Lamarckian mechanisms, although unsupported by any evidence at the time, came to play an increasingly important role in Darwin’s thinking, as criticisms of natural selection caused Darwin to place more weight on the direct influence of the environment in evolutionary change. Indeed, by the sixth edition of the Origin (1872), Darwin specifically emphasized the importance of these modes of inheritance.50
But with the rediscovery of Mendel’s laws in 1900 and the identification of chromosomes as the material entity responsible for the transmission of inheritance, Lamarckian theories of inheritance fell out of favor. Following the rise of the neo-Darwinian synthesis, most evolutionary biologists came to regard the gene as the locus of all heritable change in the organism. And after 1953, biologists equated the gene with specifically arranged nucleotide bases within the DNA molecule.
Recently, however, as more biologists have recognized that some biological information—epigenetic information—resides in structures outside of DNA, interest has grown in the possibility that these nongenetic sources of information may influence the course of evolution. The discovery that epigenetic information can be altered and directly inherited independently of DNA has attracted further attention. This discovery has, in turn, led to the formulation of a contemporary “neo-Lamarckian”51 theory that envisions changes in the nongenetic structures of an organism affecting subsequent generations.
Today, prominent defenders of neo-Lamarckism include Eva Jablonka, of Tel Aviv University, and Massimo Pigliucci, of the City University of New York. Lamarck, of course, knew nothing about the role of genes and believed that inheritance of acquired characteristics was an important driving force in evolution. Modern neo-Lamarckians, fully apprised of the reality of genetic inheritance, nevertheless think that nongenetic sources of information and structure may play some role in the evolution of biological form. According to Jablonka, neo-Lamarckism “allow[s] evolutionary possibilities denied by the ‘Modern Synthesis’ version of evolutionary theory, which states that variations are blind, are genetic (nucleic acid–based), and that saltational events do not significantly contribute to evolutionary change.”52
Jablonka has collected several categories of evidence in support of what she calls “epigenetic inheritance systems.” In the first place, in some single-celled organisms (such as E. coli and yeast) environmentally induced changes in metabolic pathways can be transmitted to the next generation independently of any changes in the cell’s DNA. Second, she notes that structural information mediating organismal form (and function) does pass from parent to offspring independently of DNA, via membranes and other three-dimensional cellular patterns.
Third, she discusses the process of DNA methylation—a process in which special enzymes attach a methyl group (CH3) to nucleotide bases within the double helix. Processes like this can alter gene regulation and chromatin structure. Jablonka notes that the changes produced by processes that alter gene regulation are often transmitted to subsequent generations of cells without any changes to DNA base sequences. Finally, she cites a process called “RNA-mediated” epigenetic inheritance, a recently discovered phenomenon. Here, small RNAs, again acting in concert with special enzymes, affect gene expression and chromatin structure, and these modifications appear to be heritable independently of genes.
Can any of these mechanisms help to explain the origin of animal form in the Cambrian explosion? Not really.
By its nature, macroevolution requires stable—meaning permanently heritable—changes. But Jablonka’s evidence shows that where nongenetic inheritance occurs in animals, it involves structures that either (a) do not change (such as membrane patterns and other persistent templates of structural information), or (b) do not persist over more than several generations. And neither case generates significant evolutionary innovation in animal form. Instead, for directional evolutionary change to occur in a population of organisms, changes must not only be heritable, but permanent. Stability—the irreversible and enduring heritability of traits—is a logically inescapable requirement for any theory of evolution. This is precisely what “descent with modification” means.
And here Jablonka’s evidence for stable nongenetic inheritance is equivocal at best, as she readily admits. Reviewing Jablonka’s assembled data for animals reveals no case where an induced epigenetic change persisted permanently in any population. The heritability of such changes is transient, lasting (depending on the species in question) from a few generations up to forty.
Jablonka candidly addresses this lack of evidence for stability, noting, “We believe that epigenetic variants in every locus in the eukaryotic genome can be inherited, but in what manner, for how long, and under what conditions, has yet to be qualified.”53 Consequently, despite its intriguing aspects, the evolutionary significance of neo-Lamarckian epigenetic inheritance remains uncertain or, in Jablonka’s own words, “inevitably, somewhat speculative.”54
Natural Genetic Engineering
University of Chicago geneticist James Shapiro has formulated another post-Darwinian perspective on how evolution works that he calls “natural genetic engineering.” Shapiro has developed an understanding of evolution that takes account of the integrated complexity of organisms as well as the importance of nonrandom mutations and variations in the evolutionary process.
He observes that organisms within a population often modify themselves in response to different environmental challenges. He cites evidence showing that when populations are challenged by environmental stresses, signals, or triggers, organisms do not generate mutations or make genetic changes randomly, that is, without respect to, or unguided by, their survival needs. Instead, they often respond to environmental stresses or signals by inducing mutations in a directed or regulated way. As he explains, “The continued insistence on the random nature of genetic change by evolutionists should be surprising for one simple reason: empirical studies of the mutational process have inevitably discovered patterns, environmental influences, and specific biological activities at the roots of novel genetic structures and altered DNA sequences.”55
The depth of Shapiro’s challenge to orthodox neo-Darwinism is profound. He rejects the randomness of novel variation that Darwin himself emphasized and that neo-Darwinian theorists throughout the twentieth century have reaffirmed.56 Instead, he favors a view of the evolutionary process that emphasizes preprogrammed adaptive capacity or “engineered” change, where organisms respond in a “cognitive” way to environmental influences, rearranging or mutating their genetic information in regulated ways to maintain viability.
As an example, Shapiro notes that—contrary to the neo-Darwinian assumption that “DNA alterations are accidental”57—all organisms possess sophisticated cellular systems for proofreading and repairing their DNA during its replication. He notes that these systems are “equivalent to a quality-control system in human manufacturing,” where the “surveillance and correction” functions represent “cognitive processes, rather than mechanical precision.”58
As an example of regulated mutation, Shapiro observes that in response to environmental assault—UV damage from sunlight or the presence of an antibiotic, for instance—bacteria activate what is known as the “SOS response” system. This system makes use of specialized error-prone DNA polymerases, normally left unexpressed, that are synthesized and set into action, allowing the population to generate a much wider range of genetic variation than usual. Bacterial cells regulate this process using a DNA-binding protein known as LexA, which normally represses the error-prone polymerases. When the SOS system is activated by environmental damage, the production of LexA first drops dramatically, allowing expression of the error-prone polymerases, but then rises, which “ensures that as soon as DNA repair occurs … LexA [will] reaccumulate and repress the SOS genes.”59 This system allows cells to “replicate DNA that carries unrepaired damage,”60 keeping their essential replication machinery moving past a stall, in the absence of which the bacterium would die.
An ana
logy may help to illustrate what the cell is doing when confronted with an environmental challenge. Imagine a military unit, a combined armor and infantry battalion, crossing an open plain. Suddenly, the battalion falls under a fierce, unrelenting enemy artillery barrage, wounding many of its soldiers. To keep the wounded alive until the barrage ceases or reinforcements arrive, the commander instructs certain members of the unit with destructive skills to disassemble (in military jargon, “cannibalize”) a few of the tanks to provide temporary armored cover from further incoming shells. His order tells them, however, to cease their tank-modifying actions as soon as the barrage ends. That is, the unit as a whole tolerates “damage” to some of its equipment to save as many of its members as possible.
In the same way, while at one level their “error-prone” role may appear counterintuitive, these mutation-generating DNA polymerases of the SOS system actually constitute essential hardware in the cell’s defensive armory.61 From Shapiro’s perspective, this survival strategy does not exemplify Darwinian randomness, but rather sophisticated preprogramming, an “apparatus that even the smallest cells possess” to maintain viability.62 What’s more, the carefully regulated expression of the SOS response provides evidence that cells employ the system only when needed.63
In addition to ramping up their mutation rates in specific sections of the genome, cells may also change the way they express the genetic information that they already carry, expressing some genes that were previously unexpressed and suppressing others. Organisms in populations under particular stresses may retrieve and access modular elements of genetic information stored in disparate locations on the genome or even on different chromosomes. Cells will then assemble, or concatenate, those modular elements to form a new gene or RNA-transcript capable of directing the synthesis of a novel protein or proteins that can help the organism survive.
Shapiro argues that these and other kinds of directed, rather than random, genetic changes and responses to stimuli occur under “algorithmic control.” He describes the cell as “a powerful real-time distributed computing system”64 implementing various “if-then” subroutines. This emphatically challenges one of the three key elements of the neo-Darwinian triad: the claim that mutations and variations occur in a strictly random way.
During the last fifteen years, Shapiro has published a series of fascinating papers about the newly discovered capacities of cells to direct or “engineer” the genetic changes they need to remain viable in a range of environmental conditions. His work represents a promising avenue of new biological research, bringing insight into how the cell’s information-processing system modifies and directs the expression of its genetic information in real time in response to different signals. Shapiro’s work also provides new insights into how observable evolutionary changes occur in living populations.
Could it, then, also provide a solution to the problem of the origin of the information necessary to build an animal body plan? It could, except for one question that Shapiro’s otherwise brilliant characterization of how organisms modify themselves doesn’t address.
Where does the programming come from that accounts for the “preprogrammed adaptive capacity” of living organisms? If, as James Shapiro argues, natural selection and exclusively random mutations don’t produce this information-rich preprogramming, then what did? In the next chapters, I’ll propose an answer to precisely this question.
17
The Possibility of Intelligent Design
The owner of a remote island estate has been murdered while out riding. When the local sheriff arrives, he learns there are several obvious suspects: the volatile gamekeeper, the owner of a neighboring estate with whom the murder victim has had a long-running feud, and the estate owner’s estranged wife, who had been living on the island in a small mother-in-law cottage. The sheriff quickly learns the basic facts of the case. The victim was found dead, facedown on the beach, with his horse standing nearby. Any one of the three suspects could have taken a rifle, from an unlocked shed at the edge of the property. All were healthy enough to have hiked to the scene of the crime. Each of them has a motive. And none has an alibi.
But as the investigation unfolds additional facts come to light. Most importantly, when the coroner arrives, he determines that although the victim was shot in the stomach and then his head was harshly bludgeoned by the butt of the rifle, these injuries served merely to conceal the bullet wound that actually killed the estate owner. The man was dead when he hit the ground. What killed him was a perfect shot entering the head just behind the right ear, exactly where an expert marksman would place a bullet. Moreover, ballistics shows that this bullet came from a different gun altogether from the one stored in the shed, a weapon likely fired from quite a distance.
The sheriff then returns to the list of suspects and, one by one, eliminates them. Abundant evidence shows that none of the three prime suspects is a particularly good shot, much less a world-class marksman. The landowner’s estranged wife has a shaky hand and no experience with firearms. The volatile gamekeeper has extremely poor eyesight. And the neighboring landowner turns out to have an alibi after all—as well as a broken arm, which would have prevented him from holding the kind of rifle from which the bullet was fired. There is, however, one other person living on the estate, though not even the other suspects suspect him. He is the victim’s loyal and longtime personal assistant, a timorous older man much beloved by both the family and the other servants. No one wants to consider him as a possible suspect. But is it possible that he could have had something to do with the crime after all? Might an unexpected suspect—indeed “the butler”—have done it?
Clearly, standard evolutionary theory has reached an impasse. Neither neo-Darwinism nor a host of more recent proposals (punctuated equilibrium, self-organization, evolutionary developmental biology, neutral evolution, epigenetic inheritance, natural genetic engineering) have succeeded in explaining the origin of the novel animal forms that arose in the Cambrian period. Yet all these evolutionary theories have two things in common: they rely on strictly material processes, and they also have failed to identify a cause capable of generating the information necessary to produce new forms of life.
This raises a question. Is it possible that a different or unexpected kind of cause might provide a more adequate explanation for the origin of the new form and information—as well as the other distinctive features—present in the Cambrian explosion? In particular, is it possible that intelligent design—the purposeful action of a conscious and rational agent—might have played a role in the Cambrian explosion?
Introducing Intelligent Design
When the case for intelligent design is made, it’s often hard to get contemporary evolutionary biologists to see why such an idea should even be considered or why discussions of design should play any role in biology at all. Though many biologists now acknowledge serious deficiencies in current strictly materialistic theories of evolution, they resist considering alternatives that involve intelligent guidance, direction, or design.
Much of this resistance seems to come simply from not understanding what the theory of intelligent design is. Many evolutionary biologists see intelligent design as a religiously based idea—a form of biblical creationism. Others think the theory denies all forms of evolutionary change. But contrary to media reports, intelligent design is not a biblically based idea, but instead an evidence-based theory about life’s origins—one that challenges some, but not all, meanings of the term “evolution.”
Perhaps the best way to explain the theory of intelligent design is to contrast it with the specific aspect of the theory of Darwinian evolution that it directly challenges. Recall from our opening discussion in Chapter 1 that the term “evolution” has many different meanings and that Darwin’s theory of evolution by natural selection affirmed several of them: first, change over time; second, universal common descent; and third, the creative power of natural selection acting on random variations. In affirming this third meaning
of evolution, both classical Darwinism and modern neo-Darwinism also affirm what neo-Darwinist Richard Dawkins has called the “blind watchmaker” hypothesis. This hypothesis holds that the mechanism of natural selection acting on random genetic variations (and mutations) can produce not just new biological form and structure, but also the appearance of design in living organisms.1
Darwin argued for this idea in The Origin of Species as well as in his letters. Recall the sheep breeding illustration from Chapter 1 where I described how both intelligent human breeders and environmental change (a series of bitterly cold winters) might produce an adaptive advantage in a population of sheep. During the nineteenth century, biologists regarded the adaptation of organisms to their environment as one of the most powerful pieces of evidence of design in the living world. By observing that natural selection had the power to produce such adaptations, Darwin not only affirmed that his mechanism could generate significant biological change, but that it could explain the appearance of design—without invoking the activity of an actual designing intelligence. In doing so, he sought to refute the design hypothesis by providing a materialistic explanation for the origin of apparent design in living organisms. Modern neo-Darwinists also affirm that organisms look as if they were designed. They also affirm the sufficiency of an unintelligent natural mechanism—mutation and natural selection—as an explanation for this appearance. Thus, in both Darwinism, and neo-Darwinism, the selection/variation (or selection/mutation) mechanism functions as a kind of “designer substitute.” As the late Harvard evolutionary biologist Ernst Mayr explains: “The real core of Darwinism … is the theory of natural selection. This theory is so important for the Darwinian because it permits the explanation of adaptation, the ‘design’ of the natural theologian, by natural means.”2 Or as another prominent evolutionary biologist, Francisco Ayala, has put it succinctly, natural selection explains “design without a designer.”3
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