Meanings of "evolution"

Summary of problems:

As used in standard biology textbooks, "evolution" has several connotations, but they all derive from a single concept. Explore Evolution obscures the relationship between these concepts by treating them as three definitions which can be taken in isolation from one another. These definitions are not actually different ideas, just different consequences of the same idea. Attempting to divide these topics and act as though students can choose which to accept a la carte is a common creationist fallacy.

Full discussion:

In describing what we now refer to as "evolution," Darwin usually used the phrase "descent with modification," using the word "evolve" only once in the The Origin of Species:

It is interesting to contemplate an entangled bank, clothed with many plants of many kinds, with birds singing on the bushes, with various insects flitting about, and with worms crawling through the damp earth, and to reflect that these elaborately constructed forms, so different from each other, and dependent on each other in so complex a manner, have all been produced by laws acting around us. These laws, taken in the largest sense, being Growth with Reproduction; Inheritance which is almost implied by reproduction; Variability from the indirect and direct action of the external conditions of life, and from use and disuse; a Ratio of Increase so high as to lead to a Struggle for Life, and as a consequence to Natural Selection, entailing Divergence of Character and the Extinction of less-improved forms. Thus, from the war of nature, from famine and death, the most exalted object which we are capable of conceiving, namely, the production of the higher animals directly follows. There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone on cycling on according to the fixed laws of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved.

Charles Darwin (1859) On the Origin of Species, 1st ed., John Murray, London (facsimile edition, Harvard University Press), p. 490

In this concluding paragraph to the book, Darwin lays out the connections between the senses of "evolution" which Explore Evolution attempts to keep separate. Traits vary between individuals, and some of those differences can be passed from parent to child. Some of those heritable differences leave the offspring at a greater advantage than others. That process of natural selection can cause one population to become increasingly different, branching off from the ancestral population. Where heritable variation exists, this branching pattern of descent is inevitable, and it is possible to trace the evidence of that common descent back through history. Thus, the existence of change over time (first definition in EE) is part and parcel with the power of evolution to produce novelty (third definition in EE), and that change over time will inevitably produce a pattern of common descent (second definition in EE).

Why do we talk about universal common descent in particular? The most basic reason is that the idea of a single origin of life is the simplest explanation for the diversity of life that we see in the world today. A scientist who wants to challenge universal common descent cannot simply say that there may be something, somewhere, which doesn't share an ancestor with the rest of life on earth (as EE's "critics" do). That scientist would have to present evidence that a particular group of organisms does not share an ancestor with the rest of life, and show how that hypothesis is better than the hypothesis of universal common descent. Explore Evolution does not propose to replace a successful hypothesis with a better hypothesis, it merely emphasizes areas of uncertainty, but doesn't provide students with the knowledge or tools to gather new knowledge or improve our existing knowledge. Thus, the textbook fails both to accurately represent how science is practiced, but also a failure to live up to its claim of being "inquiry-based."

Evolutionary mechanisms

Summary of problems:

Explore Evolution describes only two evolutionary mechanisms, yet standard biology texts describe many more. The discussion of evolutionary mechanisms completely omits any reference to genetic drift, endosymbiosis, gene flow, genetic recombination. This despite the fact that prominent biologists have argued that genetic drift and symbiosis may actually be more important to the history of life than natural selection or mutation, the only mechanisms mentioned anywhere in Explore Evolution.

Full discussion:

Biologists recognize many evolutionary mechanisms, including not only natural selection and mutation, but the effects of chance fluctuations in gene frequency (genetic drift), the effects of genetic rearrangements on a chromosome (recombination), the effects of migration of genetic variants into and out of a population (gene flow) and the effects of wholesale incorporation of genetic material by one species from another species (endosymbiosis). There is an ongoing debate within evolutionary biology over whether genetic drift is more influential than natural selection on the course of evolution. Other biologists have suggested that endosymbiosis may be even more important, and continue to test that hypothesis. If Explore Evolution really intended to present ongoing scientific controversies regarding evolution, those debates over evolutionary mechanisms would have a prominent place. And yet, in discussing "the creative power of natural selection," EE states:

Some people use the term evolution to refer to a cause or mechanism of change. When evolution is used in this way, it usually refers to the mechanism of natural selection (acting on random variations and mutations). This third use of evolution affirms that the natural selection/mutation mechanism is capable of creating new living forms, and has thus produced the major changes we see in the history of life (as represented by Darwin's Tree of Life.)

EE, p. 8

It's certainly true that scientists refer to evolution in this broad mechanistic sense, but no biologist restricts that discussion to mutation and natural selection. Biologist Michael Lynch recently pointed out that the mistake Explore Evolution makes is a common one:

Evolutionary biology is treated unlike any science by both academics and the general public. For the average person, evolution is equivalent to natural selection, and because the concept of selection is easy to grasp, a reasonable understanding of comparative biology is often taken to be a license for evolutionary speculation. It has long been known that natural selection is just one of several mechanisms of evolutionary change, but the myth that all of evolution can be explained by adaptation continues to be perpetuated by our continued homage to Darwin's treatise in the popular literature. … There is, of course, a substantial difference between the popular literature and the knowledge base that has grown from a century of evolutionary research, but this distinction is often missed by nonevolutionary biologists [including the authors of EE].
…
[E]volution is a population-genetic process governed by four fundamental forces. Darwin articulated one of those forces, the process of natural selection, for which an elaborate theory in terms of genotype frequencies now exists. The remaining three evolutionary forces are nonadaptive in the sense that they are not a function of the fitness properties of individuals: mutation is the ultimate source of variation on which natural selection acts, recombination assorts variation within and among chromosomes, and genetic drift ensures that gene frequencies will deviate a bit from generation to generation independent of other forces.
…
[A]ll four major forces play a substantial role in genomic evolution. It is impossible to understand evolution purely in terms of natural selection, and many aspects of genomic, cellular, and developmental evolution can only be understood by invoking a negligible level of adaptive involvement.

Michael Lynch (2007) "The frailty of adaptive hypotheses for the origins of organismal complexity," Proceedings of the National Academy of Sciences 104(S1):8597-8604

Explore Evolution provides a perfect example of the errors Lynch describes. Genetic drift and recombination do not occur in the index to the book, nor the glossary, nor does the EE passage quoted above even acknowledge the existence of evolutionary processes other than natural selection acting on mutations. Evolutionary biology textbooks typically devote at least a full chapter to discussing the role of genetic drift (e.g., chapter 7 in Ridley's Evolution, chapter 11 in Futuyma's Evolutionary Biology), and introductory textbooks address the topic as well (e.g., p. 400 in Miller and Levine's Biology, pp. 450-451 in Campbell and Reece's Biology, 6th ed., and pp. 393-399 in Raven and Johnson's Biology, 5th ed.). There is no way to "explore evolution" accurately without including a discussion of all the major evolutionary processes. The inaccurate and biased presentation of even such basic knowledge demonstrates how EE would misinform and miseducate students.

It should not come as a surprise to learn that the caricature of evolution as "natural selection (acting on random variations and mutations)" is a common creationist trope, and the discussion of the definitions of evolution in EE is basically identical to that in a seminal work of ID creationism, Phillip Johnson's Darwin on Trial (with one interesting omission):

"Evolution" in the Darwinist usage implies a completely naturalistic metaphysical system, in which matter evolved to its present state of organized complexity without any participation by a Creator. But "evolution" also refers to much more modest concepts, such as microevolution and biological relationship.

Phillip E. Johnson (1991) Darwin on Trial, Regnery Gateway, Washington, DC, p. 151

Explore Evolution employs the same argument, but lets innuendo replace Johnson's forthright advocacy of "a Creator." This is in keeping with EE's habit of parroting creationist criticisms of evolution and attempting to cloak the religious nature of those objections through omission and obfuscation.

Universal Common Descent

Summary of problems:

Scientists continue to research the origins of life, and to investigate the possibility that early lineages of life shared genes so freely that very early living things cannot be separated into multiple discrete lineages. The extent of that sharing is a subject of active research and scientific debate. Explore Evolution misrepresents that ongoing research as if it were between advocates of a single tree of life and supporters of a "neocreationist orchard."

Full discussion:

The nature of the Last Universal Common Ancestor is a topic of ongoing research today, and a book which intended to explore current scientific controversies within evolution would have to address that topic. A growing body of evidence suggests that there was so much sharing of genetic material among the single-celled organisms at the base of the tree of life that the different strands cannot be separated. Some scientists go so far as to treat the entire community of organisms alive at the time as essentially a single superorganism which shuffled genes freely between components. They treat that community of cells as the Last Universal Common Ancestor (LUCA). As particular genes became more tightly entwined with the functioning of other genes, the sharing decreased and lineages began to diverge.

Other scientists hold that gene transfer between organisms is not an obstacle to tracing the lineages of modern life, and insist that the branching trees of life can be traced all the way back to the earliest cell.

Explore Evolution ignores this ongoing and fascinating scientific controversy. To the extent they acknowledge its existence, it is only to misrepresent the views of participants in that debate. This statement, for example, betrays a profound lack of understanding of evolution and could hardly be more inaccurate or misleading about basic biology:

Darwin envisioned this 'Tree of Life' beginning as a simple one-celled organism that gradually developed and changed over many generations into new and more complex living forms.

EE, p.6

A central point of the Origin of Species is that evolutionary change takes place in populations of organisms, not in individuals. To elide this point, or fail to make it clear, is obviously an egregious error in a book supposed to be about evolution.

Furthermore, even in 1859 Darwin allowed for the possibility of more than one type of early organism. At the end of The Origin of Species, for example, Darwin wrote:

There is grandeur in this view of life, with its several powers, having been originally breathed by the Creator into a few forms or into one;

The Origins of Species

Since then, the evolution of the earliest cells has been and continues to be a dynamic area of research.

Neo-creationist orchard: From Kurt Wise (1990) "Baraminology: A Young-Earth Creation Biosystematic Method," in Robert E. Walsh (ed.) Proceedings of the Second International Conference on Creationism, Vol. 2. Creation Science Fellowship, Inc.: Pittsburgh, PA. p. 345-360.Furthermore, Explore Evolution badly misrepresents the state of science when it states "Other scientists doubt that all organisms have descended from one — and only one — common ancestor" (p. 9). While some scientists dispute the strict monophyly of the early history of life, but only because they think that genes from other branches of the tree of life moved between lineages, not because they dispute that life can be traced to a common ancestor. Researchers in the field do not "say that the evidence does indeed show some branching groups of organisms, but not between the larger groups" (pp. 9-10, emphasis original), and scientists absolutely reject the notion that "the history of life should … be represented … as a series of parallel lines representing an orchard of distinct trees" (p. 10). In fact, that way of talking about life's history was originated by creationists, as shown in the figure at right. In describing his "orchard" view of life, young earth creationist Kurt Wise explains:

Some modern creationists are suggesting a metaphor of their own — a metaphor which is planted between the Evolutionary Tree and the Creationist Lawn. The new metaphor may be described as the "Neo-creationist Orchard" (see figure 1C [reproduced here]). In this metaphor, life is specially created (as fruit trees are specially planted) and polyphyletic (i.e. each tree has a separate trunk and root system). There are also discontinuities between the major groups (trees are spaced so that branches do not overlap and could not and never did anastomose [grow together]) and there are constraints to change (a given tree is limited to a particular size and branching style according to its type). In these ways, the Neo-creationist Orchard is similar to the Creationist Lawn [Figure 1A]. They differ, though, in that the Neo-creationist Orchard allows change, including speciation, within each created group (each tree branches off of the main stem). Permitting this type of change (variously called by creationists 'diversification', 'variation', 'horizontal evolution', and 'microevolution') in different amounts in different groups allows the creation model to accomodate microevolutionary evidences (e.g. changing allelic rations, genetic recombination, speciation, etc.).

Kurt Wise (1990) "Baraminology: A Young-Earth Creation Biosystematic Method," in Robert E. Walsh (ed.) Proceedings of the Second International Conference on Creationism, Vol. 2. Creation Science Fellowship, Inc.: Pittsburgh, PA. p. 345

In this passage, Kurt Wise introduces his explicitly creationist concepts in the exact terms that Explore Evolution uses. Dr. Wise, is undoubtedly one of the "critics" EE refers to, but he is never cited in EE. Not surprisingly, the book doesn't mention that the young earth creationist group Answers in Genesis states that the same figure shows "the true creationist 'orchard' model."

"Creation model": Explore Evolution co-author Paul Nelson's preferred "creation model," copied from a German creationist textbook.

Paul Nelson (2001) "The Role of Theology in Current Evolution," in Intelligent Design Creationism and Its Critics Robert Pennock, ed. The MIT Press:Cambridge, MA pp. 685.

Nor does the book point out that one author, Paul Nelson, previously presented the "polyphyletic" model shown at left, writing that "creationists defend the dynamic pattern of figure 32.2," rather than the models like the lawn illustrated by part a) of Wise's figure (Paul Nelson, 2001. "The Role of Theology in Current Evolution," in Intelligent Design Creationism and Its Critics Robert Pennock, ed. The MIT Press:Cambridge, Ma. pp. 684-685). Elsewhere, Nelson and a co-author defended their young earth creationist views by arguing that "The overall geometry of the history of life … depict[s] … a forest of trees, each with its own independent root" (Paul Nelson and John Mark Reynolds, 1999, "Young Earth Creationism" in Three Views on Creation and Evolution, J. P. Moreland and John Mark Reynolds, eds. Zondervan Publishing: Grand Rapids, MI. p. 45).

This vision of multiple trees of life, totally independent of one another is a creationist concept, and bears no relationship with any position being advanced in the scientific literature. There are challenges to the idea that diversity of life followed a strict branching pattern from the earliest days, but as shown in the figure at the right, this view rests heavily on exactly the sort of mixing (or "anastomosis") that Nelson and Wise reject. The figure EE uses to illustrate its proposed alternative view of life also does not include the complex exchanges of genetic information proposed by the authors Explore Evolution cites as critics.

A modern view of the tree of life: From W. Ford Doolittle (2000) "Uprooting the tree of life." Scientific American, 282(2):90-5. Note that distances are not necessarily to scale in this image. This image reflects a view held by some practicing scientists (including Dr. Doolittle, the author of the original article) that there was a period in life's early history when genes swapped so frequently that it is impossible to treat those earlier lineages as truly distinct, nor to trace those lineages back cleanly to a single ancestor. They do not dispute that life has some common ancestor, but they do seek to clarify how we talk about that ancestor.

The scientists cited as supporting this "orchard" view of life actually advocate a tree very different from the one illustrated by Explore Evolution (figure i:4). As the figure to the right shows, the group of scientists challenging traditional views of the tree of life are not proposing the sort of orchard that EE illustrates. Where EE and its creationist antecedents' embrace "discontinuities between major groups," the objection raised by the scientists EE cites actually object that there aren't enough connections between the branches of the tree of life.

These authors do not dispute that we can talk about a single common ancestor, merely that we should talk about it in a different sense. Doolittle explains:

As Woese [an author cited as a critic of monophyly by EE] has written, "The ancestor cannot have been a particular organism, a single organismal lineage. It was communal, a loosely knit, diverse conglomeration of primitive cells that evolved as a unit, and it eventually developed to a stage where it broke into several distinct communities, which in their turn become the three primary lines of descent [eubacteria, archaea and eukaryotes]." In other words, early cells, each having relatively few genes, differed in many ways. By swapping genes freely, they shared various of their talents with their contemporaries. Eventually this collection of eclectic and changeable cells coalesced into the three basic domains known today. These domains remain recognizable because much (though by no means all) of the gene transfer that occurs these days goes on within domains.

W. Ford Doolittle (2000) "Uprooting the tree of life." Scientific American, 282(2):90-95

This is a nuanced view, one that high school students are ill-equipped to understand until they have a fuller grasp on the basic concepts of biology. As Doolittle observes, even "some biologists find these notions confusing." It is hardly reasonable to expect students who are still learning what the genome is to appreciate a debate about the ways that gene swapping between ancient bacteria would have produced the sort of communal superorganism Woese and Doolittle describe. It would pedagogically inappropriate for Explore Evolution to thrust students into the midst of that debate without any background or support. Indeed, many biology teachers would be ill-prepared to lead such a discussion. This does not excuse the failure of EE to accurately describe the nature of that scientific debate.

Woese and Doolittle do not advocate an orchard, they simply thing that the trunk of the tree of life cannot be separated into distinct strands. They are not opponents of evolution, and Explore Evolution does the authors they cite no favors when they misrepresent the underlying science. That loose treatment of the underlying science also would do students and teachers no favors. A truly inquiry-based text might be able to wring some useful educational lessons from the debate going on over the base of the tree of life, but it is doubtful that high school students would benefit from that highly technical discussion, and they could not use Explore Evolution to understand even the basic nature of that ongoing research.

"Fundamentally new" organisms

Summary of problems:

Evolutionary theory predicts relatively smooth and incremental transitions, not the sudden emergence of new traits or species. Even so, Explore Evolution discusses "whether natural selection can produce fundamentally new forms of life, or major innovations in the anatomical structure of animals" without ever explaining how students ought to distinguish "fundamentally new forms" of life from merely "new" forms, nor how "major innovations" can be distinguished from more mundane "innovations." The assumption that any trait would spring forth, fully formed, without precedent, is not a prediction of evolution, nor are these concepts in general use by biologists.

Full discussion:

As noted above, real textbooks about evolution distinguish several evolutionary mechanisms, including natural selection and mutation, but also genetic drift and gene flow, as mechanisms for evolutionary change. In particular, mutation is a change in the DNA of a cell in a single organism, and if it happens in a cell which goes on to produce an egg or sperm cell, it can be passed on to all the descendants of that individual. This makes mutation "the origin of genetic variation" (Futuyma, 1998, Evolutionary Biology, 3rd ed., ch. 7). When Explore Evolution speculates about "whether natural selection can produce fundamentally new forms of life, or major innovations" in anatomy (p. 9), it wrongly omits the generative power of mutation, as well as other evolutionary mechanisms, several of which may be more important to the course of evolution than natural selection.

The discussion of whether evolution is "creative or conservative" (section heading, p. 9) in Explore Evolution is profoundly confusing because it fails to distinguish between different evolutionary processes, and between the levels at which they operate. For instance, the discussion about whether natural selection itself is "creative" ignores the role of other mechanisms in generating variation, and the difference between novelty at a genetic level, at a genomic level, or at a population level. Also, EE's focus on whether natural selection can produce "fundamentally new forms of life" fails to describe over what time scale it might be operating, nor what processes scientists hypothesize in addition to (not instead of) natural selection.

More worrisome in the educational setting, the authors of Explore Evolution misrepresent several of the authors that they quote regarding the "creative" power of natural selection. They write:

Zoologist Ernst Mayr writes that natural selection is a "positive, constructive force," and adds "one can go even further and call natural selection a creative force."

EE, p. 9

As the footnote points out, these two quotations come from different sources; Mayr did not "add" one phrase to the other. Neither does the first quotation refer to Mayr's own views on whether natural selection was a "creative" force, he was pointing out that Charles Darwin "considered selection not a purely negative force that eliminates the unfit, but a positive, constructive force that accumulates the beneficial" (Ernst Mayr, 1964, "Introduction" to On the Origin of Species by Charles Darwin: A Facsimile of the First Edition, Harvard University Press: Cambridge, MA. p. xvii). The latter quotation comes from a passage that addresses exactly the misconceptions EE promotes, and is worth quoting at length.

An understanding of the working of natural selection is the key to the Darwinian theory of evolution. I know of no other scientific theory that has been as misunderstood and misrepresented as greatly as the theory of natural selection. First of all, it is usually represented as strictly negative, as a force that eliminates, a force that kills and destroys. Yet Darwin, by his choice of the name "selection," clearly emphasized the positive aspects of this force. Indeed, we now know that one can go even further and call natural selection a creative force. Second, natural selection is not an all-or-none phenomenon. The typologist, the follower of Plato, seems to think that alternatives are always either good or bad, black or white, worthy of preservation or doomed to rejection. This viewpoint is represented in two statements by well-known contemporary philosophers, chosen at random from the recent literature: "Natural selection requires life and death utility before it can come into play"; and "Unsuccessful types will be weeded out by the survival of the fittest but it cannot produce successful types."

Actually, types in the sense of these statements do not exist; only variable populations exist. No one will ever understand natural selection until he realizes that it is a statistical phenomenon. In order to appreciate this fully, one must think in terms of populations rather than in terms of types [or EE's "forms" -ed.].
&hellip
A further consideration will help to make the role of natural selection even clearer. Not the "naked gene" but the total phenotype is exposed to selection. A gene occurring in a population will contribute toward very many phenotypes. In some cases these phenotypes will be successful, in others they will not. The success of the phenotypes will depend on the fitness of the particular gene, within the framework of the gene pool of this population. And this again will be an essentially statistical phenomenon.

Let us also remember that recombination, not mutation as such, is the primary source of the phenotypic variation encountered by natural selection. The usual argument of the anti-Darwinian is: "How can an organism rely on the opportune occurrence of a favorable mutation whenever one is needed, considering that most mutations are deleterious? Surely all organisms would be doomed to extinction of in times of need they had to rely on such rare events?" Those who ask such questions confuse genetic variability and phenotypic variability. To be sure, mutation is ultimately the source of all genetic variation. But natural selection operates not at the level of the gene but at the level of the phenotype. Further, the main source of phenotypic variation is recombination rather than mutation, and this source of variation is ever present. With every individual differing genetically from every other one, every phenotypic character is variable, showing deviations of varying intensities and directions around the mean. Under normal conditions, selection will favor the mean (stabilizing selection), but if a deviation in any direction should be required by a newly arising selective force, the material is instantaneously available to respond to this force (directive selection).

Natural selection in this modern nontypological interpretation is an exceedingly sensitive instrument. The phenotype in nearly every case is actually a compromise between a number of conflicting selective forces.

Ernst Mayr (1962) "Accident or Design: The Paradox of Evolution," in The Evolution of Living Organisms, (proceedings of the Darwin Centenary Symposium of the Royal Society of Victoria), and reprinted in Mayr (1976) Evolution and the Diversity of Life: Selected Essays, Harvard University Press:Cambridge, MA, ch. 4, pp. 36-38

Given that it is the combinations of genes which produces the final organism, recombination of genes during cell replication and sexual reproduction plays a critical role in generating variation within the population. Natural selection acts on combinations of genes as much as it operates on the individual genes themselves, and the sum total of the selection on particular genes and particular combinations of genes can and does produce biological novelties. It is fair to say that this process of selecting genes and gene combinations makes natural selection "an editor" (EE, p. 9, emphasis original). Editing can be creative work; EE would have benefited from a particularly creative editor, and good authors often regard their editors as collaborators whose creativity is necessary for the final product.

Explore Evolution hedges a bit on this point, arguing that it is not enough for something to be new, it must be "fundamentally new." By this they seem to mean a "major innovation[] in the anatomical structure of animals" (or plants, fungi and other living things, presumably). Unfortunately, it is not clear what makes an innovation "major," any more than it is clear when a novelty is "fundamentally new," rather than simply new. More importantly, it is not clear how quickly novelties must appear in a population in order to qualify as "major innovations" or "fundamentally new." The accumulation of small novelties over many generations is the hallmark of evolutionary change. The sudden appearance of new structures without any intermediates is not an evolutionary prediction, and no examples of such a change exist to require evolutionary explanations.

There are indeed many innovations which cannot be explained by natural selection alone. The mitochondria and chloroplasts are a perfect example, discussed in more detail in our critique of the chapter on Natural Selection. Endosymbiosis, a sort of cooption at the cellular level, is comparable to the role of recombination within the genome and gene flow in populations, and the authors of Explore Evolution would have done well to have expanded their exploration to include the full range of evolutionary processes. It would have benefited their own writing, and helped any students unfortunate enough to have this book inflicted upon them.

References

Antonis Rokas, Sean B. Carroll, (2006) "Bushes in the Tree of Life," PLOS Biology 4(11): e352 doi:10.1371/journal.pbio.0040352.

Timothy D. Colmer, Timothy J. Flowers, and Rana Munns. (2006) "Use of wild relatives to improve salt tolerance in wheat," Journal of Experimental Botany 57: 1059-1078