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. 

Despite this usage, most of us know that randomness has something to do with probability, and that it often implies a lack of conscious intentionality. But what do mathematicians and scientists mean when they say something is random? Can a random process lead to an ordered, even predictable outcome? Is there evidence that God makes use of random processes to fulfill his creative purposes?

These are big questions, and we won’t address them all today. But I think randomness is an important topic to cover for two reasons: 1) it is integral to many processes in biology (and math, physics, chemistry, etc.), and 2) it is commonly misunderstood to be incompatible with Christianity.

As I said above, most of us know that randomness has something to do with probability. If you pick a card “at random” from a shuffled deck, you have a small probability of drawing an ace (4 out of 52, or a 7.7% chance). If you flip a coin, you have an equal probability of getting heads or tails.

Randomness also seems to imply a lack of intentionality or purposefulness. After all, you might hope for an ace when you draw a card, but you can’t choose one on purpose. You might call heads when you flip a coin, but you can’t know beforehand what the outcome will be. Thus the outcome is indeterminate, but is it purposeless? Not necessarily. Indeterminacy simply means the result cannot be predicted from the outset.

It should be noted that indeterminacy does not imply that God does not have foreknowledge of future events. Christians ought not to be uncomfortable with the idea of God interacting with his creation through chance. We often describe a seemingly-random (i.e. unplanned by us) sequence of events as being “providential,” or planned by God.

In biology, it is very hard or impossible to calculate precise probabilities for most processes, so when we say a process is random, we typically mean it is extremely unpredictable. Eventually we will discuss randomness within biological evolution, but first we must consider some simpler processes, like the self-assembly of a virus.

Viruses are remarkably efficient entities. Coiled tightly within a protein-based shell is a small amount of DNA needed for self-replication. The shell, called a capsid, is made of many repeating protein subunits and is therefore highly symmetrical (see figure). Important biomedical insights have certainly been gleaned from structural studies of viruses, but viruses also teach us about the emergence of order from non-order.

The virus life cycle has four main steps: 1) enter a host cell, 2) hijack the cell’s replication and translation machinery to make many copies of itself, 3) assemble into many virus particles, and 4) exit the cell to invade another host.

When I first learned about this process, I found it very hard to believe it just “happens.” The idea that a bunch of molecules bumping into each other inside a crowded cell could spontaneously assembly into a fully-functional virus seemed a bit far-fetched. Many viral capsids have over 100 protein subunits that must interact with each other in just the right way, or it won’t work. Surely there must be something driving this process, right?

There is! Random motion. I had to see it to believe it. I distinctly remember sitting in class during my first year of graduate school when the professor demonstrated self-assembly of a virus using a 3D model as shown in the following video. In less than 30 seconds, you can watch a jumbled heap of proteins become a beautifully ordered structure.

As the narrator explains, sub-assemblies form and break apart en route to the most stable structure, the full capsid. As the sub-assemblies begin to form, further associations with free subunits become more favorable and as a result occur rapidly, while the final steps may take considerably longer. While the subunits in the model are rigid, in reality the proteins take on multiple conformations, allowing the capsid to “breathe.”

Amazing as it is, the system we just considered—one virus capsid in a jar—is pretty simple. One wonders how self-assembly can happen in a crowded cell, where there are countless other molecules diffusing around, potentially getting in the way. We can’t directly see how it happens in a cell, but we can reconstitute the process in a test tube using different combinations of constituent molecules.

Consider two viruses, where each protein subunit in one virus is the mirror image of the corresponding subunit in the other. Putting the two viruses together by hand would be pretty tricky, because the constituent parts look so similar. But random motion can do the job in short order:

From this model, we can see clearly, in real-time, how distinct complex structures can arise from their parts randomly interacting with one another. Many large viruses also use special scaffolding proteins to assist in the assembly process, and some even use their own genomes as a scaffold. In addition, two closely-related viruses that happen to infect the same cell can exchange parts to create a new virus. This is one way viruses can evolve quickly to evade the host’s immune system.

Here we have seen how viruses demonstrate a principle inherent in God’s world—that order can emerge out of chaos from random processes. In my next post, we will look at some other biological processes that make use of—rather, depend on—randomness. This will set the stage for us to see that such processes can not only assemble a structure within seconds or minutes, but also generate complex, information-bearing molecules over billions of years. Even though the freedom inherent in nature sometimes produces unintelligently-designed structures (like viruses, which can kill us), we see that God has made, and continues to oversee by his providence, a good creation that, at least in part, is capable of creating itself.

Next weekend, we’ll continue this series about randomness and God’s divine will. Up next: how God created the body to heal itself, and how can random mutations can be both harmful and benign.

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

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

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

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

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

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

And who created it? Was it the good Lord?

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

We are the only ones who say: cruelty.

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

Who cannot but feel and think,

Who is kindred to us by his warmth and movement,

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

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

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

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

The Problem

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

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

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

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

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

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

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

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

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

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

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

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

Notes

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

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

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

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

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

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

Lights, camera, actualization

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

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

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

Responding to the data

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

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

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

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

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

For further reading:

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

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

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

Suppose a man falls among thieves, or wild beasts; is shipwrecked at sea by a sudden gale; is killed by a falling house or tree. Suppose another man wandering through the desert finds help in his straits; having been tossed by the waves, reaches harbor; miraculously escapes death by a finger’s breadth. Carnal reason ascribes all such happenings, whether prosperous or adverse, to fortune. But anyone who has been taught by Christ’s lips that all the hairs if his head are numbered [Matt. 10:30] will look further afield for a cause, and will consider that all events are governed by God’s secret plan.

In this passage, Calvin presents belief in “fortune” as evidence of carnal reasoning, and statements like this one have contributed to a widely-held notion that modern scientific understandings of the role that randomness plays in nature is inconsistent with belief in divine providence. In other words, if “randomness” equals blind and capricious “fortune,” then how can God be said to be working all things to his ends?

But Calvin could not have known of the very different understanding of randomness held by today’s scholars. Physical scientists, mathematicians, and statisticians have not yet agreed on a single unambiguous definition of the term “randomness,” but among these scientists, the term consistently refers to a family of related concepts focusing on unpredictability of the outcomes of single events and the absence of pattern in sequences of outcomes. I like this statement by John Polkinghorne, “Chance doesn't mean meaningless randomness, but historical contingency. This happens rather than that, and that's the way that novelty, new things, come about.” In Polkinghorne’s view, chance is an agent of creativity and can be perceived as being purposeful.

In fact, there are abundant examples of phenomena in nature in which randomness plays a role one could understand as being purposeful. For example, osmosis is a marvelous mechanism that enables all 10 trillion cells in our bodies to be nourished – it depends on the random motion of molecules. The human immune system is able to defend the body against attacks from millions of different microorganisms using a relatively small number of building blocks and random combinations of these to fashion defenses specific to each adversary. We never take a breath and find it to be all nitrogen or carbon dioxide – random motion of molecules keeps oxygen close to uniformly distributed throughout the atmosphere.

In 2007, a British statistician, David Bartholomew published God, Chance, and Purpose in which he argues that God “can have it both ways”—that he can use low level randomness to accomplish divine purposes while simultaneously maintaining order at a higher level. Of course, we cannot prove that God ordained these random processes to achieve divine purposes in the world. But to a person of faith, such an interpretation in both consistent with the observations we make in science and with the Scriptural notion of God’s providential care for the world.

Considerations like these led the John Templeton Foundation to provide a generous grant of $1.69 million to support a new research initiative on the theme of Randomness and Divine providence. Beginning this past summer, the program has the purpose of providing support for solid theoretical exploration of the kinds of ideas and possibilities expressed above—involving theology, philosophy, natural science, mathematics, and statistics. The grant will support individual scholars and teams of scholars who are willing to devote a significant amount of time between March of 2013 and June of 2015 to such work, and the project’s request for proposals suggests the following as questions researchers might pursue:

• How might God work providentially through indeterminate processes? Can recent advances in understanding the nature of randomness offered by algorithmic information theory, physics, biology, and other sciences provide insight into this question?
• Can we bring clarity to the concept of "randomness"? Philosophers and scientists have tried on occasion to give precise definitions of when a process is random, but more work needs to be done on the question. How do (or should) conceptions of randomness vary across academic disciplines?
• What are some possible implications of randomness for hiding or unfolding divine creativity and purpose in the world? Could God use randomness to (1) generate creativity, (2) hide divine actions, or (3) unfold information? Why might God do so?
• How might we identify and come to understand a significant collection of nondeterministic processes in which agents could intentionally employ randomness to bring about purposeful results?
• How might we mathematically and physically model random processes in ways that help us understand how divine providence could be exercised in a "chance-governed" world?
• How do "laws and orders" in nature interplay with "chance and randomness" in bringing about results that can be interpreted as aspects of divine providence?
• Might randomness be evidence of limitations in human knowledge but nothing more? Or might it be evidence of ontological indeterminism? Might this be tested?
• What implications does randomness have for aspects of God’s relationship with the physical world such as God’s relationship to time and God’s role in causation? How might randomness be reconciled with God’s foreknowledge?
• How might an understanding of providence based on an extended Molinism and/or open theology incorporate randomness? For example, could an extended Molinism provide a plausible account of the relationship between quantum mechanics and divine providence?
• What are some theodical implications of randomness, particularly for the issue of natural evil?
• How have the theological traditions of Augustine, Maimonides, Aquinas, Luther, and Calvin addressed chance and fortune? In what ways might they incorporate ontological randomness?
• How do or could religions other than the Judeo/Christian tradition understand and incorporate randomness?
• How is the concept of randomness understood by advocates of secularism, naturalism, and new atheism? What are the strengths and weaknesses of these usages?
• How might an understanding of randomness in the world alter our conceptions of divinity, especially our understanding of divine providence?

Despite the range of issues mentioned above, research is by no means restricted only to these topics. In fact, the structure of the program is designed to foster collaboration and build community between scholars, with the end of expanding the range and integration of their work: two conferences will be held to bring scholars together with each other and then with members of the public—one at Calvin College in 2013 and the other at Fuller Theological Seminary in 2015. To get more information and to learn how to submit a proposal, see the project website; then join us in exploring the truth that all creation glorifies God—even randomness!

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.

In my previous essay, I discussed “Darwin’s finches” and how surprisingly little Charles Darwin himself had to say about them. In fact, it was actually the British ornithologist David Lack (1910-1973) who conducted the critical research that immortalized the finches in biology textbooks and popular lore. In 1973, the eminent German zoologist Ernst Mayr wrote:

Already well known among professional ornithologists, his work on the Galapagos finches gave David Lack world fame… There is no modern textbook of zoology, evolution or ecology which does not include an account of his work.¹

Ernst W. Mayr

Decades have passed since Mayr wrote these words, and David Lack’s name has largely faded from public discourse. On the other hand, the Galapagos finches have become one of the most recognized symbols of evolution in the world today. Does it really matter whether Lack or Darwin gets credit for describing the evolution of these remarkable birds?

Insofar as evolutionary theory contrasted with religious belief, it makes a big difference. In a culture that is eager to equate evolution with atheism, it should come as no surprise that these birds are only known as “Darwin’s finches”. Darwin’s personal struggles and ultimate rejection of Christianity are well documented, and people are eager to link his loss of faith to his evolutionary theory. David Lack, on the other hand, began his scientific career as an agnostic, but shortly after publishing his famous book on the evolution of Galápagos finches, he converted to Christianity! ²

A Christian at the forefront of evolutionary biology

Lack’s Christian conversion did not mark the end of his scientific achievements, either. In fact, he continued as a prolific researcher until just weeks before he died. Among his many achievements, he was Director of the Edward Grey Institute of Field Ornithology (1945-1973), Fellow of the Royal Society, and President of both the International Ornithological Congress (1962-66) and the British Ecological Society (1964-65). His fellow scientists held him in great esteem:

He was described as one of the most outstanding among world ornithologists; he was certainly this, but he was also one of the world’s leading evolutionists. All the time one saw developing his use of birds as material for the study of wider, deeper, biological problems.³

David Lack at the International Ornithological Congress, 1962.

Clearly David Lack was an outstanding scientist, and his commitment to Christianity did not tarnish, hinder, or undermine his research on evolution. But we might also ask, what was Lack like as a Christian? Did he keep his faith hidden from view, afraid that it might compromise his reputation as a scientist? Ernst Mayr, who interacted with David Lack professionally and personally for nearly 40 years, had this to say:

I have known only few people with such deep moral convictions as David Lack. He applied very high standards to his own work and was not inclined to condone shoddiness, superficiality and lack of sincerity in others. This did not always go well with those who preferred to compromise in favour of temporary expediency. David had been raised in an environment in which great stress was layed on moral principles and this attitude was later reinforced by his Christian faith. This explains his extraordinary unselfishness and modesty, and his great devotion to his family, to his students, to his friends, and to all the things that he lived for. The equanimity, indeed serenity, with which he faced death after his terminal cancer had been diagnosed is further evidence of the strength which his faith gave him.⁴

Like Asa Gray⁵ before him, and Francis Collins⁶ after, David Lack was an sincere, devout Christian, as well as a leading scientist who employed evolutionary theory to make brilliant discoveries about the natural world. Though Lack did not see any conflict between his scientific and Christian beliefs, he was sympathetic to the concerns of his fellow Christians. Therefore, ten years after publishing his masterpiece on Darwin’s Finches, Lack wrote another book entitled Evolutionary Theory and Christian Belief: The Unresolved Conflict.

Originally published in 1957, this book deals with the very same science and faith questions that Christians struggle with today— topics like randomness and chance, death in nature, miracles, and evolutionary ethics. While it would be unreasonable to expect anyone to completely resolve these matters, Lack offered numerous insights both as a devout Christian and one of the world’s leading biologists.

Let’s take a brief look at how Lack addressed some of these questions.

Blind Chance or Divine Plan?

Evolutionary theory does not invoke supernatural forces in explaining the history of life on Earth; instead, it relies on naturally-occurring processes to account for the vast diversity of life. Additionally, it explains animal behavior largely in terms of survival and reproduction, without appealing to any higher purpose of life. Taken together, does this imply that God is absent, and that our lives are ultimately meaningless?

David Lack responded,

Behind the criticism that Darwinism means that evolution is either random or rigidly determined lies the fear that evolution proceeds blindly, and not in accordance with a divine plan. This is another problem that really lies outside the terms of reference of biology. It is true that biologists have inferred that, because evolution occurs by natural selection, there is no divine plan; but they are being as illogical as those theologians whom they rightly criticize for inferring that, because there is a divine plan, evolution cannot be the result of natural selection.⁷

When rendering judgment on the ultimate meaning of life, biologists are speaking from their person beliefs, not from scientific authority. Moreover, Lack pointed out that many science enthusiasts have employed the concept of “randomness” in ambiguous and misleading ways:

Mutations are random in relation to the needs of the animal, but natural selection is not. Selection, as the word implies, is the reverse of chance.⁸

In support of his view, Lack pointed out that convergent evolution has produced uncanny resemblances between distantly-related species across the world, notably among marsupials in Australia. Different evolutionary trajectories can lead to very similar results.⁹

Death in Nature

After addressing concerns about the seeming “randomness” of evolution, Lack turned to another great concern, the role of death in natural selection:

Various writers–some Christian and others agnostic–have been troubled about natural selection not only because it seems too random, but also because it is so unpleasant.¹⁰

Image courtesy John Marsh Photography via Flikr

Genetic mutations are generally harmful, and for evolution by natural selection to produce new forms of life, an awful lot of organisms must die. For many Christians, it is inconceivable that a loving and merciful God would allow death on such a vast scale.

But Lack also pointed out that rejecting evolutionary theory doesn’t actually get rid of the problem of death. Regardless of what we think about evolution, the brute fact of mass extinction remains. Fossils of innumerable animals, plants, and microorganisms clearly demonstrate that the vast majority of species that have ever lived are now dead. It may be quite troubling for us to observe that our planet is a giant graveyard of natural history, but rejecting evolution will not change this fact.

Some Christians conclude that death could not have been part of the divine plan; instead, it must be the work of the devil, or the result of human sin. But this interpretation contains an implicit assumption that death is always evil. Is this really true? David Lack offered two intriguing insights:

Blue-cheeked Bee-eater (Merops persicus) pair in
courtship, seen in Basai, Gurgaon, India.
Image courtesy Koshy Koshy.

1. For a population to maintain a stable size, all births must be balanced by a corresponding number of deaths. A world in which no animals die is a world in which no animals are born. That means no reproduction, no courtship, and by implication, no singing birds—much to the dismay of ornithologists and people in love!

2. Some people, taking cues from Isaiah 11:6-7, suppose that in a perfect world, animals only eat plants. But in fact, plants themselves depend on the bacterial decay of dead organisms. If animals didn't die, then essential nutrients would disappear from the ground, and plants could not continue to grow. Eventually, there would be nothing left for animals to eat, and all life would cease.¹¹

Miracles

Many Christians are uncomfortable with evolutionary theory because it denies a miraculous, supernatural origin of life. They fear that if those miracles are denied, it might lead people to reject the possibility of miracles altogether, including the central feature of the Christian faith—the resurrection of Jesus from the dead.

As a devout Christian, David Lack certainly affirmed the fundamental tenets of the gospel. But at the same time, he explained to his readers that invoking miracles to account for unusual features of the natural world is not particularly helpful when trying to deepen our understanding of God’s great multitude of creatures:

[The biologist's] research depends on repeated observations. It need not, as popularly supposed, consist solely, or even mainly of measurements and experiments, but unless events are repeated, they cannot be assessed by science. Hence truly unique events come outside the domain of science, though biologists are not usually convinced when told they must, therefore, leave such problems as miracles to others. For one of the chief ways in which research has advanced is through the discovery of apparent exceptions to the known rules, and if further study shows the exceptions to be replicable, new regularities are revealed from which modified rules can be propounded. This method has been so successful that the biologist tends to doubt whether there are any types of irregularity, or seeming irregularity, that will not yield to it.¹²

But just because a scientist cannot repeat a particular event doesn’t mean it didn’t happen. Both natural history and human history contain unique events that only happened once. As we peer into the past, the difficulty of discerning fact from fiction inspires us to further investigate the mysteries that surround us.

Conclusion

David Lack’s book Evolutionary Theory and Christian Belief was quite insightful, but his enduring achievements took place in evolutionary biology, a place where many Christians are afraid to tread. While it is significant that he himself found no contradiction between his faith and his science, perhaps the greatest testament to the compatibility between Christian faith and evolution is the life he led as a believer in both. As we saw in Ernst Mayr’s candid praise, Lack reflected the light of Christ through both his personal and his professional relationships.

Today, many voices in our culture still insist that evolution is incompatible with a sincere faith in Jesus, but a careful look at history demonstrates otherwise. In the future, perhaps more people of faith will have confidence to study biology knowing that one of the most iconic symbols of evolution—the Galapagos finches—owe their fame in large part to a devout Christian named David Lack.

Notes

1. Mayr (1973) “David L. Lack.” Ibis: 433.
2. Larson, E. J. Evolution's Workshop: God and Science on the Galapagos Islands. New York, Basic Books, 2001: 218. See also Lack, David. (1973) “My life as an amateur ornithologist.” Ibis: 431.
3. Alister C. Hardy (1973). "David L. Lack." Ibis: 436.
4. Mayr (1973) “David L. Lack.” Ibis: 433.
5. For more about Asa Gray, see the BioLogos FAQ “How have Christians responded to Darwin’s Origin of Species?”
6. See Francis Collins’ autobiography The Language of God: A Scientist Presents Evidence for his Belief (New York: Free Press, 2007) (book info)
7. Lack, David. Evolutionary Theory and Christian Belief: The Unresolved Conflict. Methuen & Co., 1957: 67.
8. Lack, p65.
9. For more on convergent evolution and the possibility that evolution could be compatible with some form of divine purpose, see the work of Simon Conway Morris, especially The Deep Structure of Biology: Is Convergence Sufficiently Ubiquitous to Give a Directional Signal? Templeton Press, 2008.
10. Lack, p72.
11. Lack, pp75-76.
12. Lack, p82.

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

For more, be sure to read Randall Pruim's recent series Randomness and God’s Governance, Kathryn Applegate's post That's Random: A Look at Viral Self-Assembly, and our FAQ How Do Randomness and Chance Align with Belief in God's Sovereignty and Purpose?.

Author's Note

I am so thankful that I grew up in a Christian environment, which both kindled and nurtured my relationship with Jesus Christ. The Biblical instruction I received from my parents, pastors, and teachers has been invaluable as I walk out my love for the Lord from day to day. However, there was one specific topic growing up which was not fully addressed, namely evolutionary theory.

Coming from a conservative Christian background, evolution was given little or no thought because of its seeming contradiction to the creation story in Genesis. To me, evolution meant a monkey became a human, and as far as I knew, I had never seen that happen! So, of course, it appeared too improbable to hold any truth. When it was discussed, an inadequate picture of its ideas was often painted, which caused immediate suspicion and rejection of the theory. I don’t think this was intentional, but most Christians have never learned an unbiased, in-depth theory of evolution that is completely detached from societal agendas and philosophical conclusions. Therefore, their explanations of the theory are often misinformed.

My senior year of high school, I took AP Biology, and finally learned the scientific reasoning supporting this theory. I was surprised by how logical and obvious the mechanisms of change (such as mutations, natural selection, genetic drift, and so on) were that gave rise to new species. My subsequent response was, “No wonder people believe evolution occurred.” At that point, I was convinced that microevolution (evolution within a species) existed, but I was still questioning macroevolution.

Now, being at Point Loma Nazarene University as an undergrad in the Biology-Chemistry major and a year-round, student intern at BioLogos, my understanding of evolution has expanded enormously. I have enjoyed critically thinking through the evidence for evolution and reading articles that tackle difficult issues at the interface of science and Christian faith. Ultimately, I know that God has created all things, but the processes he used surpass my small understanding.

My personal wrestling with evolution and quest for truth has led to times of prayer and studying God’s Word, which has deepened my love for him in ways I cannot express. The first chapters of Genesis, in particular, have come alive. My whole life, the creation story was a straightforward list of facts about the creation of the world; I never searched further. I didn’t even perceive the truths Genesis declared over my very identity and God’s character. The more I study his Word and handiwork, I glimpse the awesomeness and majesty of the Creator, who loves me much more than I know. There is still so much to learn, but I am confident that he will lead me into all truth as I seek him out.

I desire to give others the opportunity to see evolution accurately and to distinguish it from the traditional, philosophical, and personal conclusions that too often cloud the scientific theory. I believe these conclusions alienate Christians from evolution more than the scientific theory itself. Ultimately, I do not mean to convince someone about evolution, but simply to give them the freedom to understand it.

Therefore, my goal for this podcast is two-fold:

• First, to offer a new perspective on randomness within natural processes that removes its negative connotations (especially as it relates to evolution).
• Second, to expose why evolution is powerless to support conclusions beyond the physical realm.

This will hopefully encourage others to study evolutionary theory and draw their own conclusions about its meaning in the framework of their faith.

Many of the games I enjoyed playing involve a combination of strategy and randomness: card games of various sorts, backgammon, and board games like Monopoly and Parcheesi. Some games that rely exclusively on chance (like War and Candy Land) or too heavily on chance (like Sorry) quickly became uninteresting to me. In fact, for Sorry, War, and several other games, I introduced additional rules to change the balance of strategy and luck—for example, by allowing each player to hold a hand of cards rather than merely flip a card and follow its bidding.

When my children were young, I played many games with them, especially those involving some amount of chance. I always play to win, so games of pure strategy like chess gave me too great an advantage—at least when they were still young. I still remember the first time I played the German game Mitternachtspartie with my children and some of their cousins. The game uses a die on which the number 5 has been replaced with the image of Hugo the ghost. Each player rolls the die and moves one of his figures the specified number of squares, unless Hugo is rolled, in which case Hugo moves instead.

I quickly worked out the expected distance Hugo would move for each of my turns and the expected number of squares I would get to move my own figures each turn. Using that information, I could strategically place my figures in the opening portion of the game. I fully expected to win this first game, since my young children were going to have to learn from experience what I already knew by the mathematics of probability. I lost—badly. As it turned out, the die had two Hugos on it. So compared to my expectations, Hugo moved twice as often, and my figures moved slightly less far. That combination turned the carefully calculated positioning of my figures into a disaster.

From Fun and Games to Science

I still enjoy playing games, including games that involve chance. But these days I encounter randomness even more often in my profession. I was trained as a mathematician and now work at the intersection of mathematics, statistics, and computer science. Like many scientists, I use randomness on a daily basis as part of our toolkit for modeling and investigating all sorts of phenomena. Models known as stochastic models, which explicitly incorporate random components, often via simulation in computer software, are used to model everything from diffusion to genetics to quantum mechanics. Insurance companies and financial institutions use stochastic models to manage risk. If we include all the applications of statistics, then almost no area of science is untouched by the use of randomness.

Most of the time, scientists and game players alike don’t devote much thought to just what makes randomness tick. But they both know that the better they understand the probabilities, the more successful they are. Nevertheless, if you ask many of them what it means for something to be random, they may struggle to put it into words. I won’t try to give a precise definition either, but it is important that we have some idea what we are talking about, so let’s consider one of the prototypical examples of randomness: the tossing of a fair coin.

If I flip a coin, the result could be heads or tails. Until I flip the coin, I don’t know which it will be. In this sense, the coin toss is unpredictable. If the coin is fair, each result is equally likely, so while I cannot say in advance whether a particular result will be heads or tails, I can say something about a large number of flips: approximately half should be heads and the other half tails.

A little mathematics even allows me to determine a range around 50% in which the percentage will almost surely lie. For example, if I flip a fair coin 1,000 times, the percentage of heads will most likely be between 45% and 55% (where “most likely” means a 99% chance). If the percentage of heads lies outside this range—especially if it is quite far outside this range—I am going to be suspicious that the coin flipping process is not fair. That’s one of the key ideas in statistics: not only can we calculate the frequency with which an event occurs, but we can compare data to a stochastic model to see if they are compatible or incompatible.

There are several interesting things we can learn by considering a coin toss. First, probability calculations rely on assumptions. If the assumptions are incorrect, then the probability calculations will also be incorrect. For example, if the coin is biased (such as one that is heads 60% of the time), but we assume it is fair, then the probability calculations given above will be wrong. Of course, if the assumptions are not too far from correct, the results may still be sufficiently accurate for scientific conclusions. If we have an appropriate way to collect data, then we can test our assumptions by comparing data to projections made based on the assumptions.

Second, “random” does not imply “equally likely.” A fair coin should have equal probabilities of heads or tails, but a biased coin is no less random. It’s just different. It is not as simple to handle arithmetically as a situation in which all outcomes are equally likely, but it is not otherwise special. It is a common mistake to assume random events are equally likely when they are not (or when that assumption is not justified).

Third, randomness is about the process. It is a fun experiment to flip a penny 100 times, then spin a penny 100 times and record the side that is showing when it finally tips over, then to stand the penny on end (this takes a steady hand and a little practice) and record which side is showing after pounding the table. These are three different processes, and they do not yield the same results.

Fourth, random processes produce patterns. I sometimes ask my students to mentally flip a coin and record the results as a sequence of letters (e.g., “HTTHHTHT”). Then I have them actually flip a coin and record the results. If the sequences are long enough, I can almost always tell them which is which. The sequences imagined by the students tend to have too few runs of consecutive heads or tails. The sequences based on real coin flips usually include several heads in a row. People not familiar with randomness are often surprised at the patterns that result and assume that the process must not have been random when they perceive a pattern. Our eyes and minds are drawn to similarities and patterns—even those that are produced purely randomly. This can lead us to draw false conclusions from coincidences of all sorts.

Consider the image in Figure 1. It was constructed using a computer to randomly throw 300 darts at a square board. Every position on the board was equally likely to be hit by a dart. This does not, however, mean that the dots are evenly spaced. There are 100 smaller squares. The average is three dots per square. But your eye is likely drawn to some clusters and voids. My eye also catches a graceful downward swoop in the lower part of the upper left quarter. All of this is exactly what we should expect from this random process. If we repeated this experiment, we should expect similar results. Several of the smaller squares would be empty and some others would have two or three times the average number of dots, but these clusters and voids would appear in different places.

Finally, randomness can be used to produce patterns intentionally. Consider the two pictures in Figure 2. You may think the two pictures are identical, but they are not. However, they were each constructed using the same random process:

1. Start at the lower left corner of the big triangle.
2. Randomly choose one of the three corners of the big triangle.
3. Move half way to that corner, placing a dot at the new location.
4. Repeat steps 2 and 3, 50,000 times.

The first few steps of this process for each image are illustrated in Figure 3. Although the final images look very similar, the route taken to get there is very different. In fact, the only point the two images have in common is the starting point. As the creator of the program that generated these images, I knew full well that the result would resemble a fractal image known to mathematicians as Sierpinski’s Triangle, even though I did not know or exercise any control over how the individual points would be selected.

Despite our familiarity with children’s games and the importance of stochastic models throughout the sciences, many Christians have a reaction to randomness that falls somewhere between uneasy and antagonistic. And yet, those same Christians may well watch the evening news to learn about public opinion polls forecasting upcoming elections, take prescription drugs approved by the FDA based on statistics found in clinical trials, obtain electrical power from a nuclear power plant that uses random fission reactions, and insure their cars with companies that rely on stochastic models to set the rates. The foundation of each of these activities is a thorough understanding of randomness that begins with the simple description above.

So where does the uneasiness come from? Likely it comes from the feeling that taking randomness seriously means not taking God seriously. Or put more strongly, it comes from a fear that believing in randomness means not believing in God. Next week we’ll address that problem by asking the question, “Could God use randomness to achieve his purposes?”

In the 1950s, Cage began using various methods of “casting lots” to determine how elements of his music would be chosen and arranged—principally the Chinese system of I Ching. His controversial program was to distance himself from his own creative process, and he explored many additional strategies to transform the role of “creator” into one of “observer.” Most famous of these was his musical composition, “4.33,” which consisted of a pianist sitting at the instrument doing nothing at all for four minutes and thirty-three seconds, while musician and audience listened to the ambient sounds of the concert hall. Yet contrary to that main thrust of Cage’s work, a description of the activities during the week-long residency at the Mountain Lake Workshop where the New River Watercolor Series were made suggests that choice, constraint, and intention were integral and inescapable tools in putting randomness to work for creative ends.

Here’s art historian and theorist Howard Risatti’s description of Cage’s plan of action for the New River Watercolors, from the website of artist Ray Kass, who runs the Mountain Lake program and was Cage’s collaborator for his work there:

Following upon [a previous (1983) Mountain Lake workshop] “painting experiment,” stones collected from the New River were sorted into three groups according to size, which were separately numbered; numerous and varied brushes were divided into two separately numbered groups; likewise, feathers to paint with, colors and washes, and papers were also divided and numbered. In this way, chance procedures using pages of random numbers that were now generated by a computer program could be used to determine the specific materials utilized for each painting (e.g., which painting instruments, what type of paper and which colors, how many washes, which stones to paint around, where to locate the stones on the paper).

While this list enumerates all the specific variables that Cage and his team submitted to chance, there was an incredible level of personal engagement with the materials: Cage didn’t just show us drawings of where the I Ching said the rocks ought to be, he (or his assistants) placed them on the paper and used them as guides to paint around. Large custom brushes were constructed to lay on washes of color, and even the paints were hand mixed, combined, and diluted according to his desires.

Cage’s use of chance, then, was not a “hands off” process, but neither was it a matter of total control: Cage selected processes to create a space of play between himself and the materials he used: the feather between himself and the paper, for instance, introduced variability of resistance and spring, its ability to hold paint, the width of the line. All of these things were elements of material ‘freedom,’ areas in which Cage asked the stuff he used to make the paintings to take part in the process—to contribute its own identity to the intentional, purposeful, and determined work of creating “based on chance.” This should not be surprising, as all art, all creation that we can observe, happens as a dialectic between materials and the creator, and such engagement and interaction in no way lessons the purpose of making, the end in sight.

Kass’ book The Sight of Silence: John Cage’s Complete Watercolors, gives a much more complete account of the tools, processes, and interpersonal reactions between Cage, Kass, and the team of student assistants who helped at almost every stage of the creation of the works. The book goes to great length to honor Cage’s ideal of being present in but not controlling the outcomes (not least by nearly always putting words like “choice” in quotation marks), but the description of his process makes the centrality of Cage’s personal aesthetic and artistic motives inescapable, even more than his physical engagement. What comes through perhaps even more than the way Cage intended to allow chance to ‘guide the creative process’ is that way Cage, himself, not only set the parameters of the chance he allowed into the system, not only engaged directly with the materials during the process, but also exercised judgment over the results, both in process and at the end:

“Cage decided he didn’t want the images of the stones to overlap or go off the sides of the paper. To guarantee this restriction, he created conditions and rules to limit their possible placements.” (p. 51)

“For this single painting [Series IV, #1, pictured above] Cage chose to confine the images of the rocks to a lower area of the paper that represented the proportion of the “golden rectangle. . .” (p. 57)

“While “choice” established much of the work’s nature, “chance” highlighted the intrinsic nature of the materials to reveal a refreshing presence.” (p. 59)

“[H]e initially decided to remove [the first painting of Series III] from the group, and then, liking it more, changed his mind and returned it to the group that would be signed.” (p. 56)

This last note is particularly interesting in that it highlights the fact that Cage was claiming these paintings, naming himself as their author, and was attentive to which ones he approved of enough to call his own. There is no way around the fact that Cage was subjectively as well as objectively the maker of these works: the author of the procedures by which they came to be, but well as the judge (and sometimes redeemer) of the results. For Cage, randomness was a tool, no different than the brushes or rocks or paints is that its specific parameters were chosen at the outset, and always used within the context of his over-arching vision. Perhaps we may likewise think of God’s use of chance—constrained by and tuned to the material conditions he established at the birth of the cosmos—as a way to both engage with and allow freedom for the creation itself.

With any work of art it is reasonable to ask, “Is it beautiful?” or more tellingly, “Would I hang this on my wall?” Seeing Cage’s watercolors for first time without any knowledge of the process or the relative fame of Cage himself, some might be intrigued by the structure of the work (the proportions of the golden rectangle, the overlapping stone shapes, the colors of the paint) while others would be completely uninterested, perhaps even after hearing about how they were made and seeing them in the context of the rest of the New River Watercolor series. But if you had been there in the shop as an assistant, or even observer, if you had been party to the relationships that developed even over the few days Cage spent at the Mountain Lake Workshop, your sense of the beauty of these paintings (and perhaps even scraps of paper Cage used to try out brushes or washes), would take on a different meaning, in much the way we treasure the crayon drawings of our children not because they are spectacular art, but because they are tokens of our relationship.

I make that observation to emphasize one other aspect of Cage’s creative process: that Cage was the instigator first and foremost of relationships of creation. His process created not only paintings but the fellowship that developed as the work was being done. That social, interpersonal dimension is what gives the objects a depth of meaning beyond their material composition, and suggests the particular roles humanity has been given by God. One role is to join into the creative process as lesser, but not unimportant co-creators with him; the other is to observe, recognize and celebrate his activity in the world. Where some will see randomness as evidence of an absent God, our knowledge of this most personal and participatory aspect of creation points us to the God who is with us.

With God’s creation as with human art, we may (or may not) marvel at any one particular “work,” or even think the specifics of how it was made are interesting or attractive; but knowledge of and fellowship with the artist transforms our appreciation of the process as well as its results. When we know the maker, we come to recognize and treasure even the most “random” bits of his handiwork, and name them as his, nonetheless.

For Further Reading:

Ray Kass. The Sight of Silence: John Cage’s Complete Watercolors, 2011.

Website for John Cage Centennial Festival, Washington, DC. September 2012.



]]> Sun, 13 May 12 12:53:04 -0700 Mark Sprinkle http://biologos.org/blog/southern-baptist-voices-a-biologos-response-to-william-dembski-part-ii?utm_source=RSS_Feed&utm_medium=RSS&utm_campaign=RSS_Syndication http://biologos.org/blog/southern-baptist-voices-a-biologos-response-to-william-dembski-part-ii?utm_source=RSS_Feed&utm_medium=RSS&utm_campaign=RSS_Syndication I now respond directly to Dembski’s analysis of “Darwinism” and how BioLogos differs from the view he critiques. Is Darwinism Theologically Neutral?

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.

Perusing the writings of atheistic scientists and philosophers like Daniel Dennett, one could easily get the impression that arriving at a simpler explanation for something equates to a revelation that things are “lower, cruder, and more trivial.” But at the heart of Barr’s critique is the observation that in fundamental physics and advanced mathematics, “simpler” does not mean more chaotic and inchoate, but rather more elegant and beautiful. Those who hold to a philosophical reductionism “overlook the hidden forces and principles” that govern the processes of cosmic evolution.

Barr’s article lays out the way that the work of scientists and mathematicians exploring the fundamental principles of physics (from Kepler to Einstein to those currently running the Large Hadron Collider in Switzerland) actually suggests “that order does not really emerge from chaos, as we might naively assume; it always emerges from greater and more impressive order already present at a deeper level.” This excerpt gives his first example, the starting point from which he guides us into strangely beautiful world of particle physics, and towards the discovery that “matter, although mindless itself, is the product of a Mind of infinite profundity and infinite simplicity.”

Fearful Symmetries

“Let’s start with a simple but instructive example of how order can appear to emerge spontaneously from mere chaos through the operation of natural forces. Imagine a large number of identical marbles rolling around randomly in a shoe box. If the box is tilted, all the marbles will roll down into a corner and arrange themselves into what is called the “hexagonal closest packing” pattern. (This is the same pattern one sees in oranges stacked on a fruit stand or in cells in a beehive.) This orderly structure emerges as the result of blind physical forces and mathematical laws. There is no hand arranging it. Physics requires the marbles to lower their gravitational potential energy as much as possible by squeezing down into the corner, which leads to the geometry of hexagonal packing.

At this point it seems as though order has indeed sprung from mere chaos. To see why this is wrong, however, consider a genuinely chaotic situation: a typical teenager’s bedroom. Imagine a huge jack tilting the bedroom so that everything in it slides into a corner. The result would not be an orderly pattern but instead a jumbled heap of lamps, furniture, books, clothing, and what have you.

Why the difference? Part of the answer is that, unlike the objects in the bedroom, the marbles in the box all have the same size and shape. But there’s more to it. Put a number of spoons of the same size and shape into a box and tilt it, and the result will be a jumbled heap. Marbles differ from spoons because their shape is spherical. When spoons tumble into a corner, they end up pointing every which way, but marbles don’t point every which way, because no matter which way a sphere is turned it looks exactly the same.

These two crucial features of the marbles—having the same shape and having a spherical shape—should be understood as principles of order that are already present in the supposedly chaotic situation before the box was tilted. In fact, the more we reduce to deeper explanations, the higher we go. This is because, in a sense that can be made mathematically precise, the preexisting order inherent in the marbles is greater than the order that emerges after the marbles arrange themselves. This requires some explanation.

Both the preexisting order and the order that emerges involve symmetry, a concept of central importance in modern physics, as we’ll see. Mathematicians and physicists have a peculiar way of thinking about symmetry: A symmetry is something that is done. For example, if one rotates a square by 90 degrees, it looks the same, so rotating by 90 degrees is said to be a symmetry of the square. So is rotating by 180 degrees, 270 degrees, or a full 360 degrees. A square thus has exactly four symmetries.

Not surprisingly, the hexagonal pattern the marbles form has six symmetries (rotating by any multiple of 60 degrees: 60, 120, 180, 240, 300, and 360 degrees). A sphere, on the other hand, has an infinite number of symmetries—doubly infinite, in fact, since rotating a sphere by any angle about any axis leaves it looking the same. And, what’s more, the symmetries of a sphere include all the symmetries of a hexagon.

If we think this way about symmetry, careful analysis shows that, when marbles arrange themselves into the hexagonal pattern, just six of the infinite number of symmetries in the shape of the marbles are ex-pressed or manifested in their final arrangement. The rest of the symmetries are said, in the jargon of physics, to be spontaneously broken. So, in the simple example of marbles in a tilted box, we can see that symmetry isn’t popping out of nowhere. It is being distilled out of a greater symmetry already present within the spherical shape of the marbles.”

In the full essay, Barr gives a richer description of how this most basic kind of symmetry is just one sort of order, and how even this form points to other much more complex kinds of symmetry whose properties may be described only through the tools of complex mathematics. As he says, “the symmetries that characterize the deepest laws of physics are mathematically richer and stranger than the ones we encounter in everyday life.” But even more important than the fact that such mathematical concepts exist and are beautiful, more important even than the way such esoteric mathematical symmetries have suggested imminently practical experimental projects, is the way they point to a universe that is anything but brutish and trivial, though its elegance may be hard to see:

“It is true that the cosmos was at one point a swirling mass of gas and dust out of which has come the extraordinary complexity of life as we experience it. Yet, at every moment in this process of development, a greater and more impressive order operates within—an order that did not develop but was there from the beginning. In the upper world, mind, thought, and ideas make their appearance as fruit on the topmost branches of an evolutionary tree. Below the surface, we see the taproots of reality, the fundamental laws of physics that shimmer with ideas of profound simplicity.”

This essay appears with the permission of First Things. To read Barr’s complete essay, please click here.

Evolution: just a theory

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

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

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

Whale evolution: an example of converging lines of evidence

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

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

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

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

Going out on a limb

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

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

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

… and passing the test

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

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

For further reading

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

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

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

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

Transcript

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Along for the ride, but looking out for number 1

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

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

Rags to riches: converting transposons to functional sequences

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

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

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

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

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

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

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

The genomic recycling bin

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

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

For further reading

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

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

Today's video is courtesy of filmmaker Ryan Pettey, director/editor of Satellite Pictures and features physicist Ard Louis.

In today's video, Oxford physicist Ard Louis discusses the famous debate between renowned evolutionary biologists Stephen Jay Gould and Simon Conway Morris. Gould believed (and wrote in his book Wonderful Life) that if the "tape" of evolution were rerun, the chance that anything like human intelligence would emerge is essentially zero. In other words, humanity is here through random accident. Gould pointed to the work of Morris and fellow scientists in their research of the Burgess Shale as evidence for this view.

However, Morris himself disagrees, pointing to what is called evolutionary convergence. As Morris notes, there are numerous examples of identical features evolving multiple times throughout the history of life independently. Morris believes that if the tape of life were replayed, we would see something like humans emerge. A Christian might say, it looks like we were planned.

Some Christians might find Simon Conway Morris' viewpoint, with its implicit teleology, more attractive. Others, perhaps motivated by a high view of providence, may find Gould's emphasis on contingency equally congenial to their faith. What do you think?

As we noted in our response to the June article in Christianity Today “The Search for the Historical Adam,” the evidence for gradual creation is overwhelming, with more studies supporting the evolutionary process being published each year. We’ve looked at many of these evidences: from fossils, from comparative anatomy, from genetics. Today, we’d like to highlight for our readers a compelling video from the annual TED Conference featuring geneticist Svante Pääbo. You may remember Pääbo from his efforts to extract and sequence DNA from 30,000(+) year old Neanderthal bones (we mentioned his work here).

In this eighteen minute video, Pääbo covers a lot of ground, noting several lines of genetic evidence for the evolution of modern humans from earlier hominids in Africa, as well as for the interbreeding between early humans and Neanderthals. We’ve covered some of this data before, but it’s particularly compelling to hear it described by one of the scientists leading the field of study.

However, our goal at The BioLogos Foundation isn’t just to make the Church aware of the fascinating and convincing scientific evidence for gradual creation. As we have said before:

BioLogos exists to help Christians think carefully about the ramifications of these new data in light of long-standing traditional ways of viewing human creation. We have some re-thinking to do, but it can be done and will be done within the context of a Christian faith that is fully orthodox and thoroughly evangelical. Any time we draw closer to truth, to God’s truth, we have nothing to fear. There is still much to learn, but we can look back at what we have learned with awe—absolute awe.

It is truly amazing that we know so much now about our early days. For example, Africans do not have DNA which is specifically derived from Neanderthals, whereas people in the rest of the world do carry a small amount. This confirms the picture of human history derived from studying fossils. Neanderthal bones have not been found in Africa, so it isn’t surprising that their DNA is not there either. The fact that non-Africans have some of the DNA found in Neanderthal bones confirms that which geneticists knew from other studies: we have two distinct groups of human ancestors—those who left Africa in ancient times and those who stayed.

God chose to reveal himself and to begin working with a distinct sub-group of ancient humans, those descended from Abraham and Sarah. To Abraham, God made a marvelous promise. Drawing his attention to the stars above, God said that someday Abraham’s descendents would outnumber the countable stars in the universe. And so it came to be. Indeed through our adoption into the family, we are all children of Abraham. The God of Abraham is our God too and each one of us is one of those stars too numerous for Abraham to count.

Sometimes, it seems that we are uncomfortable with the notion that God made us through a gradual process that included apes in our family tree. It is almost as though we would prefer dirt to apes. Perhaps, in at least some cases, this is due to an inadequate appreciation for the fact that God loves, really loves, all of creation, not just us. As special as we know we are, we can’t read Psalm 104, Genesis 1, Genesis 9 (where the covenant is not just with Noah but with all living creatures), or Job 38-41 without being reminded that all living creatures are God’s creation (see here). The Neanderthals, the Denisovans, Homo erectus, and the australopithecines were God’s creation too! Still, we modern humans have been singled out. We’ve been called out.

True our family tree, as Pääbo shows here, is intriguing. But let us never forget, that the most important thing about this tree is that God is the vine which exists at its core, and we are called to be the branches which bear fruit. The fact that many of us have a small amount of Neanderthal DNA, some of us have Denisovan DNA, and others have neither is interesting, but it is really just a side issue for people of faith. As a result of God’s visit to Abraham, followed eventually by God’s taking on flesh in the person of Jesus of Nazareth, we can all know God as our heavenly Father. We are children of God and as such, we are God’s representatives. We are called to image God. We are called to love God. And we are called to love each other and to deeply respect all that he has made.