Understanding Evolution

Evolutionary Biology and Intelligent Design

In the previous chapter, I have briefly explained some features of life which the ID theorists see as evidence of design. But as noted, the ID movement’s biological design arguments include critiques of naturalistic explanations of the biological order of nature. Darwinian evolutionary theory agrees with ID that the functional complexity of biology requires an explanation – the explanation given is just different. But what exactly is Darwinian evolutionary theory and what parts do the ID theorists accept or reject?

Ernst Mayr, one of the 20^th century’s leading evolutionary biologists, divided Darwinian evolutionary theory into five distinct parts. First, (1) there is the general thesis of evolution as such. This states the changeability of species as opposed to a constant, unchanging world. Second (2), there is common descent, the thesis that all different branches of animal species share a common ancestor. Third (3), there is the thesis of gradualness, which states that species change by small, successive and cumulative mutations. Thus there are no big “jumps” in evolution where a completely new form of animal is formed through just one mutation. Fourth (4), there is the thesis of populational speciation, which states that new species can emerge from existing populations through changes. Fifth (5), there is natural selection – the Darwinian mechanism for explaining evolutionary adaptations.⁶⁶¹ As Mayr argues, it is in principle possible to accept just parts of Darwinian evolutionary theory. For example, many of Darwin’s contemporaries did not accept natural selection as the mechanism of evolutionary change, but accepted the thesis of common descent.⁶⁶² Modern expansions of the evolutionary synthesis also tend to modify one of these parts. For example, there are different views about the relative importance of natural selection and how large the mutations can be.⁶⁶³

There is a broad variety of different views within modern evolutionary biology, as well. Recent discussion on evolutionary theory has complicated the picture. For example, there has been discussion of evo-devo, neutral evolution, endosymbiosis, punctuated equilibirium and even “natural genetic engineering” as complementary mechanisms to Darwinian natural selection.⁶⁶⁴ However, the standard Darwinian mechanism is typically still

661 Mayr 2002, 94-95.

662 Mayr 2002, 95. See also Bowler 2009, chapters 6 and 7, particularly pages 196-199.

663 Pigliücci & Muller 2010.

664 See e.g. Cunningham 2010, Cobb 2008 and Noble 2013 for discussions emphasizing the breadth and continuing development of evolutionary theory; see Shapiro 2011 & Wilkins 2012 for discussion on natural genetic engineering.

seen as the only way to explain the presence of complex biological adaptations, such as the eye which appears to be formed for the purpose of sight and other such examples of biological “teleology” or whatever name we wish to use of this feature of life.⁶⁶⁵

In any case, Mayr and the mainstream of current evolutionary biologists still regard accepting the whole package of Darwinism as the most consistent and scientifically reasonable thing to do. New developments in evolutionary biology are seen as supplementing the basic naturalistic picture of neo-Darwinism rather than overthrowing it and returning to a Paleyan understanding of the origin of species. Evolutionary biologist Mark Ridley summarizes four main lines of evidence for Darwinian evolutionary theory.⁶⁶⁶ First, (1) small scale changes in organisms can be directly observed. It is then extrapolated that past changes in organisms can be explained through the same evolutionary mechanisms observed in the present. Second (2), the similarities of living things can be explained by the proposition that they are descended with modification from a common ancestor. Such similarities can be seen both in the appearance (phenotype) and the genetic structure (genotype) of organisms. The classification of living things into different species and classes by pre-Darwinian biologists was historically necessary for the emergence of Darwinian theory. It then became possible to argue (for example) that all different cats were descended from the same cat-like ancestors, all mammals from the same ancestors and so on.⁶⁶⁷ Third, (3) the geological evidence demonstrates that past forms of life were different from those that now live, and fits well with the supposition of descent with modification. Fourth (4), evolutionary biology acts as a unifying theory for all of biology and helps explain many details which seem to be without any other explanation.⁶⁶⁸ As Theodosiuz Dobzhansky famously stated in 1974, “nothing in biology makes sense except in the light of evolution.”⁶⁶⁹ Dobzhansky admitted that not all details about how evolution happens have been worked out, but this should not stop us from accepting the general picture given by the theory as correct. The logic of the inference to the best explanation does not demand that all questions related to a hypothesis are resolved before it can emerge as a clearly better explanation than any rival hypothesis.⁶⁷⁰

665 E.g. Freeman & Herron 2007, 98-99. Even Fodor & Piattelloi-Palmarini (2011, chapter 8) recognize in their critique of neo-Darwinian theory that this is the strongest argument in favour of the importance of natural selection; similarly Cunningham (2010, chapter 3) notes the importance of natural selection in explaining adaptations, while otherwise emphasizing the importance of other factors in evolution.

666 Ridley 2004, 66. There are other ways of summing the evidence for evolution. Campbell and Reece (2007) add the evidence from biogeography to this list: similar animals live close to each other. This is better explained by assuming that these species have a history of common ancestry and migration, rather than assuming that all species are created by God in the places which they are found.

667 See Bowler 2009, chapter 3 for this history. See also Freeman & Herron 2007, Dawkins 2009 and Coyne 2009 for presentations of the evidence for common descent.

668 As Dawes (2007, 80) notes, there is massive amount of research in evolutionary biology. It is now over 140 years from the publication of Darwin’s Origin of Species (1859) and evolutionary biology has since been worked on by generations of biologists.

669 Dobzhansky 1974.

670 Lipton 2003, Sober 2008.

In addition to these four reasons, many defenders of evolutionary biology also reference philosophical and theological arguments as powerful reasons for accepting Darwinian evolutionary biology over any idea of creation involving miracles and gaps in nature. I will analyse some such reasons further in chapters 7, 8 and 9.

The ID movement's critique of evolutionary biology is mostly aimed at the sufficiency of the Darwinian mechanism for explaining the origin of complex functional order in life (part 5 in Mayr’s division above). As John G. West puts it, “intelligent design is simply the effort to investigate empirically whether the exquisitely coordinated features we find throughout nature are the result of an intelligent cause rather than a blind and undirected process like natural selection.”⁶⁷¹ All of the ID movement’s main thinkers similarly affirm the compatibility of common descent and ID’s biological design arguments. This theme is already present in Johnson’s Darwin on Trial⁶⁷², and continues in later ID works. Dembski, for example, argues that

“intelligent design is also fully compatible with large-scale evolution over the course of natural history, all the way up to what biologists refer to as “common descent” (i.e., the full genealogical interconnectedness of all organisms.)”⁶⁷³The reason for this is that the thesis of common descent does not by itself provide any explanation for biological adaptations, and thus does not compete with design as an explanation, whereas the Darwinian mechanism is understood to compete with design. ⁶⁷⁴

However, Behe is the only major ID theorists who actually believes in common descent as the best explanation of the similarities of living beings and who restricts his critique to naturalistic mechanisms of evolution. All of the other major ID theorists do recognize Behe’s position as coherent and as part of ID. However, they also make extended critiques of standard evidence for common descent, including ID textbooks like the The Design of Life (2007) by Dembski and Jonathan Wells.⁶⁷⁵ This critique is thus a part of ID, but the major ID theorists do not consider it a necessary part of ID’s project or its design argument. Therefore I will leave discussion of the first four parts of Mayr’s thesis aside and focus on the central question of natural selection as the mechanism driving the evolution of new functional structures.⁶⁷⁶

671 Gauger, Axe & Luskin 2012, 11.

672 Johnson (1993, 4) argues that one can be a creationist in the broad sense and accept evolution, as long as one believes that the process of evolution was directed by God.

673 See also Meyer 2010. I will have more to say about ID’s relationship to theistic evolution in chapter 8.

674 The ID theorists’ engagement with evolutionary mechanisms other than the standard neo-Darwinian account has been limited. Behe’s analysis of Lynn Margulis’ theory of endosymbiosis (2006, 26-31) and evo-devo (2007, chapter 9) is one exception.

675 Jonathan Wells’ (2002a and 2002b) critiques of standard evidences for common descent are among the deepest in the ID movement.

676 Though many sources (e.g. Mayr 2002, Bowler 2009) argue that the idea of common descent was historically acceptable without accepting the other parts of Darwinian evolutionary theory such as gradualism and natural selection, Korthof (2005) argues that there is tension between Behe’s acceptance of common descent and his rejection of the Darwinian mechanism as the explanation for macroevolution. Common descent, gradualism and the Darwinian mechanism fit in well together, but I find Korthof’s argument unpersuasive. It seems that other evolutionary theories also imply some degree of discontinuity between parents and their offspring, as long as there is change from generation to generation.

According to evolutionary biologists Stanley Freeman and Jon C. Herron, evolution by natural selection is the logical outcome of the following four facts. First (1), individuals vary in most or all traits. Second, (2) some of this variation is genetically based and can be passed on to offspring. Third (3) there is differential reproduction: some organisms are more successful than others in passing on their genes. Fourth (4), reproductive success is not completely random. Rather, the better adapted (or more fit) individuals in the population will reproduce the most.⁶⁷⁷ But this results only in a proving a very general definition of evolution defined as a change in the genetic makeup of the population over time. This definition does not yet tell us what sort of variations occur and whether the cumulation of these variations over time can explain even complex, functional biological structures. One of the best discussions of this is still Richard Dawkins’ classic The Blind Watchmaker – also a central text discussed by the ID movement.⁶⁷⁸

The ID movement’s thinkers admit the powers of naturalistic evolutionary mechanisms in explaining minor changes, but do not accept them as a sufficient explanation for all of life’s complexity. In other terms, at issue is the extrapolation from microevolution to macroevolution.⁶⁷⁹ According to Johnson, “If empiricism were the primary value at stake, Darwinism would long ago have been limited to microevolution, where it would have no important theological or philosophical implications.”⁶⁸⁰In the ID movement’s terminology, microevolution is “small-scale genetic and structural changes in organisms”, whereas macroevolution means large-scale genetic and structural changes “leading to new and higher level of complexity.”⁶⁸¹ In the Edge of Evolution (2007), Behe attempts to determine the limits of Darwinian evolutionary mechanisms and concludes that Darwinian evolution is likely possible beyond the species level and the limits of Darwinian mechanisms are somewhere on the levels of animal genera, families and orders. For the ID theorists, the boundaries of the system of classification are not what limit the possibilities of the Darwinian mechanisms. Rather, the argument is that though this mechanism can explain some features of life, there are many features which it cannot explain. Thus Behe writes that “the major architectural features of life – molecular

677 Freeman & Herron 2007, 105.

678 For example, Freeman & Herron (2007, 98-99) and Ridley (2004, 70) direct the reader to Dawkins for the best defence of the powers of the Darwinian mechanism and reference Dawkins’ ideas about evolution as the “blind watchmaker.”

679 The distinction is also common in creationism. See Ratzsch 1996, 86-90. For an example within ID see Dembski

& Wells 2007, 102-104.

680 Johnson 1993, 118.

681 Dembski & Wells 2007, 315-316. Unfortunately there are several different ways of making the distinction between microevolution and macroevolution, leading to misunderstandings. In the standard terminology of evolutionary biology, microevolution refers to the evolutionary change within the species, while macroevolution refers to evolutionary change above the species level. However, the biological species line (meaning a reproductively isolated population) can be crossed without changes that the ID theorists would term macroevolution. (Dembski & Wells 2009, chapter 4). Nevertheless, similar broader definitions of micro- and macroevolution are also used within the philosophy of biology, and the question is typically seen as a valid one.

(See Sepkoski 2008 for discussion)

machinery, cells, genetic circuitry, and probably more – are purposely designed. But the architectural constraints leave spandrels that can be filled with Darwinian adaptations.”⁶⁸²

Philosopher of biology David Sepkoski formulates the basic question in the move from micro- to macroevolution as follows: “Do major taxonomical groups represent real, ontologically distinct entities with their own emergent properties, and are the factors that govern their development discontinuous with the mechanisms that produce variation and fitness among individuals?”⁶⁸³ In the typical usage of the terms in Neo-Darwinian biology, macroevolution has been understood as the same process as microevolution, only on a bigger scale. In this understanding, there is no qualitative difference between microevolution and macroevolution. Rather, if there is a sufficient amount of time, microevolution can lead to macroevolution without the need for further mechanisms.⁶⁸⁴ It is tempting to see a parallel between the arguments for natural selection and design as the best explanations for functional biological complexity. In chapter 4, I argued that ID’s design inference is best formulated as an inference to the best explanation where inductive and analogical arguments are used to support design as an explanation. Similarly, natural selection can be defended as the best explanation of functional biological complexity, and its capabilities for explaining this type of order can be defended using inductive arguments, just as is done for design. The Darwinian mechanism is observed to do similar work on a smaller scale today; therefore we can infer that it has the capabilities required for producing macroevolutionary changes given a much larger amount of time.

This comes very close to the way the case for the Darwinian extrapolation is often made.⁶⁸⁵ There are some important differences in the arguments for the Darwinian mechanism and design, however. Both the ID theorists and the Darwinians agree that the existence of the Darwinian mechanism in the past is not in doubt. The existence of the Darwinian mechanism is guaranteed by the existence of variation, inheritance and differential reproduction, as we saw above. Darwinian evolutionary biologists also argue that this mechanism fits with what we know about the progress of evolution from fossils and homological evidence, though ID theorists argue that these do not demonstrate the mechanism of evolution.⁶⁸⁶ By contrast, as I showed in chapters 4.4 and 4.5, design arguments are often critiqued for lack of independent

682 Behe 2007a, 202.

683 Sepkoski 2008, 212.

684 Sepkoski 2008, 213-216. As Sepkoski notes, there is some dispute about whether the (well-evidenced) mechanisms of microevolution can be extrapolated to also explain macroevolution. The majority opinion within evolutionary biology is that the extrapolation can be made, but there is a growing number of biologists who would supplement the basic Neo-Darwinian understanding with other mechanisms. These include appeals to mechanisms working on a larger scale, such as selection on the level of groups and species rather than individuals, large-scale events such as extinctions, epigenetic evolution, macromutations, endosymbiosis, structural constraints and other factors.

685 E.g. Ridley 2004, 54-55.

686 Ridley 2004, 54-55. Behe 2006a, 22: “The fossil record has nothing to tell us about whether the interactions of 11-cis-retinal with rhodopsin, transducin and phosphodinesterase could have developed step-by-step.” The existence of natural selection is already accepted by Phillip Johnson in his Darwin on Trial (1993, chapter 2). Though Johnson discusses the critique that natural selection is a tautology and meaningless, he goes on to state that it can be formulated in a meaningful way and indeed works in explaining microevolution.

evidence of the designer’s existence and characteristics. For the ID theorists, the crucial question is not the existence of natural selection in the past, but the causal powers attributed to it. The reliability of the extrapolation from miroevolution to macroevolution is denied. The observed evolutionary changes are not thought to demonstrate the possibility of much larger or qualitatively different evolutionary changes through the same mechanism.

ID and Macroevolution

But what is it that, in the ID theorists’ view, stops the processes of microevolution from leading to macroevolution? How do the ID theorists justify their rejection of the Darwinian mechanism’s capabilities for macroevolution? Their basic idea is that though small gradual changes are known to produce some positive changes in modern-day organisms, explaining all of life’s features through the same process is difficult. I will now summarize four features of biological order the ID theorists believe are resistant to Darwinian explanations. These are (1) irreducibly complex molecular machines, (2) proteins and genes, (3) animal body plans, and (4) the pattern of the fossil record.

(1) Irreducibly complex molecular machines. Both critics and defenders of ID have identified Behe’s irreducible complexity (IC) as ID’s most central argument against the Darwinian extrapolation.⁶⁸⁷ Behe focuses on biochemical machines which he believes are not credibly explained by a gradual process, because producing the function of these machines requires the interaction of several fine-tuned parts. In recent ID literature, there seems to be a move away from using IC as the central ID argument. Rather, the ID theorists are starting to argue that producing even one part of an IC machine is beyond the capabilities of the Darwinian mechanism. IC is then used to argue for the severity of the problem – if producing even one new protein is beyond the capacities of the Darwinian mechanism, then surely producing a new machine requiring tens of such proteins is utterly incredible.⁶⁸⁸ I will have more to say about this argument and its critique in chapter 6.3.

(2) Proteins and genes. Proteins are the basic building blocks of life. For example, the parts of the biochemical machines described by Behe’s argument are proteins. Proponents of ID argue that new proteins are themselves beyond the capacities of evolution. Based on research into protein evolution, Douglax Axe and Ann Gauger have argued that the structures of many proteins are very sensitive to changes. The amino acids have to be in the right places for the protein to fold into a functional three-dimensional form. While proteins can sustain some mutations without breaking, too many changes result in the loss of protein function. Axe estimates that only about 1 / 10⁶⁴ protein folds are functional. If this is correct, then explaining the emergence of new protein folds through a random search is

687 E.g. Shanks 2003, 160. and Woodward 2003, 155. The argument from irreducible complexity takes much space in many sources both for and against ID. For examples, see Dembski 2002a, chapter 5; Shanks 2003, chapter 5;

Dawkins 2006, 144-150; Miller 2002, chapter 5.

688 E.g. Gauger, Axe & Luskin 2012; Meyer 2013, 205-206.

implausible.⁶⁸⁹ Axe admits that random mutations can make small beneficial changes to

implausible.⁶⁸⁹ Axe admits that random mutations can make small beneficial changes to