, and experimental hypothesis testing.

Artificial and Natural Selection

Explore Evolution begins its discussion of natural selection with a discussion of artificial selection. Artificial selection, in which differential survival and reproduction in animals, plants, or other organisms is driven by the choices of human breeders selecting among natural variations in a population, is treated as an analogy for natural selection, in which differential survival and reproduction of organisms is driven by natural processes acting on natural variation in a population.

This is a dubious beginning, as natural and artificial selection are, in fact, different aspects of the same process. While Darwin's early understanding of natural selection was influenced by his ability to draw analogies between natural observations he made and the actions of humans breeding pigeons and dogs for special traits, it is wrong to suggest that our modern understanding of these processes is merely analogical, rather than treating artificial selection as a special application of the principles behind natural selection.

Explore Evolution further errs in presenting results from a few hundred years of intensive breeding in dogs and horses as evidence for limits in evolutionary processes over thousands, millions, and indeed billions of years. Even if horses and dogs demonstrated the limits claimed by the authors, it would be foolish to extrapolate limits found under the special conditions of horse-breeding and dog-breeding to the longer-term and more complex conditions which natural selection must confront in its more general form. Given the track record of Explore Evolution, it is hardly surprising that artificial selection in dogs and in horses has not actually reached clear limits, and what limits can be inferred from those cases shows that the variation which can be produced in even a thousand years or so is greater than that seen in all of the members of the mammalian family Carnivora other than dogs. If such extrapolation is legitimate, the actual evidence undermines the point Explore Evolution seeks to make with those data.

Artificial vs. Natural Selection

Summary of problems:

Artificial selection and natural selection are different forms of the same process. Treating the relationship as a mere analogy assumes that differences are greater than they actually are.

Full discussion:

Natural selection simply requires certain conditions. When they occur, natural selection will occur:

  1. There must be variation within the population of organisms.
  2. That variation must be heritable.
  3. There must be differences in reproductive success based on those heritable differences.

The only difference between natural selection and artificial selection is whether the difference in reproductive success is driven by naturally occurring processes, or whether the selection is imposed by humans. Explore Evolution obscures this in two ways. First, by asserting that the relationship is an analogy, rather than a generalization from the human activity. Second, by referring not to a human activity, but to the action of "intelligence."

This shift is subtle, but is a powerful rhetorical opening move. After introducing an example of shepherds selectively breeding woollier sheep, Explore Evolution asks:

Is it possible that something like this process occurs in nature—only without any intelligence to guide it?
Explore Evolution, p. 87

The same question could as easily be posed whether "something like this process occurs in nature—only without any [human] to guide it," but would seem much less profound. And as Explore Evolution acknowledges, it is easy to see how forces other than humans could exert selective pressure on populations of living things.

Horses and Dogs

Summary of problems:

The claim that there are limits on evolution – as evidenced by the limits on the speed of horses or the size of domestic dogs – is essentially a restatement of the creationist doctrine that types (or baramins) cannot evolve into one another. Explore Evolution argues that if natural selection cannot produce a certain change in a matter of decades, it could never produce that change. This is nonsensical on its face, and does not accurately reflect basic knowledge about natural selection and population genetics stretching back to the 1920s. It also misstates the effects that animal husbandry has been shown to have on domestic species.

Full discussion:

Explore Evolution invites readers to imagine a dog as small as a pair of glasses, or larger than a horse, concludes "this is comical," and states that unnamed "critics" think "there are limits to how much an animal can change [via natural selection]" (p. 90). Setting aside that natural selection does not change "an animal," but operates over many generations of a population or species of animals, plants or other organisms, the claim that limits on natural selection are such that they would prevent speciation or other "large-scale changes" is simply not correct.

Explore Evolution states that "Horse breeders have not significantly increased the running speed of thoroughbreds, despite more than 70 years of trying" (p. 90), a claim which is inaccurate on at least one count, and which misrepresents the source they cite. Gaffney and Cunningham (1988), the paper they cite to justify the sentence, do find that winning race times have not changed, but end the paper stating, "We conclude that the explanation for the lack of progress in winning times is not due to a lack of genetic gain in the thoroughbred population as a whole." Genetic gain in the population as a result of selective breeding is the very definition of selection. Furthermore,

breeders and horse-racing enthusiasts state they pay little attention to winning times. Instead, riders, horse owners, breeders, and bettors are rewarded for horses that win races, regardless of time, and little effort is made to "beat the clock." Furthermore, "fast tracks" are notoriously bad for the health of horses, causing damage to bones and tendons. Consequently, track surfaces are often treated to be softer, slower, and less likely to cause stress on the horse. Thus, modern racetracks may be slower than the tracks of 50 years ago.
Ernest Bailey (1998), "Odds on the FAST gene," Genome Research, 8(6):569-571

Thus, it is not the case that horse breeders have tried to increase the absolute time in which their horses complete races, but to ensure that their horses run faster than the other horses in a given race. It is therefore impossible to know whether contemporary horses would run faster than famous racehorses like Seabiscuit or Secretariat if they ran against one another, or whether contemporary horses as a whole are faster in absolute terms than horses were 70 years ago.

The book's dismissal of variation within dogs is, if possible, even more disingenuous.

Dog limbs vs. wild canids: Fig. 7 from Wayne (1986), "Limb morphology of domestic and wild canids: The influence of development on morphologic change," Journal of Morphology 187(3):301-319. It shows an analysis of limb measurements from several species of domestic dogs (dots), other members of the genus Canis (labeled 1), fox-sized species (labeled 2-5) and other species: la) Canis lupus, the grey wolf; 6a) Speothos venaticus, the bushdog; 6b) Nyctereutes procyonoides, the raccoon dog; 6c) Atelocynus microtis, the short-eared dog; A) Chihuahua; B) Irish wolfhound. It shows that dog limbs are much more varied than those of all other members of the family Canidae, including foxes, wolves, and coyotes.Dog limbs vs. wild canids: Fig. 7 from Wayne (1986), "Limb morphology of domestic and wild canids: The influence of development on morphologic change," Journal of Morphology 187(3):301-319. It shows an analysis of limb measurements from several species of domestic dogs (dots), other members of the genus Canis (labeled 1), fox-sized species (labeled 2-5) and other species: la) Canis lupus, the grey wolf; 6a) Speothos venaticus, the bushdog; 6b) Nyctereutes procyonoides, the raccoon dog; 6c) Atelocynus microtis, the short-eared dog; A) Chihuahua; B) Irish wolfhound.

It shows that dog limbs are much more varied than those of all other members of the family Canidae, including foxes, wolves, and coyotes.
Dog skulls vs. wild canids: Fig. 3 from Robert K. Wayne (1986) "Cranial Morphology of Domestic and Wild Canids: The Influence of Development on Morphological Change," Evolution, 40(2):243-261. It shows an analysis of skull measurements from several species of domestic dogs (dots), other members of the genus Canis (labeled 1), fox-sized species (labeled 2-5), other species (labeled 6), and Canis lupus, the grey wolf (labeled 1a).Dog skulls vs. wild canids: Fig. 3 from Robert K. Wayne (1986) "Cranial Morphology of Domestic and Wild Canids: The Influence of Development on Morphological Change," Evolution, 40(2):243-261. It shows an analysis of skull measurements from several species of domestic dogs (dots), other members of the genus Canis (labeled 1), fox-sized species (labeled 2-5), other species (labeled 6), and Canis lupus, the grey wolf (labeled 1a). As with limb morphology, the variability in skull size and shape in dogs exceeds that found within all other canids. Morphometric studies of dog limbs and skulls have found that the variation within the domestic dog, Canis familiaris, is greater than the variation within the entire family to which that species belongs, and indeed greater than the variation within the order Carnivora. The range of sizes is many times greater (axis 1 in both figures). The shapes of the dogs' limbs (axis two in the first image) only slightly overlap the shapes found in other canids, including other members of the genus Canis. The shapes of the skulls (axis two in the second figure) completely overlap the shapes of non-Canis canid skulls, and the range of dog skull shapes is matched only by variation among other members of the genus.

There is no evidence in these data to suggest that dogs have reached any inherent limits to their evolution or to the powers of natural selection. What these data show is that dog breeders have already managed to produce animals which break new morphological ground. Whatever limits might seem to exist if we look at the shapes and sizes of wild canids have been surpassed by the work of dog breeders. Whatever limits natural selection has, they have prevented the evolution of variation beyond that seen within the rest of the entire order Carnivora (dogs, cats, bears, foxes, weasels, etc.), all within the last few thousand years. Natural selection may well have limits, but if the limits are that loose, they would not prevent the diversification of life as we know it over the course of several billion years.

There is little doubt that limits on natural selection do in fact exist. Because selection operates on existing variation, there is a balance between the rate of mutation and the force of selection. This balance was first described in the 1920s, and modern textbooks describe this mutation-selection balance (e.g., p. 115 in Ridley's Evolution, p. 438 in Futuyma's Evolutionary Biology, or p. 461 in Campbell and Reece's Biology). In a hypothetical case where mutation does not occur, strong enough selection would eventually stabilize all of the genes relevant to a given trait. Similarly, in the absence of selection, mutation would gradually increase the number of mutants in the population to some equilibrium. Depending on the amount of selection and the amount of mutation, the amount of variation available to select on will vary.

The limits selection might face because of limited natural variability within a single generation will get progressively broader as the number of generations increases. Modern racing horses can trace over half of their genes to 10 horses of the late 18th century, and over 80% to only 31 ancestors from that era. Despite that highly constrained gene pool, the speed of horses has risen (whether or not it plateaued in the 1950s as discussed above). Similarly, much of the morphological evolution in dogs took place over a similar time period, beginning in the 18th century as breeders began paying more careful attention to studbooks.

Experiments

In its effort to debunk natural selection, Explore Evolution reiterates the debunked claims from the creationist book Icons of Evolution. That book claimed that textbooks misrepresented evolution by incorrectly characterizing certain popular experiments. Explore Evolution repeats the earlier book's arguments, reuses several of that books images without change (or attribution), and does not update its arguments to reflect more recent research.

The most fundamental error here is the claim that research on peppered moths and work on the Galápagos finches are the only, or at least major, examples offered for natural selection in textbooks. Those examples are frequently cited, but modern textbooks cite many other examples to show how natural selection works. Nor do modern textbooks cite those bodies of research for the purposes claimed in Explore Evolution. The treatment of natural selection in this book focuses exclusively on whether natural selection can generate biological novelty. That is an interesting topic, but not the only relevant topic for students to learn about natural selection, and Explore Evolution does students a disservice by treating an important and multi-faceted topic like natural selection through such a limited lens.

Turning to the details of the critiques offered for the peppered moth work and the Galápagos finch research, one finds that Explore Evolution describes that research inaccurately, and ignores recent work which directly contradicts the book's claims. For instance, it presents a graph of finch evolution which bears no relationship at all with any measurements reported by any researchers in the field, and criticizes the 50 year old work of Bernard Kettlewell on peppered moths without any discussion of research from the 1990s which tested several of the authors' criticisms of Kettlewell, and found that Kettlewell's results were unaltered by those criticisms.

Biology Texts

Summary of problems:

Darwin's finches and peppered moths are unquestionably examples of natural selection. They are far from the only examples offered in biology textbooks.

Full discussion:

Explore Evolution claims:

Biology textbooks cite two classic examples to support the claim that natural selection can produce small-scale change over a short time.
Explore Evolution, p. 88

Campbell and Reece's Biology (6th edition) has a section in the chapter on evolution entitled, "Examples of natural selection provide evidence of evolution." It begins:

Natural selection and the adaptive evolution it causes are observable phenomena. As described in the interview at the beginning of this unit, Peter and Rosemary Grant of Princeton University are documenting natural selection and evolution in populations of finches in the Galápagos [Darwin's finches]. We will now look at two additional examples of natural selection as a pervasive mechanism of evolution in populations.
Neil A. Campbell and Jane B. Reece, Biology, 6th ed.

Those examples include the evolution of HIV and insects in response to drugs and insecticides, yet neither HIV nor insecticide even rates a mention in the index of Explore Evolution. In Chapter 9, Explore Evolution addresses antibiotic resistance, but only to discuss the origins of mutations conferring resistance, not to point out that natural selection is what causes that resistance to spread.

Sickle cell anemia also makes an appearance in Chapter 9, again purely as an example of a mutation. In Raven and Johnson's Biology (5th edition), however, it is the first example of natural selection described in the section entitled "Natural selection explains adaptive microevolution." Explore Evolution mentions that sickle cell anemia can be beneficial under some circumstances, but misses the chance to either discuss how natural selection makes it more common in human populations traditionally occupying malarial areas, or to employ a truly inquiry based approach by inviting students to develop and test hypotheses about malarial resistance in order to actually explore evolution.

Earlier, Raven and Johnson discuss examples of natural selection including its ability to maintain persistent latitudinal gradients in the oxygen-carrying hemoglobin molecule in ocean fish, differences which make northern fish more efficient in cold water and southern fish more efficient in warmer water. They also describe how selection improves the camouflage of butterfly caterpillars and allows snail populations to adapt to different local ground coloration, as well as pesticide resistance in tobacco budworms and agricultural weeds. Only later do they discuss industrial melanism in peppered moths or the beaks of Darwin's finches.

That introductory textbook authors tend to focus on a few common examples does not detract from the fact that natural selection is commonplace, easy to observe, and widely documented. Specialized textbooks on evolutionary biology present an even wider array of examples of natural selection. For instance, the chapter on natural selection in Futuyma's Evolutionary Biology discusses how selection produces a north-south gradient in the frequency of alleles of a certain gene in Drosophila flies, a pattern repeated on multiple continents. Similar patterns exist for field crickets. Later, Futuyma describes how guppies in streams without predators have brighter coloration than closely related guppies in streams with predators. In the example of snail shells also used by Raven and Johnson, Futuyma points to paleontological studies showing that the genetic polymorphism seen in the population today has persisted for thousands or millions of years — clear evidence of stabilizing selection — and studies of broken snail shells allow an evaluation of rates of predation on various color morphs — allowing an assessment of the selective pressures acting on the population.

The emphasis on two examples of natural selection, and the complete disregard for the myriad other examples in active use by introductory and advanced textbooks, reflects a common creationist strategy. Jonathan Wells, a creationist author at the Discovery Institute, has made a career of attacking the Galápagos finches and the peppered moth, perhaps in the belief that all of the other examples of natural selection would go away if he could disprove one or two well-known examples.

It is noteworthy that several figures in this chapter are drawn from Jonathan Wells' Icons of Evolution, a creationist work aimed at critiquing the content of common biology textbooks and common examples used to illustrate and explain evolutionary processes. While Wells is not credited in this chapter, many of the arguments are the same as in his earlier work (critiqued by NCSE's Alan Gishlick), as are the illustrations. Explore Evolution repeats many of the errors previously identified in Wells' work. Just as the authors of Explore Evolution have a well-documented religious agenda which belies the scientific appearance of their book, Wells is famous for his religious reasons for obtaining a PhD in biology and attacking evolution, rooted in his involvement with the Unification Church (better known as "Moonies"), led by Sun Myung Moon, or, as Wells refers to him, "Father":

I asked God what He wanted me to do with my life, and the answer came not only through my prayers, but also through Father's many talks to us, and through my studies.…

He also spoke out against the evils in the world; among them, he frequently criticized Darwin's theory that living things originated without God's purposeful, creative activity.…

Father's words, my studies, and my prayers convinced me that I should devote my life to destroying Darwinism, just as many of my fellow Unificationists had already devoted their lives to destroying Marxism. When Father chose me (along with about a dozen other seminary graduates) to enter a Ph.D. program in 1978, I welcomed the opportunity to prepare myself for battle.

Explore Evolution, like Wells' earlier work, is rooted in a religious aversion to evolution, not in actual science. Scientists have sought to correct the erroneous claims displayed in Explore Evolution in their earlier incarnations, and the refusal to accept those corrections, or even to acknowledge those criticisms, recommends strongly against adopting this work into science classes.

Modern Galapagos Finches

Summary of problems:

The hybridization observed in the finches is not enough to merge two species, and observations in the field have actually shown substantial evidence of incipient speciation.

Full discussion:

Explore Evolution argues that
…after the rains returned [to the Galápagos], the Grants notices that several separate species of finches were interbreeding. No only were no new species springing forth, but existing varieties actually seemed to be merging. Critics therefore conclude that the finch beak example of microevolution actually suggests that biological change has limits.
Explore Evolution , p. 93

Explore Evolution versus the data: Actual measurements of G. scandens finches compared to Explore Evolution's presentation of data over the same time period.  EE arbitrarily compresses the Y-axis to minimize actual variability, introduces an "extrapolation" which bears no resemblance to what any scientist has predicted, and uses the unjustified claim of oscillation in the data to produce their own extrapolation — limits on the power of evolution.Explore Evolution versus the data: Actual measurements of G. scandens finches compared to Explore Evolution's presentation of data over the same time period. EE arbitrarily compresses the Y-axis to minimize actual variability, introduces an "extrapolation" which bears no resemblance to what any scientist has predicted, and uses the unjustified claim of oscillation in the data to produce their own extrapolation — limits on the power of evolution.

Given that this passage follows right after their complaints about the dangers of extrapolation, it is rich to find them claiming that anything that didn't happen in a 30 year study could never happen. The sole basis for the claim that limits exists seems to be that something did not occur in the course of a single study. By that standard, I could predict that I will never die, since I am thirty and have not been observed to die.

Furthermore, the citation the authors use to explain that hybridization occurred points out that genetic novelty accompanies such unusual matings, and explains why those matings do not mean that the species are merging. The ongoing changes in beak shape (shown in part F of the figure above) cannot be explained by natural selection alone. They can only be explained by invoking the combination of two of the 4 major evolutionary mechanisms: natural selection and gene flow. Natural selection explains the initial changes, but the flow of genes between species provided the ongoing evolutionary pressure towards blunter beaks. Peter and Rosemary Grant explain:

The proportionally greater gene flow from G. fortis to G. scandens than vice versa has an ecological explanation. Adult sex ratios of G. scandens became male biased after [the extremely hot and wet] 1983 as a result of heavy mortality of the socially subordinate females. High mortality was caused by the decline of their principal dry-season food, Opuntia cactus seeds and flowers; rampantly growing vines smothered the bushes. G. fortis, more dependent on small seeds of several other plant species, retained a sex ratio close to 1:1. Thus, when breeding resumed in 1987 after 2 years of drought, competition among females for mates was greater in G. fortis than in G. scandens. All 23 G. scandens females paired with G. scandens males, but two of 115 G. fortis females paired interspecifically. All their F1 offspring later bred with G. scandens because choice of mates is largely determined by a sexual imprinting-like process on paternal song.
Grant, P. R. and B. R. Grant (2002), "Unpredictable evolution in a 30-year study of Darwin's finches." Science 296:707-711

There are two important things to understand about that. First, that the hybridization was a result of unusual environmental conditions and an excess in the number of males of one species. Those males competed for access to any female at all, and were prepared to overcome pre-mating barriers to hybridization. Second, the main force limiting hybridization is that different species of finches select mates with songs similar to those of their fathers. Elsewhere, the Grants explain:

Hybridization occurs sometimes as a result of miscopying of song by a male; a female pairs with a heterospecific male that sings the same song as that sung by her misimprinted father. On Daphne Major island, hybrid females bred with males that sang the same species song as their fathers. All G. fortis × G. scandens F1 hybrid females whose fathers sang a G. fortis song paired with G. fortis males, whereas all those whose fathers sang a G. scandens song paired with G. scandens males. Offspring of the two hybrid groups (the backcrosses) paired within their own song groups as well. The same consistency was shown by the G. fortis × G. fuliginosa F1 hybrid females and all their daughters, which backcrossed to G. fortis. Thus mating of females was strictly along the lines of paternal song.
Peter R. Grant and B. Rosemary Grant (1997). "Genetics and the origin of bird species," Proceedings of the National Academy of Sciences, 94:7768–7775

The Grants go on to discuss how this helps explain the speciation of Galápagos finches.

Experiments show that birds are less responsive to the songs of conspecifics from different islands than to songs from their own island. Even though the changes are small, the process of cultural drift is enough to begin isolating these populations. In addition, the finches show a preference for the morphology of birds from their own island to members of the same species from other islands, even independent of song differences. The forces driving natural selection on different islands will differ, and that will produce morphological differences, which will combine with differences in songs to make hybridization less likely.

Thus, the observation of hybridization does not provide evidence that two species will merge into one. Instead, it helps test the process by which species separate. Furthermore, the hybridization observed had an effect which directly contradicts the claim that novelty cannot originate through evolutionary processes. Because of genes flowing in from another species, G. scandens experienced substantial evolutionary change, and acquired novel traits.

The Grants point out that this sort of gene exchange is important to understanding speciation and evolution in general:

Introgressive hybridization [as seen in Darwin's finches] has the potential of leading to further evolutionary change as a result of enhancing genetic variances, in some cases lowering genetic covariances), introducing new alleles, and creating new combinations of alleles, some of which might be favored by natural selection or sexual selection. Svärdson believed that introgression in coregonid fishes has replaced mutation as the major source of evolutionary novelty. Introgression and mutation are not independent; introgressive hybridization may elevate mutation rates.



The relevance to speciation lies in the fact that regions of introgression are peripheral areas, which could become isolated from the main range of the species through a change in climate and habitat: they are potential sites of speciation.
Grant, P. R. and B. R. Grant (1997)

Far from demonstrating limits to the power of evolution, the rare hybridizations between species demonstrate how strong pre-mating isolation is, illustrate an important source of variation, and provide evidence about the process of speciation and the origins of genetic novelty. The fact that Explore Evolution never mentions two of the four major mechanisms of evolution (gene flow and genetic drift), speaks poorly of the authors' commitment to a serious examination of evolutionary biology.

Peppered Moths

Summary of problems with claim:

Textbooks do not use peppered moths as an example of something new being created, they use it to demonstrate what natural selection can do in mere decades.

Full discussion:

Explore Evolution claims:
Critics question whether the peppered moth story shows that microevolution can eventually produce large-scale change. They point out that nothing new emerged.
Explore Evolution, p. 93, emphasis original

Textbooks which present this example typically use it to illustrate the process by which biologists investigate natural selection, not to demonstrate the origins of biological novelty. In Raven and Johnson's Biology (5th edition), the discussion of peppered moths and industrial melanism is in a section titled "Natural selection explains adaptive microevolution," and never claims that the example illustrates anything other than the process by which scientists have investigated the effects of natural selection. Ridley's Evolution (2nd ed.) discusses peppered moths first in a section explaining how "Natural selection operates if some conditions are met," and later in a chapter entitled "The Theory of Natural Selection," in a section discussing how "the model of selection can be applied to the peppered moth." Ridley first demonstrates the reasons why natural selection was invoked by observers of a pattern, and then proceeds to describe the particular ways in which researchers investigated the hypothesis: determining the heritability of coloration, experimenting to determine the fitnesses of various genotypes under different conditions, and concluding with a discussion of ways in which "the details of the story are now known to be more complex."

As Ridley explains:

In conclusion, the industrial melanism of the peppered moth is a classic example of natural selection, and illustrates the one-locus, two-allele model of selection. The model can be used to make a rough estimate of the difference in fitness between the two forms of moth using their frequencies at different times; the fitnesses can also be estimated from mark-recapture experiments. However, the one-locus, two-allele model is only an approximation to reality. In fact, several alleles are present (and their dominance relations are not simple); selection is not simply a matter of bird predation in relation to camouflage; and it seems that migration, as well as selection, is needed to explain the geographic pattern of gene frequencies.
Mark Ridley (1996), Evolution, 2nd ed., p. 109

Explore Evolution claims that "the experiment [does] not show what the story says it's supposed to," but misrepresents what scientists claim it illustrates. It is not an experiment meant to illustrate speciation, and Explore Evolution does not discuss those experiments, such as the examples in Drosophila discussed by Ridley in his chapter on speciation.

In fact, Explore Evolution does not even discuss the process by which melanism would have originated in peppered moths. The genetics of melanism have been well understood since the 1960s, when researchers showed how several different mutations to the same genes could produce similar sorts of melanism (Lees, David R., 1968, "Genetic Control of the Melanic Form Insularia of the Peppered Moth Biston betularia (L.)," Nature 220(5173):1249-1250). Natural selection is the process by which those mutations increased in frequency over several generations, exactly what scientists and textbook authors claim this example demonstrates.

Kettlewell's Experiments

Summary of problems:

Research scientists do not find Kettlewell's work invalid because he released moths in the daytime. This claim is found nowhere in the research literature.

Full discussion:

Bernard Kettlewell did several experiments on peppered moths, to explore the factors driving their observed evolution from lighter to darker forms over a relatively short time period. The research most relevant to this claim are the mark-recapture experiments where moths were captured, marked, released onto trees and recaptured the following night.

In these experiments the moths were placed onto trunks and branches at dawn, not day time, and allowed to take up their own resting places, as described in Kettlewell's 1958 paper "The importance of the micro-environment to evolutionary trends in the Lepidoptera" (Entomologist, 91:214-224). This is exactly what the moths do naturally. In one experiment, as a control, Kettlewell released moths earlier, and allowed them to fly on to the trees themselves. The recapture patterns from this experiment were no different from the recapture patterns with the moths placed on branches and trunks (Kettlewell, 1956, "Further experiments on industrial melanism in Lepidoptera" Heredity, 10: 287-301).

As well, some of the moths that were released in the mark-recapture-experiments stayed out for two nights before being captured. That is, they had been flying free at night and had found their own location during the morning. The distribution of those moths that did freely choose their own resting places is no different from those that were placed on trunks and branches (as shown in Kettlewell, 1956, and in his 1955 paper "Selection experiments on industrial melanism in Lepidoptera," (Heredity, 9: 323-342).

While there were legitimate reasons why scientists did criticize Kettlewell’s experiments (including Bruce Grant's 1999 paper "Fine tuning the peppered moth paradigm," Evolution 53. 980-984 and Michael Majerus's 1998 Melanism: evolution in action, Oxford University Press, Oxford, chapters 5 and 6), none of these criticisms (density and resting place choice) involve the moths being sleepy or sluggish, and no serious experimenter suggested that Kettlewell’s results were invalid. Indeed, subsequent experiments to test these criticisms broadly confirmed Kettlewell’s results (again, see Grant, 1999, Majerus 1998, and Majerus' 2007 talk "The Peppered Moth: The Proof of Darwinian Evolution," given at the ESAB meeting in Uppsala on 23 August – also available as Powerpoint, as well as his 2009 paper "Industrial melanism in the peppered moth, Biston betularia: an excellent teaching example of Darwinian evolution in action," Evolution: Education and Outreach 2(1):63-74). Further details of these experiments are discussed in "Where Peppered Moths Rest," below.

Where Peppered Moths Rest

Summary of problems:

Peppered moths do rest on trunks. Kettlewell placed moths on both branches and trunks, covering the spectrum of moth resting places.

Full discussion:

Kettlewell was aware that peppered moths rested on both trunks and branches. In Kettlewell’s experiments, he actually placed the moths on trunks and branches, in relatively unexposed locations, thus covering the natural resting places of the peppered moth.

In a comprehensive study of peppered moth resting places in the wild, fully 25% of moths were found resting on trunks (Majerus, 1998, cited above). Of the remainder, roughly 25% were found on branches, and 50% at branch/trunk junctions. Furthermore, in the branch/trunk junction category, the moths are actually resting on the trunks, 2-3 inches below the branch. In a later, extensive 6 year study 37% of peppered moths were found on trunks (Majerus, 2007, cited above).

Peppered moths in situ: Peppered moths in their natural resting places on horizontal tree branches (above) and vertical tree trunks (below).  From figures 4 and 5 in Michael E. N. Majerus (2009), "Industrial melanism in the peppered moth, Biston betularia: an excellent teaching example of Darwinian evolution in action," Evolution: Education and Outreach 2(1):63-74.Peppered moths in situ: Peppered moths in their natural resting places on horizontal tree branches (above) and vertical tree trunks (below). From figures 4 and 5 in Michael E. N. Majerus (2009), "Industrial melanism in the peppered moth, Biston betularia: an excellent teaching example of Darwinian evolution in action," Evolution: Education and Outreach 2(1):63-74.

It is important to note that Kettlewell performed several different experiments; direct observations, filmed observations of birds taking moths from exposed trunks, indirect observations of moth predation where moths were released onto relatively unexposed trunks and branches and allowed to chose their resting places, and mark-recapture experiments, where again moths were released onto relatively unexposed trunks and branches to choose their own resting places (Kettlewell, 1955, 1956, both cited above). So when Kettlewell put his moths on trunks and branches (Kettlewell, 1955, 1956), he was placing them where the majority of all moths rest naturally, as far as we can tell (even more if we count the trunk-resting moths at the trunk/branch junctions).

Michael Majerus has repeated Kettlewell’s experiments using moths resting on the undersides of branches (Majerus 1998, 2007). In both cases, differential predation was found that confirmed Kettlewell’s original observations. Furthermore, in Majerus’s 6-year experiment, measured predation intensity at the experimental sites predicted the population frequencies of moths found in the wild (Majerus, 2007).

While the authors of Explore Evolution could not have been expected to have had access to Majerus’s 2007 results, Majerus’s 1998 results, as well as Kettlewell’s description of the original experiments (Kettlewell, 1955, 1956) alone are enough to show that Explore Evolution is completely wrong on this point.

Since Kettlewell's original experiments were published, they have been independently replicated at least 6 times (See for example Grant 1999, Majerus 1998, and Majerus 2007, all cited above, for reviews). All of these experiments have addressed one or more criticisms of the original study, and all have broadly confirmed Kettlewell's experiments. Thus we can say that Kettlewell's experiments have stood the test of time.

An inquiry-based book could have used this history of successive investigations to explore the practice of science as a self-correcting enterprise, and the importance of replicability to the scientific process. Students could have been asked to devise their own experiments based on criticisms of Kettlewell's early work, and then teachers could reveal data from experiments like those performed by Majerus to evaluate the results of those new experiments. Instead, students are presented with erroneous critiques of Kettlewell's work, given none of the more recent vindicating evidence, and instructed to believe that this flawed exploration demonstrates a weakness in natural selection. In fact, it reflects only the weaknesses of Explore Evolution, and of its authors' approach to evolution and science in general.

Extrapolation

Natural selection operates at different speeds under different circumstances. Scientists agree that natural selection over long periods of time can produce larger evolutionary change than natural selection can produce in shorter periods, but exactly how much more is a subject of ongoing research.

Explore Evolution claims that there are inherent limits to the amount of change that evolutionary processes can produce, and that these limits make it improper to extrapolate from short-term research on natural selection in explaining the long-term evolutionary change we see in the fossil record. Alas, their argument for inherent limits to evolutionary change is rooted in exactly the sort of fallacious extrapolation they decry. The work scientists do bears little, if any, resemblance to these sorts of erroneous extrapolation.

To illustrate the claim of improper extrapolation, Explore Evolution actually invents data from whole cloth, presenting a graph of finch beak size "extrapolation" vs. "data" which is actually contradicted by the data obtained from field research. Where the text and graph suggest constant oscillations within fixed limits, research on the Galápagos finches show directional change in beak shape in addition to cyclical changes in beak size. Furthermore, those cycles match the cyclical environment the birds live in, so it is inappropriate to treat those oscillations as inherent limits to the birds' evolutionary capacity, rather than a reflection of their ability to rapidly adapt to large environmental changes with equally large evolutionary change.

As always, Explore Evolution passes up any opportunity to give students the data or opportunity to propose their own tests of any of these claims, belying the book's claim to be inquiry-based. Students are expected to learn by rote that limits exist on evolutionary change. They are never told how researchers actually investigate the ways in which various factors do limit evolutionary change.

Exrapolating microevolution to macroevolution

Summary of problems with claim:

The link between evolution on short timescales and longer-term evolutionary processes is thoroughly testable and not a mere extrapolation.

Full discussion:

Anyone who denies the logical link between genetic changes within a population ("microevolution") and speciation ("macroevolution") is similar to someone who watches the sun come up in the east and move west across the sky, but denies that it will set in the west. The only difference between genetic changes within a population and generation of a new species from that population is time. Given enough time, the sun will set in the west. Given enough time, speciation will occur.

This claim is related to the "young earth" creationist belief that the earth is only a few thousand years old. In this belief system, there has not been enough time for speciation to occur, given the rate of change that we can observe in most populations. So it is necessary for them to deny reality (observations of speciation) in order to validate a creationist perspective on the age of the earth. An age, by the way, that is about 0.00000002% of the approximately 3 billion years over which biological evolution has proceeded.

Limits on Evolution

Summary of problems:

Explore Evolution never defines "biological information," except through error-laden analogies to computers. Biologists have no trouble showing how new information (in the sense used by information theorists) originates, nor how new genes, kinds of cells or tissues evolve.

Full discussion:

Nowhere in the discussion of "the information problem" is there any attempt to formally define how students should measure "information." At one point, the authors introduce a strained analogy between upgrading computer software and adding biological information, but never quite explain the analogy. Later they observe that scientists have occasionally referred to DNA as if it were analogous to a computer program. Based on this informal analogical reasoning, they declare "So, biological information is stored in DNA" (p. 94). Teachers who wish to actually discuss this idea in class would be stranded utterly not only by Explore Evolution's treatment of the subject, but by the equally vague attempts by the ID creationists on whose work this section draws.

The field of mathematics known as information theory was developed to address the transmission of information, and it both defines information and describes how information is created. In essence, a mathematically random sequence of symbols (whether letters, DNA bases, or computer bits) has the highest information content possible. A completely predictable sequence contains only as much information as it would otherwise take to accurately predict the sequence. Thus, in information theory, adding random noise actually increases the amount of information being transmitted. Whether that information is useful or not to a listener is a separate matter.

This is where the misuse of "information" throughout Explore Evolution can be confusing. We usually have a very specific expectation for information transmitted over a telephone line, so random static on the line reduces the amount of information we can use. Randomness adds mathematical information, but decreases immediately usable information. A process of selection, mutation, and drift acting on such random information will, in time, extract new elements which are usable.

Evolution itself has no expectations about what data will be transmitted from generation to generation. Random mutations add information to the genome, and natural selection (or artificial selection) acts against those mutations which are not useful at a given moment, promotes those mutations which happen to benefit the organisms possessing them, and has no particular effect on mutations which do not influence the organism's fitness.

Biologists have incorporated this insight into their studies of the evolution of new genes. Gene duplication are common events, resulting from small errors in the process of cell replication. Once a gene is duplicated it is possible for one copy to mutate, adding information without risking the functioning of the pre-existing gene.

The process of gene duplication has been known since at least 1936; its possible significance for producing the raw material for the evolution of genetic novelty was recognized as early as 1951 (see Zhang 2003 for more on this history).

Examples of New Genes of Known Age (from Long, 2003), table 2)
Genes Age Evolutionary feature
Drosophila
jingwei 2.5 my A standard chimeric structure with rapid sequence evolution
Sdic <3 my Rapid structural evolution for a specific function in sperm tails
sphinx <3 my A non-coding RNA gene that rapidly evolved new splice sites and sequence
Cid Function diverged in the past 3 my Co-evolved with centromeres under positive Darwinian selection
Dntf-2r 3-12 my Origin of new late testis promoter for its male-specific functions.
Adh-Finnegan 30 my Recruited a peptide from an unknown source and evolved at a faster rate than its parent gene
Primates
FOXP2 100,000 y A selective sweep in this gene, which has language and speech function, took place recently
RNASE1B 4 my Positive selection detected, which corresponds with new biological traits in leaf-eating monkeys
PMCHL2 5 my Expression is specifically and differentially regulated in testis
PMCHL1 20 my A new exon-intron in the 3' coding region created de novo and an intron-containing gene structure created by retroposition
Morpheus 12-25 Strong positive selection in human-chimpanzee lineages
TRE2 21-33 my A hominoid-specific chimeric gene with testis=specific expression
FUT3/FUT6 35 my New regulatory untranslated exons created de novo in new gene copies; the family has been shaped by exon shuffling, transposation, point mutations and duplications
CGß 34-50 my One of two subunits of placentally expressed hormone; the rich biological data clearly detail its function
BC200 35-55 my A non-coding RNA gene that is expressed in nerve cells.
Rodents
4.5Si RNA 25-55 my A non-coding RNA gene that is expressed ubiquitously
BC1 RNA 60-110 my A neural RNA that originated from an unusual source: tRNA
Fish
Arctic AFGP 2.5 my Convergent evolution; antifreeze protein created from an unexpected source driven by the freezing environment
Antarctic AFGP 5-14 my Convergent evolution; antifreeze protein created from an unexpected source driven by the freezing environment
Plants
Sanguinaria rps1 <45 my A chimeric gene structure created by lateral gene transfer
Cytochrome c1 110 my Origin of mitochondrial-targeting function by exon shuffling
Protozoa
N-acetylenuraminate lyase << 15 my A laterally transferred gene from proteobacteria that recruited a signal peptide

As it has become more practical to trace the sequences of genes in multiple species, scientists have been able to identify genes which went through these processes, acquiring new functions within relatively recent history. That research systematically refutes the claim in Explore Evolution that "whether you're talking about artificial selection or about microevolution that occurs naturally, changes in the sub-population take place as genetic information is lost to that population" (p. 95). In fact, a recent review of the processes by which new genes and new gene functions evolved drew the exact opposite conclusion:

The origination of new genes was previously thought to be a rare event at the level of the genome. This is understandable because, for example, only 1% of human genes have no similarity with the genes of other animals, and only 0.4% of mouse genes have no human homologues, although it is unclear whether these orphan genes are new arrivals, old survivors or genes that lost their identity with homologues in other organisms. However, it does not take many sequence changes to evolve a new function. For example, with only 3% sequence changes from its paralogues, RNASE1B has developed a new optimal pH that is essential for the newly evolved digestive function in the leaf-eating monkey. Although it will take a systematic effort to pinpoint the rate at which new genes evolve, there is increasing evidence from Drosophila and mammalian systems that new genes might not be rare. Patthy compiled 250 metazoan [multicellular animal] modular protein families that were probably created by exon shuffling. Todd et al. investigated 31 diverse structural enzyme superfamilies for which structural data were available, and found that almost all have functional diversity among their members that is generated by domain shuffling as well as sequence changes.
Manyuan Long, Esther Betrán, Kevin Thornton and Wen Wang (2003) "The Origin of New Genes: Glimpses from the Young and Old," Nature Reviews: Genetics, 4:865

The table at the right describes a few well-studied examples of recently evolved genes, and a summary of what scientists have learned about the processes by which those genes evolved. The processes are the same sorts of small-scale mutational changes that we observe in existing populations. It was not necessary to invoke previously undescribed processes, merely to understand how known processes could produce the patterns observed in nature. That is the way scientists typically work, and an inquiry-based textbook ought to teach students to apply those methods. Instead, Explore Evolution ignores actual knowledge, criticizes the scientists who produced that knowledge, and discourages scientific inquiry from students, in favor of vague and untestable speculation.

Biologists do not dispute that limits to evolution may exist, and conduct research to test whether such limits exist. For instance, biologists wonder why no marsupials evolved flight or the sorts of adaptations to swimming seen in other mammals. It is hypothesized that the young marsupials' early crawl to the teat (see our discussion of marsupial reproduction in chapter 12) may place a constraint on the possible final forms the marsupial shoulder can take. While placental mammals give birth to offspring that are self-sufficient, marsupials give birth before major nerves, muscles and bones have formed, and must crawl to the teat (an exception is found in bandicoots of the genus Isoodon, which have a backwards-facing pouch into which the newborn can drop or slither without using its arms). That crawl requires that a functional shoulder exist early in fetal development, and the necessity of forming that functional shoulder so early may prevent the sort of limb diversification seen in other mammals, which range from the bat's wing to the cat's leg and on to the whale's flipper.

To test this, Dr. Karen Sears measured the adult and fetal shoulderblades of a dozens of marsupial and placental mammals, and performed a statistical analysis of the changes in shape.

Ontogenetic Trajectories: Growth of the shoulderblade in marsupials and placentals. The ontogenetic trajectories of individual marsupial and placental species are plotted in a morphospace representing general scapular shape (PC2 and PC3 are the 2nd and 3rd principal component; the first principal component is just size). Marsupials, with the exception of the bandicoot Isoodon, are represented by solid black arrows (w, Macropus [Tammar wallaby] t, Trichosurus [Australian possum] m, Monodelphis [South American opossum]). Isoodon (i) is represented by the white arrow with the black border. Placentals are represented by solid gray arrows. The ontogenetic trajectories of marsupials, with the exception of Isoodon, are remarkably similar, whereas the trajectories of placentals vary greatly.  Isoodon does not crawl to the pouch, and so its fetus does not experience the same developmental constraints as other marsupials. (Figure 7 from Karen E. Sears. 2004. "Constraints on the Morphological Evolution of Marsupial Shoulder Girdles," Evolution 58(10):2353–2370.)Ontogenetic Trajectories: Growth of the shoulderblade in marsupials and placentals. The ontogenetic trajectories of individual marsupial and placental species are plotted in a morphospace representing general scapular shape (PC2 and PC3 are the 2nd and 3rd principal component; the first principal component is just size). Marsupials, with the exception of the bandicoot Isoodon, are represented by solid black arrows (w, Macropus [Tammar wallaby] t, Trichosurus [Australian possum] m, Monodelphis [South American opossum]). Isoodon (i) is represented by the white arrow with the black border. Placentals are represented by solid gray arrows. The ontogenetic trajectories of marsupials, with the exception of Isoodon, are remarkably similar, whereas the trajectories of placentals vary greatly. Isoodon does not crawl to the pouch, and so its fetus does not experience the same developmental constraints as other marsupials. (Figure 7 from Karen E. Sears. 2004. "Constraints on the Morphological Evolution of Marsupial Shoulder Girdles," Evolution 58(10):2353–2370.)

As shown in the figure here, the placental mammals changed shoulder shape in many directions as they grew in size, while all of the marsupial limbs moved in the same direction. All but Isoodon, which doesn't use the shoulder during its move from womb to pouch, and so does not face the same developmental constraints.

This insight that developmental constraints can limit what evolutionary processes can produce is not new, and is well integrated into textbooks on biology and evolutionary biology (for a recent review, see J. L. Hendrikse, T. E. Parsons and B. Hallgrímsson. 2007. "Evolvability as the proper focus of evolutionary developmental biology," Evolution & Development, 9(4):393–401. For examples of textbook coverage, see pp. 352-365 of Ridley's Evolution, with sections titled: "Genetic constraints may cause imperfect adaptations," "Developmental constraints may cause adaptive imperfection," "Historical constraints may cause adaptive imperfection," "An organism's design may be a trade-off between different adaptive needs" and "Conclusion: constraints on adaptation.")

Other scientists confronting apparent biological constraints did not merely criticize, they proposed new evolutionary mechanisms which would not face those same limitations. The origins of mitochondria and other cellular structures is a case in point. The mitochondrion is the part of the cell in which oxygen is converted into usable energy. Without mitochondria, oxygen would poison every cell in our bodies, and without the molecular energy they produce, each of our cells would starve.

Our cells each have several mitochondria within them. Each of those mitochondria has its own circular genome with which it produces the proteins it needs to process oxygen. Each of the mitochondria possess two or more cell membranes, rather than the one found around all of our cells. It is impossible to imagine how a cell could exist with only part of a mitochondria, nor why a cell before the era of oxygen might have any of the unique parts present in the mitochondria found in nearly every eukaryotic cell. Even more mysterious was why the mitochondrial genome should be so different from that of every eukaryote. It is much more similar to that of a bacterium.

In the late 1970s, Lynn Margulis proposed that the mitochondria and several other parts of the eukaryotic cell might actually be the descendants of bacteria which were engulfed by the ancestors of all eukaryotes. This would explain the odd genome, and would explain the multiple membranes. The inner membrane is like that possessed by the free-living ancestor of mitochondria, while the outer membranes are the remnants of the vacuole within which that bacterium was captured to be digested. For whatever reason, it wasn't digested, instead helping process oxygen and cellular waste into useful molecular energy.

This theory proposed an entirely novel evolutionary mechanism, endosymbiosis. While some of the endosymbiotic relationships Margulis proposed are seen as unlikely, her explanation of the origin of mitochondria and chloroplasts have become widely accepted within the scientific community. Again, her discovery could form the basis for an inquiry-based discussion of evolutionary mechanisms, and could be enhanced by evidence of transitional stages in the evolution of endosymbiosis found today. Scientists in Japan recently described one such case (Noriko Okamoto and Isao Inouye. 2005. "A Secondary Symbiosis in Progress?" Science, 310(5746):287), and researchers recently showed that a bacterium which commonly invades insect cells, sometimes integrates its genes into the host cell, exactly like mitochondria sometimes do (Julie C. Dunning Hotopp, et al. 2007. "Widespread Lateral Gene Transfer from Intracellular Bacteria to Multicellular Eukaryotes," Science [DOI: 10.1126/science.1142490]).

Explore Evolution never mentions this process, despite its obvious pedagogical value, and its utility in addressing the limits of more commonly observed evolutionary mechanisms.

Oscillations

Summary of problems with claim:

When the sizes of finch beaks oscillates, it is because of an oscillating environment. The size changes within a species are large enough to explain the differences between the various species of Galápagos finches, species Charles Darwin initially thought belonged to several different families of bird. Not all of these changes oscillate, the evolution of Darwin's finches has been directional in some aspects.

Full discussion:

Finch Sizes: Morphological trajectories of adult Geospiza fortis (A to C) and G. scandens (D to F). In the absence of change, mean trait values should have remained within the 95% confidence intervals (horizontal broken lines) of the estimates from the 1973 samples (body size: G. fortis, n = 115, G. scandens, n = 37; beak traits: G. fortis, n = 173, G. scandens, n = 62). Sample sizes varied from 45 (1997) to 976 (1991) for G. fortis and from 30 (1999) to 336 (1983) for G. scandens. The 1972 sample is composed of the adults (=1 year old) in 1973.  (From [http://www.sciencemag.org/cgi/content/full/296/5568/707 Peter R. Grant and B. Rosemary Grant, 2002, "Unpredictable Evolution in a 30-Year Study of Darwin's Finches," Science 296(5568):707-711].Finch Sizes: Morphological trajectories of adult Geospiza fortis (A to C) and G. scandens (D to F). In the absence of change, mean trait values should have remained within the 95% confidence intervals (horizontal broken lines) of the estimates from the 1973 samples (body size: G. fortis, n = 115, G. scandens, n = 37; beak traits: G. fortis, n = 173, G. scandens, n = 62). Sample sizes varied from 45 (1997) to 976 (1991) for G. fortis and from 30 (1999) to 336 (1983) for G. scandens. The 1972 sample is composed of the adults (=1 year old) in 1973. (From [http://www.sciencemag.org/cgi/content/full/296/5568/707 Peter R. Grant and B. Rosemary Grant, 2002, "Unpredictable Evolution in a 30-Year Study of Darwin's Finches," Science 296(5568):707-711].

The figure shown here illustrates that, as the climate in the Galápagos has changed due to the multiyear El Niño cycle, the finches have changed body size, beak size, and beak shape (a measure of width, length and depth). Some of those measurements have returned to levels that were seen historically (inside the faint horizontal lines in the figure), while other measurements continue to diverge.

As the Grants describe in "Unpredictable Evolution in a 30-Year Study of Darwin's Finches", "The temporal pattern of change shows that reversals in the direction of selection do not necessarily return a population to its earlier phenotypic state." This is the opposite of what Explore Evolution describes:

After the heavy rains of 1983, the depth of the average finch beak went back to its pre-drought size, and the so-called "evolutionary change" was reversed.
Explore Evolution, p. 93

While one species did wind up at roughly the same beak size, the beaks at the end were sharper than they had been at the beginning, while the other species has a smaller and blunter beak than it had to begin with.

Does this demonstrate that evolution has limits? Not at all. We would not expect finches to evolve more rapidly over 30 typical years. Over the thirty years, the environment oscillated within limits, and the finches evolved and adapted to that changing climate. When the climate returned to the state it had been in at the beginning of the study, the finches became more similar, but not identical, to their initial state. Why students ought to assume that finches could not have changed more if the environment had changed more is not at all clear, especially since the size and shape of finches and their beaks continues to change and to cross historical limits.

Of course, the climate is not constant, either. Peter Grant explains:

The climate of the Galápagos has not remained stable over the last 50,000 years. This is known from an analysis of particles and plant products in cores taken from the sediment of El Junco lake on the summit of San Cristobal (Colinvaux 1972, 1984). Inferences can be made about changes in water level, cloud cover, and heat budget from the composition of the cores at different levels.

The present climate has persisted for the last 3,000 years, and it also prevailed about 6,200 and 8,000 years ago. In the intervening period of 3,200 years it was drier, and possibly hotter, than now. Going back further, it was drier before 8,000 years ago. The most different climate regime from the present one occurred from about 10,000 to 34,000 years ago; this was a time of little precipitation or evaporation.
Grant, P. R. (1999) Ecology and Evolution of Darwin's Finches, Princeton University Press, Princeton, NJ, pp. 29-30

We know that finches can and do undergo significant morphological change when the climate changes. We know the climate changes. Explore Evolution simply insists that we should not follow the syllogism to its conclusion, and decide that the finches would have undergone large changes during periods of large environmental change. Explore Evolution invokes limits, but provides no actual evidence that inherent limits on evolution operate beyond those imposed by limited environmental variability. This is not, needless to say, how science proceeds, and it is not what we would expect from an inquiry-based approach to science. Unanswered questions are not places where scientists draw lines, they are opportunities to make new discoveries. An inquiry-based text should invite students to propose hypotheses about finch evolution, and provide teachers with a suite of data for students to test their hypotheses.