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.

During the past year the first results were published from the "Encyclopedia of DNA elements" project ('ENCODE'), revealing that at least 20 percent of the genome, perhaps more, is involved in regulating the expression of its 21,000 protein-encoding genes. The "selfish gene" had its day in the sun, but has now been replaced by the image of a finely tuned genomic system in which each type of gene product cooperates via an intricate networking complex to generate the music of life. The vast array of epigenetic signals whereby genes are switched on or off ensures a steady flow of two-way communication between the genome and its wider environments.

The human as a complex, interactive and highly integrated system might not on the face of it seem a fruitful hunting ground for those who see the genes as pulling the strings of life. Nevertheless, the past year has continued to see a growing love affair between the social sciences and genomics. This is well illustrated by a recent article in Nature entitled: "The anatomy of politics -- from genes to hormone levels, biology may help to shape political behavior." The author writes that "An increasing number of studies suggest that biology can exert a significant influence on political beliefs and behaviors," reporting that "genes could exert a pull on attitudes concerning topics such as abortion, immigration, the death penalty and pacifism." The political scientist John Hibbing is quoted as saying that "...it is difficult to change someone's mind about political issues because their reactions are rooted in their physiology."

Geneticists have highlighted the suspect nature of such claims from a purely scientific perspective. But in our present context it is the way that the genetic results are reported that is most striking. Note the dualist language involved and its assumption of genetic determinism. Genes and physiology are seen as something different from "us" and "our mind," and they seem to be controlling us, so we can't even change our mind. Humans are presented as pawns of their biology, puppets dancing to the tune of their genetic masters.

What has all this to do with the "big idea" concerning human identity that the Imago Dei provides? More, it turns out, than initially meets the eye. The clash of ideas here between theology and science comes not at the level of the science itself, which, in this case, remains ambiguous and disputed, but at the level of the ideological packaging of scientific ideas. To see where the clash comes from, we first need to understand the revolutionary nature of the Imago Dei idea in its original context in the texts of Genesis.

For millennia it was uniquely the pharaoh or the king who was seen as being in the "image of a god" in the polytheistic political systems of ancient Egypt and Mesopotamia. Adad-shum-ussur, a court astrologer and cultic official in the seventh century B.C. royal court of Nineveh, made clear that the Assyrian king Esarhaddon is the very image of Bel (Marduk), the top god of that era:

A (free) man is as the shadow of god, the slave is as the shadow of a (free) man; but the king, he is like unto the (very) image of god.

Richard Middleton provides further examples in his book, The Liberating Image, which describes how the stratified urban society of great cities such as Babylon was structured politically, socially and economically round the king's court and the cultic practices of temple worship of the various polytheistic deities of the city. Social destinies were unchanging because rooted in powerful creation myths. Power was in the hands of the privileged few and true freedom belonged only to the king, for only he was in the image of a powerful god.

Would Hebrew thinkers and writers have been familiar with this idea? Almost certainly, yes, since Israel had significant cultural and economic contact with both Egypt and Mesopotamia over prolonged periods, not least during their periods of exile. So how would the original readers of that wonderful theological essay, Genesis chapter 1, have understood these words?:

Then God said, "Let us make adam [humankind] in our image, in our likeness, and let them rule over the fish of the sea and the birds of the air, over the livestock, over all the earth, and over all the creatures that move along the ground." So God created adam in his own image, in the image of God he created him; male and female he created them. [Genesis 1:26-27].

In its historical context, the implications were revolutionary: the kingly and priestly male roles previously allocated to the privileged few by a pantheon of gods were now being delegated instead by the one creator God to the whole of humanity, male and female. In a stroke the entire ruling and priestly structure of Mesopotamian society was delegitimized. The Imago Dei was being democratized and it was now humankind who were to be the significant players in the arena of earthly life, the mandate to rule underlying their new responsibilities. Above all, humanity was set free by the one true God to determine their own destiny, no longer under the yoke of all-powerful dictators, nor under the baleful astrological control of the moon and stars.

Yet, ever since, humans have become experts at re-enslaving themselves, refusing the responsibilities that come with free-choice and submitting instead to narratives of fate and destiny. It seems ironic that today it is not the creation myths of ancient Babylon but the ideological interpretations of biology that provide the narratives of fate, in which genes "pull" humans toward certain political views and people cannot change their minds because their convictions are "rooted in their physiology."

"It's in his or her DNA" is a new phrase becoming increasingly embedded in our language, referring to something that cannot apparently be changed. On Sept. 8, 2012, Brad Pitt was quoted by the Daily Mail as saying that "America is a country founded on guns. It's in our DNA. It's very strange but I feel better having a gun." No it's not in our DNA, Mr. Pitt, either literally or metaphorically. People have choices -- they are the prisoners neither of their genetics, nor of their physiology, nor indeed of their environments. Human beings made in the image of God are free to chart their own destiny in a way that preserves human value and dignity. On that we can leave the last word to Abraham Lincoln: "...nothing stamped with the Divine image and likeness was sent into the world to be trodden on, and degraded, and imbruted by its fellows" (Aug. 17, 1858).

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.

If a cadre of outspoken, strong atheists wrote a litmus test for scientists, that might very well be question #1.

"Scientists, if you're not an atheist, you're not doing science right," PZ Myers -- a well-known blogger, biology professor and atheist -- regularly preaches.

But if this is true, then as many as half of scientists are doing science wrong. A 2009 study from the Pew Research Center polled members of the American Association for the Advancement of Science (AAAS). Fifty-one percent of respondents reported a belief in a higher power. Does this mean that it's too late for science? Has religion already pillaged the minds of researchers worldwide? No, of course it hasn't.

"It seems to me that we as a society have lately been caught in this false dichotomy where it's either God as the guy with the beard on the cloud or nothing at all," neuroscientist David Eagleman told Discovery News.

Staunch atheists often falsely characterize followers of religion as being "all-in" with their beliefs, opining that they ascribe to the whole creationist, woo-y shebang. "Where's your evidence?" atheists mockingly question. "You can't prove that God exists!" they accuse (correctly). Yet, hypocritically, strict atheists are guilty of the exact same crime: belief without evidence.

"We know too little to commit to a position of strict atheism. [But] we know way too much to commit to any particular religious story," Eagleman said.

Just as it's a leap of faith for a religious person to assert that God incontrovertibly exists, it's an equally large leap for a strict atheist to declare, without question, that God does not exist. As Carl Sagan eloquently explained:

An atheist is someone who is certain that God does not exist, someone who has compelling evidence against the existence of God. I know of no such compelling evidence. Because God can be relegated to remote times and places and to ultimate causes, we would have to know a great deal more about the universe than we do now to be sure that no such God exists. To be certain of the existence of God and to be certain of the nonexistence of God seem to me to be the confident extremes in a subject so riddled with doubt and uncertainty as to inspire very little confidence indeed.

Absence of evidence is not evidence of absence. As this statement applies to science, so does it apply to religion. History is replete with signs that an all-powerful deity may not exist, but such substantiation is nowhere near tantamount to proof -- especially, as Albert Einstein said, in a universe as incomprehensibly vast as our own:

The human mind, no matter how highly trained, cannot grasp the universe. We are in the position of a little child, entering a huge library whose walls are covered to the ceiling with books in many different tongues. The child knows that someone must have written those books. It does not know who or how. It does not understand the languages in which they are written. The child notes a definite plan in the arrangement of the books, a mysterious order, which it does not comprehend, but only dimly suspects. That, it seems to me, is the attitude of the human mind, even the greatest and most cultured, toward God. We see a universe marvelously arranged, obeying certain laws, but we understand the laws only dimly.

Ultimately, the key is not to be swayed to one extreme or the other -- fundamentalist religion or strict atheism -- but to walk a reasoned middle path. Eagleman believes that path is "possibilianism," the concept of holding multiple beliefs or hypotheses whilst exploring new ideas.

"The goal is to avoid committing to any particular story," Eagleman told Discovery News, "whether that's religious fundamentalism or strict atheism. The goal of possibilianism is to retain the wonder that drives us all into science in the first place and to avoid acting as though we know the answers to things we can't possibly know at the moment."

Strict atheists do the world an incredible service by promoting the scientific method, skepticism, and critical thinking. But they do a disservice by campaigning against religion or touting -- as pure truth -- the non-existence of God, for those actions (especially the latter) are just as unscientific as a blind belief in all aspects of religion.

This summer, a worldwide poll showed that atheism is on the rise and religiosity is on the decline. It is my hope that these "New Atheists" and agnostics won't narrowly focus on denigrating religion, but will instead focus on encouraging open-mindedness and discouraging fundamentalism.

That would surely make the world a more enlightened place.

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).

There are more things in heaven and earth, Horatio, than are dreamt of in your philosophy.

—Hamlet Act 1, Scene 5

We live in a world driven by the gods of economics, technology and science. Particularly in a time of economic austerity, it is tempting to see the arts or humanities as an optional “extra”—a happy by-product of those true engines of society when they are running smoothly. But in this article we will look at how a biblically informed worldview might turn this perspective on its head, and what the humanities might have to tell us about the present contours of the science and faith conversation.

In his iconic 1959 Rede lecture, “The Two Cultures,” CP Snow noted the dysfunctional relationship between science and the humanities, arguing that the situation is principally the result of our educational system in the West. Ken Arnold, from the medicine and arts focused Wellcome Collection in London, believes that the split continues today, but with the further extension that

In emerging countries . . . amongst the middle classes there is a strong pressure to join the ranks of doctors and scientists and engineers because they see that as the place where future economies are growing. . . . In some ways you could almost begin to feel sorry for the arts and the humanities because they seem to be worth less than the sciences.¹

Is Protestant Christianity also peculiarly prone to such thinking? A skepticism of art in religious spaces as a result of iconoclasm and the reformation, combined with a proud history of the protestant work ethic, economic success, and a profound influence on the history of science, might lead Protestants to be more inclined towards the sciences and technology than to the arts. However, there are more corrosive reasons that science has usurped the humanities in our culture than merely educational or theological bias.

In the early 20th century, logical positivists regarded the humanities as expressions merely of our inner states and desires, but having nothing to do with objective reality. Such imperialistic claims to knowledge denied that other knowledge claims referred to any true reality, and were therefore not really forms of knowledge at all. Bertrand Russell writes,

But if there is a world which is not physical, or not in space-time, it may have a structure which we can never hope to express or to know … Perhaps that is why we know so much physics and so little of anything else.²

Christian scientists are of course very sensitive to this, and work hard to explain that science cannot answer questions of ultimate meaning or the existence of God, which are beyond the scope of science. Often, this line of thinking can be narrow in focus, delineating the limits of the science, and naming those assumptions made by science that cannot be justified empirically. Such arguments can be very fruitful within this narrow context, but we should not be led into thinking that our true perception of reality is limited to such analytic and evidential approaches. There are fields of inquiry that science isn’t able to explain (such as metaphysical judgments, ethics, and beauty), and even our confidence in mathematics— upon which so much of science itself is based—rests upon assumptions that cannot be experimentally demonstrated.

The human condition

Mathematics and the sciences do seem to provide tools by which we are able to perceive the external world and its regularities. However, the arts and humanities, too, are a way of understanding reality, and they tell us less about external reality than the internal human condition. The problem is that the ‘human condition’ seems to have been relegated by many to the realm of mere desire and subjective feeling and, therefore, not reality.

The modernist account of science is that, through our reason, we are somehow able to get outside of nature and describe it objectively. The biblical account, though, has human beings as part of the created order, and so embedded in nature—made from the dust of the earth. Given that, human thought life is also part of the natural world, even despite the fact that it is not best described by the sciences.

The works of Shakespeare, for instance, are part of the created order, as are the poems of Wordsworth, the sculptures of Michaelangelo, and the music of Bach, not to mention children’s nursery rhymes, home decoration, and humming tunes whilst waiting for the bus. As C. S. Lewis wrote, "This is not panache, it is our nature." ³

A little reflection on life reveals something very strange going on here. Somehow, the mythic ‘war’ between science and religion has become the dominant battleground for defending the Christian faith, and competing explanations of the material world are used as apologetic weapons. But the reality is that science plays a peripheral role in our experience of life, not least our life as Christians. Of course that is not to deny the enormous impact of science on the material conditions of our lives, or the prevalence of the products of science. Instead, it is to observe that science plays a facilitatatory role, enabling us to carry out the real core business of our lives, which does not revolve around science. Cars, trains and airplanes are modes of transport to take us to work, or to see family, or go on holiday. Social media provide another way of being in relationship with people. Health services are not an end in themselves, but aim to make people well, so that they can get on with their lives. Why then, when life is not about science, does science dominate our way of thinking about life?

In focusing so much energy on opposing positivism are we not being inadvertently drawn into a positivist way of thinking, that science and material explanations of things are, indeed, our basic reality, what is ultimately true?

A biblical model

“We feel,” wrote the philosopher Ludwig Wittgenstein, “that even when all possible scientific questions have been answered, the problems of life remain completely untouched.” ⁴ Likewise, philosopher Susanne Langer questions any philosophy which claims to be able to explain everything:

Philosophers in every age have attempted to give an account of as much experience as they could. Some have indeed pretended that what they could not explain did not exist; but all the great philosophers have allowed for more than they could explain, and have, therefore, signed beforehand, if not dated, the death-warrant of their philosophies.⁵

Fortunately, the Bible preserves us from total positivist oblivion. There are a great many types of literature represented in the Bible, with the notable exception of scientific writing. If we long to be able to express our deepest emotions, we have the psalms; if we are looking for wise advice, we have the proverbs; if philosophical reflection, Ecclesiastes. There is poetry, song, history, biography, but there is no science. In addition, the Bible refers to the use of the visual arts in, for example, the designs of the tabernacle and temple. The Bible does seem to think the arts and humanities are fundamental for human life, but it doesn’t seem to think that what we think the physical world is constructed of matters much at all.

Do we sometimes read the Bible more like a science textbook than a novel or a poem? Most will agree that each type of literature needs to be read in its own way, but lip-service to that idea notwithstanding, recent arguments prove that it is still possible to read a poem with a scientific mentality—looking out for the ‘facts.’ Is that because we have too high a view of science, or because we have too low a view of the humanities? To say something is poetic is not to declare it ultimately untrue, futile and meaningless—it is to say it is more profound and meaningful and true than many other modes of expression.

According to Langer, part of the problem is the priority that has been accorded to discursive language as the only valid way we have of representing reality to each other. She observes that a study of symbolism shows us that this is actually only one way humans use to abstract from reality, and in fact, the situation even with discursive language isn’t as simple as has been made out. She notes that our sensory organs mediate our perceptions of the world and are already on the job— formulating, framing the world to us—before our cognitive apparatus gets to work. It must be so, or we would not be able to evaluate the importance of the vast array of sensory data we receive and reality would appear as a blur.

A linguistic symbol carries a concept we associate with it, which in turn denotes a reality. In language there is a commonly agreed definition for each word we use, thus enabling communication. But each person also has associations unique to him or her which color any particular concept. Though such personal associations with words are present all at once, they can only be expressed and communicated one at a time, because language is also sequential.

A picture also acts symbolically, though in a different way. Even something as ‘realistic’ as a photograph is likewise a representation of reality and not the reality itself. It also carries with it layers of meaning which reflect the subjective intentions of the person who took the photograph, and opens up for interpretations and associations of the person ‘reading’ the picture. A picture, though, is not sequential. All the information comes at once, and individual blotches of color carry no significance on their own, but only as part of the whole.

No amount of words could ever describe a picture in full. The number of blotches of color and their relations to each other are vast in their complexity, and one could never read words quickly enough to carry the meaning a picture brings in an instant, even if it warrants a far longer period of contemplation. Indeed, though we are only speaking here of visual perception, the same is true of our other sensory inputs, too: they all carry knowledge in quite distinct and profound ways, whilst we, in line with the Greeks, have tended to give sight a special place as the most ‘objective’ of our senses.

As we dig down into empirical science and explore the mechanisms by which sights and sounds and textures are transmitted and processed by the brain, we discover that the meaning of the sense-data which we perceive and which we attempt to describe is likewise profoundly limited by the use of words—much less mathematics—and that our science, as such, represents a tiny fraction of reality.

To suggest, then, that science is the only true way of representing reality—as positivism has done—or to exclude the humanities from our world, leaves us without a proper or even adequate means of expressing the significance we attach to even the most mundane day-to-day activities. Science is very good at describing the regularities of the physical world, but the experience of being human is no less part of the real natural world than are the structure of proteins or the movement of planets, and science does not have the appropriate tools to explore our inner worlds.

Nowadays it seems that Christian cultural life has also too-often failed to fully acknowledge other ways of representing reality than materialist science—ironic because this state of affairs is so at odds with the Bible’s model of using the arts and humanities to profoundly explore the human condition. Perhaps it is time to recover that side of the biblical witness, and remind ourselves that there are more ways of representing the world to each other than positivism has ever dreamt.

Notes

1. BBC Radio 4, “The Life Scientific”, Tuesday 25th September 2012.
2. Bertrand Russell, “Philosophy”, New York. W.W.Norton &Co, 1927, page 265, quoted by Susanne K. Langer, Philosophy in a New Key, Harvard University Press, 1979, page 88.
3. C. S. Lewis, “Learning in War Time” in Fernseed and Elephants and other Essays on Christianity, Fontana, 1975, page 28.
4. Ludwig Wittgenstein, Tractatus Logico-Philosophicus. Routledge and Kegan Paul, 1951, page 187.
5. Susanne K. Langer, Philosophy in a New Key: A Study in the Symbolism of Reason, Rite and Art. Harvard University Press, 1979, p 5.

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.

There are several different kinds of arguments that people bring along these lines; I want to talk about just one. So first… the Heidelberg catechism, one of the forms of unity of the church I go to (the Christian Reformed Church), says

Providence is the almighty and ever-present power of God, by which he upholds as with his hand heaven and Earth and all creatures and so rules them, that leaf and blade, rain and drought, fruitful and lean years, food and drink, health and sickness, prosperity and poverty. All things, in fact, come to us not by chance, but from his fatherly hand.

And part of the way it comes to us—not by chance, but from his fatherly hand—part of the way God has designed our world, is that there is a great deal of regularity and dependability in our world. Of course, if it were not for this regularity and dependability, we couldn’t do the things that we actually do. I mean, for example, if I just wanted to walk off the stage—if, for example, all the sudden those stairs over there suddenly turned into a ladder going up—well, that would make it really difficult.

If you are trying to build a house, for example, you have this hammer, but all the sudden the hammer turns in to a goose or a pigeon. Again, that would make things really difficult…or if the nail turned into a worm…or if you get in the car and turn the key and the car turns into a camel, things would be really hard, much harder than they are. This regularity and dependability in our world is an essential condition of our being able to live in the world in which we actually do.

If the world were irregular enough, we would not even be able to live in it, but there are also, according to classical Christianity here (the Heidelberg catechism, for example) there are also special divine actions; sometimes God does things specially. There are miracles in Scripture: the parting of the Red Sea, for example, Jesus walking on water, Jesus changing water into wine. There are miraculous healings: Jesus rising from the dead, Jesus raising Lazarus from the dead, and so on. And according to classical Christians, many of them, perhaps most of them, are special divine actions. God, for example, responds to prayers. He works in the hearts and minds of his children to effect sanctification. There is, what Calvin called, the internal testimony or witness of the Holy Spirit, and there is what Thomas Aquinas called the internal instigation of the Holy Spirit. So, these things are all special actions on the part of God. God constantly causes events in the world. Ok, so far fair enough—what is the problem?

Many theologians seem to think there is a science-religion problem here. I don’t think any of the theologians of Biola think this, (I don’t know, but I doubt it) but many theologians do. For example, Rudolf Bultmann says, “The historical method,” which of course he thinks that is the method we should use, “includes the presupposition that history is a unity in the sense of a closed continuum of effects in which individual events are connected by the succession of cause and effect. This continuum, furthermore, cannot be rent by the interference of supernatural, transcendent powers.”

That’s what he says. Alright, there is this continuum that cannot be rent by the interference of supernatural (that would be God) or transcendent powers. So, it is a little bit like the laws of the Medes and Persians. You probably remember Daniel. Daniel was a favorite of King Darius, and well, the other courtiers became jealous of Daniel (they didn’t like it that the king liked him so well). So, they came to the king and said, “Oh king, live forever, we think it would be a great idea if you passed an edict to the effect that you alone can be worshipped. Everybody has to worship you and nothing else.” Well the king thought that over for a minute, and that sounded pretty good to him so he said, “I guess that it is a pretty good idea.” So he made this edict; he made this declaration: “Only King Darius is to be worshipped—no one else, nothing else.”

These courtiers knew that Daniel worshipped God, and they thought probably Daniel would keep right on worshipping God despite this edict. So they were watching Daniel, and he was, in fact, worshipping God. So they came to the king. Now the penalty for worshipping something else was to be thrown into the lion’s den and they said, “Well, king live forever, looks like Daniel has been violating this edict. You have got to throw him in the lion’s den.”

Well, the king didn’t want to do this because he really liked Daniel. He thought this was a miserable way to proceed, and he didn’t want to do it, but then they said to him, “O king live forever, and remember a law of the Medes and Persians cannot be abrogated, even by the king himself.” So once it’s put in place, not even the king himself can change it or abrogate it or go against it.

That is sort of the suggestion that you get here from Bultmann. Bultmann thinks, “Maybe God created the world and set it up in a certain way, but once he did that, not even he can interfere in it”—he uses that word interference—“not even he can do anything in it. He just has to keep hands off.” It is like the law of the Medes and the Persians.

Another theologian who agrees is John Macquarrie, who says,

The way of understanding miracle (and that would be one kind of special divine action) that appeals to breaks in the natural order and to supernatural intervention belongs to the mythological outlook, and cannot commend itself in a post-mythological climate of thought. The traditional conception of miracle is irreconcilable with our modern understanding of both science and history. Science proceeds on the assumption that whatever events occur in the world, can be accounted for in terms of other events that also belong within the world, and if on some occasion, we are unable to give a complete account of some happening, the scientific conviction is that further research will bring to light further factors in the situation that will turn out to be just as imminent and this worldly as the factors already known.

Ok again, no room there for special action. And the third thinker here, Langdon Gilkey (still another theologian), says something similar, but I will pass. I will not read that one in the interest of saving a little bit of time, but these three theologians, plus many others want to assert that there is something wrong with the idea of God acting in the world, acting in the world in a way that goes beyond creation and sustaining, or creation and holding things in existence. So they think, “Ok, God created the world; God sustains it in existence”…that is ok with them, but anything beyond that, God performing any miracles, raising Jesus from the dead, or for that matter working in somebody’s heart and mind in a special way, that, they say, is a real problem. The question is, what is the problem?

Well, the next little bit here…according to the Christian and theistic idea, God is a person; he has knowledge, loves, and hates. He has aims and ends. He acts on the basis of his knowledge to achieve his ends. He is all-powerful, all-knowing, and wholly good. Thirdly (noted above by the Heidelberg catechism), God has created the world. Fourth is God conserves and sustains and maintains in being this world he created, but fifth, at least sometimes, God acts in a way going beyond creation and conservation in miracles, but also in his providential guiding of history, his working in the hearts of people, his internal instigation of the Holy Spirit, and so on, and it is with that fifth category that these people have a problem. It is God’s special action in the world—action beyond conservation and creation—and miracles would be an example.

So we might think of these theologians as endorsing what we could call hands off theology. God has got to keep his hands off. God could create the world. God conserves the world, sustains it in being, but he can’t do anything else—that is as far as he could go. It is hands off theology, and Bultmann, even in this context, even talks about interfering. I mean if God did something in the world that would be interfering, which, when you think about it, is a sort of strange thing to say—I mean if God created the world, he is the omnipotent, omniscient, holy, good creator of the world—when you accuse someone of interfering, you are saying they are doing something they should not be doing, right?

So Bultmann thinks if God did something in the world that would be interfering, and he should be ashamed of himself. Ok, now why is this a problem? Their suggestion is that somehow it is contrary to science. It is contrary to science the suggestion that God acts specially in the world. I didn’t read that bit, but Gilkey says, "The causal nexus in space and time which the enlightenment science and philosophy introduced into the western mind is also assumed by modern theologians and scholars. Since they participate in the modern world of science, both intellectually and existentially, they can scarcely do anything else.”

From a presentation sponsored by Biola University’s Center for Christian Thought, and delivered February 12, 2012 at EV Free Church, Fullerton, CA. Used by permission.

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

Judging from the flurry of headlines over the past week, one might be tempted to think that proof positive of God’s existence (or lack thereof) had just appeared out of a 27-km-tunnel buried beneath the Swiss-French border. This frenzy of news headlines and blog titles hailed the recent news that CERN’s Large Hadron Collider has discovered a brand new particle of a mass of 125-126 GeV, which is assumed to be the Higgs boson, or the so-called “God particle.” The discovery of the Higgs boson would certainly be a breakthrough for particle physics and cosmology, but would such a finding also radically redefine theology’s understanding of God or challenge the existence of such a deity? Is there actually any theological or religious significance in Higgs physics at all?

The short answer is “no,” which becomes apparent when one considers the widely-reported story of how it got named. In 1993, Nobel Laureate physicist Leon Lederman, along with science writer Dick Teresi, wrote a book detailing the history of particle physics starting with Pre-Socratic Greek philosophy Democritus and culminating with the hunt for the Higgs boson. Until this latest discovery, the Higgs boson was the elusive final missing piece of the puzzle known as the Standard Model—a collection of the fundamental particles that constitute our universe and the complex and mathematically-sophisticated relationships between them. Considering how incredibly difficult finding the Higgs boson was proving to be, Lederman wanted to name the book after that “goddamn particle,” according to some of his collaborators. His editor, however, would not allow it and so the name was shortened to “The God Particle: If the Universe Is the Answer, What is the Question?” And thus ‘the God particle’ was born, carrying with it more than enough social baggage for such a miniscule particle.

Particle physicist Dr. Zosia Krusberg (at right) is visiting assistant professor of physics and astronomy at Vassar College and thinks “the term ‘god particle’ is unfortunate. The Higgs boson is no more (or less) divine or spiritually significant than any other elementary particle within the standard model of particle physics.” It may be fundamental to explaining one of the most basic characteristics of the universe—namely the existence of matter and mass in addition to energy—but “it is no more (or less) important than any other physics principle underlying the Standard Model.”

Last week’s discovery was monumental in that it may have finally provided experimental evidence for the Higgs Mechanism and defined the specific energy of the resulting Higgs boson, but even this “breakthrough” for particle physics leaves many scientific questions unresolved. Finding the Higgs boson completes the Standard Model, but it does not do away with many other questions and shortcomings of the current state of particle physics, such as the constituent particles of dark matter, a quantum theory of gravity, and other “mathematically subtle problems.” Not to mention that there is still significant work to be done to determine the exact nature of this newly-found particle. According to Dr. Krusberg, this particle might behave just as the Standard Model predicts or it could instead be “a Higgs-like particle that will serve as a gateway into explorations of physics beyond the Standard Model." Krusberg continued, “And I guarantee that it is this latter scenario that most of us are hoping for: physicists love nothing more than discovering the shortcomings of their theories, since this is the first step toward more fundamental theories with even more predictive power!”

No, finding the Higgs boson does not answer all the questions of particle physics, much less lend insight into the existence (or not) of God. For that reason, Dr. Krusberg (like most physicists) bemoans the term ‘God particle’ and insists, “There really is nothing either literally or metaphorically god-like about the Higgs boson.” Indeed, one writer for the British journal The Guardian reached such a point of frustration about the name that he ran a competition for alternatives. The winner was “the champagne flute boson,” ostensibly because the bottom of a champagne bottle is an excellent and oft-used demonstration of the energy potential of the Higgs Mechanism. Or then again, perhaps it is simply because physicists thought that finally finding this shy particle would call for some of the bubbly.

On the other hand, some science writers and scientists can appreciate the ‘educational benefits’ of such a mysterious and controversial name because it attracts the attention of the general public and puts a relatable face on an extremely esoteric physics concept. Krusberg herself admits that “People are naturally drawn to the mysterious and the controversial, providing educators with great teaching opportunities.” But she worries about the larger social implications involved in “mixing the vernacular of physics and spirituality,” not least because such uncritical mixing can lead the non-scientific community to draw conclusions about the authority and reach of science that are not justified.

Understanding that the Higgs boson is not the literal stuff of God and that it does not prove or disprove God’s existence (as the name seems to suggest) extinguishes the fire under any sort of religious outcry. But this does not mean that its discovery is irrelevant to the discussion of science and faith, nor to the Christian community as a whole. As Dr. Krusberg remarks, “The recent discovery of [this] new boson at the LHC perfectly embodies the scientific process at its best (and thereby illustrates to the public why and how science works).” Scientific exploration of nature is not a fool-proof endeavor; healthy skepticism and accountability to a wide community of other researchers are absolutely critical to its success. But such evidence of the power and finesse of well-executed science as we saw last week is a testament to our ability to explore and understand the ‘how’ of the universe. God has equipped humanity with the desire, the intellectual abilities, and the collective will to recognize and explore the cosmic order and beauty of his creation. God has made our home knowable, and has given us the tools and capacities by which to know it.

At left, Cern researchers present their findings to a few hundred of their colleagues in Melbourne, Australia. Image © 2012 CERN

It is valuable, then, for the Christian community to understand and appreciate how science works, in part to recognize that there are many instances in which science and the church work in tandem in order to better understand and better serve the world. But I think there is something else we can draw from the story of the Higgs boson, too. The nickname ‘the God particle’ has touched nerves in religious communities because it implies that science has the ability to prove or disprove divine existence by physical means. Even though the physics community is by no means claiming insight into the divine, it is sometimes assumed by the religious community that scientists view their work as chipping away at God’s existence when they begin to understand something that was previously unknown, or known only “by faith” in esoteric theories and models.

And yet, regardless of motives or metaphysical interpretations, perhaps physicists' search for the Higgs boson is in fact an apt picture of our own search for God. How many times have we stared up at the starry ceiling in times of crisis and prayed fervently for some kind of sign from God to assure us of his presence? And how many times has that much-desired evidence appeared only in retrospect, when we look back to see God’s hand faithfully and elegantly working in ways inscrutable at the time? It took a community of physicists to discern the presence of the Higgs boson. But even so, they could only do so after the fact from the cascade of particle decays it sparked; they could not observe the particle itself directly. In a similar way, though we often do not see the working of God directly, “in the moment,” we still trust in his presence and providence, often depending on friends, family and the community of the church to help us see his hand in hindsight.

So while the discovery of the Higgs boson does not itself explain God, we rejoice at the subtle yet striking new insight we have into God’s creative genius via the Higgs boson and at the way God gives evidence of his faithfulness in the ordered creation itself. Perhaps, however, the greatest insight we can glean from this breakthrough is an analogy for the way God calls us to seek him and find him together, in the community of those who follow his son.

Tomorrow, Baylor University physicist Gerald Cleaver answers the question, "What is the Higgs boson?"

A scientist, my dear friends, is a man who foresees; it is because science provides the means to predict that it is useful, and the scientists are superior to all other men. --Henri de Saint-Simon¹

Scientism is a rather strange word, but for reasons that we shall see, a useful one. Though this term has been coined rather recently, it is associated with many other “isms” with long and turbulent histories: materialism, naturalism, reductionism, empiricism, and positivism. Rather than tangle with each of these concepts separately, we’ll begin with a working definition of scientism and proceed from there.

Historian Richard G. Olson defines scientism as “efforts to extend scientific ideas, methods, practices, and attitudes to matters of human social and political concern.” ² But this formulation is so broad as to render it virtually useless. Philosopher Tom Sorell offers a more precise definition: “Scientism is a matter of putting too high a value on natural science in comparison with other branches of learning or culture.” ³ MIT physicist Ian Hutchinson offers a closely related version, but more extreme: “Science, modeled on the natural sciences, is the only source of real knowledge.” ⁴ The latter two definitions are far more precise and will better help us evaluate scientism’s merit.

A History of Scientism

The roots of scientism extend as far back as early 17th century Europe, an era that came to be known as the Scientific Revolution. Up to that point, most scholars had been highly deferential to intellectual tradition, largely a combination of Judeo-Christian scripture and ancient Greek philosophy. But a torrent of new learning during the late Renaissance began to challenge the authority of the ancients, and long-established intellectual foundations began to crack. The Englishman Francis Bacon, the Frenchman Rene Descartes, and the Italian Galileo Galilei spearheaded an international movement proclaiming a new foundation for learning, one that involved careful scrutiny of nature instead of analysis of ancient texts.

Descartes and Bacon used particularly strong rhetoric to carve out space for their new methods. They claimed that by learning how the physical world worked, we could become “masters and possessors of nature.” ⁵ In doing so, humans could overcome hunger through innovations in agriculture, eliminate disease through medical research, and dramatically improve overall quality of life through technology and industry. Ultimately, science would save humans from unnecessary suffering and their self-destructive tendencies. And it promised to achieve these goals in this world, not the afterlife. It was a bold, prophetic vision.

As this new method found great success, the specter of scientism began to emerge. Both Bacon and Descartes elevated the use of reason and logic by denigrating other human faculties such as creativity, memory, and imagination. Bacon’s classification of learning demoted poetry and history to second-class status.⁶ Descartes’ rendering of the entire universe as a giant machine left little room for the arts or other forms of human expression. In one sense, the rhetoric of these visionaries opened great new vistas for intellectual inquiry. But on the other hand, it proposed a vastly narrower range of which human activities were considered worthwhile.

The Enlightenment

A century later, many of the Enlightenment intellectuals continued their love-affair with the power of natural science. They claimed that not only could science enhance the quality of human life, it could even promote moral improvement. The Encyclopedist Denis Diderot aimed to collect, organize, and preserve all human knowledge so that “our children, becoming better instructed, may become at the same time more virtuous and happy.” ⁷ Many of the French philosophes even claimed that science could be a substitute for religion. In fact, during the French Revolution, numerous Catholic churches were converted into “Temples of Reason” and held quasi-religious services for the worship of science.⁸

Positivism

The 19th century witnessed the most powerful and enduring formulation of scientism, a system called positivism. Its founder was August Comte, who built his positive philosophy from a deep commitment to David Hume’s empiricism and skepticism. Comte claimed that the only valid data is acquired through the senses. Nothing was transcendent, and nothing metaphysical could have any claim to validity.⁹ The task of scientists was twofold—first, to demonstrate how all phenomena, including human behavior, are subject to invariable natural laws.¹⁰ Second, they would reduce these natural laws to the smallest possible number, and ultimately unify them under the laws of physics.¹¹

Comte also subsumed all of human intellectual history into a single process which he called the Law of Three Stages. In his view, each branch of knowledge passes through three stages: the theological or fictitious, the metaphysical or abstract, and lastly the scientific or positive state. He believed that through the continual advancement of human understanding, religion would fade away, philosophy and the humanities would be transformed into a naturalistic basis, and all human knowledge would eventually become a product of science. Any ideas outside that realm would be pure fantasy or superstition.

Logical Positivism

Positivism did not lose its appeal in the 20th century. To the contrary, a group known collectively as The Vienna Circle reinvigorated the fundamental tenets of positivism with enhanced symbolic logic and semantic theory. They called their approach, fittingly, logical positivism. In this system, there are only two kinds of meaningful statements: analytic statements (including logic and mathematics), and empirical statements, subject to experimental verification. Anything outside of this framework is an empty concept.¹²

Given its sweeping claims, logical positivism came under heavy scrutiny. Karl Popper pointed out that few statements in science can actually be completely verified. However, a single observation has the potential to invalidate a hypothesis, and even an entire theory. Therefore, he proposed that instead of experimental verification, the principle of falsifiability should demarcate what qualified as science, and by extension, what can qualify as knowledge.¹³

Another weakness of the positivist position is its reliance on a complete distinction between theory and observation. Observations, essential to the empirical approach of science, were claimed by positivists to be brute facts which one could use to establish, evaluate, and compare the theories. However, W.O. Quine pointed out in his “Two Dogmas of Empiricism” that observations themselves are partly shaped by theory (“theory-laden”).¹⁴ What counts as an observation, how to construct an experiment, and what data you think your instruments are collecting—all require an interpretive theoretical framework. This realization does not deal a death-blow to the practice of science (as some post-modernists like to claim), but it does undermine the positivist claim that science rests entirely on facts, and is thus an indisputable foundation for knowledge.

Scientism of Today

Scientism today is alive and well, as evidenced by the statements of our celebrity scientists:

The Cosmos is all that is or ever was or ever will be. –Carl Sagan, Cosmos

The more the universe seems comprehensible, the more it also seems pointless. –Stephen Weinburg, The First Three Minutes

We can be proud as a species because, having discovered that we are alone, we owe the gods very little. –E.O. Wilson, Consilience

While these men are certainly entitled to their personal opinions and the freedom to express them, the fact that they make such bold claims in their popular science literature blurs the line between solid, evidence-based science, and rampant philosophical speculation. Whether one agrees with the sentiments of these scientists or not, the result of these public pronouncements has served to alienate a large segment of American society. And that is a serious problem, since scientific research relies heavily upon public support for its funding, and environmental policy is shaped by lawmakers who listen to their constituents. From a purely pragmatic standpoint, it would be wise to try a different approach.

Physicist Ian Hutchinson offers an insightful metaphor for the current controversies over science:

The health of science is in fact jeopardized by scientism, not promoted by it. At the very least, scientism provokes a defensive, immunological, aggressive response from other intellectual communities, in return for its own arrogance and intellectual bullyism. It taints science itself by association.¹⁵

Noting that most Americans enthusiastically welcome scientific advancements, particularly those in health care, transportation, and communications, Hutchinson suggests that perhaps what the public is rejecting is not actually science itself, but a worldview that closely aligns itself with science—scientism.¹⁶ By disentangling these two concepts, we have a much better chance for enlisting public support for scientific research than we would by trying to convince millions of people to embrace a materialistic, godless universe in which science is our only remaining hope.

Distinguishing science from scientism

So if science is distinct from scientism, what is it? Science is an activity that seeks to explore the natural world using well-established, clearly-delineated methods. Given the complexity of the universe, from the very big to very small, from inorganic to organic, there is a vast array of scientific disciplines, each with its own specific techniques. The number of different specializations is constantly increasing, leading to more questions and areas of exploration than ever before. Science expands our understanding, rather than limiting it.

Scientism, on the other hand, is a speculative worldview about the ultimate reality of the universe and its meaning. Despite the fact that there are millions of species on our planet, scientism focuses an inordinate amount of its attention on human behavior and beliefs. Rather than working within carefully constructed boundaries and methodologies established by researchers, it broadly generalizes entire fields of academic expertise and dismisses many of them as inferior. With scientism, you will regularly hear explanations that rely on words like “merely”, “only”, “simply”, or “nothing more than”. Scientism restricts human inquiry.

It is one thing to celebrate science for its achievements and remarkable ability to explain a wide variety of phenomena in the natural world. But to claim there is nothing knowable outside the scope of science would be similar to a successful fisherman saying that whatever he can't catch in his nets does not exist.¹⁷ Once you accept that science is the only source of human knowledge, you have adopted a philosophical position (scientism) that cannot be verified, or falsified, by science itself. It is, in a word, unscientific.

Notes

1. "Un savant, mes amis, est un homme qui prévoit; c’est par la raison que la science donne le moyen de prédire qu’elle est utile, et que les savants sont supérieurs à tous les autres hommes." Translated into English by Valence Ionescu in The Political Thought of Saint-Simon. Oxford University Press, 1976. Page 76
2. Olson, Richard G. Science and Scientism in Nineteenth-Century Europe. Urbana, University of Illinois Press, 2008.
3. Sorell, Tom. Scientism: Philosophy and the Infatuation with Science. New York: Routledge, 1991.
4. Hutchinson, Ian. Monopolizing Knowledge: A Scientist Refutes Religion-Denying, Reason-Destroying Scientism. Belmont, MA: Fias Publishing, 2011.
5. Descartes, Rene. Discourse on Method
6. Sorell, p176
7. Sorell, p35
8. Ozouf, Mona. Festivals and the French Revolution. Harvard University Press, 1988.
9. Zammito, John H. A Nice Derangement of Epistemes : Post-Positivism in the Study of Science from Quine to Latour. Chicago: University of Chicago Press, 2004.
10. This view is a form of strict determinism, and current popularizers of continue to enthusiastically endorse it. Perhaps they are “determined” to do so?
11. This view is a form of extreme reductionism, also widely endorsed by current popularizers of science.
12. Zammito, p8
13. Popper, Karl. Logic of Scientific Discovery. 1959
14. For an extended discussion, read Zammito’s chapter “The Perils of Semantic Ascent: Quine and Post-positivism in the Philosophy of Science” in A Nice Derangement of Epistemes. University of Chicago Press, 2004.
15. Hutchinson, p143
16. Hutchinson, p109
17. Giberson, Karl, and Mariano Artigas. Oracles of Science: Celebrity Scientists Versus God and Religion. Oxford: Oxford University Press, 2009.

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.

Ultimately, however, Finch remarks that "science can neither prove nor disprove the existence of God." To him, those who proselytize atheism under the banner of "science" do a disservice to science. The goal of scientists is to understand the physical world around us, and most scientists go into their labs to discover something wonderful about the world, rather than to comment on the existence of God.

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.”