That may seem strange. Many people wouldn’t start with the Bible when talking about a scientific theory. But I’m a theologian, and I take the Bible with utmost seriousness. Talking about the Bible is a natural place for me to begin, both because the Bible was principally important in my youth, and because it remains so for me today.

I don’t mean to snub science. Science is important too. I read a lot in the sciences, and I think the evidence supporting the theory of evolution is strong. I try to take this and other evidence with great seriousness.

But the real story – for me – starts with the Bible.

Centrality of Scripture

Fortunately, my parents were committed Christians. Our family was one of those “attend-church-three-times-a-week-and-more” families. My parents were significant leaders in our local congregation, and I began following their footsteps early in life.

I doubt I missed more than a handful of Sunday school classes before I was twenty years old. And I always attended Vacation Bible School – even winning Bible memorizing competitions on occasion. (John 11:35 was my friend!) I participated on youth Bible quizzing team for a while too.

While growing up, I don’t recall anyone telling me that the Bible was the inerrant Word of God. But my passion for Scripture and my Evangelical community inclined me toward that position. Scripture was central in my life.

Besides, I wanted a failsafe foundation for my beliefs. And how could I convince my Mormon friends to become Christians if the Bible was not true in every sense, including literally true about what it said about the natural world? Witnessing to God’s truth seemed to require that I believe the Bible was without error on all matters, including matters related to science.

An Inerrant Bible?

My view of the Bible began to change when I went to college. It wasn’t that a liberal Bible professor brainwashed me away from the positions of my youth. Instead, I started reading the Bible carefully and the work of biblical scholars. I began to think it important to love God with my mind in a more consistent way.

And then I took a class in koine Greek, the language of the New Testament. In this course, I discovered several things. First, we have differing English translations of the New Testament, because the biblical text allows for a number of valid translation options. (When I later took Hebrew class, I found the diversity of valid translations even greater!) Second, we do not have access to the original biblical manuscripts/autographs. Our Bibles come from later manuscripts, the earliest of which are not complete. And, third, the oldest texts we have differ in many ways – although most differences are minor.

I also discovered discrepancies in the Bible. For instance, in Matthew’s gospel, Jesus curses a fig tree and it withers immediately (21:18-20). But in Mark’s version of the same story, the fig tree does not wither immediately and the disciples find it withered the next morning (11:12-14; 20-21). Mark says that Jesus heals one demon-possessed man at Gerasenes (5:1-20), while Matthew says there were two demon-possessed men involved in that same miracle (8:28-34). Jesus tells the disciples to take a staff on their journey as recorded in Mark 6:8, but Matthew says Jesus told the disciples not to take a staff (10:9-10). Jesus says Jonah was three days and three nights in the whale's belly. Then, making an analogy with his own death, he says the Son of Man will be three days and three nights in the heart of the earth (Mt 12:40). But Jesus was not dead three days and three nights!

I mention only a few of the many internal discrepancies. Once I discovered a few, I noticed more. This, of course, made me question whether I should say the Bible is inerrant in all ways.

What’s the Bible For?

I’m persistent. I don’t settle for easy answers, ignore problems, or appeal to mystery at the drop of a hat. I want to give a plausible account of the hope within me.

My quest for better ways to think about the Bible prompted me to read theologians and Bible scholars from the past and present. What I found surprised me! I had assumed believing the Bible is inerrant in all ways was the traditional position of Christians throughout the ages. I assumed it was the position of my own Christian tradition. I was wrong.

Few if any great theologians argued the Bible was absolutely inerrant. Augustine did not affirm inerrancy in this way. Thomas Aquinas didn’t. Neither did Martin Luther or John Wesley – a least in a consistent way. And I discovered through reading and conversations that those considered the leading biblical scholars and theologians today also reject absolute biblical inerrancy.

I did find a few teachers who said the Bible was inerrant. But when I read their explanations of the Bible’s discrepancies and their views about the differences between the oldest manuscripts, I found they stretched the word “inerrant” beyond recognition. Their meaning of “inerrant” was nothing like the usual meaning. And it was certainly not what most Evangelicals meant when they called the Bible the inerrant Word of God.

Perhaps even more important was my discovery that great theologians and biblical scholars of yesteryear believed the Bible’s basic purpose was to reveal God’s desire for our salvation. Many giants of the Christian faith could agree with John Wesley who said, “The Scriptures are a complete rule of faith and practice; and they are clear in all necessary points.”

The necessary points of Scripture refer to instruction for our salvation. They indicate that, as the Apostle Paul puts it, Scripture is inspired and “useful for teaching, for reproof, for correction, and for training in righteousness, so that everyone who belongs to God may be proficient, equipped for every good work” (2 Tim. 3:16-17). The purpose of the Bible is our salvation!

I also discovered Christian leaders over the centuries did not feel required to search the Bible for truths about science. In fact, they sometimes used allegorical interpretations that seem silly to me now. The vast majority of Evangelical scholars with whom I talked also didn’t think the Bible has to be inerrant about scientific matters.

After my studies, I came to believe that the Bible tells us how to find abundant life. But it does not provide the science for how life became abundant.

Tomorrow, Tom will discuss what his evolving view of the Bible has to do with evolution.

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. 

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.

One of the more outspoken proponents of this view is Sam Harris, a leading figure among the New Atheists, and a fierce antitheist. Harris has written a book and given talks on the idea that morality—broadly, the act of discerning good from bad—can be derived from science.

On the face of it, this seems strange, since the scientific consensus, especially in evolutionary biology, has always been that nature is morally neutral. We know, as scientists, that sharks are not “bad” any more than dolphins are “good.” The true evolutionary view (I always thought) was that fitness is related to success, not goodness.

The problem is that as human beings, we know that goodness exists, so it must be accounted for, and if one is a staunch believer in scientism, it must be accounted for scientifically. In some situations, this accounting seems to be possible. There is a large literature on kin selection as the basis for some kinds of altruism, and Dawkins has made the case that what he calls “misfiring of genes” for kin altruism are responsible for human goodness.

Harris claims that moral values can be based on scientific principles, and that no kind of cultural context, especially faith-based context, is necessary for humans to have a code of morals. He bases this argument on the idea that moral values are based on facts, and that these facts can be tested for their truthfulness. To some extent, this is an old idea. Murder, adultery, theft and lying—some of the best-recognized universal moral prohibitions, all tend to destabilize the coherence of social groups and would therefore be selected against in all societies.

But Harris goes much further, using arguments and examples that are anything but scientific. Since Harris is a leader of the antitheistic movement, and is interested in finding examples of religious practices that he believes can be scientifically proven to be immoral. He cites the abusive treatment of women in Islamic societies as a main example, and he mentions corporal punishment of children as a slap at Christianity.

So how does Harris prove scientifically that forcing women to cover their bodies, and hitting school children with rulers are morally wrong? He doesn’t. Here is what he actually says:

But we can ask the obvious question: Is it a good idea, generally speaking, to subject children to pain and violence and public humiliation as a way of encouraging healthy emotional development and good behavior? Is there any doubt that this question has an answer, and that it matters?

Harris clearly believes the answer to that question is no, and I agree with him. But where is the science here? Has he data to show that children who were subjected to corporal punishment had worse emotional development and behavior than children who did not undergo such punishment? No. He has no such data, and in fact while he considers the wrongness of corporal punishment to be an obvious fact, there are millions of people who consider it to be just the reverse. There is no science here; there is simply a basic underlying moral idea, which Harris shares with others.

Harris touts the evils of Islamic fundamentalism as morally indefensible from a scientific point of view. But what kind of fact is it to say that making women cover their bodies is wrong, other than the “fact” that Harris thinks it is? Is there a science for determining the optimal way to treat women? If there is, it isn’t mentioned by Harris. 

While it may seem obvious that the oppression of women is morally wrong, proving scientifically that its disadvantageous to the thriving of our species is more tricky. In fact, the moral values of Harris, which are typical Western Judeo-Christian values, are largely counter-evolutionary. What we see when we look at history or sociology, is a background of true selection-positive behavior—indiscriminate killing of enemies, sexual aggression, concentration of power in a dominant faction—on which has been superimposed a moral code, followed and enforced despite its anti-evolutionary tendency. The real question to ask is: How is it that humans obey any of these moral codes that do not help them survive as individuals or as members of a culture?

In truth, there is no science at all behind Harris’s grand claim of factual moral values, (beyond such obvious things as it isn’t a good idea to add cholera germs to the water supply). He even admits this by stating:

Now the irony, from my perspective, is that the only people who seem to generally agree with me and who think that there are right and wrong answers to moral questions are religious demagogues of one form or another.

Of course that is correct, because both Harris, and the people whom he calls “religious demagogues,” have formulated moral codes that they hold to in the absence of any “scientific” data. 

The argument that morality is outside the scope of science is not a hard one to make, but it isn’t only morality that must be excluded from the domain of science. The more important argument is that very few of the ideas of evolutionism are based on anything remotely scientific. This is because the evolutionism paradigm includes many distortions of Darwin’s great theory, and too many of these distortions have become accepted by an antitheistic academic culture without proper rigorous analysis. 

Like Steven Jay Gould, I see no evidence that the biological mechanisms of evolution by natural selection can be extrapolated beyond the bounds of biology. Gould devotes several chapters in The Richness of Life to attacking the “adaptationist paradigm,” which is a central part of evolutionism. In responding to Daniel Dennet’s assertion that adaptation and selection explain just about everything, Gould says:

The fallacy of Dennet’s argument undermines his other imperialist hope that the universal acid of natural selection might reduce human cultural change to the Darwinian algorithm as well … The chief strategy proposed by evolutionary psychologists for identifying adaptation is untestable and therefore unscientific.

Cunningham has also explored this issue in Darwin’s Pious Idea. Social Darwinism, eugenics, evolutionary psychology, sociobiology, mimetics and other nonbiological applications of Darwin’s theory are not rationally consistent with the fundamental properties of evolution by natural selection. 

Evolutionism has been used to “explain” all sorts of dynamics in culture, using evolutionary concepts. But, while the evolution of devices that play music (as an example) might bear a resemblance to the evolution of carnivores, it is a superficial resemblance. Devices do not replicate themselves, so they cannot be the target of selection. 

Scientism is a failed philosophical approach to the pursuit of universal truth. Its failure should be evident especially to scientists who, more than most, understand the limits of their fields of study, as well as the enormous effort it takes to wrest nuggets of pure truth from nature. We must, as previous generations of enlightened thinkers have done, admit that issues of morality, beauty, thought, love, art, and culture are not approachable by scientific methodology or tools, or we risk losing a huge part of our human endowment of special (if not divine) genius.

Genesis 8:1: But God remembered Noah and all the wild animals and all the domestic animals that were with him in the ark. And God made a wind blow over the earth, and the waters subsided; 2 the fountains of the deep and the windows of the heavens were closed, the rain from the heavens was restrained, 3 and the waters gradually receded from the earth.

The Flood narrative of Genesis 7-9 has played a prominent role in science and religion debates for over three hundred years and gave rise in earlier centuries to geological theories such as old earth catastrophism. While literary studies have uncovered the chiastic structure of the Flood story (see Gordon Wenham, “The Coherence of the Flood Narrative” Vetus Testamentum 28 (1978):336-48) and with it the theological pivot point of the entire narrative (Gen. 8:1 – “And God remembered Noah…), much of the popular attention remains on the questions regarding details (Is there THAT much water in the world to cover ALL the mountains to a depth of 15 cubits? Could you really fit two or seven of every animal species in an ark that size?)

Looking at a smaller matter, we find at the beginning and the middle of the narrative indications of an ancient Near Eastern worldview. As the story is told, the flood was not merely the result of excessive rain, but actually the convergence of the waters above the earth with the waters below the earth. It is, as one translation puts it, as if the sluice gates at the deep and of the heavens were thrown open and water poured in from above and below. This is a consistent picture from the Old Testament of a three-tiered universe—a dome above the earth holding back the heavenly waters, a flat earth with water on its surface, and water under an earth which is held up by pillars.

That the story is told using the cosmology of its time should not be unduly unsettling, nor that the story is reinterpreted as new understandings of the universe come into favor. By way of example, consider John Calvin and his understanding of the structure of the universe. Although committed to the principle of sola Scriptura, Calvin recognized that the Bible would have been written in terms its original recipients would have understood.

Calvin inherited the medieval cosmology of his time, a way of viewing the world heavily influenced by Greek thought and one which was about to receive shocks from astronomers such as Copernicus and Galileo. But not just yet. Calvin still subscribed to the common conception of his day in which the four elements—earth, air, fire, and water—comprised the earthly sphere and possessed unique characteristics. The nature of air and fire was to rise, while the nature of earth and water is to sink. Earth, being heavier than water, should sink to the center of the cosmos and water should compose the next layer. Both earth and water are spherical, i.e., naturally form spherically around the cosmic center. Thus the heavier spherical element of earth should be encased entirely within the lighter spherical element of water.

Notice what this does to the flood story. For Calvin, the amazing thing is that the world isn’t constantly under water and subject to flooding. In the cosmology of Calvin’s day, it does not take an act of God to cause a universal flood, but rather an actively present and restraining hand of God to keep the waters back in everyday circumstances and make inundation by water something other than universal.

Obviously, Calvin was wrong. Or perhaps we should say that medieval cosmology was flawed and justifiably gave way to new conceptions of the universe. The answer is not to return to an ancient Near Eastern cosmology, but to reinterpret cautiously within new and better cosmologies and to pay closest attention to the text and the theology of scripture.

The geological and planetary sciences bring their own unique contributions and are of more interest than the latest expedition to discover the ark on Mt. Ararat. Is the flood story a universalization of a catastrophic regional event that burned itself into the psyche of ancient cultures in the Mediterranean basin? Various theories regarding a Black Sea venue for a catastrophic flood event are still in process of being sorted out. It’s intriguing. Or the question where the water on Planet Earth comes from? Was it always here as an emanation of vapors from the earth’s crust in its early formation, or has it accumulated over eons through the steady bombardment of earth by small, icy comets? It’s an intriguing scientific question that is in the midst of determination through testing.

Preaching Suggestions

When preaching on the story of the Flood, it is easy to get lost in the debates over particulars. As mentioned elsewhere, to tackle all the peripheral issues threatens to turn a sermon into a geology lecture. Other settings are better suited to addressing those questions, and those are best addressed open-endedly.

A brief explanation of ancient Near Eastern cosmology can be helpful to contextualize the story. If there are those who are tempted to think that a cosmology embedded in the Bible must be inspired and definitive, one can note that cosmology has changed by the New Testament. The Bible itself isn’t wed to a particular structure of the universe.

What is important is to keep the theology of the text front and center, and in that theology there are at least three non-negotiables from the flood narrative. First, human sin and violence threatens to undo a good creation (the flood is a de-creation event, a return of the waters mentioned in Genesis 1:2). Second, God remembers Noah, and never forgets his promises. Third, the end of the flood is a covenant with the whole earth regarding the stability and endurance of the natural order.

Morality, or more strictly our belief in morality, is merely an adaptation put in place to further our reproductive end.

Important scientific theories invite philosophical and theological reflection. Dawkins, Ruse, and Wilson, have described their conclusions. But scientific theories are often compatible with multiple philosophical and religious interpretations. For example, Newton's laws of motion and gravity allow several competing theistic and atheistic interpretations.

To avoid Ruse and Wilson's philosophical conclusion, we need not dispute their scientific hypothesis about how morality evolved. We need only dispute their philosophical extrapolation as to why morality exists. Even if we restrict ourselves to an atheistic worldview, this extrapolation is questionable. Donald MacKay (1965) would call this an example of "the fallacy of nothing but-tery". This is the assertion that a description of something at one level renders other levels of description meaningless. From our everyday experience, we know that a successful description on one level does not invalidate other levels of description. For example. one might assert that a Shakespeare sonnet is "nothing but" ink blots on a page (MacKay 1965). True, one way to describe a sonnet is to precisely specify the page coordinates of every ink blot. This description is valid and complete on its own level; however, one could also analyze the sonnet linguistically, emotionally, socially, historically, and on other levels. If one is programming an inkjet printer, the most important description is in terms of ink blot coordinates. For almost every other purpose in life, however, that is an unimportant level of description. In the same way, a complete evolutionary description of the existence of morality does not necessarily invalidate the truth, utility, or significance of other levels of description of morality.

If we do not restrict ourselves to atheism and instead allow for the existence of a creator, the extrapolation from how morality evolved to why morality exists fails further. Consider an analogy. Suppose an inventor builds a robot which could do a variety of useful things-- mow the lawn, clean the house, grade homework, write book chapters, and so on. One thing this robot can do, given a complete set of spare parts, is build a replica of itself. Whenever the inventor needs another robot, she gives one robot a set of spare parts and has it build a replica of itself. Amongst all the software subroutines within this robot, there is a set of subroutines that govern the robot's self-replication, including the replication of those self-replication subroutines. Would it be correct to say that the purpose of the robot's existence is merely to reproduce those particular self-replication subroutines? Do all of the other software and hardware of the robot--which allow it to mow the lawn, and so on-- merely further the reproductive ends of those self-replication subroutines? At one level, the robot's hardware and software do serve to reproduce those self-replication software routines. At another level of analysis, however, those self-replication software routines serve the robot to produce more copies of itself. At still another level, those self-replication software routines serve the robot's creator. The creator of the robot should get the last world as to which of those levels of description is most important.

In humans, does morality exist to further the reproduction of certain genes, or do those genes exist in order to allow for the production of new human beings who can behave morally? If human beings have a creator, the creator gets the final word on the question of purpose. The mechanism which the creator used to make those genes-- whether de novo or via evolution-- is secondary. The creator's purpose in creating those genes decides the issue.

References

• Dawkins, Richard. 1976. Pp. 1-11 in The Selfish Gene. Oxford: Oxford University Press.
• MacKay, Donald. 1965. Christianity in a Mechanistic Universe. Chicago: InterVarsity.
• Ruse, Michael, and Edward O. Wilson. 1993. The approach of sociobiology: The evolution of ethics. In Religion and the Natural Sciences, ed. James E. Huchingson. Fort Worth: Harcourt Brace Javonovich.

Today, as I write, I am no longer in the desert of southern California, nor in the beech-maple forest of New Hampshire, but on a glacial drumlin in Waubesa Wetlands—a large marsh four miles south of Madison, Wisconsin. Here Ruth and I have our home, and here I study creatures whose watery habitats my neighbors and I have worked to save from eventual destruction. While my desert study site now is covered by a city where people live alone in the land—absent the desert creatures—my wetland study site remains occupied by all kinds of native plants and animals. Embracing it is the Town of Dunn, whose land stewardship plan helps people understand, serve, and maintain this and the other ecosystems. Our town stewardship plan encourages restoration of the landscape, protects agricultural lands, and strives to transmit an intergenerational heritage of secure and wholesome homes, livelihoods, and habitats for the animals, plants, and people that live here. We live largely in harmony and accord.

House-building on slabs poured onto desert sands first alerted me to the question of praxis, the third point on the napkin. But it was later, in my work as organizer of the Waubesa Wetlands Scientific and Agricultural Preserve, and as supervisor and later as chair of the Town of Dunn, that I came to realize that science and ethics do no earthly good unless put into practice. In serving my town, I came to apply what I had learned in the desert: praxis uninformed by science and ethics usually creates more problems than are solved.

“How do you put it all together?” those students in New Hampshire wanted to know. For me, it was building a framework for stewardship that simultaneously considered the questions “How does the world work?” “What is right?” and “What then must we do?” This science-ethics-praxis triad is a framework for living, for learning, for teaching, and most importantly for acting. It is a framework for stewardship.

In order to live and act rightly in the world, we need to know how the world works. We need to know how the systems that sustain us work, and how we interact with them. Without such knowledge we could drown in a flash flood, have our homes undercut by desert winds, cross the street in the path of an oncoming car, or get sick from consuming foods with toxic ingredients. As human beings develop more and more of the world, and as the reach of human actions extends regionally and globally, our knowledge must increase accordingly. This knowledge is not limited to what we acquire from a formal education; it also includes the knowledge we gain from family and friends, and from experience and experiment. In order to live and act rightly in the world, we need to know how the world works.

In order to live and act rightly in the world, we need to know what we ought to do. A century ago, this question was addressed in many colleges across America in a course for graduating seniors on moral philosophy. The purpose of this course was to convict students that they should apply their knowledge for the pursuit of good instead of pursuing self at others’ expense. At my university, this aspect of college education is expressed in a quotation from Abraham Lincoln carved in stone on a bench behind Lincoln’s statue at the top of Bascom Hill: “Let us have faith that right makes might, and in that faith, dare to do our duty.” The question “What is right?” is represented by the ethics corner of our triad. Moving directly from the Science corner to the praxis corner, or from the ethics corner to the praxis corner, proves problematic, even disastrous. Consider the result of going from knowledge of nuclear fission (science) directly to producing and dropping an atomic bomb (praxis), or moving from the belief that death is bad (ethics) to removing dead wood from forests (praxis); both are examples of these disastrous shortcuts.

But knowing the science and observing the ethics of this stewardship framework does absolutely no good if it is not put into practice—placed into service. By themselves, the very best science and the most substantial ethics are no substitutes for action. We need to act appropriately and deliberately in the light of scientific and ethical knowledge. Praxis by itself, without being grounded in science and ethics, results in mere activism—activism that is unlikely to do good and that may produce harm. All three corners of the triad are essential—but not by themselves. Taken together and working interactively, they provide a framework for stewardship.

But will these three operate in dynamic interaction? Will they interact in ways that preserve and achieve the integrity of human life and the environment? The answer depends on what we know and understand about ourselves and the world (science), what we believe we should do (ethics), and what we in fact do, and how we respond to our successes and failures (praxis). It depends on our will, our motivation, our determination, and our dedication to strive for a harmonious world of creatures before their Creator. What might make us strive for such a world?

Part 3 explores the challenge of translating ideals into concrete actions.

A careful study of this chapter is important because it gives us a beautiful picture of the proper relationships we should have with God, the natural world, and each other. Numerous posts could be written on each of these relationships, but in this post I’d like to focus on how Genesis 2 describes our relationship to the rest of creation. These relationships are given deeper significance when we recognize that the garden is being described as a temple-like “sacred space,” not just an ordinary garden. There are numerous clues in the passage that this is the case. John Walton writes that the Garden/temple parallels “are givens that are simply assumed by the author and audience” ¹ of Genesis, but we completely miss them if we take fail to read the text the way the ancient author and audience would have.

Temples and Gardens

In the Ancient Near East (ANE), all sacred space was conceived of as something like a temple; it was a place where humans would serve God and experience their closest access to Him. Thus in ANE cultures, a temple complex was seen as being the apex and a microcosm of creation and the earthly abode of the god(s). Descriptions of temples often pictured a river flowing from under the temple and flowing out through an adjacent garden, symbolizing the fertile extravagance of the divine provision. A temple garden would be no mere backyard vegetable patch, but rather an elaborate, beautifully landscaped botanical park.

The same temple/river picture can be seen in the description of the eschatological temple in Ezekiel (ch. 47) and Revelation (chs. 21-22, where the final temple is God Himself). Sound familiar? In Genesis 2 we also have a river flowing “from Eden [‘Abundance’] to water the garden” (v. 10).² Not only is the Garden filled with “every beautiful tree with edible fruit” (v. 9), but the area itself is rich with gold, resins, and gemstones (sometimes translated “bdellium and onyx”), the same materials later used to decorate Israel’s tabernacle, temple, and priestly garments. Furthermore, many scholars are convinced that the design of temple’s Menorah (candlestick) deliberately echoes the Garden’s Tree of Life, and some also think that the Ark of the Covenant in the temple parallels the Tree of the Knowledge of Good and Evil.³

Made for Sacred Service

As inhabitants of this temple-garden, it comes as no surprise that Adam and Eve enjoyed a special closeness to God’s presence (Gen. 3:8 pictures God taking an evening walk through the Garden). But as inhabitants of the Garden, they had special responsibilities as well; they were told “to farm it and take care of it” (v. 15). The two Hebrew words used here have a broader range of meaning than their English translations suggest. As John Walton writes, the broader meaning of the word here translated “to farm” (particularly when used in a sacred context) “is often connected to religious service deemed as worship (e.g., Ex. 3:12) or of priestly functionaries serving in the temple precinct (e.g., Num. 3:7-10).” ⁴

The usage in Genesis 2 seems to have two layers of meaning: “farm/cultivate the Garden” (since it is an agricultural space) and “serve/worship God” (since the Garden is also a sacred space). The dual meanings are as intertwined in Hebrew grammar as they are intended to be in practice. The second Hebrew word (translated “take care of”) has a deeper religious meaning as well. The word can refer to protecting farmland from external threats, but in a danger-free sacred space like the Garden, the word more generally refers to “performing duties on the [temple] grounds,” that is, to “sacred service.”⁵

Walton therefore translates these two Hebrew words as “serve and preserve.” These same words appear again together several times in Numbers to describe the priest’s duties in the temple. Because of all this, Gordon Wenham describes Adam as “perhaps…an archetypal Levite” with a “quasi-priestly” role in the garden.⁸ Eve was created as Adam’s companion and “helper” in his work, a word which nowhere in the OT refers to a subordinate assistant, but rather to one who is at least equal to the one being helped.⁹

Genesis 2 should banish from our minds any idea that creation care is somehow “secular” work for a Christian, or that it is not even our responsibility. This was the first task given to humanity, to serve and worship God by cultivating and protecting the natural world. The centrality of our responsibility in this regard is even clearer when we back up to the beginning of the chapter. We know there was a river “flow[ing] from Eden to water the garden” (v. 10), symbolizing that “all fertility emanates from the presence of God.” ¹⁰ Nonetheless there could be no cultivated plants in the garden because “there was still no human being to farm the fertile land” (v. 5). With no gardener and no rain, the ground was watered indiscriminately; a human was needed to irrigate the waters and support a garden.¹¹ Therefore, God “formed the human from the topsoil” (Hebrew wordplay equivalent to “human from the humus”) before planting the garden. God certainly could have watered it another way without needing us, but He chose not to, and the resulting collaborative picture here is a beautiful one. All provision flows from God, but He has chosen to give us an essential part in further channeling his provisions in the natural world. Far from countering God’s creative work by destroying nature, we are intended to work with Him to preserve and further it.

Of course, though created primarily to glorify God, the world was also made to provide us abundantly with the food and resources that we need to live (Gen. 2:16). Yet we don’t need to look far to see that we have often failed in our responsibility to properly care for creation. We live in a fallen world, and sin has fractured the intended harmony of our relationships with God, creation, and each other (as described in Genesis 3:14-24).

I recently heard a striking crystallization of this fallen perspective in Spencer Tracy’s narration in the opening scene of the sprawling 1962 western film “How the West Was Won.” As the camera flies over majestic Western fields and mountains, the narrator tells us that “This land has a name today, and is marked on maps. But the names and the maps all had to be won, won from nature and from primitive man.” This is the fallen perspective – advancing our human purpose on earth is done through defeating nature and other people (derogatively labeled “primitive,” as well) apart from God. This perspective perfectly illustrates the conflict-based relationships that sin brings about, already described for us back in the first chapters of the Bible.

Are we doomed, then, to live helplessly in this way? If this is just the way the world is and the way we are, shouldn’t we just accept that? Apart from Christ the answer would be “yes,” but the New Testament makes it clear that though we are still fallen, the saving work of Christ has brought about a profound change in us. As N.T. Wright makes clear in his book Surprised by Hope, Jesus taught (and the Resurrection vindicated) that the Kingdom of God “was and is breaking in to the present world, to earth.” ¹² Christ’s Resurrection was the first act of the future new creation. If we are truly “born again” into this new reality, this new way of living, we must strive (in the Spirit’s power) to live lives of wholeness and right relationships, putting our sinful nature to death (Colossians 3). In doing so, we would be wise to include Genesis 2 as we seek to follow God’s will and God’s Kingdom, “on earth as it is in heaven” (Matt. 6:10).

In part 2 of this series, David describes how Genesis 1, Genesis 2, and modern scientific accounts offer complementary and mutually enriching perspectives in our understanding of God's creation.

Notes

1. John H. Walton, Ancient Near Eastern Thought and the Old Testament: Introducing the Conceptual World of the Hebrew Bible (Grand Rapids, MI: Baker Academic, 2006), 125.
2. Biblical quotations are from the Common English Bible unless otherwise noted.
3. Both symbolized divine wisdom that humans had to receive from God obediently, with the proper “fear of God” that the Old Testament wisdom literature stresses as a prerequisite. Disobediently eating the Tree’s fruit would lead to death and disobeying God would lead to expulsion from the Garden. Similarly, disobediently touching the Ark brought death (Num. 4:15, 2 Sam. 6:1-7) and disobeying God’s instruction led to Israel’s exile from their Eden, the land of Canaan.
4. John H. Walton, Genesis (Grand Rapids, MI: Zondervan, 2001), 172.
5. Ibid., 173.
6. Ibid., 192.
7. See Numbers 3:7-8, 8:26, 18:5-6.
8. Gordon J. Wenham, “Sanctuary Symbolism in the Garden of Eden Story,” in “I Studied Inscriptions from Before the Flood”: Ancient Near Eastern, Literary and Linguistic Approaches to Genesis 1-11, ed. Richard S. Hess and David Toshio Tsumura (Winona Lake, IN: Eisenbrauns, 1994), 401.
9. Walton, Genesis, 176.
10. Ibid., 170.
11. This follows Walton’s illuminating exegesis of this passage in Genesis, 164-65.
12. N.T. Wright, Surprised by Hope: Rethinking Heaven, the Resurrection, and the Mission of the Church (New York: HarperOne, 2008), 201.

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.

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.

Scripture and the Authority of God: How to Read the Bible Today

My title reflects the book that I published six years ago as The Last Word, which has recently reappeared as Scripture and the Authority of God: How to Read the Bible Today. In this new edition I have included two substantial new chapters explaining more fully how the model I propose works out in practice. Both versions of the book and the paper I wrote some years before that (from which this series of posts is adapted) cast light on a puzzle which became clearer to me in the early years of the century. At that time I was involved in many discussions within the Anglican Communion on the one hand, and in dialogue with Roman Catholic theologians on the other, in which reference to scripture and its authority was ubiquitous but frequently opaque. That is, everybody says that scripture is authoritative, but few stop to explain what that means in practice. My book gets off to its start by pointing out that in scripture itself, it is God who is authoritative. This may be obvious, but when you chase through the ramifications it becomes less so.

The Christian tradition has assumed, of course, that what scripture says, God says. But even those who were most concerned to make this point – specifically the Protestant reformers – were often, from our perspective, somewhat cavalier in how they applied this. Some reformers were eager to draw on Old Testament narratives and prophecies in order to instruct the princes of their day – I think of Latimer preaching before Edward VI – while others, notably Martin Luther, could say such things as ‘Moses knows nothing of Christ’. What’s more, the idea of the authority of scripture was used as a limiting statute in the sixteenth century (i.e. one should only insist on that which could be plainly shown from scripture, and not insist, on pain of damnation, upon dogmas that did not have scriptural warrant). But in more recent western church life the phrase ‘authority of scripture’ has been used in a maximal sense, especially of course within fundamentalism. And yet the underlying problems of a Christian ‘authoritative’ reading of scripture have not gone away, but only been parked.

The question before us, then, is: how can the Bible be authoritative? This way of putting it carries two different though related meanings, and I shall look at them in turn. First, how can there be such a thing as an authoritative book? What sort of a claim are we making about a book when we say that it is ‘authoritative’? Second, by what means can the Bible actually exercise its authority? How is it to be used so that its authority becomes effective? The first question subdivides further, and I want to argue two things as we look at it:

(1) I shall argue that usual views of the Bible—including usual evangelical views of the Bible—are actually too low, and do not give it the sufficient weight that it ought to have.

(2) I shall then suggest a different way of envisioning authority from that which I think most Christians normally take.

Authority?

Our generation has a problem about authority. In church and in state we use the word ‘authority’ in different ways, some positive and some negative. We use it in secular senses. We say of a great footballer that he stamped his authority on the game. Or we say of a great musician that he or she gave an authoritative performance of a particular concerto. Within more structured social gatherings the question ‘Who’s in charge?’ has particular function. For instance, if someone came into a lecture-room and asked ‘Who’s in charge?’ the answer would presumably be either the lecturer or the chairman, if any. If, however, a group of people went out to dinner at a restaurant and somebody suddenly came in and said, ‘Who’s in charge here?’ the question might not actually make any sense. We might be a bit puzzled as to what authority might mean in that structure. Within a more definite structure, however, such as a law court or a college or a business, the question ‘Who’s in charge?’ or ‘What does authority mean here?’ would have a very definite meaning, and could expect a fairly clear answer. The meaning of ‘authority’, then, varies considerably according to the context within which the discourse is taking place. It is important to realize this from the start, not least because one of my central contentions is going to be that we have tended to let the word ‘authority’ be the fixed point and have adjusted ‘scripture’ to meet it, instead of the other way round.

Authority in the Church

Within the church, the question of what we mean by authority has had particular focal points. It has had practical questions attached to it. How are things to be organized within church life? What are the boundaries of allowable behavior and doctrine? In particular, to use the sixteenth-century formulation, what are those things ‘necessary to be believed upon pain of damnation’? But it has also had theoretical sides to it. What are we looking for when we are looking for authority in the church? Where would we find it? How would we know when we had found it? What would we do with authoritative documents, people or whatever, if we had them? It is within that context that the familiar debates have taken place, advocating the relative weight to be given to scripture, tradition and reason, or (if you like, and again in sixteenth-century terms) to Bible, Pope and Scholar. Within the last century or so we have seen a fourth, to rival those three, namely emotion or feeling. Various attempts are still being made to draw up satisfactory formulations of how these things fit together in some sort of a hierarchy.

Evangelical Views

Most heirs of the Reformation, not least evangelicals, take it for granted that we are to give scripture the primary place and that everything else has to be lined up in relation to scripture. There is, indeed, an evangelical assumption, common in some circles, that evangelicals do not have any tradition. We simply open the scripture, read what it says, and take it as applying to ourselves: there the matter ends, and we do not have any ‘tradition’. This is rather like the frequent Anglican assumption (being an Anglican myself I rather cherish this) that Anglicans have no doctrine peculiar to themselves: it is merely that if something is true the Church of England believes it. This, though not itself a refutation of the claim not to have any ‘tradition’, is for the moment sufficient indication of the inherent unlikeliness of the claim’s truth, and I am confident that most people, facing the question explicitly, will not wish that the claim be pressed.

But I still find two things to be the case, both of which give me some cause for concern. First, there is an implied, and quite unwarranted, positivism: we imagine that we are ‘reading the text, straight’, and that if somebody disagrees with us it must be because they, unlike we ourselves, are secretly using ‘presuppositions’ of this or that sort. This is simply naïve, and actually astonishingly arrogant and dangerous. It fuels the second point, which is that evangelicals often use the phrase ‘authority of scripture’ when they mean the authority of evangelical, or Protestant, theology. The assumption is made that we (evangelicals, or Protestants) are the ones who know and believe what the Bible is saying. And, though there is more than a grain of truth in such claims, they are by no means the whole truth, and to imagine that they are is to move from theology to ideology. If we are not careful, the phrase ‘authority of scripture’ can, by such routes, come to mean simply ‘the authority of evangelical tradition.


The next part of our series explores whether we are unwittingly “belittling the Bible” by appealing to the wrong kind of authority.

(Originally published in Vox Evangelica, 1991, 21, 7–32. Reproduced by permission of the author.)

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

Today's video features theologian Rev. Lincoln Harvey and is courtesy of filmmaker Ryan Pettey, director/editor of Satellite Pictures.

In today's video, Rev. Lincoln Harvey discusses our desire to "domesticate" the liveliness and abundance of God. Harvey notes that the Trinity highlights both the manyness and oneness of God, which can be hard to Christians to fully understand. While this lack of understanding can be unsettling, Harvey encourages Christians not too force God into too neat of a box. Often, this desire to domesticate can be found in our interaction with Scripture. The Scriptures can be understood, but there is still something lively, mysterious, and beautiful in them that resists our desire to tame them. We should instead approach Scripture, as we approach God, with a spirit of humility and openness.