My editorial policy for these excerpts is explained at the bottom of this post.

Motivated Belief (part 3)

Jesus had a comparatively short public ministry, but it had enormous local impact, drawing crowds who were anxious to hear his words and who often sought the healing ministry that he exercised. Then, on a last visit to Jerusalem, it all seemed to fall apart. The authorities, civil (Roman) and religious (Jewish) acting together, moved in to avoid trouble. Jesus was arrested and hastily executed, suffering the painful and shameful fate of crucifixion, the kind of death reserved for slaves and rebels and seen by pious Jews as being a sign of God’s rejection (“any one hung on a tree is under God’s curse,” Deuteronomy 21:23). Except for a few staunch women, his followers ran away, overcome by despair and disappointment. From the place of execution there came the cry “My God, my God, why have you forsaken me?” (Matthew 27:46; Mark 15:34).

Giotto di Bondone, The Arrest of Christ (Kiss of Judas)
(ca. 1304-06), fresco, Cappella Scrovegni, Padua

On the face of it, Jesus’s death seems a moment of pathetic failure, the final disillusionment of the followers of a rejected man whose grand pretensions had suddenly and definitively been found wanting. If that really was the end of the story of Jesus, I believe that most of us would never have heard of him. At best he would have seemed to be no better than other first-century messianic pretenders whose causes also finally failed. So the first remarkable thing about Jesus is that he is known to all of us. We need to look closer into the New Testament to find out why, against all reasonable expectation, his story continued beyond his death.

Amid the variety of its component writings, there are certain common themes that recur in the New Testament. Three of the most important themes are:

(1) All the [biblical] writers believe that the story of Jesus continued because God raised him from the dead on the third day after his crucifixion. We shall have to pay further attention to this extraordinary claim, but the existence of the New Testament, and the character of its contents, are unintelligible without the recognition that this is what its writers are affirming.

(2) In wrestling with what they believe to be their experience of the risen Christ, the writers are driven, in their different ways, to speak of Jesus in a quite extraordinary manner. They know that he was a man living in Palestine in their own times, yet in the accounts they give they often seem driven to employ not only obvious human categories, but also to use language that is only appropriate to deity. The Pauline epistles are probably of the earliest Christian writings known to us, certainly antedating the gospels. Already Jesus of Nazareth is being referred to in remarkable terms. Paul begins almost all his letters with some such phrase as “Grace to you and peace from God our Father and the Lord Jesus Christ” (Romans 1:7; 1 Corinthians 1:3; and so on). Not only is Jesus being bracketed with God in a manner that would, for example, have been inappropriate for a pious Jew to use in relation to Moses, the servant of God, but he is also accorded the title “Lord.” While this word (kyrios) had a widespread secular usage amounting to no more than politeness of address, its Hebrew counterpart, adonai, also had a special Jewish religious usage as an acceptable circumlocution in place of the unutterable divine name, YHWH, a particular significance which the religious context of Paul’s greeting could scarcely fail to invoke. The gospel of John portrays Jesus as claiming unity with God (John 10:30, words uttered in a situation where the hostile crowd are shown as having no difficulty in detecting what they see as the blasphemous implication), and it assigns to Jesus the use of images (the bread of life, the true vine, and so on) which carry implications of more than human status. The Writer to the Hebrews proclaims that “in these last days [God] has spoken to us by a Son, whom he appointed the heir of all things and through whom he also created the worlds” (Hebrews 1:2). Examples could easily be multiplied.

It is clear that when it comes to Jesus, the New Testament writers cannot rest content with the standard Jewish repertoire for speaking of people with special gifts from God—the categories of prophet, teacher, healer—but, against all their instincts as monotheistic Jews, they are driven to use divine-sounding language about him. Remember that they are referring to a near contemporary, and not to some shadowy figure of a legendary past. The New Testament very seldom out and out calls Jesus God (the confession of Thomas in John 20:28 is perhaps the clearest example), but its pages manifest a continual tension between the use of human and divine manners of speaking about him. The problem thus posed is unresolved in the New Testament itself, but succeeding Christian generations had to address it and eventually the Church was led to the distinctive and extraordinary doctrinal concept of the incarnation, the affirmation of the presence of deity in the life of this first-century Jew, who truly was the Son of God.

(3) Coupled with this recourse to divine language, and fuelling its fire, was a firm conviction among those first-generation Christians that the risen Christ had brought into their lives a new and transforming experience of saving power. Paul wrote to the Corinthians, “if anyone is in Christ, there is a new creation: everything old has passed away; see everything has become new!” (2 Corinthians 5:17). I believe that an adequate Christology (a true understanding of the nature of Jesus) must satisfy the criterion of affording an adequate soteriology (a true understanding of the power of Christ in human lives, to which the Church has continued to give its testimony down through the centuries). The doctrine of the incarnation implies that in the Word made flesh a unique bridge was established between the created life of humanity and the uncreated life of God, and in this meeting of divine power and human nature there lies a way of understanding the fulfillment of the soteriological criterion.

​
Giotto di Bondone, Resurrection (Do not Touch Me) (ca. 1304-06), fresco, Cappella Scrovegni, Padua

These three lines of testimony need to be presented for consideration by anyone seeking to understand the significance that Jesus of Nazareth holds for Christian belief. In the context of science the discussion of the persuasiveness of that belief cannot be conducted satisfactorily without a detailed engagement with these claims. The task is indispensable to honest enquiry and it is made all the more important today by the fact that many people seem to have so little knowledge of what the New Testament actually says.

The pivot on which the claim of a unique and transcendent significance for Jesus must turn is clearly the resurrection. If in fact he was raised from the dead to a new and unending life of glory, then it is indeed credible that he has an altogether unique status and role in salvation history. If, sadly, his life ended in failure and his body was left to molder in the grave, then he seems at best little different from many other prophetic figures who have suffered martyrdom for holding fast to the integrity of their beliefs. The quest for motivated Christian faith has to begin by focusing on the question of the resurrection. I believe that it would be a serious apologetic mistake if Christian theology thought that operating in the context of science should somehow discourage it from laying proper emphasis on the essential centrality of Christ’s resurrection, however counterintuitive that belief may seem in the light of mundane expectation.

As a preliminary one must first face the general issue of miracle. It was as clear in the first century as it is today, that it is wholly contrary to any reasonable natural expectation that a man should be resurrected within history. While there were parties in first-century Judaism which expected a general resurrection at the end of history [for example, the Pharisees], none expected the resurrection of a specific person to take place within history, even if there was some hope that a prophetic figure, such as Elijah, might have been stored up in heaven in order to be returned for a further spell of earthly life at some critical juncture in Jewish history. It is important here to recognize the distinction between resuscitation and resurrection. The former applies to someone like Lazarus, who is portrayed in John’s gospel as being called out of the tomb after an apparent death (John 11), but who was undoubtedly expected by all to die again in due course. Resuscitation is only a temporary reprieve from mortality. Resurrection, on the other hand, implies a transition from this mortal life to a new form of glorified life, lived without end in the presence of God. Resurrection is a permanent victory over mortality. The possibility of resurrection lies wholly outside the context of scientific explanation. If the resurrection of Jesus happened, it could only have been through a special exercise of divine power. In short, resurrection is, in the strict sense of the word, a miracle.

The real problem of belief in miracle is properly a theological issue, not a scientific one, since claims of unique historical occurrences lie outside science’s competence to adjudicate. All it can do is reinforce the commonsense recognition that something like a resurrection does not usually happen. The real challenge to belief in miracle lies elsewhere. It is theologically inconceivable that God should act capriciously as a kind of celestial conjurer, doing a turn today that God did not think of doing yesterday and won’t be bothered to do tomorrow. The theological problem of miracle is that of discerning divine consistency in the face of a claim of radically novel action. How that consistency is understood depends upon a proper understanding of what is involved in speaking of God in personal terms. I have already said that divine action is not to be assimilated to a kind of impersonal and unchanging process, similar to that which characterizes the law of gravity. If personal language is to mean anything when used about God, it must imply a divine freedom to respond in particular and different ways to particular and different situations, including even the rational possibility of unprecedented action in unprecedented circumstances.

Once again we encounter the unavoidable necessity of hermeneutic circularity. Of course, persons are not normally resurrected in history, but if there is something truly unique about Jesus (the Son of God), then his story could conceivably have included unique events. Equally, if he was resurrected, this was surely a sign that he indeed did have an altogether unique status. However, if he was just another prophet, then the story of his resurrection is likely to be no more than a touching legend. Both possibilities have to be considered. To believe in the resurrection rightly requires significant motivating evidence, a question to which we shall turn shortly, but its possibility should not be ruled out absolutely from the beginning, before even considering what evidence there might be for this counterintuitive belief. Moreover, it is important to note that the Christian understanding of Christ’s resurrection is that it occurred within history as the unique seed event from which a resurrected destiny for all people will come about beyond history (“for as all die in Adam, so all will be made alive in Christ”; 1 Corinthians 15:22). In this sense, what Christian theology sees as unique about the resurrection is its timing, rather than its occurrence. Further consideration will be given to this point in the succeeding chapter.

​Giotto di Bondone, The Last Judgment (detail, ca. 1304-06),
fresco, Cappella Scrovegni, Padua

[The succeeding chapter, which will not be part of this series, deals with eschatology. Polkinghorne’s reference in the penultimate sentence to the unique timing of the resurrection can be fleshed out by quoting from the chapter on eschatology: “The eschatological destinies of human beings and of the whole universe lie together in the world of God’s new creation. <SNIP> In Christian thinking, the seed event from which this new creation has already begun to grow is the resurrection of Christ. His tomb was empty because the matter of his corpse had been transmuted into the ‘matter’ of the new creation, to become his risen and glorified body in which he appeared to the first witnesses.” In other words, the resurrected Jesus is “the first fruits of them that sleep,” in the glorious words of 1 Corinthians 15:20.]

Looking Ahead

In about two weeks, we will see how Polkinghorne brings his search for “motivated belief” to bear on the biblical narratives about the Resurrection.

References and Credits

Excerpts from John Polkinghorne, Theology in the Context of Science (2009), copyright Yale University Press, are reproduced by permission of Yale University Press. We gratefully acknowledge their cooperation in bringing this material to our readers.

Editorial Policy

Most of the editing for these excerpts involves breaking longer paragraphs into multiple parts, altering the spelling and punctuation from British to American, removing the odd sentence or two—which I indicate by putting [SNIP] at the appropriate point(s)—and sometimes inserting annotations where warranted [also enclosed in square brackets] to provide background information. Polkinghorne uses footnotes a bit sparingly, and I usually find another way to include that information if it’s important for our readers.

So, I’ve decided to try a slightly different approach for the next while—one that has these sorts of folks in mind. From time to time, you can still expect those more in-depth, technical articles, or perhaps a discussion of some new research that makes the popular press, or even an analysis of some new argument from the IDM or RTB. These will be breaks from the new routine, however. For the most part, we’re going to stick to the basics, much like you would if you took an introductory evolution course at a university. Don’t worry, though: this course doesn’t have any prerequisites! All that’s needed is a willingness to learn.

What you can expect

The goal of this course is straightforward: to provide evangelical Christians with a step-by-step introduction to the science of evolutionary biology.  This will provide benefits beyond just the joy of learning more about God’s wonderful creation. An understanding of the basic science of evolution is of great benefit for reflecting on its theological implications, since this reflection can then be done from a scientifically-informed perspective. From time to time we might comment briefly on some issues of theological interest (and suggest resources for those looking to explore those issues further), but for the most part, we’re going to focus on the science. For folks interested in the interaction between science and Christianity, I heartily recommend Ted Davis’ recent series as a fabulous introduction to the topic.

You can also expect a slow, patient pace. Since this course is intended for folks with little or no background in biology, we’re going to take our time to make sure no one gets left behind. This might be frustrating to folks who already know a fair bit about evolution. Hopefully even more knowledgeable readers will learn some new and interesting details along the way—but the goal will primarily be to help folks who are less well versed in evolution increase their understanding.

You can also expect a survey of many different areas that have some bearing on evolution. We’ll examine geology, paleontology, biogeography, genetics, and a host of other topics in order to provide a “big picture” overview. This broad-brush approach means that any given individual post will not necessarily be “convincing” to folks who have doubts about evolution. Think about assembling a large jigsaw puzzle: placing any individual piece, on its own, doesn’t convincingly demonstrate what the overall picture will show. This course will be like that. Each topic we cover will put a few pieces in place here and there, slowly building towards the final overall picture.

Since evolution is an active science, this process will also highlight where there are “missing pieces” that are still being sought by scientists. All of this is well and good, since the purpose of this course is not so much to convince anyone of the validity of evolutionary theory, but rather to inform readers about the nature and scope of evolution as a scientific theory in the present day. My goal is to provide readers with a basic understanding of what evolution is and how it works. Given that as the primary goal, if one finds the scope of the evidence ultimately convincing (or not) is somewhat beside the point. The intent here is to provide readers with information they can use to make their own, informed decision.

How you can help

First and foremost, you can help by spreading the word about this series to folks you think would be interested in learning more about evolution in a non-threatening environment. Secondly, you can help me by asking questions in the comments. One of the challenges of being a specialist is having the ability to put oneself in the shoes of someone just starting out. What might seem obvious to me may not seem obvious to you, and I hope you’ll feel that no question is too basic or too simplistic. If you’re wondering about something, it’s almost guaranteed that other folks are, too! So, please don’t be shy. I’ll do my best to answer questions in the comments, though I hope that some of our more skilled commenters will (respectfully!) help out here, as well. Finally, you can help by letting me know what broader areas of evolution you find confusing. I have my own ideas about what areas of evolution are commonly misunderstood, but I’d love to hear from readers about what areas they find difficult to understand. I’ll use this input to shape the topics I will cover as we go forward.

Getting started

In the next post in this course, we’ll dive into the course content by introducing two key areas: how scientific theories work in general, and how evolution in particular works as the current organizing theory of modern biology. 

"Anyone approaching the Resurrection accounts in the belief that he knows what rising from the dead means will inevitably misunderstand those accounts and will then dismiss them as meaningless" (p. 243).

In fact, if Jesus' Resurrection were "merely" coming back to life in any way that we might comprehend, then it would be of little significance.

"Now it must be acknowledged that if in Jesus' Resurrection we were dealing simply with the miracle of a resuscitated corpse, it would ultimately be of no concern to us" (p. 243).

So what then does Resurrection mean? For Benedict it represents a new dimension of reality breaking through into human experience. It is not a violation of the old; it is the manifestation of something new.

"Jesus had not returned to a normal human life in this world like Lazarus and the others whom Jesus raised from the dead. He has entered upon a different life, a new life -- he has entered the vast breadth of God himself..." (p. 244).

Because it is something entirely new, it cannot represent a violation of natural law as understood by science.

"Naturally there can be no contradiction of clear scientific data. The Resurrection accounts certainly speak of something outside our world of experience. They speak of something new, something unprecedented -- a new dimension of reality that is revealed. What already exists is not called into question. Rather we are told that there is a further dimension, beyond what was previously known. Does that contradict science? Can there really only ever be what there has always been? Can there not be something unexpected, something unimaginable, something new? If there really is a God, is he not able to create a new dimension of human existence, a new dimension of reality altogether?" (p. 246-7)

Thus, in this view, Resurrection (as with all true miracles) is not contrary to science, but an indicator that science does not (yet?) describe the full expanse of reality. Indeed, some may argue that science itself contains similar "indicators." The 11 (or so) dimensional universe required by some versions of string theory, the multiverse theory of the universe where ours is but one of an infinite array of universes with variable physical laws, quantum entanglements, "spooky" action at a distance, the mysterious emergence of consciousness from inorganic matter -- all push the limits of human reason and imagination, suggesting to some that reality may be far more complex than the human mind can grasp.

For a moment, let us entertain the possibility that Resurrection is as Benedict interprets it: not a violation of natural law but an indicator of something beyond our scientific understanding of the universe. This has interesting implications for understanding how believers and skeptics approach the issue. If Resurrection does not violate science, then science does not necessarily constitute an impediment to accepting the reality of Resurrection. If the difference between the skeptic and believer is not science, then is it just a matter of imagination? The believer imagines greater possibilities for the universe than the non-believer. While this is possible, it seems questionable. To my knowledge, no research has found differences in imaginative abilities between religious and non-religious people. Moreover, contrarian examples easily come to mind: Isaac Asimov was an atheist but hardly lacking in imagination when it came to science fiction. I tend to think that both believers and non-believers can imagine (with varying degrees of effort, I'm sure) the new possibilities implied by Resurrection.

Thus, if it is neither imagination nor science that prompts skepticism about Resurrection, then what is left? I suggest that it comes down to a question of authority: At what point does one allow imaginative possibilities to have authority over how one lives? To the believer, Resurrection has an authority that science fiction does not. Resurrection is not thought-provoking entertainment. It requires far more than just imagining greater possibilities for the universe. It requires a change of life, here and now. Unlike the microscopic hidden dimensions of string theory, the new dimension implied by Resurrection has "broken though" into everyday reality and demands a response -- even if that response is to actively ignore it.

Now, what convinces the believer that Resurrection merits such authority when other imaginative possibilities such as extraterrestrial life or time-travel do not? The answer here appears to be historical commitment. There's no record of people committing themselves to the point of martyrdom to other imaginative possibilities as they have to Resurrection. The earliest example of such commitment being found, of course, in the dramatic post-crucifixion turn-around of the Apostles. Such an astounding change of heart, followed by an unwavering commitment capable of altering human history demands a categorically unique explanation: Resurrection.

The believer's argument, however, remains unconvincing to the skeptic. However impressive they might be, a change of heart and steadfast commitment do not necessarily add up to a new dimension of reality. Extraordinary claims require extraordinary evidence. Fair enough. So a key question regarding the interpretation of Resurrection is this: Is the post-crucifixion history of Christianity extraordinary? Does it compel the dispassionate observer to concede that a categorically unique event could plausibly be its best explanation?

It ought to be upon questions such as those above that skeptics and believers respectfully engage one another, rather than the simplistic and often acrimonious sloganeering that has increasingly become the norm.

Antibody fine-tuning

At this moment, millions of B cells are patrolling my spleen and lymph nodes, each sporting a different antibody on its surface. If a foreign molecule from the cold virus happens to stick to an antibody on a particular B cell, the cell can get “activated.”

Pathogens are like cockroaches. If you see one roach, you can bet there are many more lurking under cupboards and between walls. Just as one shoe won’t kill them all, one B cell can’t make enough antibodies to deal with an infection. Activation causes the B cell to reproduce, creating more and more B cells that can produce the same kind of antibody.

As is typical during cell division, most of the DNA in dividing B cells is copied with extremely high accuracy. But in the gene segments coding for the variable region of the antibody, mutations accumulate about a million times more often than normal. Why would this be? Isn’t the point of B cell replication to make more identical antibodies?

Almost. It turns out that these frequent random mutations contribute to optimize the antibody. A shopping story helps to illustrate. I was recently at the mall and found a fabulous pair of shoes on sale. Sadly they were out of my size, but it was such a good sale that I decided to buy the half-size down, figuring the shoes might stretch out a little and grow more comfortable with time. Bad idea! That great bargain turned out to be pretty expensive when I got blisters and never wore the shoes again. Clearly this was not an optimized choice.

Just because you can get your foot into a shoe does not mean it fits. Likewise, just because an antibody binds to an antigen does not mean the two are perfectly complementary. Descendents of the activated B cell have a mechanism to induce mutations so each one can make a slightly different version of the antibody. If one of the resulting B cells makes a better-fitting antibody than its kin, it will have a selective advantage and proliferate. The other cells will not become activated as often and will end up dying by apoptosis, a kind of cellular suicide. This mechanism of mutation and selection, called affinity maturation, produces a highly specific, strong interaction between the antigen and the antibody.

Antibody production and evolution both involve mutation and selection

I believe God is sovereign over all of creation, but I don’t imagine he is presently curing my cold by directly controlling the specific gene rearrangements and optimizing mutations in each of the millions of B cells in my body. Could he do so? Of course! But if that were the case, why bother making billions of antibodies in the first place? The evidence suggests that God has chosen to work through a random process, one which involves the routine creation and destruction of millions of cells that never get used. This is the ordinary means by which God maintains our health. The miracles of healing recorded in the Bible are miraculous precisely because they don’t occur by this normal, natural process.

In my last post, I stated that the generation of antibody diversity is an example in which God uses a “blind” system to sustain and preserve life. I then suggested a link to evolution by asking, “If God uses natural mechanisms that work over short time scales (less than a week) to evolve life-giving solutions to disease, could he also use a similarly elegant approach to create life over long periods of time?”

Some may argue that a small-scale process like antibody production isn’t comparable to the processes of mutation and natural selection that are supposed to have caused macro-evolution. Intelligent Design proponent Michael Behe, for example, accepts that all creatures (including humans) have a common ancestor, but he believes random mutations are not powerful enough to have brought about the diversity of life we see today. He argues that there is an “edge” of evolution: mutation can bring about drug resistance and other small-scale adaptations, but beyond a certain point it can’t really produce anything new.

Clearly, antibody production creates something new: the random recombining of whole gene segments generates highly specific, never-before-seen protein functionality within just a few days. The body can respond to any foreign entity, simply by sorting through billions of ready-made possibilities. Furthermore, a pretty-good solution can be made even better by generating many variations on a theme and sorting through these for the optimal antibody.

Evolution works by the same kinds of mechanisms, except the mutations occur in germ cells (which give rise to egg and sperm) rather than in B cells, and the sorting (selection) process occurs at the population level rather than the cellular level.

Though often neutral or destructive, mutations sometimes create new functionality

Most people are familiar with point mutations, in which a single DNA “letter,” or base, gets changed. However, mutations come in several other varieties. Short sequences of DNA can be inserted or deleted at random. Chunks of DNA can get cut out and inserted in the opposite direction. Individual genes or even whole chromosomes can get lost or duplicated. In rare cases, the entire genome can get duplicated!

The effect of a mutation principally depends on where it occurs, not on the size of the DNA segment affected. A large deletion occurring within a long stretch between two genes may do nothing at all. On the other hand, a single point mutation within a critical gene may cause a devastating disease. There is also a third possibility though: new functionality may emerge as a result of a mutation.

Let’s consider the protein hemoglobin, for example, which binds oxygen and transports it throughout the body in the blood. Hemoglobin is made from two pairs each of two amino acid chains, called α and β (blue and red in the figure at right). The corresponding genes that code for α and β have similar sequences to each other, and are believed to have arisen when an ancestral globin gene (still present in marine worms, insects, and some fish) duplicated and slowly changed over time. While the ancestral form can bind oxygen just fine, the four chains of hemoglobin cooperate to do so even better.

Both the α and β genes have undergone further duplications followed by smaller mutations. As expected, many of the resulting genes have become irreparably damaged by mutations, but they continue to exist in the genome as inert DNA “fossils.” Others, however, remain active and now perform specialized functions. For instance, one set of β genes binds more tightly to oxygen than the others; it becomes active only during development to ensure that the fetus gets enough oxygen from the mother’s bloodstream. A few months after birth, fetal hemoglobin turns off and the adult form turns on.

To summarize, mutations come in many forms (e.g. rearrangements, insertions, deletions, duplications) and can lead to good, bad, or neutral effects within an individual. B cells depend on random mutations to produce novel antibodies. A few are productive, but the vast majority of B cells die unused. Yet the entire process works for our good! In the same way, mutations in germ cells can lead to no effect, disease, or new and better solutions, as we saw in the hemoglobin example. These are the ordinary (but masterful!) means by which God creates and sustains life.

Editor's Note: For more on the evolution of the immune system, read Randy's Isaac's post "Complex Specified Information Without an Intelligent Source" at the ASA website.

Tonight and tomorrow, Christians around the world stop to remember and celebrate the birth of Jesus in Bethlehem just over two thousand years ago. The familiar narrative of Joseph leading Mary to the stable to give birth to the Messiah, of the angels telling the shepherds in the fields of the great event that was happening nearby, and of the three men from the east who came to pay homage to the new King of Israel is re-told or acted out in countless churches, schools and homes. And from countless pulpits, the message goes out that those events are not just a quaint story and an excuse to give gifts, but the central mystery of our faith—that God himself became one of us in order to redeem us and the cosmos from our bondage to sin and death. That mystery—that the Creator God is also the Redeemer Christ—has been to focus of our worship since the first days of the church, and is the subject of the 7th-century Latin hymn Conditor alme siderum, presented here in a new setting from Alex Mejias and High Street Hymns.

While this recording includes only verses one and three from the original text (given in full below), it adds a refrain that catches the spirit of the whole hymn and emphasizes the longing we still feel even in our Christmas joy—the “already, but not yet” state in which we find ourselves today, living between that first Advent and the second Advent yet to be: “Come, O come to us!” For while we know that God has come to us in Jesus—that his death and resurrection have redeemed us and the universe—we are still waiting for that final consummation, depending on the Spirit to be working out our salvation even now. Until the time when, as the hymn says, “all hearts must bow,” the entire BioLogos community invites you to join us in the blessed work of declaring, celebrating, and following the Christ who is both Creator and Savior.

Creator of the Stars at Night

Alex Mejias is the founder and director of High Street Hymns, a non-profit music ministry that exists to spread the Gospel and worship the Triune God in spirit and truth through hymns, psalms and spiritual songs. Alex grew up in New Jersey and outside Washington, DC, receiving a BA in Religious Studies from the University of Virginia and a J.D. from the University of Virginia School of Law. For the past 15 years he has been leading worship for churches and ministries, writing and recording both new and old hymns, and touring the east coast as a singer-songwriter. Alex is also committed to the power of the creative arts to advance the Gospel and promote justice and healing in the name of Christ, serving, supporting, and collaborating with several other non-profit ministries.

When he opened the sixth seal, I looked, and behold, there was a great earthquake, and the sun became black as sackcloth, the full moon became like blood, and the stars of the sky fell to the earth as the fig tree sheds its winter fruit when shaken by a gale. The sky vanished like a scroll that is being rolled up, and every mountain and island was removed from its place. (Revelation 6:12–14)

The non-concordist view of science and Scripture argues that Biblical texts about creation were never intended to concord with modern scientific theories. Thus, Genesis 1 is not cryptically describing the Big Bang or instant fiat, a young earth or old earth, special creation or evolutionary creation. It is not “literal” language describing the physics of the universe; it is “literary” genre describing God’s sovereignty over creation and most likely his covenantal relationship with his people.

But the argument against literalism of language of the creation of the heavens and the earth is also applicable to the language of the destruction of the heavens and the earth, or what the Bible calls, “the last days,” “the end of the age,” “the end of days,” or “the Day of the Lord.” Christians often refer to this as “the end times,” but the technical theological term is eschatology, which means “the study of end things.”

Regarding the end times, the modern Evangelical popular imagination has been deeply influenced and at times dominated by a theological construct that is best reflected in the 1970s bestselling The Late Great Planet Earth by Hal Lindsey and the newer bestselling fictional phenomenon Left Behind by Tim LaHaye and Jerry Jenkins.

This view believes that the Bible foretells an as-yet future scenario on the earth of a rapture of Christians, followed by the rise of an “Anti-Christ,” a world dictator who initiates a Great Tribulation on the earth, requires a “Mark of the Beast,” and assembles global forces for a battle of Armageddon against Israel, resulting in the Second Coming of Christ who replaces the universe with a new heavens and earth to rule forever. The technical theological term for this view is futurism, the belief that prophecies about the end times are yet to be fulfilled in the future.¹

In this article, I will address the hermeneutic or interpretive approach used by this futurist perspective and apply it to the particular aspect of creation language, or in this case, decreation language -- the collapsing universe and the destruction of the heavens and the earth.

In short, the language of cosmic catastrophe often interpreted literally as referring to the end of the space-time universe is actually used by Biblical authors to figuratively express the cosmic significance of the covenantal relationship between God and humanity.

The tendency of modern literalism is to interpret descriptions of signs in the heavens and earth as being quite literal events of the heavens and earth shaking, stars falling from the sky, the moon turning blood red, and the sky rolling up like a scroll. The problem with this hermeneutic is that it assumes the priority of modernity over the ancient world. Rather than seeking to understand the origins of symbols and images used by the writers within their ancient context, this literalism often suggests the writer was seeing events that would occur in our modern day but did not understand them, so he used his ancient “primitive” language to describe it.

So for instance when the apostle John saw modern day tools of war in his revelation, such as battle helicopters, he did not know what they were so he described them in ancient terms that he did understand such as locusts with the sting of scorpions, breastplates of iron, a crown of gold and human faces, whose chopper blades made the “noise of many chariots with horses rushing into battle” (Rev 9:3-9).

I was taught this modernist interpretation and lived by it for many years. When I read about Jesus explaining the “end of the age” I would assume he meant the “end of the space-time universe” because that’s the kind of language I, a post-Enlightened modern scientific mind, would use to describe such an event. When he spoke of the moon turning blood red and the sun being darkened, I assumed such events were easy miracles for God, so if you considered them figurative, you were falling down the slippery slope of neo-orthodoxy. When Jesus said stars would fall from the sky, you had better bet stars would literally fall from the sky (a primitive description of meteors²) or else you’re a liberal who doesn’t believe in the literal accuracy of the Bible.

But all that changed when I sought to understand the prophetic discourse on its own terms within its ancient cultural context instead of from my own cultural bias. I now propose that the ancient writers did understand what they were seeing, but were using symbols and images they were culturally steeped in, symbols and images with a history of usage from the Old Testament, their cultural context – not mine.

In this essay, I will argue that the decreation language of a collapsing universe with falling stars and signs in the heavens was actually symbolic discourse about world-changing events and powers related to the end of the old covenant and the coming of the new covenant as God’s “new world order.” In this interpretation, predictions of the collapsing universe were figuratively fulfilled in the historic past of the first century. The technical theological term for this view is preterism, the belief that most or all prophecies about the end times have been fulfilled in the past.³

Notes

1. The Left Behind series is a particular version of futurism called Dispensational Premillennialism. For a more in depth presentation of these varieties of eschatology see Bock, Darrell L. ed., Three Views on the Millennium and Beyond. Grand Rapids, MI: Zondervan, 1999.
2. Interestingly, as soon as the interpreter thinks falling stars are meteors, he has just engaged in figurative speculation, which is not literal.
3. Some examples of orthodox scholars who hold to this view are Sproul, R.C. The Last Days According to Jesus. Grand Rapids, MI: Baker, 1998; and Gentry, Kenneth L. Jr. Navigating the Book of Revelation. Fountain Inn: SC, Goodbirth Ministries, 2009.

Introduction

One of the reasons that some of us are hesitant to accept evolutionary creation is that it seems to make God responsible for the suffering and death of innumerable creatures over millions of years—before humans ever existed or sinned against their creator. Since we believe in and worship a God who is loving, benevolent, and all-powerful, it sounds quite implausible that our God would have created a world like that; therefore, any scientific evidence for evolution must be incorrect.

Other people look at the scientific evidence for evolution and find a compelling case that it has taken place during our earth's history. On this basis they may conclude that if evolution is true, then the belief in an all-powerful, perfectly good God must be false!

The trouble with both of these views is that they tend to invoke a completely abstract, philosophical god, not the living God of the Bible—the God who became a human being, experienced unimaginable suffering, and died in a grotesque and humiliating public display. The death of Jesus completely defied the expectations (and common sense) of his followers, as well as the expectations of any “rational” understanding of the way the Creator of the universe should act in the world. On the cross, in the person of Jesus, God took upon himself far more suffering than any creature has ever experienced.

If God himself is willing to die, particularly in such a gruesome way, then perhaps we should at least consider the possibility of God allowing the death of other creatures, too. But would this really be compatible with what we know of God through Scripture? In this essay, we will explore this quandary through a “theology of the cross”, a concept articulated by pastor George Murphy in his book Cosmos in the Light of the Cross.¹

Theology of the cross

Before we jump into the theological problems associated with evolution, let’s take a look at how we understand Christian theology itself. For the reformer Martin Luther, any theology (or science) that tries to reach knowledge of God apart from the cross is bad theology.² Instead, Luther pointed to a theologia crucis, in which the true God is seen first and foremost “through suffering and the cross”. To make his point even clearer, Luther insisted that “the CROSS alone is our theology”.³ It is the lens through which we view everything.

Of course Martin Luther, having lived in the 16th century, was not aware of the vast history of life on our planet (or any other aspect of modern science, for that matter), but George Murphy draws from Luther’s teachings the foundation that all human knowledge begins with the Word made flesh and crucified.⁴ With the cross of Christ as the ultimate framework through which we view reality, we are bound to view the processes of nature quite differently. As Murphy explains it,

A theology of the cross is an explication of belief in a God who becomes a participant in the history of the universe and thereby shares in the suffering, loss, and death that are part of worldly experience.⁵

God does not sit idly by and watch unaffected as his creatures suffer, but neither does he swoop in and make everything completely effortless and easy. Instead he chose another way, the crucifixion of Jesus—certainly not the approach that we would have preferred! The apostle Peter went so far as to try to talk Jesus out of it, but he was met with a stern rebuke (Matthew 16:21-23).

Why is evolution so disconcerting to Christians?

The problem of suffering throughout all of human history is troubling enough for us to reconcile with a loving, personal God. But in addition to that, the discovery of vast numbers of fossils reveals that death has taken place on a far greater scale than we had ever imagined. Both the wide variety of extinct creatures and their sheer numbers is quite staggering, and it raises questions about our Creator:

The picture of a God who is immune from suffering and death but who forces organisms through millions of generations and extinction is disturbing to those who believe in a God of love.⁷

The mass extinction of life on earth was already well established by the early 19th century—decades before Darwin’s research—and extinction can be empirically verified independent of any theory of evolution.⁸ The fact that the earth’s crust is a veritable graveyard of long-lost creatures is deeply troubling, and as late as the 1790’s, distinguished intellectuals such as Thomas Jefferson denied the very possibility of extinction.⁹

But in addition to the reality of species extinction, the theory of evolution by natural selection proposes that new species also arise in an environment containing widespread pain and death. Both the creatures that are now living and those that are gone are tainted by an “acrid smell of death”.¹⁰ It makes us wonder, if our Creator is not the God of the dead, but of the living (Mk. 12:27), where is God’s presence in the evolutionary picture?

In all honesty, creation through evolution is not what we would expect from God, but Scripture is full of examples in which God acts in unexpected ways. After all, God’s choosing to undergo an agonizing death on a cross is not what we would expect from the all-powerful Creator of the universe, either. In both cases, new life comes about through pain, suffering, and death. As George Murphy puts it,

A priori ideas about God have to be overcome, and God's character has to be learned from God's self-revelation.¹¹

God’s fullest self-expression is in Jesus Christ himself, one who is intimately familiar with and personally endured creaturely pain and death. The theology of the cross reveals that God's self-revelation takes place in situations of suffering, loss, and apparent hopelessness, much like situations that occur through natural selection.¹²

The crucifixion is disconcerting too

Not only is creation through evolution an unexpected and unsettling process, but so is the crucifixion of Jesus! Killing someone by hanging them on a cross is an unbearably painful, prolonged, humiliating form of death. It was such a horrific type of public execution that it wasn't until after the Roman Empire stopped the practice of crucifixion—and people no longer witnessed it personally—did the cross become a visual object of devotion.¹³ Our culture is sufficiently removed from crucifixion that we are desensitized to its original significance, but to connect it to our current context, imagine the reaction you would get by wearing jewelry designed to look like an electric chair.¹⁴

Once we are more attuned to the brutality of crucifixion, it seems all the more striking that the cross is the sign of God’s work, what George Murphy calls “the trademark of God”.¹⁵ The suffering and death of Jesus is featured prominently in the Gospels, but the crucifixion-resurrection pattern is strongly resonant within the Old Testament, too. Israel suffered and toiled as slaves in Egypt for centuries before they were rescued in the Exodus, bringing life to a people who were spiritually dead. Centuries later, the nation of Israel would experience death again when the Babylonians destroyed the Davidic monarchy, burned their Temple, killed their people, and sent many into exile.¹⁶ Neither Israel (God’s chosen people) nor Jesus (God’s own son) were spared from death and suffering; rather, suffering seems to have been the way in which God re-forms and renews humanity to fully bear His own image.

Redemption extends to all of creation

Fortunately, God’s story does not end with death. God gives new life after his creatures have been subjected to terrible circumstances. Redemption was promised to Israel itself—Ezekiel’s vision of the valley of dry bones describes how God would renew His chosen people (Ezek 37:1-14). Later, the astonishing resurrection of Jesus made salvation possible not only for Jews, but for all people in Christ (Gal 3:26-29). Ultimately, the New Testament makes it clear that God’s renewal will encompass the entire Creation:

For God was pleased to have all his fullness dwell in him, and through him to reconcile to himself all things, whether things on earth or things in heaven, by making peace through his blood, shed on the cross. (Colossians 1:19-20)

With all wisdom and understanding, he made known to us the mystery of his will according to his good pleasure, which he purposed in Christ, to be put into effect when the times reach their fulfillment—to bring unity to all things in heaven and on earth under Christ. (Ephesians 1:8-10)

Christians are accustomed to thinking of the death of Christ in regard to humans, but our culture rarely acknowledges God plan for the redemption of His entire creation. This is partly attributable to the fact that discussions of creation and origins are often separated from the topic of salvation.¹⁷ In doing so we tend to marginalize Jesus as we argue about Genesis. Rather than fall into this trap, if we view nature through a theology of the cross, we will see Christ as both the alpha and the omega point in discussions of life’s history and life’s future. With this perspective, we are more apt to sense our solidarity with the rest of creation as we wait in eager anticipation of a glorious future:

The creation waits in eager expectation for the children of God to be revealed. For the creation was subjected to frustration, not by its own choice, but by the will of the one who subjected it, in hope that the creation itself will be liberated from its bondage to decay and brought into the freedom and glory of the children of God. (Romans 8:19-21)

Conclusion

As part of the Church’s conversation about the problem of natural evil, this essay is meant to be a brief introduction to a “theology of the cross”. One can explore this concept in greater detail in Murphy’s book The Cosmos in the Light of the Cross. While there is a lot more to be said, let me conclude with the following observation: though evolution may not be compatible with some interpretations of Christianity, evolutionary creation is certainly compatible with the crucified Christ and the theology of the cross. In the person of Jesus, God suffers with the world and ultimately redeems it. As George Murphy puts in, “The world's pains are God's stigmata.”¹⁸

Explore this Topic Further

• Miller, Keith. “And God saw that it was good”: Death and Pain in the Created Order. BioLogos series
• Murphy, George L. The Cosmos in the Light of the Cross. Harrisburg, PA: Trinity Press, 2003.
• Murphy, George L. “Cross, Evolution, and Theodicy: Telling It Like It Is”. In The Evolution of Evil. Edited by G. Bennett, M.J. Hewlett, T. Peters, and R.J. Russell. Göttingen: Vandenhoeck & Ruprecht, 2008.
• Southgate, Christopher. The Groaning of Creation: God, Evolution, and the Problem of Evil. Louisville, KY: Westminister John Knox Press, 2008.

Notes

1. Murphy, George L. The Cosmos in the Light of the Cross. Harrisburg, PA: Trinity Press, 2003.
2. Murphy, p34
3. “CRUX Sola Est Nostra Theologia,” in D. Martin Luthers Werke, Kritische Gesammtausgabe (Weimar: Hermann Boehlau, 1892), 5:172. The captitalization is in the original. Cited in Murphy, p26.
4. Murphy, p108
5. Murphy, p4
6. Murphy, p43
7. Murphy, p3
8. Some Christians ascribe animal death to some combination of Adam’s fall and Noah’s flood, but this does not resolve the problem that the animals are still suffering and dying through no fault of their own. See Keith Miller’s BioLogos series Death and Pain in the Created Order for the limitations inherent in a fall-based theodicy.
9. Rudwick, Martin. The meaning of fossils: Episodes in the history of paleontology. Chicago, University of Chicago Press, 1985.
10. See Jeff Schloss’ BioLogos essay Evolution, Creation, and the Sting of Death
11. Murphy, p63
12. Murphy, p122
13. Murphy, p27
14. This example is drawn from an evangelical outreach event held by a Christian student group in Innsbruck, Austria. On campus one day, they started conversations with their classmates by asking the question, “Would you wear an electric chair on your neck?”
15. Murphy, George L. The Trademark of God: A Christian Course in Creation, Evolution, and Salvation. Wilton, Conn.: Morehouse-Barlow, 1986.
16. Murphy, Cosmos in the Light of the Cross, p 31-32.
17. Murphy, p35
18. Murphy, p87

My valiant helper, a small-sized tiger
Sleeps sweetly on my desk, by the computer,
Unaware that you insult his tribe.

Cats play with a mouse or
with a half-dead mole.
You are wrong, though: it’s not out of cruelty.
They simply like a thing that moves.

For, after all, we know that only consciousness
Can for a moment move into the Other,
Empathize with the pain and panic of a mouse.

And such as cats are, all of Nature is.
Indifferent, alas, to the good and the evil.
Quite a problem for us, I am afraid.

Natural history has its museums,
But why should our children learn about monsters,
An earth of snakes and reptiles for millions of years?

Nature devouring, nature devoured,
Butchery day and night smoking with blood.

And who created it? Was it the good Lord?

Yes, undoubtedly, they are innocent,
Spiders, mantises, sharks, pythons.

We are the only ones who say: cruelty.

Our consciousness and our conscience
Alone in the pale anthill of galaxies
Put their hope in a humane God.

Who cannot but feel and think,

Who is kindred to us by his warmth and movement,

For we are, as he told us, similar to Him.

Yet if it is so, then He takes pity
On every mauled mouse, every wounded bird.
Then the universe for him is like a Crucifixion.

Such is the outcome of your attack on the cat:
A theological, Augustinian grimace,
Which makes difficult our walking on this earth.

–Czeslaw Milosz,¹
 translated by the author and Robert Hass

The Problem

The poem above communicates in a very poignant and profound way the essence of the theological problem of death, pain, and suffering in the natural world—what has been referred to as “natural evil.” As we will see, it may also point to at least one aspect of a Christian response.

I have become convinced that one of the fundamental issues underlying much of the resistance of many Christians to an ancient, evolving creation is that of the problem of “natural evil.” “Natural evil” is also very often a primary focus of those who reject a personal and compassionate God, as it was for Darwin himself. The issue of theodicy thus seems not only to drive many people of Christian faith away from an acceptance of the conclusions of modern science, but also to drive members of the scientific community away from a serious consideration of the claims of the Christian faith. The topic is important, then not because its solution is central to the validity of the Christian faith, but because it often serves as an unnecessary stumbling block to a productive engagement of both science and faith.

The tension generated by our understanding of God’s character, as revealed in the Bible, and by the reality of the natural world around us has been the focus of much theological and philosophical debate within the Christian church since the first century. This article sets out to examine critically several of the proposed solutions to this problem, viewing them from the perspective of a geologist, paleontologist, and orthodox evangelical Christian.

The theological problem of death and pain emerges from the following propositional statements:

1. Scripture consistently declares the absolute goodness of God and the very goodness of his creation. Furthermore, Scripture declares God’s love and care for creation, and the glory and praise it returns to him.
2. Scripture also confesses a transcendent God who is omnipotent in power, yet immanent in creation as well. God’s creative activity is not described as being confined to some past event at the beginning of time, but as a present and continuing reality. God upholds creation in its being from moment to moment, and is creatively active in its history. This understanding of God’s relationship to creation has been well articulated by Jürgen Moltmann.²
3. In seeming conflict with these confessions of God’s character, we observe death, pain, and suffering as ubiquitous, even integral, aspects of the creation around us.

The apparent conflict between God’s goodness and the presence of pain and suffering is made especially acute when we consider the nonhuman creation.³ How can we accommodate the death and suffering of animals within a theology that declares both God’s omnipotence and goodness? C. S. Lewis forcefully puts the issue before us in his book The Problem of Pain:

The problem of animal suffering is appalling; not because the animals are so numerous ... but because the Christian explanation of human pain cannot be extended to animal pain. So far as we know beasts are incapable either of sin or virtue: therefore they can neither deserve pain nor be improved by it.⁴

Because the issue of animal pain so directly impacts our understanding of the goodness of creation, I will focus particularly on solutions to the problem as posed by Lewis.

How do we then reconcile the goodness of God who is immanent and active in his creation with the death, pain, and suffering we see embedded within it? There seem to be two basic alternative approaches to this dilemma.⁵

1. Natural evil can be attributed to something independent of God and acting against his will. This position threatens to limit God’s power and freedom.
2. Natural evil can be considered a part of God’s good purpose for creation, and either directly willed or permitted by him. Such a view would seem to bring into question God’s goodness and love for his creatures.

The tension between these alternatives—and efforts to avoid their negative theological consequences—surface in many of the proposed solutions to this problem.

In part 2, we start to look at some of the proposed solutions, beginning with the idea that a perfect creation was corrupted by a fall.

Notes

1. This poem was included in a collection of poems that was one of two works by Czeslaw Milosz mentioned in a review article by Michael Ignatieff, “The Art of Witness,” New York Review of Books (March 23, 1995). I thank Carol Regehr for bringing my attention to this work.
2. Moltmann refers to this aspect of God’s creative activity in history as “continuous creation.” Jürgen Moltmann, God in Creation (Minneapolis, MN: Fortress Press, 1993), 206–14.
3. I will not address here arguments concerning the degree to which animals experience pain. This issue is considered by Robert Wennberg in “Animal Suffering and the Problem of Evil,” Christian Scholar’s Review 21 (1991): 120–40. It is obvious to me that, for many animals at least, pain and suffering are a very real conscious experience.
4. C. S. Lewis, The Problem of Pain (New York: Macmillan Publishing, 1962), 129.
5. As stated by John Hick, in Evil and the God of Love, rev. ed. (New York: HarperCollins Publishers, 1977): “For every position that maintains the perfect goodness of God is bound either to let go the absolute divine power and freedom, or else to hold that evil exists ultimately within God’s good purpose” (pp. 149–50).

As we discussed yesterday, the most dramatic innovation yet observed in the E. coli Long Term Evolution Experiment (LTEE) was the ability, acquired by one of the twelve cultures, to use citrate as a carbon source under aerobic conditions. When we last discussed the LTEE in 2011, we noted what was known then about the mutations that eventually combined to produce the Cit+ trait:

Tracking down the nature of this dramatic change led to some interesting findings. The ability to use citrate as a food source did not arise in a single step, but rather as a series of steps, some of which are separated by thousands of generations:

1. The first step is a mutation that arose at around generation 20,000. This mutation on its own does not allow the bacteria to use citrate, but without this mutation in place, later generations cannot evolve the ability to use citrate. Lenski and colleagues were careful to determine that this mutation is not simply a mutation that increases the background mutation rate. In other words, a portion of what later becomes “specified information for using citrate” arises thousands of generations before citrate is ever used.
2. The earliest mutants that can use citrate as a food source do so very, very poorly – once they use up the available glucose, they take a long time to switch over to using citrate. These “early adopters” are a tiny fraction of the overall population. The “specified information for using citrate” at this stage is pretty poor.
3. Once the (poor) ability to use citrate shows up, other mutations arise that greatly improve this new ability. Soon, bacteria that use citrate dominate the population. The “specified information for using citrate” has now been honed by further mutation and natural selection.
4. Despite the “takeover”, a fraction of the population unable to use citrate persists as a minority. These cells eke out a living by being “glucose specialists” – they are better at using up glucose rapidly and then going into stasis before the slightly slower citrate-eaters catch up. So, new “specified information to get the glucose quickly before those pesky citrate-eaters do” allows these bacteria to survive. As such, the two lineages in this population have partitioned the available resources and now occupy two different ecological niches in the same environment. As such, they are well on their way to becoming different bacterial species.

As such, we noted three distinct steps observed by the Lenski group: steps they call potentiation, actualization, and refinement. Potentiation mutations do not themselves result in the ability to use citrate under aerobic conditions, but they are necessary for it to appear later. Actualization is the mutation that first brings about the Cit+ trait, though, as we noted, this step produced only a very weak Cit+ effect. This nascent ability, however, then undergoes refinement through additional mutations and selection to give the final, robust Cit+ trait observed in the culture.

While some things were known about these steps when the Lenski group last published on this topic (in 2008), the precise details remained unclear. What was needed was a complete characterization of the Cit+ bacteria through whole-genome sequencing to help indentify the changes. These long-awaited results are now available in a new paper published last month by the Lenski group, and they shed light on all three stages of the process.

Lights, camera, actualization

The key step - and the one of greatest interest - is of course actualization: the mutation that converted a Cit- cell to a Cit+ one. This is also one of the easiest steps to study, since the mutation provides the cell with a new feature that can be detected experimentally. Though E. coli cannot use citrate as a carbon source in the presence of oxygen, they are capable of using citrate in anoxic conditions (i.e. when oxygen is absent). To do so, they employ a protein that imports citrate in to the cell while at the same time exporting a compound called succinate. Since this protein is already present in the E. coli genome, it was long suspected that a genetic regulatory change that turned on its production in the presence of oxygen could be the key innovation that produced the first Cit+ bacterium in the culture. As we discussed yesterday, Behe notes that this change could result from a loss-of-FCT or a gain-of-FCT mutation:

“If the phenotype of the Lenski Cit+ strain is caused by the loss of the activity of a normal genetic regulatory element, such as a repressor binding site or other FCT, it will, of course, be a loss-of-FCT mutation, despite its highly adaptive effects in the presence of citrate. If the phenotype is due to one or more mutations that result in, for example, the addition of a novel genetic regulatory element, gene duplication with sequence divergence, or the gain of a new binding site, then it will be a noteworthy gain-of-FCT mutation.”

Interestingly, the actualization mutation was indeed a change of regulation of the anoxic citrate / succinate transporter, and it arose through a gain-of-FCT mutation. The mutation turned out to be a side-by-side duplication of the citrate / succinate transporter gene, as well as portions of two genes on either side of it. This imprecise duplication placed a partial fusion of these flanking genes next door to one of the copies of the citrate / succinate transporter gene. This brought the copy under the control of promoter sequences derived from of one of its neighbors, a gene that is active when oxygen is present. The resulting product was a copy of the citrate / succinate transporter gene that was now very weakly expressed in aerobic conditions. Since this is an example of a mutation that duplicates a gene and simultaneously creates a new regulatory element for it (causing significant sequence divergence), this is a clear-cut example of a gain-of-FCT mutation.

Responding to the data

While Behe has not yet, to my knowledge commented on this particular development within the LTEE, one of his colleagues in the Intelligent Design Movement (IDM), microbiologist Ann Gauger, has offered her thoughts. Two themes emerge in her commentary: that the Cit+ trait is “not new”, and that the number of mutations it required were within the bounds set out by Behe and another member of the IDM, structural biologist Douglas Axe:

When is an innovation not an innovation? If by innovation you mean the evolution of something new, a feature not present before, then it would be stretching it to call the trait described by Blount et al. in "Genomic analysis of a key innovation in an experimental Escherichia coli population" an innovation [...]

The total number of mutations postulated for this adaptation is two or three, within the limits proposed for complex adaptations by Axe (2010) and Behe in Edge of Evolution. Because the enabling pre-adaptive mutations could not be identified, though, we don't know whether this was one mutation, a simple step-wise series of adaptive mutations, or a complex adaptation requiring one or two pre-adaptations before the big event.

But does this adaptation constitute a genuine innovation? That depends on the definition of innovation you use. It certainly is an example of reusing existing information in a new context, thus producing a new niche for E. coli in lab cultures. But if the definition of innovation is something genuinely new, such as a new transport molecule or a new enzyme, then no, this adaptation falls short as an innovation. And no one should be surprised.

While Gauger does not speak to the tension between her description of the Cit+ mutation as “not genuinely new” and Behe’s criteria that this should be classified as a gain-of-FCT mutation, it is clear that she views this event as within Behe’s “edge” – i.e. within the bounds of “what Darwinism can do.” Additionally, she sees it as falling within the scope of what is evolutionarily possible as proposed by Axe’s work. In the next installment of this series, we’ll revisit how Behe defines his (claimed) limit of what evolutionary processes can accomplish, with this new evidence in hand. In doing so, a careful examination of the potentiation and refinement phases of the Cit+ transition will be informative.

For further reading:

Blount, Z.D., Barrick, J.E., Davidson, C.J. and Lenski, R.E. (2012). Genomic analysis of a key innovation in an experimental Escherichia coli population. Nature 489; 513- 518.

Michael J. Behe, The Edge of Evolution: The Search for the Limits of Darwinism (New York: Free Press, 2007).

Michael J. Behe (2010). Experimental evolution, loss-of-function mutations, and “The first rule of adaptive evolution”. The Quarterly Review of Biology 85(4); 419-445.

[T]he purpose of Jesus’ “art” was to give verbal, visual, and dramatic forms to those complicated and confounding relationships and symmetries and harmonies between Himself (and the Father and Spirit) and the world, ourselves included in the latter. Such creative expressions did and do not make everything clear, but rather resist simple clarity, forcing their hearers to come at the whole complicated, opaque truth from a position of intellectual and spiritual humility.

Speaking in parables is indeed similar to an artist’s craft. Neither are systematic, logical arguments aimed at intellectual persuasion. Rather, they create impressions, whole new worlds of meaning intended to turn old worlds on their heads. Further, they do not always clarify, but actually can by design obscure a deeper reality. To apprehend that deeper reality, one must—like a patron facing a timeless painting—continue to seek, ponder, and meditate on what is being said.

Parables are radical pieces of communication meant to disorient the hearers and then reorient them to an entirely new way of thinking. The reason Jesus does so much story telling is because stories—not debate or other “proofs”—are best suited for such a whole scale reorientation. Jesus’ preaching, after all, was about the kingdom of heaven (or of God). This kingdom was not about where one goes after death, but a here-and-now transformation of how people thought about God and their relationship to him.

Jesus “explains” this new kingdom in several ways, one of which is the Sermon on the Mount (Matthew 5-7), where Jesus lays out the types of behaviors that should now characterize the people of God. These new behaviors contrast again and again with the old and are fully at odds with what the religious leaders of the time were teaching the people. Jesus’ kingdom is counter-cultural.

But Jesus more often “shows” the people what this kingdom looks like by telling a good story, which regularly begins, “The kingdom of heaven is like….” Sometimes the best way to get an idea across is to paint a verbal picture, which is precisely what Jesus does in the parables.

Jesus’ stories are not like Aesop’s Fables (as interesting as they are), where there is a moral to the story. The parables are not about playing nice with each other. They actually plant you in a different world where things are running according to a wholly different set of rules of the kingdom of heaven.

We can see this by looking at one of Jesus’ favorite topics in the parables: how Jews related to Gentiles. Jewish identity was an extremely important and touchy issue in Jesus’ day. Even though the Jews had returned to their land after the exile (539 BC), they had been guests in their own land—first of the Persians, then Greeks, and now the Romans. How Jews could maintain their ethnic and religious identity in such a pressure cooker of pagan Greek and Roman ideas, not to mention the embarrassment of pagan rulers telling them what to do, was a sore point.

So, one can understand why Jewish attitudes towards tax collectors, for example, are a repeated concern in the Gospels. Tax collectors were fellow Jews who were traitors to their own people by collecting taxes for the Romans. They were even spoken of in the same breath as prostitutes (e.g., Matthew 21:31-32).

No “good Jew” committed to maintaining his or her identity amid a pagan world would lower themselves to work alongside the Romans. Yet, what does Jesus do? He associates with these (and other) “sinners” on a regular basis, and even calls a tax collector (Matthew) to be among his select group of followers. By his actions Jesus demonstrates that his kingdom operates by different, counter-intuitive, counter-cultural rules.

These types of concrete actions were supported again and again by Jesus’ parables. Such a radical change in how Jews viewed God, the world, and their place in it—where sinners and other outsiders were welcome—required a communication strategy that was up for the task.

Stories are that communication strategy. Parables were Jesus’ canvas for “painting” a new vision for what life in his kingdom should look like. And in Jesus’ kingdom, there was no longer any place for maintaining those fundamental ethnic and religious distinctions by which the Jews had been operating.

We can go to virtually any parable to make this point, but the well-known parable of the Good Samaritan works as well as any (Luke 10:30-37). We recall that what drove Jesus to tell this story was the question asked by the “expert in the law” (v. 25): “Who is my neighbor?” Jesus’ answer was this parable, and it carries a double punch.

First, the Jewish leaders step around the beaten man on the road—certainly a non-Jew—feeling no obligation to come to his aid. The point is that the leaders of Israel, of all people, should know enough of God’s character to stop and help him. They shouldn’t ask whether he is “one of us,” an insider. All one needs to know is that this human being needs help. In Jesus’ kingdom, carefully drawn lines of ethnic and religious separation are a thing of the past.

But second, on a deeper level, Jesus’ point is far more threatening. By calling upon a Samaritan as the “good guy” in this story—with all of the backdrop of cultural hostility—Jesus is making a more pressing point than “be good to everyone” (which is where the Sunday School lesson typically ends). The hated Samaritan sees the man lying there, and without asking questions about who he is—whether Jew, Samaritan, Greek, Roman, or anything else for that matter—helps him. The Samaritan, of all people, acts like a neighbor toward the man who needed help, the very thing the Jewish leaders failed to do.

By telling Jewish leaders that they have something to learn about their own God from, of all people, Samaritans, is not a suggestion to be more open-minded and tolerant. It is nothing less than a rewriting of the Jewish narrative or religious and ethnic identity. Jesus uses a story to paint a vivid mental and emotional picture for his hearers. No other medium would do.

It is sometimes thought that Jesus told stories because he wanted to persuade the masses, the common people who are not used to debating fine points of theology like the scribes and priests. This is partially true, but it is also true that the radical message of the kingdom of heaven required a means of communication that was best suited for it. Like any work of art, stories “create” new ways of seeing the world—and it is, after all, a new world that Jesus means to create.

Let me put this another way: Jesus himself communicated the deep mysteries of a new way of being through the use of such things as vivid imagery, symbolism, metaphors, and other devices common to artistic expression. In fact, the incarnation, God in human flesh, is not a debate or argument about the nature of God that appeals primarily to the intellect. It is a vivid—and true—demonstration, a portrait, of a radically new and mysterious way of thinking about God, the world, and our place in it.

If this is how God chooses to communicate at the incarnation—the very climax and epicenter of his story—we should not be surprised to see God painting vivid portraits elsewhere in Scripture. This is especially true of Genesis and creation. Something so fundamental to God’s story may need to be told in a way that transcends the limitations of purely intellectual engagement. Genesis may be written more to show us—by grabbing us with its images than laying out a timeline of cause and effect events—that God is the central figure on the biblical drama.

Originally posted February 1, 2011.

A Christology for Science

The theologian Robert Barron has nicely clarified much of what lies behind recent conflicts over human origins that feature supposedly biblical truths contending against supposedly scientific conclusions.

In his words, “recent debates concerning evolutionist and ‘creationist’ accounts of the origins of nature are marked through and through by modern assumptions about a distant, competitive, and occasionally intervening God, whether the existence of such a God is affirmed or denied.”¹ Barron’s response to these modern debates is a sophisticated exposition of classical Christology aimed at his theological peers. My effort is much simpler and is aimed at academics in general, but it comes from the same christological perspective.

Christ as Creator, Sustainer, Redeemer

Classical Christian orthodoxy as expressed in the creeds that summarize the Scriptures begins at the beginning: nature owes its existence to and is sustained by Jesus Christ. From this starting point several important ramifications follow naturally.

One is the implication that the best way of finding out about nature is to look at nature. This implication comes directly from the christological principle of contingency. As described in the Gospels, individuals who wanted to learn the truth about Jesus had to “come and see.” Likewise, to find out what might be true in nature, it is necessary to “come and see.”

The process of “coming and seeing” does not lead to infallible truth about the physical world since there is no special inspiration from the Holy Spirit for the Book of Nature as there is for the Book of Scripture. But “coming and seeing” is still the method that belief in Christ as Savior privileges for learning about all other objects, including nature. This privileging means that scientific results coming from thoughtful, organized, and carefully checked investigations of natural phenomena must, for Christ-centered reasons, be taken seriously.

From this perspective, the successes of modern science in recent centuries testify implicitly to the existence of a creating and redeeming God. To once again quote Robert Barron, scientific activity by its very nature “implies . . . an unavoidable correspondence between the activity of the mind and the structure of being: intelligence will find its fulfillment in this universal and inescapable intelligibility.” But how can this implication be justified? According to Barron,

The universality of objective intelligibility (assumed by any honest scientist) can be explained only through recourse to a transcendent subjective intelligence that has thought the world into being, so that every act of knowing a worldly object or event is, literally, a recognition, a thinking again of what has already been thought by a primordial divine knower.²

In lay language, the “transcendent subjective intelligence” and the “primordial divine knower” guarantee the possibility that a researcher’s mind can grasp something real about the world beyond the mind. The Scriptures—in John 1, Colossians 1, and Hebrews 1 — provide a name for that “intelligence” and that “knower.” In these terms, the existence of nature and the possibility of understanding nature presuppose Jesus Christ.

A second implication arising from the centrality of Christ in creation concerns the interpretation of Scripture. Classic biblical texts about the purpose of the Bible reinforce the foundational principle that the believers’ confidence in Scripture rests on its message of salvation in Jesus Christ. Thus, in John 20, the Gospel story has been written down so “that you may believe that Jesus is the Christ, the Son of God, and that by believing you may have life in his name” (20:31). In 2 Timothy 3, the inspired or God-breathed “holy scriptures” have as their main purpose instruction “for salvation through faith in Christ Jesus” (3:15). And in 2 Peter 1, “the word of the prophets made more certain” as these prophets were “carried along by the Holy Spirit” (1:19, 21) deals preeminently with “the power and coming of our Lord Jesus Christ” (1:16).

As these passages suggest, salvation in Christ anchors the believer’s confidence that all of Scripture is trustworthy.³ But because of that supreme fact, the effort to understand how Scripture is trustworthy for questions like the ordering of nature should never stray far from consideration of Christ and his work. Yet as we have seen, “Christ and his work” includes, as an object, the material world of creation, and as a method, “come and see.” In other words, following the Christ revealed in Scripture as Redeemer means following the Christ who made it possible for humans to understand the physical world and offered a means (“come and see”) for gaining that understanding.

Final and ultimate disharmony between what “come and see” demonstrates about Christ and what “come and see” reveals about the world of nature is impossible. This Christ is the same one through whom God has worked “to reconcile to himself all things . . . making peace through his blood, shed on the cross” (Col. 1:20) and in whom “all things were created” and in whom “all things hold together” (1:16-17).

Yet it is indisputable that on some science-theology questions, trust in Christ (and therefore trust in Scripture) has seemed to conflict with trusting in what Christ-authorized procedure (“come and see”) reveals about a Christ-created and Christ-sustained world. The parade of difficult questions arising from the effort to bring together standard interpretations of Scripture and standard interpretations of the natural world is a long one. Trying to answer these questions has been a consistent feature of the modern scientific age.

• In the nineteenth century, many earnest believers were wondering, if “coming and seeing” in geology and astronomy led to the conclusion that material existence has a very long history, should the “days” of Genesis 1 be understood as long periods of time or should a new interpretation of Genesis 1:1 be adopted that posits a “gap” between “in the beginning” and “God created”?

• More recent advances in both historical understanding (the ancient Near East) and empirical science (genetics, biology, astronomy) have prompted questions about the creation accounts of early Genesis. Well-trained scientists with strong Christian convictions have followed the Christ-rooted procedure of “coming and seeing” in their study of physical evidence for the origin of the universe and have concluded that much of standard evolutionary theory seems well grounded.⁴ Similarly, well-trained biblical scholars with strong Christian convictions have followed the Christ-rooted procedure of “coming and seeing” in their study of ancient Near Eastern cultures and have concluded that the early chapters of Genesis seem to be directly concerned about attacking idol-worship that substituted the sun or the moon for God.⁵ Given the combination of these two streams of testimony, should it be thought that early Genesis is not concerned with modern scientific questions but is very much concerned about encouraging worship of the one true God who is the originator and sustainer of all things?

• Even more recently, the rough consensus on evolutionary change assembled from many scientific disciplines makes for even more complex questions: for example, if human evolution seems indicated by a wide range of responsible scientific procedures (“come and see”), how might responsible biblical interpretation understand the New Testament stress on Christ (very definitely in historical time and historical space) as overcoming the sinfulness inherited from Adam and Eve, whom Scripture, at least on a surface level, also represents as individuals in historical time and historical space?

All such questions caused understandable consternation when they were first raised, since they challenged specific interpretations of Scripture that had been tightly interwoven with basic interpretations of the entire Bible. Even after long and hard thought, such questions continue to pose definite challenges.

Answering such questions responsibly requires sophistication in scientific knowledge and sophistication in biblical interpretation — exercised humbly, teachably, and nondefensively. Unfortunately, these traits and capacities have not always predominated when such questions are addressed. But the difficult questions will almost certainly only continue to multiply because of two ongoing realities: the Holy Spirit continues to bestow new life in Christ through the message of the cross found in Scripture, and responsible investigations lead plausibly to further evolutionary conclusions from the relevant scientific disciplines.

This excerpt was drawn from chapter 3 of Mark Noll's book Jesus Christ and the Life of the Mind. If you would like to read the whole chapter, click here. First posted August 30, 2011.

Notes

1. Robert Barron, The Priority of Christ: Toward a Postliberal Catholicism (Grand Rapids: Brazos, 2007), 221. For convenience, I return several times in the following paragraphs to this book by Robert Barron. But there are other parallel efforts, for example from the physicist and Anglican theologian John C. Polkinghorne, in books like Belief in God in an Age of Science (New Haven: Yale University Press, 1998), and Science and the Trinity; The Christian Encounter with Reality (New Haven: Yale University Press, 2004).
2. Barron, Priority of Christ, 154.
3. See above on providence.
4. Barron, Priority of Christ, 13.
5. A Summa of the Summa, ed. Peter Kreeft (San Francisco: Ignatius, 1990), 174 (from Thomas Aquinas, Summa Theologica, I, 22, 4).

In his essay for that series, Jeff Schloss addressed the question of whether animal death is a natural evil, but also noted that such theological considerations aside, death does not actually “drive evolution” in the way most people imagine—especially when they think of violence in the natural world. This more complicated sense of death’s role is partially the result of modern evolutionary science recognizing the importance of cooperation and inter-relation among species, rather than just direct competition. But just as important is the knowledge that evolution is significantly shaped not by the deaths of individual creatures, but by extinction, the loss of species over time. In this post, we explore some aspects of how extinction acts as both a destructive and creative force in evolutionary history, including the evolutionary history of mammals.

Sporadic extinction

Extinction is actually a common feature of life on earth when viewed over long (e.g. geological) timescales. By some estimates, over 99% of the species that have ever lived have gone extinct. One factor that promotes extinction is the fact that evolution does not produce species that are optimally adapted to their environment, but only better adapted than their local competitors. Invasive species testify to this fact: local (endemic) species are not always the best-adapted species for their own environment. Examples abound where species from other environments are actually better-suited to out-compete endemic species. Here in my own province, the invasive Himilayan blackberry (Rubis discolor) easily outcompetes many endemic species. If endemic species were optimally adapted to their environment, this would not be possible, as they would outcompete all exotic species. Instead, exotic species, by chance, might be better adapted to an ecosystem they did not evolve in. These exotics may be capable of eliminating endemic species altogether.

Such an extinction event (of a single species, or perhaps a handful of species) alters the environment of other remaining species in an ecosystem. This, in turn, may influence the ability of some of these remaining species to reproduce compared to other species. For example, the extinction of a competitor might allow a species to increase in population size. Conversely, the extinction of a species that provides a benefit (such as a pollinator) may reduce a species in number. As the ecosystem landscape shifts due to loss of species, new biological opportunities, or niches, might arise. These new niches are then available to support new species to fill them.

Extinction, en masse

One way to appreciate how extinction opens up new niches is to examine mass extinction events – geologically brief periods where large numbers of species go extinct at the same time. Over the history of life on our planet there have been several mass extinction events. The largest such event, at the end of the Permian (~250 million years ago) appears to have been caused, at least in part, by intense volcanic activity over several hundred thousand years. This activity likely shifted CO2 levels and eventually led to a “runaway” greenhouse effect that dramatically raised global temperatures and led to anoxic (i.e. oxygen-depleted) oceans, though the exact contributions of these varied factors remains an area of scientific debate. What appears certain is that during this period environmental changes were too rapid for most species to keep evolutionary pace with, and as a result over 90% of the world’s species alive at that time went extinct. Obviously this represents destruction of biodiversity on an unimaginable scale, and the destructive effects of this event are with us to this day.

Speciation, en masse

This destruction, however, is not the whole story. Following on from the Permian mass extinction, we observe a steady increase in new species. These are species previously unknown in the fossil record. In fact, this pattern (a “radiation” of new species following an extinction event) is the rule, not an exception – we see the same effect after every mass extinction in the fossil record. Extinction is a driving force for novelty.

Perhaps the most famous mass extinction event is the Cretaceous – Paleogene (KPg) extinction, and it too follows this standard pattern. This mass extinction took place 65 million years ago when an asteroid ~10 kilometers in diameter struck the Yucatan peninsula. (Note: this event was formerly known as the Cretaceous – Tertiary (K-T) extinction, but that terminology is in decline within the scientific community). This extinction event is famous since it is the one that eliminated the dinosaurs (with the exception of the ancestors of modern birds). As with the Permian extinction, the elimination of so many species shifted the evolutionary landscape for the remaining species, and the result was a burst of speciation that appears rapid when viewed in geological time. Significantly for our own species, following the KPg extinction event is a burst in mammalian speciation, as small mammals that survived the event diverge and fill niches left empty by the dinosaurs. Without this event, the trajectory of mammalian evolution would certainly look very different.

Clearing the deck, and re-filling the niches

One interesting fact to note is that biological features that make a species resistant to usual, sporadic extinction are not necessarily the same features that will be useful during a mass extinction event. While species are continually under selection at the local level, there is no mechanism for (pre) selection to survive a mass extinction. As such, only species that happen to have the right combination of traits will survive, and often spread widely after a mass extinction. These so-called “disaster species” are usually generalists, and will later be displaced by more specialized species as they arise. As such, where sporadic extinction allows for more gradual turnover in species, mass extinction events are major “resets” of evolution that can radically shift what constitutes “well adapted” in a geological eyeblink. For mammals at the KPg boundary, small body size and an omnivorous diet (including the ability to scavenge detritus) were the “winning” combination of traits that allowed them to survive where larger, more specialized animals (think Tyrannosaurus rex) could not. From this rather humble station, mammals would come to dominate the world’s ecosystems over the coming eons – including a lineage that would someday lead to our own species. Far from only a destructive force, extinction is a powerful mechanism to allow evolutionary innovation, and one that was of significant importance to us.

For further reading:

Meredith, R.W. et al (2011). Impacts of the Cretaceous Terrestrial Revolution and KPg Extinction on Mammal Diversification. Science 334; 521-524.

Fastovsky, D.E. (2005). The Extinction of the Dinosaurs in North America. GSA Today (15); 1052-5173.

Benton, M.J. and Twitchett, R.J. (2003). How to kill (almost) all life: the end-Permian extinction event. TRENDS in Ecology and Evolution (18); 358-365.

The Evolutionary Role of Death & Natural Evil

In addition to providing a general theological critique of the endemic—as opposed to post-hoc or intrusive—origins of death in the natural world, John Laing’s imminently fair-minded essay also takes theological aim at the role death and natural evil play in the evolutionary diversification of life. It is one thing to say that death is primordial; it is another to view it not just as an ancient byproduct, but as the central means of creation. The understandable theological uneasiness expressed by John and many others about this issue ultimately rests not just on an understanding of God’s creative activity, but also on a particular representation of evolution. In this regard John makes two important claims:

• a) “…natural selection, with its emphasis on a natural state characterized by competition for limited resources and a general struggle for survival, is the primary means by which speciation takes place…”
• b) “death actually functions as a mechanism for life. Death plays a vital role in natural selection by rooting out weakness and driving evolutionary development.”

For reasons I discussed in the previous section, it is not entirely clear that death constitutes an evil that is incommensurate with divine activity. However, the fact is that the above depiction of evolution—which is not unique to John amongst public commentators and is largely commensurate with Darwin’s own views—does not adequately portray current discussions within evolutionary biology. There are three problems with this portrayal that I’d like to address in turn—three aspects of evolutionary theory that need to be better understood.

First, while there is no uncertainty about common descent or about natural selection as a cause of evolutionary change, there is considerable discussion over the extent to which natural selection is “the primary means” by which speciation takes place. For one thing, there are manifold other agents of evolutionary change: drift, gene flow, systems of mating, mutation itself unfiltered by selection. A tremendous amount of variation may be adaptively neutral, being invisible to natural selection. For another thing, some claim that evolution proceeds most rapidly and speciation occurs most precipitously in the relaxation of selection—when ecological times are good and the culling effects of the environment are minimized. We may see this in the contingency-driven formation or colonization of a new habitat or the exploitation of a new resource that does not displace previous variants. Or, speciation events or species-level innovations may be the results of chromosomal rearrangements or symbiogenesis that are not the cumulative results of selection. Finally, there exist manifold and admittedly controversial proposals that are critical of neo-Darwinism as a whole, claiming that natural selection may be a necessary, but is neither a sufficient nor a primary cause of large-scale evolutionary change.¹

Second, notwithstanding Darwin’s formulation of natural selection in terms of competitive struggle as (accurately) cited by John, the modern understanding of evolution and competition is considerably more differentiated and complicated. For one thing, competition is neither a necessary nor a sufficient condition for natural selection. Natural selection is formally defined as the differential reproduction of genotypes (or information.) Some sets of genes are replicated with greater efficiency than are others. Competition is formally defined as the negative impact of two organisms (or two species) on one another’s fitness. You can have all sorts of competition that does not result in natural selection. And importantly, you can have differential reproduction by natural selection without the negative fitness impacts of competition. Colonists to a new under-exploited habitat, or two species that are partitioned onto separate resources in a way that minimizes competition might well have some variants that leave more offspring than others without displacing them. This is natural selection.

Indeed, imagine an infinite habitat with non-limiting resources and no competition at all: as long as there were adaptively salient mutations, there would be natural selection—some of those new genotypes would reproduce more effectively than others. Competition, to whatever extent it exists in nature, is a consequence of finitude and not a necessary precondition of natural selection. And finally, the role of cooperation in evolution has itself been massively reconsidered in recent years. It would not be entirely unfair to say that on the basis of mathematical models and empirical data, the proposal that cooperation “is now seen as a primary creative force”² and a “fundamental principle of evolution”³ has moved from being a cult-alternative to a widely accepted paradigm. Indeed, cooperation and increasing scales of cooperative interdependence are seen not only as a formative process but also as a recurring product of evolutionary change, which may even be viewed as “progress.”⁴ A biologically significant and theologically salient thematic trend across major evolutionary transitions, is that cooperative interdependence itself – and the wondrous properties of life mentioned in the first installment of this essay – seem to be amplified through selection.⁴ Through evolution, God may be seen to confer life and confer it in greater abundance.

Third, the claim that “death drives evolutionary development” turns out to be problematic. Recent discussions of death and senescence (organismic decay) between various branches of the biosciences are spirited and fascinating. One of the vexing characteristics of living creatures is the internalization of death and senescence: even if an individual is not killed by external forces, it will die from the inside out—virtually no species is immortal.⁶ One account of this—the rate of living theory of senescence—understands it not in terms of selection for reduced mortality but in terms of biophysical or allometric constraints relating rate of metabolism to rate of wearing out. Though it views senescence differently, the prevailing evolutionary theory of senescence, with several variants, does not affirm death or decay—at least the kind of death and decay that is intrinsic to organismic development—as a prerequisite to evolution by natural selection either.⁷

Indeed, internalized death is viewed not as driving but as deriving from, not as a necessary requirement for but as a byproduct of, natural selection. Specifically, mutations or traits with detrimental impacts later in life may not be eliminated by or may even be favored by selection if their contribution to reproduction early in life is sufficient. Now, neither theory completely dismisses the shaping role of death. Under certain but not all conditions, differential mortality may have adaptive import (and it is not even the longer-lived organisms that always have adaptive advantage). Extrinsic sources of death may also shape the internalization of death.⁸ But the view that death drives evolution does not adequately represent emerging scientific understanding of the relationship between natural selection and senescence.

Scientifically death does not “drive” evolution. And theologically, although neither evolutionary change nor ecological interaction “solve” the ultimate puzzle of human death, they may nevertheless mitigate the proximal existence of creaturely death by amplifying the complexity and vibrant abundance of living forms.

Darwin famously closed The Origin by observing “There is a grandeur in this view of life, with its several powers, having been originally breathed by the Creator into a few forms or into one…from so simple a beginning endless forms most beautiful and most wonderful have been, and are being evolved.”⁹ Unlike John, I do not see anything in evolutionary theory to reduce, and I see much to augment the sense of grandeur and (for that matter) the appreciation of sheer goodness—both earthly and divine—evoked by the wonders of the living world.

Yet grandeur and goodness are not perfection. My Dad is still dying. I still wince at the suffering of clearly sentient animals. And, truth be told, I tremble at the biblical images of universal herbivory: even metaphors are metaphors of something, and in the case of biblical revelation, that something can be taken to be real and important. So like John, I confess to profound gratitude tempered with a lingering unease at the state of nature. Though I believe in a Fall, this unease is not rationally relieved by attributing to an Adam the present state of all nature. Nor is it resolved by the various alternative considerations I’ve described and which, taken together, seem to have considerable merit but not sufficiency. Notwithstanding, I thankfully affirm that “I have known the goodness of the Lord in the land of the living.” And I look to the day when we may say together, “My ears had heard of You, but now my eyes have seen You.” (Job 42:5)

Notes

1. E.g., Salthe, S. 2008. “An Anti-Neo-Darwinian View of Evolution.” Artificial Life. 14:231-233; David Depew and Bruce Weber (eds). Darwinism Evolving: Systems Dynamics and the Genealogy of Natural Selection. 2004. MIT Press
2. Michod, Richard and Denis Roze. 2001. “Cooperation and Conflict in the Evolution of Multicellularity.” Heredity. 86:1-7. Page 2
3. Nowak, Martin. Evolution, Games, and God: The Principle of Cooperation. Martin Nowak & Sarah Coakley, eds. Forthcoming from Harvard University Press.
4. Sigmund, Karl and Eörs Szathmáry. 1998. “Merging Lines and Emerging Levels.” Nature. 392: 439-441.
5. John Maynard Smith and Eörs Szathmáry. 1998. The Major Transitions in Evolution. Oxford University Press. Brett Calcott & Kim Sterelny (eds). 2011. The Major Transitions in Evolution Revisited. MIT Press.
6. “Virtually” is an important qualifier: while senescence has been documented in nearly all organisms examined, there are some cell lines and species in which this may not be the case.
7. Williams, George. 1957. “Pleiotropy, Natural Selection, and the Evolution of Senescence.” Evolution. 11:398-411.
8. This relationship is complex and not invariant. E.g., Williams, Paul and Day, Troy. 2003. “Antagonistic Pleiotropy, Mortality Source Interactions, and the Evolutionary Theory of Senescence.” Evolution. 57(7): 1478-1488.
9. Darwin, Charles. 1876. The Origin of Species By Means of Natural Selection, or the Preservation of Favored Races in the Struggle for Life. 6th Edition. John Murray. p. 429.

Recently, an elegant and powerful experiment was done to further investigate a question of interest to many evangelicals: how is it that we are so different from our closest biological relative (the chimpanzee) when our DNA is so very similar? Even when using estimates that maximize the differences, our genomes are 95% identical. The conclusion, that I have discussed here in the past is that a dispersed set of numerous small changes can have large effects on the form and function of an organism. Of course, small changes are what evolution specializes in: tinkering here and there, one mutation at a time, as we have directly observed in laboratory experiments. Before we discuss how this pivotal new study was done, however, a brief review of how genes work is in order.

Review: gene structure and function

If you’ve been following the ongoing Understanding Evolution series here at BioLogos, you will recall that we discussed gene structure and function not long ago, in the context of discussing non-functional DNA sequences (so-called “junk DNA”):

Genes have a typical structure (obviously simplified here somewhat). First off, there is the actual DNA sequence that specifies the protein product sequence (the so-called “coding sequence”, shown in blue). This sequence is usually broken up into segments in mammalian genes, and these sequences are spliced together when the DNA sequence of the gene is transcribed into a “working copy” called mRNA – a short duplicate of the code that can be used by the cell’s machinery to actually build the specified protein.

In addition to the actual coding sequences, other sequences are needed to tell the cell when and where certain genes should be transcribed into mRNA. Every cell in an organism has the same genes in their chromosomes, but not all are transcribed. Using different genes in different combinations is what makes cells take on distinct roles – for example, cells in your small intestine need different genes (for absorption of nutrients) than do cells of the immune system (for fighting off pathogens). Regulatory sequences make sure any given cell type has the right genes transcribed and made into protein products. Some of these sequences are part of the mRNA transcript (shown in red), and others are not transcribed but only part of the chromosomal DNA sequence (such as the “promoter” region that directs the enzymes responsible for making the mRNA transcript (shown in blue).

With this background in mind, we can now extend our understanding slightly further. DNA in cells is “packaged up” when not in use by winding it around a class of proteins called histones. This packaging keeps the DNA in a compact form, and it is useful in helping cells prevent genes they don’t need from being transcribed. For any given chromosome - which is one long strand of DNA – some regions will be packed away (and the genes there not transcribed), while other regions are unpacked (less tightly associated with histones) with the genes there actively undergoing transcription. The open regions allow for transcription because enzymes and other proteins needed for the process can gain access to the DNA there.

Comparing gene transcription across species at the genomic level

Because of the overwhelming similarity between the human and chimpanzee genomes (and the even greater similarity when examining only their protein-coding regions) it has long been hypothesized that changes in “where and when” genes are transcribed will be a major player in what makes our two species different (in contrast to the idea that we are different because of the relatively tiny changes in the coding regions of our genes). From an evolutionary point of view, there are a few ways to explore how differences in gene transcription arise once species go their separate ways, such as when our ancestors parted ways with our last common ancestor with chimps around 4-6 million years ago. The main idea is to compare the same cell type in both species: human skin cells versus chimp skin cells, for example. Determining what specific genes are transcribed (or not) in human cells and comparing the results to chimpanzee cells gives us an idea of how gene transcription differences arose in the two lineages since they last shared a common ancestor. The challenge, up until now, is that there was no easy way to indentify the changes in regulatory DNA that led to those differences in transcription. The problem arises because of the overwhelming similarities between our genomes: changes in transcription due to changes in DNA sequence are hard to find simply by looking for sequence differences, since in most cases the differences will be very small. There are also many small differences between our genomes that have no effect on gene transcription, so we cannot simply look for any difference at all. What we need is a way to identify which small changes led to differences in gene transcription.

Old hypotheses, new technology

Back in 2008, a method for addressing this issue was devised. As we have seen, DNA undergoing transcription is “unpacked” and accessible to enzymes. Researchers have long known about a certain enzyme, called DNAse I, that can cut exposed DNA but leave histone-packaged DNA alone. This means that DNA from any given cell type can be cut using this enzyme specifically at “DNAse I hypersensitive sites” (DHS’s) where regulatory DNA is unpackaged and a nearby gene is being transcribed. While this technique is decades old, what is new is a way to then go on to sequence the DNA next to each of these sites. This requires what is known as “next-generation” or “deep” DNA sequencing methods that can use a linker sequence to attach to the DNAse I cut sites and then amplify and sequence individual DNA fragments attached to the linker. Since we have the entire genome sequence of humans and chimps it is then trivial to take the sequencing results and map them to either genome. The results are a detailed map of what chromosome regions are unpacked and regulating transcription in each cell type. These maps can then be compared with related species across entire genomes.

It was only a matter of time before these powerful methods were applied to the human-chimp question, and the first results became available last month. The research group was of course interested in differences between the two species, and the results are fascinating. The researchers looked at several different cell types, and found similar results in all cases. The results for any given gene fall into one of several categories when compared to the human-chimp (H-C) last common ancestor:

• No differences in regulatory DNA relative to the H-C last common ancestor (1259 genes)
• Gain of regulatory DNA in humans relative to the H-C last common ancestor (836 genes)
• Loss of regulatory DNA in humans relative to the H-C last common ancestor (286 genes)
• Gain of regulatory DNA in chimpanzees relative to the H-C last common ancestor (676 genes)
• Loss of regulatory DNA in chimpanzees relative to the last common ancestor (211 genes)

While it was not surprising to find a significant percentage of unchanged genes, it was interesting to note the large percentage of differences in regulatory DNA, despite the overwhelming genomic similarity between the two species. Small changes had a large impact on gene regulation. The researchers went on to examine the new regulatory regions they had identified, and found that they showed evidence of being under natural selection. These mutations had not only brought change, but provided an advantage to their hosts.

These results underscore a few important points:

• Species become different because differences accumulate in both lineages once a common ancestral population splits into two. The differences we see in modern species are due to changes both species have accumulated over time.
• Tweaking the regulation of numerous genes appears to be a widespread mechanism for generating evolutionary novelty. Both gaining and losing regulatory sequences is common.
• These gains or losses in regulatory DNA require only very small changes at the DNA sequence level, but they can have profound impacts on how genes are transcribed.
• These changes appear to be widespread in genomes, and able to accrue in short evolutionary timescales.
• Small changes are exactly the sort of thing that evolution is known to be able to accomplish easily, one mutation at a time.
• These small changes bear the marks of natural selection, indicating that they were selected for as they arose.
• Anyone who wishes to call these differences “insignificant” will have to contend with the observation that the biological differences we observe between humans and chimpanzees are significant.
• Small, incremental changes at the genomic level fit nicely with the fossil evidence for human evolution, which, though fragmentary, indicates gradual changes in skeletal morphology over the same timescale.

Of course, this study is just the beginning, and future studies are sure to examine and compare additional cell types found in humans and our evolutionary cousins. These results have already added to the troubles of antievolutionary groups that wish to portray the differences between us as too great for evolutionary mechanisms to bridge. I suspect these troubles will only worsen in the coming years as these new techniques come into their own.

For further reading:

Shibata Y, Sheffield NC, Fedrigo O, Babbitt CC, Wortham M, et al. (2012). Extensive Evolutionary Changes in Regulatory Element Activity during Human Origins Are Associated with Altered Gene Expression and Positive Selection. PLoS Genetics 8(6): e1002789. doi:10.1371/journal.pgen.1002789

http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002789

With the first part of my essay as background, I now respond directly to Dembski’s analysis of “Darwinism” and how BioLogos differs from the view he critiques. He begins by posing a question, “Is Darwinism theologically neutral?” He goes on to describe two contrasting views:

1. Those of the agnostic philosopher, Michael Ruse, who claims Christianity and Darwinian evolution are compatible and,
2. Those of individuals who hold a young earth view and claim Christianity and Darwinian evolution are incompatible.

Dembski suggests that Ruse, in order to claim compatibility (neutrality), redefines Christianity. I agree he does this. Without belief in the bodily resurrection of Jesus, Christianity is dead and, as Paul says, Christians are of all people most to pitied. (1 Corinthians 15:19).

Dembski also states that a belief in common descent can be consistent with Christian faith (i.e. neutral), and here I agree with Dembski again. As he points out, Christianity is not defined by the mechanism that God chose to use in accomplishing his purposes in creation.

So far we are on exactly the same page. Ruse claims Darwinism is neutral, but only by departing from Christian theology. Some young earth creationists claim Darwinism is not neutral, but they focus on common descent and this, by itself, does not depart from Christian theology. However, as Dembski quickly notes at that point in his essay, he has not yet carefully defined Darwinism and Christianity. He goes on to describe what he considers to be some non-negotiables of each.

Dembski suggests that among the core non-negotiable principle beliefs of Christianity are: (a) divine creation, (b) reflected glory, (c) human exceptionalism, and (d) bodily resurrection of Jesus. I agree that these are non-negotiables; take away any of these beliefs and you no longer have Christianity. We’re still on the same page.

What about non-negotiables of “Darwinism?” They are, he says, (a) common descent, (b) natural selection, (c) human continuity, (d) methodological naturalism. With that, he proceeds to analyze each.

Common Descent

Common descent, which today is at the core of the biological sciences, was a fundamental tenet for Darwin. Dembski sees no significant theological problem with common descent. “By themselves [the Christian non-negotiables described above] allow that God might have specially created living forms or brought them about via an evolutionary process,” he writes. He sees no theological conflict with this Darwinian tenet, even though he does not subscribe to it.

Natural Selection

Dembski indicates that natural selection, as defined by Darwin, is in tension with two of the four Christian non-negotiables—divine creation and reflected glory. His primary concern is that Darwin’s view of natural selection is non-teleological. Insomuch as this is true (and Darwin’s views on teleology are complex and contested), I agree. If Darwin’s non-teleological views were correct, this would be incompatible with some of the non-negotiables in Christianity. As Dembski says, “to say that something is undetectable is not to say that it doesn’t exist....” I concur that Darwin had no scientific basis for concluding that the evolutionary process did not end up exactly the way that God intended in the beginning. If Darwin reached non-teleological conclusions on the basis of his data then he allowed his philosophical and theological commitments to influence his conclusions. Like Dembski, I believe God did call our existence into being; there is a teleological basis for our presence on earth. We are by no means an accident and to the extent that Darwin thought we are, he was wrong.

So far, I see no significant difference between BioLogos and the non-negotiables presented by Dembski. Intriguingly, however, Dembski goes on to state, “it seems odd, given C1—[divine creation], that God would create by Darwinian processes, which suggest that unguided forces can do all the work necessary for biological evolution.” Here we part company. As indicated in my introductory comments above, I believe that the natural activity of God is not less divine than the supernatural activity of God, something borne out by the Scriptures themselves. This does not mean that I think that no supernatural activity occurred in life’s history; I just don’t see why it would be “odd” if God chose to create life’s diversity through his natural activity. How would we know what is odd as it relates to the activity of God? The only reliable source of what is odd and what is not is God’s revelation through his Word. But I see no scripturally-based rationale for determining the expected ratio of natural vs. supernatural divine activity in creation. Scripture is silent on the issue and so far at least, science is as well—other than demonstrating that many biological features and mechanisms previously thought by some to be evidence of supernatural action can now be explained via God’s regular activity—that associated with his natural laws. For the present, I think it is best to withhold judgment about the extent to which God suspends his ongoing regular activity in favor of miraculous supernatural activity in the history of the creating life’s diversity.

I now come to the most fundamental point of disagreement between the Intelligent Design movement and BioLogos. Dembski states:

Given that science is widely regarded as our most reliable universal form of knowledge, the failure of science to provide evidence of God, and in particular Darwin’s exclusion of design from biological origins, undercuts C2 [reflected glory].

Furthermore, he also writes:

If God does occlude his purposeful activity in nature, that raises a tension with (C2), which states that the world clearly reflects God’s glory (Psalm 19) and that this fact should be evident to all humanity (Romans 1).

I don’t think that God occludes or masks his activity. Thanks in no small part to science, we now recognize that there are “signposts” (C.S. Lewis’s term) all over the place directing our attention to the existence of our Creator. The question is whether those “signposts” can be developed into scientific hypotheses that can be scientifically tested in a manner that parallels how one goes about testing the hypothesis that smoking causes cancer or that DNA is the genetic material. The heavens do declare the glory of God (Psalm 19), and, “ever since the creation of the world, his eternal power and divine nature, invisible though they are, have been understood and seen through the things he has made” (Romans 1:20). God has not occluded his activity. It is all around us. From the birth of a baby to the birth of a star; from a universe which is mathematically coherent to one which is exquisitely fine-tuned; from our sense of shame to our ability to recognize the good and the right—from all of these and so much more, we see signposts all pointing to our Creator. Individually each hints at something beyond ourselves. Together they shout out with the message of God’s glory. Still, can they be tested scientifically—in a manner that parallels whether penicillin kills bacteria or the mitochondrion is the cell’s energy factory—to determine whether God is at work in them? Can intelligent people who choose not to believe come up with feasible alternative explanations that do not include God? Sure, they do it all the time and, as Romans 1 tells us, they have been doing it from the beginning of human existence.

Given the way that God has worked through his regular natural activity, why should we expect to be able to develop a test for the activity of God? God is always active, but scientific testing of God’s activity would require a “control” where God is not active. How can we conduct an experiment which studies the “presence vs. absence of God” when God is always present as sustainer as well as creator?

Human Continuity

Dembski quotes from Darwin’s Descent of Man:

The difference in mind between man and the higher animals, great as it is, certainly is one of degree and not of kind. We have seen that the senses and intuitions, the various emotions and faculties, such as love, memory, attention, curiosity, imitation, reason, etc., of which man boasts, may be found in an incipient, or even sometimes in a well-developed condition, in the lower animals.

Even if all that Darwin says here were more or less true, it would still say nothing about that which makes humans truly exceptional, because—our linguistic and cognitive abilities aside—what makes us truly exceptional has less to do with biology than with the fact that God chose to enter into a unique relationship with humankind. Dembski paraphrases an ideologically strict Darwinian view of man as "not worthy of special divine attention, and with no prerogatives above the rest of the animal world." But Christians recognize that our material ordinariness is radically transformed by the presence and promises of God. Exactly as with the people of Israel among the nations, so humans among the animals: our special identity rests in the free choice of the Creator to give us his himself and his name. If we recognize that human specialness rests on God’s fellowship with and call upon us, and that we—alone of all creatures—are enabled by God to bear his image in the world, then anything Darwin said about the physical continuity between humans and animals is irrelevant. In the way that matters most, we are not continuous with animals. For philosophical and theological reasons, Darwin did not recognize this. Darwin, I believe, was wrong. I, like Dembski and like Southern Baptists in general, am not a Darwinist.

Methodological Naturalism

Dembski defines methodological naturalism in the following way:

The physical world, for purposes of scientific inquiry, may be assumed to operate by unbroken natural law.

He goes on from there to write that if one assumes that miracles were performed in salvation history, then it would seem to be arbitrary to assume that God would not also perform miracles in natural history as well. Although I do not rule out the occurrence of miracles in natural history, the purpose of miracles in the biblical narrative seems to stem from God’s desire to reveal himself to humankind, reminding us of and guiding us in our relationship with him and each other. Given that, I do not see why it is arbitrary to think that God may not have used miracles to accomplish his purposes in nature before humans were around to observe them.

However, I strongly disagree with Dembski that if one believes God has worked primarily through natural processes in creation as a whole, this makes belief in the resurrection less tenable. The two ought not to be tied together in this way, especially since I have already stated that I reject the notion that the ordinary and regular processes of creation are any less God’s—than what I have called supernatural processes. One’s conclusion about the mechanism of creation has no logical extension to one’s views about the historicity of the bodily resurrection of Jesus.

In conclusion, I think Dembski takes some steps that are both theologically unnecessary and scientifically unjustified in rejecting what careful study tells us about God’s marvelously ordinary processes of creation: ordinary because they follow his natural laws so faithfully, marvelous because they have resulted in a world of complex and beautiful life. On the other hand, I agree with Dembksi that Darwin’s views were not theologically neutral. Darwin’s views on teleology, human exceptionalism, and miracles were not compatible with Christianity. Quite simply, this is why I do not consider my views to be Darwinian and why I am not a Darwinist.

For further reading:

The BioLogos website offers many resources to acquaint readers with the incredibly strong scientific evidence for common descent and other facets of evolutionary biology.

An example of the way poetry helps re-make our interpretive framework is Richard Wilbur’s poem, Still, Citizen Sparrow. Directly addressing our “natural” revulsion for death and those contaminated with it, the poem contrasts the small “darting” sparrow with the vulture—an unwelcome visitor in the sparrow’s space. Surely, the vulture must seem an awkward and ungainly abomination in the fruitful orderliness the smaller bird inhabits, for those “orchard aisles” hint at both a garden and a church. Yet the poem also presents a two-fold defense of this most un-clean of birds, beginning with the difference between how it seems on the ground and how it is in its own element, at the “tip of the sky.” “[N]o more beautiful bird is in heaven's height “, Wilbur tells us, “No wider more placid wings, no watchfuller flight.” But more than just his aeronautic skills are at issue. It is the vulture’s “rotten office”—the very thing that makes it so repulsive to our sensibilities—that Wilbur names as its saving grace.

The “naked-headed one. . . Devours death, mocks mutability, / Has heart to make an end, keeps nature new.” This description of the vulture could be a purely naturalistic assessment of the importance of biological recycling, but a turn at the poem’s fourth stanza takes its imagery in an explicitly scriptural direction. From here on, it connects the vulture with Noah, and the sparrows (and implicitly us) as those “who would have died / Gladly with all [they] knew” rather than put up with the tedium and apparent foolishness of Noah’s incessant sawing and hammering. At last, Wilbur implores the sparrows to consider how “high and lonely” was Noah’s time on the waters as “He rocked his only world, and everyone's.”

The vulture here is more than just “the hero” of the poem, as Wilbur puts it, but exactly what he stands for is not immediately clear. In terms of the great narrative of the Bible, we are used to thinking of ourselves and all humanity as “Adam’s sons,” and even as the “sons of Abraham”; in Christ, both of those images are completed and fulfilled, and all of us redeemed. But Still, Citizen Sparrow ends not with a claim of kinship with Adam or Abraham, but with this: “all men are Noah's sons.” Might Noah also be a type of Christ? How does the all-too-natural vulture connect with it, deepening our understanding the role and experience of Jesus as the Messiah?

Following Wilbur’s account of the nobility of the vulture, we can make the connection between it and Jesus’ role of overcoming death. But what unites them more subtly (and perhaps even more poignantly in this season of Lent) is shame and rejection, even exile. These terms are not at all unrelated to death, for touching the dead was one of the things that made an Israelite ceremonially unclean, and vultures’ ordinary habits might account for their similarly-rejected status in the Jewish bestiary. Elsewhere in the Bible, the characteristic baldness of the vulture provides imagery of shame, despair and humiliation, as in Micah 1:16: Make yourselves bald and cut off your hair, for the children of your delight; make yourselves as bald as the vulture, for they shall go from you into exile.

Surely the vulture is an unlikely symbol for Christ, especially when wrapped up with the character of Noah. But the key insight of the poem and the image actually lies in the relationship between the vulture and the sparrow, the latter of which serves as our stand-in. We are too often like that small bird in Wilbur’s account, wanting a more noble and glorious emblem than this of how the Kingdom bears on our world, wishing ever still to banish the unclean from our presence and keep our own lives neat and tidy. The cause of Christ is not neat or tidy, though, and brings ridicule and rejection from our peers more often than it brings honor. As we draw close to Jerusalem with Jesus, may we be willing to accept the “rotten office” ourselves, and to take his (and the vulture’s) perspective on rejection—in his story, and in our own.

“Still, Citizen Sparrow”

by Richard Wilbur

Still, citizen sparrow, this vulture which you call
Unnatural, let him but lumber again to air
Over the rotten office, let him bear
The carrion ballast up, and at the tall

Tip of the sky lie cruising. Then you'll see
That no more beautiful bird is in heaven's height,
No wider more placid wings, no watchfuller flight;
He shoulders nature there, the frightfully free,

The naked-headed one. Pardon him, you
Who dart in the orchard aisles, for it is he
Devours death, mocks mutability,
Has heart to make an end, keeps nature new.

Thinking of Noah, childheart, try to forget
How for so many bedlam hours his saw
Soured the song of birds with its wheezy gnaw,
And the slam of his hammer all the day beset

The people's ears. Forget that he could bear
To see the towns like coral under the keel,
And the fields so dismal deep. Try rather to feel
How high and weary it was, on the waters where

He rocked his only world, and everyone's.
Forgive the hero, you who would have died
Gladly with all you knew; he rode that tide
To Ararat; all men are Noah's sons.

From Richard Wilbur: New and Collected Poems. San Diego: Harcourt Brace Jovanovich, 1988: p. 318. ©Richard Wilbur.

Richard Wilbur is a poet, translator, and playwright, and was appointed as the second Poet Laureate of the United States in 1987. Please read the poem aloud, then click here to buy your own copy of Wilbur’s latest work, Anterooms: New Poems and Translations.

Evolution: just a theory

One game that my (young) children like to play is a guessing game where both players select a character from among many choices, and by process of elimination, tries to guess the character the other has selected. Questions like “does your character have red hair? glasses?” etc., are used to narrow down the possibilities. Once you have guessed correctly which character your opponent has selected, you can perfectly predict the answer to every question thereafter (and a good many parents likely prolong the questioning to keep the hopes of victory alive for their children). When considered separately, the individual features of each character—glasses, brown hair, purple hat, and so on—mean almost nothing, since they could be features shared with other characters in the game. Only the convergence of multiple features is indicative of a good guess, and the accuracy of that guess is put to the test every time a new question is asked.

A good theory is something like this: an educated guess, based on and consistent with all past work on the topic to date. It allows you to predict how future tests should pan out. In the guessing game, there are limited options to choose from (so the analogy, like all analogies, eventually breaks down). In science, we don’t really know the true way things actually work. What we have are theories—broad explanatory frameworks supported by experimentation, that make sense of our current collection of facts—that we can use to make testable predictions about the natural world. All theories in science are provisional in that they are not complete descriptions of how the world actually works and are subject to future revision; but at the same time they are robust frameworks that can be used to predict how experiments should behave with almost boring regularity. So, far from the colloquial usage of “theory” as speculation, “just a theory” is high praise in science.

The current understanding of evolutionary theory in all its scope and diversity is far more complex than Darwin himself could have ever envisaged. (As a geneticist, I’ve often wished I could have a cup of tea with him to show him how far his theory has grown, especially given his confusion about how heredity worked.) Our understanding of how evolution works has grown by leaps and bounds since the 1850s. What is remarkable is just how much Darwin got “right” given his time and place. His main hypotheses—that species descend from ancestral forms through descent with modification, that and natural selection acting on heritable variation is a significant force in that process—remains the core of modern evolutionary theory. We’ve added a lot of detail since then (population genetics, kin selection, neutral evolution/genetic drift, symbiosis, horizontal gene transfer, molecular exaptation, and so on), but Darwin’s core ideas have produced a wealth of successful predictions. They were a very good “guess” that continues to pay rich scientific dividends.

Whale evolution: an example of converging lines of evidence

One of the things I personally find quite enjoyable about evolutionary theory is the counter-intuitiveness of some of the predictions it makes. One example that is a personal favorite, and one I often use to illustrate how evolution makes sense of converging lines of evidence, is cetacean (whale) evolution. Let’s set up the “problem” that evolutionary biology forces upon us:

• Modern cetaceans are mammals – they nourish their young in utero through a placenta, give birth to live young, and feed newborns with milk – all features of standard mammalian biology.
• Mammals are tetrapods – organisms with four limbs. Mammalian life shows up in the fossil record as an innovation within tetrapods, so mammals are “nested within the set” of tetrapod forms. Not all tetrapods are mammals (amphibians, for example) but all mammals are tetrapods.
• Tetrapods are by and large terrestrial creatures. Having four limbs for locomotion is a distinctly land-based adaptation.

The “problem”, of course, is that modern whales are emphatically not terrestrial, nor do they have four limbs – they have two front flippers and a tail, with no hind limbs in sight. Yet they are mammals, which forces evolution’s hand as it were. Evolution thus is dragged, under protest, to the prediction that modern whales, as mammals, are descended, with modification, from ancestral terrestrial, tetrapod ancestors. Instantly this prediction raises a host of uncomfortable questions: where did their hind limbs go? How did they acquire a blowhole on the top of their heads when other mammals have two nostrils on the front of their faces? How did they transition to giving birth in the water? What happened to the teeth of the baleen whales? What happened to the hair characteristic of mammals? and so on. In some ways, evolutionary thinking about whales creates more difficulties than it appears to solve.

And yet, these difficulties are the stuff of science. If indeed our “educated guess” of terrestrial, tetrapod ancestry for whales is correct, the evidence will show that these transitions, challenging though they may seem, did indeed occur on the road to becoming “truly cetacean”.

Going out on a limb

Anyone who has seen a modern whale skeleton in a museum and noted it carefully may have noticed that though whales lack hind limbs, they do have a bit of bone back there where the hind limbs ought to be. While this is suggestive of a vestigial characteristic (a feature in a modern organism that has a reduced role relative to the role the structure played in an ancestral species), it’s hardly a smoking gun for evolution. Still, it’s consistent with the idea.

When we look at the cetacean fossil record, we also see forms suggestive of a progressive loss of hind limb function and structure over time, as David Kerk and Darrel Falk have elegantly explained before. Again, if one were resistant to evolutionary explanations, it would be possible (if a bit strained) to interpret these creatures as having been created directly as we find them in the fossil record. The facts that we do not see these forms in the present day, and that they seem to blur the distinctions between terrestrial tetrapods and whales might make one a bit uncomfortable, however.

Recent work on cetacean embryogenesis (how whales and their relatives develop from fertilized eggs into fully-formed baby whales) has shed even more light on the issue for modern species, however. Dolphin embryos actually have four limbs early in their development, as well as a few facial hairs, just as any good mammal should have. The hind limbs and hairs are lost later in development, and work on the molecular signaling events that halt hind limb growth and cause the limb bud to regress into the body wall have now been worked out in some detail. Moreover, early in dolphin development the nostrils are distinct and on the front of the face, and only fuse into a blowhole and migrate to the top of the head later in development. Early dolphin embryogenesis is distinctly mammalian and uncannily tetrapod-like.

… and passing the test

Taken in isolation, these facts about whales are interesting trivia. Taken together, however, they begin to form a picture entirely consistent with the prediction that modern whales are derived from terrestrial ancestors. The true strength of evolution as a scientific theory for the origin of whales is this: not that we can prove it, (for no theory is ever proven in science due to its permanently provisional nature), nor that we have full access to every bit of data we would like (consider how fragmentary the fossil record is, for example), but rather that we haven’t been able to disprove it yet, despite our best efforts. Descent with modification remains a productive educated guess that grows stronger with each investigation.

In the next post in this series, we’ll explore some additional lines of evidence for cetacean evolution that further illustrate the predictive power of evolutionary theory.

For further reading

Evidences for Evolution, Part 2a: The Whale's Tale

Evidences for Evolution, Part 2b: The Whale's Tale
J. G. M. Thewissen, M. J. Cohn, L. S. Stevens, S. Bajpai, J. Heyning, and W. E. Horton, Jr. (2006). Developmental basis for hind-limb loss in dolphins and origin of the cetacean bodyplan. Proceedings of the National Academy of Sciences 103 (22), 8414–8418. available freely online.

In our last two BioLogos podcasts, we looked at the question of transitional fossils and the genetic evidence for evolution. In our final installment of this three part series, we move on to the question of speciation and macroevolution. A common challenge to evolutionary theory is that while life does indeed change over time (what is known as microevolution), no one has ever seen one species evolve into another species (macroevolution). For example, no one has seen a dog evolve into something other than a dog. Because speciation has never been observed, and because science is based on observation, evolution cannot be considered scientific.

In fact, examples of speciation have been observed by scientists. We must also remember that we are able to observe just a tiny window of the long history of life on Earth, and the fact that any speciation has been noted at all is impressive indeed.

Transcript

It’s pretty clear to most of us that life can change over time. For those who aren’t convinced, just take a quick trip to your local animal shelter. Each of the dog breeds there, from the Great Dane to the Chihuahua, descended from a single ancestral population. As you probably already know, that ancestral group was a wolf-like species. -How did these drastic changes take place? Well, basically, genetic variation within that original population was acted upon by selective forces. Now, just to be clear, the selection at work here wasn’t natural. It was the result of breeding done over hundreds of years. But the basic principle is the same. Genetic variation plus some sort of selection results in genetic change. This is evolution.

For the most part we are ok with accepting this. Yet many people still have a problem with the Theory of Evolution. Those suspicious of evolutionary Theory generally split evolution into two categories. Instead of arguing that evolution is completely impossible, they will say something like, “I know microevolution is real, but I just can’t accept macroevolution.”

Kent Hovind, an especially outspoken opponent of evolutionary theory, often makes this argument in his presentations:

“Maybe you’re talking about macroevolution. That’s where an animal changes into a different kind of animal. Nobody’s ever seen that. Nobody’s seen a dog produce a non-dog. I mean you may get a big dog or a little dog, I understand, but you’re going to get a dog, okay?” (source)

But what does this mean? What is the difference between micro and macroevolution anyway, and why is one of them ok while the other is condemned?

Well, like many terms used in the evolution debate, the definitions tend to differ depending on who you talk to. This can make rational discussion difficult. Most opponents of evolution, like Kent Hovind, say that macroevolution refers to one “type” or “kind” of organism evolving into another “kind”. Microevolution, they might say, is evolution within a “kind”. Evolution of one dog breed into another, they would say, is microevolution. Evolution of a “dog into a non-dog”, as Hovind puts it, would be “macroevolution.”’

One big problem with this argument is that “kind” is not clearly defined. It is a subjective term referring to organisms that seem similar to each other. Now, this is a definition that can easily be manipulated. And it doesn’t work very well when asking scientific questions. Because there is disagreement about what they actually mean, the terms micro and macroevolution aren’t often used in scientific literature. But when biologists do refer to “macroevolution”, most define it as “evolution above the species level”.

(Sources: http://ib.berkeley.edu/courses/ib200a/lect/ib200a_lect26_Lindberg_macroevolution.pdf, http://www.nescent.org/media/NABT/, http://evolution.berkeley.edu/evosite/evo101/VIADefinition.shtml, http://www.nhm.ac.uk/hosted_sites/paleonet/paleo21/mevolution.html)

In other words, at the smallest scale, macroevolution is the development of a new species. This definition is more useful because you can objectively determine whether two organisms are members the same species, but “kind” has no specific definition.

So what does “species” mean anyway? How is it different from “kind?” Well, the term species can be hard to define. Life is complex, and categorizing it into clear groups can be tricky. The currently accepted definition of species comes from what we call the “biological species concept.” Basically, the biological species concept says that a species is made of populations that actually or potentially interbreed in nature.

So, two populations that cannot mate to produce successful offspring are by definition separate species. Now, this definition doesn’t always work. For example, when you have a species that reproduces asexually, finding the boundaries between species can be a little tricky. But in most cases it does a pretty good job. It’s a good way to objectively determine where one species stops and another one begins.

The Biological Species Concept is especially useful when you have two species that look and act very similar. Eastern and Western Meadowlarks are a good example of this. They look almost exactly the same. But they cannot interbreed successfully. Therefore, they are separate species. This definition also helps when we study evolution. Where can we draw the line between microevolution and macroevolution? Well, it’s never easy, but having a working definition of this thing called a species helps out a lot. When enough genetic changes accumulate in a population, eventually it loses the ability to mate with others of its species. Then, by definition, it becomes a new species. In other words, macroevolution has occurred.

As we just discussed, many critics claim that macroevolution can never happen—one species can never cross over to become another one. This statement might sound valid, but a little bit of investigation shows that it is not well supported by evidence. For one thing, the only difference between micro and macroevolution is scope. When enough micro changes accumulate, a population will eventually lose its ability to interbreed with other members of its species. At this point, we say that macroevolution has occurred.

The same processes—random mutation and natural selection—cause both micro and macro evolution. There are no invisible boundaries that prevent organisms from evolving into new species. It just takes time. Usually, the amount time required for macroevolution to occur is significant—on the order of thousands or millions of years. That’s why you don’t normally see brand new forms of life appear every time you step out your front door. And that’s also why some people think that speciation never happens at all.

But sometimes macroevolution doesn’t take that much time. In fact, the evolution of new species sometimes happens so quickly that we can actually see it take place! Let’s look at a few recent examples.

Biologists Peter and Rosemary Grant had been studying finches since 1973. They lived on an island called Daphne Major in the Galapagos. It was here that they conducted their studies. When they first began their studies, only two species of Finch lived on Daphne Major: the medium ground finch and the cactus finch. But, in 1981, Peter and Rosemary noticed that an odd new finch had immigrated to the island. It was a hybrid, a mix between a cactus finch and a medium ground finch. It didn’t quite fit in with the other birds. The odd misfit had an extra large beak, an unusual hybrid genome, and a new kind of song. But somehow he was still able to find a mate. The female was also a bit of a misfit and had some hybrid chromosomes of her own. So their offspring were very different from the other birds on the island.

Rosemary and Peter continued to carefully watch the odd hybrid line. They wondered if the birds would become isolated from the other finch species on the island or if they would eventually re-assimilate. After four finch generations, a drought killed off many of the birds on Daphne Major. In fact, almost the entire hybrid line was exterminated. Only a brother and sister pair remained. The two family members mated with each other, producing offspring that were even more unique than their parent line. From that point on, as far as biologists Peter and Rosemary could tell, the odd population of finches mated only with each other. They were never seen to breed with the cactus finches or the medium ground finches on the island. The finches with the strange song had become a brand new species.

(Source: http://www.pnas.org/content/106/48/20141.full)

Another example of speciation, or macroevolution, also took place on an island—this time, on the beautiful Portuguese island of Madeira. According to history books, the Island of Madeira was colonized by the Portuguese about 600 years ago. The colonizers brought with them a few unassuming European House Mice, which they accidentally left on the island. It’s also possible that a group of Portuguese House Mice was dropped off later on.

Recently, Britton-Davidian, an evolutionary biologist at University Montpellier 2 in France, decided to collect samples of the Madeira mice and see how those original populations had changed over time. What she found was surprising. Rather than just one or two species of mouse, she found several. In only a few hundred years, the original populations of Mice had separated into six genetically unique species. The first mouse populations had 40 chromosomes altogether. But the new ones were quite different. Each new variety had its own unique combination of chromosomes, which ranged in number from 22 to 30.

What seems to have happened is that, over time, the mice spread out across the island and split into separate groups. Madeira is a rugged volcanic island with crags and cliffs. So it makes sense that this would have been easy to do. There were many isolated corners for the mice to occupy. Over time, random mutations occurred—some chromosomes became fused together.

Now, In order to reproduce successfully, both parents must have the same number of chromosomes. So when a population develops a chromosome fusion, suddenly that group cannot mate with the other members of its species. It becomes a brand new species. That’s exactly what happened on Madeira. And because of this phenomenon, 6 new species evolved from just 1 or 2 in an extremely short amount of time.

(Sources: http://onlinelibrary.wiley.com/doi/10.1111/j.1365-294X.2009.04345.x/full, http://www.genomenewsnetwork.org/articles/04_00/island_mice.shtml, http://www.nature.com/hdy/journal/v99/n4/full/6801021a.html)

Another fascinating example of macroevolution was recently observed by researchers at Pennsylvania State University. This time, two species combined to make a single new one. In 1997, researchers at Penn State noticed a fruit maggot infestation on some recently introduced Asian Honeysuckle bushes. They decided to investigate the Honeysuckle fly population and determine how it was related to the other flies nearby. When they examined the honeysuckle fly’s genes, the researchers discovered something interesting. The fly appeared to be a hybrid of two native species—the blueberry fly and the snowberry fly.

But the honeysuckle fly’s genetic material was not an exact balance between that of the two parent species. The ratios of DNA varied from fly to fly. This showed the researchers that the honeysuckle flies had been breeding amongst themselves for many generations—probably at least 100. Also, they found that the Honeysuckle Flies were very unlikely to breed with any other species. They bred only on their host Honeysuckle plants. So they weren’t likely to mix with flies that lived on a different host.

According to Dr. Dietmar Schwarz, post-doctoral researcher in entomology, as far as the researchers can tell, “The new species is already reproductively isolated. They seem to be in a niche on the brushy honeysuckle where the parent species cannot compete."

(Source: http://www.psiee.psu.edu/news/2005_news/july_2005/hybrid_insects.asp)

While this kind of speciation—two species hybridizing to create a new one—seems odd, it is a significant mechanism of macroevolution. And it’s especially common in plants. In fact, a new species of weed recently arose this way in Great Britain. In 1991, Richard Abbot, a plant evolutionary biologist from St. Andrews University, noticed an unusual weed growing next to a car park in York. He discovered that the species, an unassuming scruffy weed, was a natural hybrid between the common groundsel and the Oxford ragwort, a plant that was introduced to Britain only 300 years ago. The York Groundsel lives in a different niche, or microenvironment, than either of its parent species. It is able to breed and reproduce, but only with other York Groundsel plants. It cannot successfully reproduce with any other species, including either of its parent plants. Thus, by definition, the York Groundsel is its own new species.

(Sources: http://www.nerc.ac.uk/publications/planetearth/2003/summer/sum03-evolution.pdf, http://www.nature.com/hdy/journal/v69/n5/abs/hdy1992147a.html)

So, as we have seen, macroevolution is an established process. Usually it takes thousands of years to occur, but sometimes we get lucky and catch it in the act. When Kent Hovind said that, “no one has ever seen a dog produce a non-dog” he was technically quite correct. But this statement infers that macroevolution means a drastic and obvious change from one type of organism into another. Those who think this way believe that macroevolution is something like two dogs breeding to suddenly produce a cat, or two guinea pigs mating to produce a mouse.

But this is not how evolution works at all. Over millions of years, a dog-like animal may indeed evolve into a something that looks completely unlike a dog. However, this is not something that we would expect to be able to observe. It just takes too much time. To put the scale of evolution into perspective, consider this. If the average lifespan of a United Stated citizen, 78 years, were a single minute, then single-celled life has been around for nearly 100 years. On this scale, all we get to see is one minute. And even in that time frame we sometimes see new species forming. God’s time is not our time and we tend to forget this. What we do expect to observe is a very slow step-by-step accumulation of tiny genetic changes that eventually result in speciation. And indeed, as we discussed today, this is exactly the sort of evidence revealed in nature.

So, macroevolution is not a “myth” by any means. It is supported by a vast amount of evidence. That evidence includes the fossil record and genetics, as discussed in previous BioLogos podcasts, and, when we get lucky, direct observation of speciation. God, being who God is, could conceivably have created species out of thin air in a single instant. But what if instead if God created and sustained the process by which new species are created? Does that make him less powerful or less "god-like"? Is it somehow more God’s process if it happened in an instant, than it is if it happened over a long period of time? Presumably even if it happened in an instant, it would still happen by some sort of process—only faster.

God’s time is not our time, and perhaps it’s a good idea for all of us to simply stand back in amazement while God does God’s work in God’s time through God’s process.

Today's video is courtesy of filmmaker Ryan Pettey, director/editor of Satellite Pictures, and features Dr. Rick Colling, biologist and author of Random Designer.

In today’s video, Dr. Rick Colling states that one of the biggest difficulties in communicating compatibility between evolution and faith is a misunderstanding of what evolution is. Evolution is not, he says, about the imposition of death and destruction and survival of the fittest. Rather, it is about second chances. Our bodies contain thousands of genes, which duplicate like a computer back-up copy and can serve as raw material. When an organism encounters adverse environmental condition, this raw material can be used to help adapt and survive.

“God is so creative," says Colling, "that he’s actually put into place a mechanism to start doing these gene changes in advance before they’re even needed. And God has given us a second change through the evolutionary process of creating duplicate genes that give rise to new raw material that give rise to new possibilities, and that really more accurately describes the process of evolution. It’s redemption, it’s possibility, and it’s hope.”

As we saw in the last post, only a small fraction of the human genome appears to be subject to selection (on the order of 5-6%). The rest appears free to mutate freely without consequence to mammalian biology, and as such constitutes good evidence that it performs no particular function. An additional line of evidence in favor of non functionality in the human genome is the observation that a large fraction of our genetic material is made up of what are known as mobile genetic elements, or “transposons.” These little snippets of DNA are well known and well studied in many organisms, including humans. So, what are they, and what are they up to?

Along for the ride, but looking out for number 1

Non-biologists are usually somewhat taken aback when they learn about transposons. Transposons are small segments of DNA inserted into in the genomes of many organisms that are little worlds unto themselves: they have a few genes that serve only to copy themselves and move themselves to new locations in a genome. That’s it! On the scale of biodiversity, transposons are less life-like even than viruses. They are the perfect parasites: using their host to provide resources so they can replicate themselves, and with a “lifestyle” so simple that replication is essentially its only feature. Their origins, like the origins of viruses, is somewhat of a mystery.

Despite their somewhat mysterious nature, transposon sequences make up a staggering 45% or more of our genome. That’s about 1.4 billion DNA base pairs of our genetic material that is recognizable as functional transposons or their mutated, fragmentary remains. Not surprisingly, nearly all transposon sequences in the human genome are not under selection – they are free to accumulate mutations. These mutations have no effect on us since they do not alter any function we require.

Rags to riches: converting transposons to functional sequences

Despite their parasitic nature, sometimes the host species can exploit transposons as a source of genetic novelty. The ability of transposons to copy and spread themselves around in genomes raises the intriguing possibility that they can acquire a function if they land in the right chromosomal area. While it is difficult (though not impossible) for a transposon to acquire a function as gene coding sequence (i.e. becoming a host protein product), it is comparatively easy for a transposon to pick up a function as a regulatory sequence: a segment of DNA that directs when and where a certain host gene product should be made. Transposons contain regulatory sequences for their own genes already, and these sequences can potentially interact with regulatory sequences in the host genome.

Perhaps a review of gene structure and function would be helpful at this point. Genes are portions of the long DNA sequences that make up chromosomes (each chromosome is one very long DNA molecule). As we have seen above, a good proportion of these sequences are either transposons or the defective fragments of transposons, as well as other DNA that is not under selection and is free to mutate. Interspersed in this sea of non-selected sequences are genes: segments of chromosomes that code for protein products that carry out functions within the cell: enzymatic functions, structural functions, and so on. These sequences stand out because they are subject to selection, and thus do not change at the same rate as sequences that are free to mutate (as we discussed previously).

Genes have a typical structure (obviously simplified here somewhat). First off, there is the actual DNA sequence that specifies the protein product sequence (the so-called “coding sequence”, shown in blue). This sequence is usually broken up into segments in mammalian genes, and these sequences are spliced together when the DNA sequence of the gene is transcribed into a “working copy” called mRNA – a short duplicate of the code that can be used by the cell’s machinery to actually build the specified protein.

In addition to the actual coding sequences, other sequences are needed to tell the cell when and where certain genes should be transcribed into mRNA. Every cell in an organism has the same genes in their chromosomes, but not all are transcribed. Using different genes in different combinations is what makes cells take on distinct roles – for example, cells in your small intestine need different genes (for absorption of nutrients) than do cells of the immune system (for fighting off pathogens). Regulatory sequences make sure any given cell type has the right genes transcribed and made into protein products. Some of these sequences are part of the mRNA transcript (shown in red), and others are not transcribed but only part of the chromosomal DNA sequence (such as the “promoter” region that directs the enzymes responsible for making the mRNA transcript (shown in blue).

So, what happens when a transposon inserts into the regulatory sequence of a gene? In many cases, this mutation (the insertion event) will cause a problem (perhaps the gene is no longer transcribed in the right way, for example). In some cases, however, the gene can tolerate such an insertion. Regulatory DNA is more able to accept changes than is coding sequence DNA, so it is quite possible that an insertion may not harm the function of a gene.

In some cases, sequences from the transposon can participate in the regulation of the neighboring gene. If these changes are beneficial, as they sometimes are, then the transposon sequences involved in regulation come under selection. Some parts of the transposon mutate away beyond recognition, and the useful bits remain since they, now being under selection, are not (as) free to mutate. The end result is a gene that has co-opted a fortuitous event (a transposon insertion) and, through mutation and selection, honed it to serve a new function (altered regulation of its product). This is an example of exaptation, the conversion of one function to another through mutation and subsequent selection. In this case the old function (a “self-serving” transposon) has had a portion of its sequence exapted to become part of the host regulatory DNA.

Recent work comparing 29 different mammals has shown there are about 280,000 examples of exapted transposon fragments in mammalian genomes. Despite this large number, the absolute fraction of human DNA that falls into this category is tiny: of our 3 billion base pairs of DNA, only about 7 million are the detectable remnants of exapted transposons. The vast majority of transposon and transposon fragments in the human genome (as we mentioned, totaling around 1.4 billion base pairs) are not under selection and are free to mutate without affecting any function.

The genomic recycling bin

So, transposons are at once a good example of non-functional DNA in genomes (indeed, nearly half of our own genome is made up of them), and an example of how evolutionary processes can convert non-functional DNA into functional DNA through mutation and selection. While I did not discuss exapted transposons in my previous series, this is another clear example of how evolution can produce novel information within the genome: by “recycling” small amounts of its junk to produce new functions. Note well, however: the fact that a small fraction of transposons have been exapted into functional sequences does not “confer” functionality on all transposons. We see the signs of selection on only a tiny minority, and even then typically only on fragmentary remains.

In the next installment of this series, we’ll examine another form of non-functional DNA present in genomes: processed pseudogenes.

For further reading

International Human Genome Sequencing Consortium, (2001). Initial sequencing and analysis of the human genome. Nature 409, 860-921. http://www.nature.com/nature/journal/v409/n6822/full/409860a0.html

Lindblad-Toh, K., et al. (2011). A high-resolution map of human evolutionary constraint using 29 mammals. Nature 478, 476-482. http://www.nature.com/nature/journal/v478/n7370/full/nature10530.html