Many things we have learned contradicts much of what we previously thought about the mind.  For example, it is quite common and sensible to believe that we come into the world with minds that are essentially “blank slates,” and that what we know is written on those slates by experience alone.  But that view appears to be wrong.

The human mind consists of a variety of distinct and interacting mental tools, each of which comes pre-loaded with some quite specific content and some processing algorithms.  For example, it is now clearly demonstrated that human beings are naturally endowed with what we might reasonably describe as innate beliefs and innate cognitive processors.

On the belief side, developmental psychologists have identified numerous domains of understanding that are native to us, such as folk physics, folk biology, folk psychology, agency detection tendencies, and so on. What these discoveries seem to show is that our minds are pre-disposed to come to think about the world in very specific ways—ways that are determined by the kinds of minds we have.

So it looks like from birth, or rather through a regular and maturationally natural process, we have dispositions for form beliefs in the following domains.

“Folks Physics”:

• Objects move on inertial paths
• Objects cannot move through other objects
• Objects must move through space
• Objects must be supported

“Folk Psychology”:

• Agents act to satisfy desires
• Agents have beliefs

“Folk Biology”:

• Animals bear young similar to themselves
• Living things need nutrients

In addition to these innate dispositions toward certain kinds of beliefs, we also seem to have cognitive mechanisms that dispose us to crunch sensory inputs in specific ways. We might call these “innate cognitive processors.” Examples of these would include things like contagion avoidance and agency detection.

Contagion avoidance is a natural aversion human beings share to things like dead bodies, animal waste and vomit, rotting food, etc. These things “gross us out” from a very early age.  Indeed, the aversions we have towards them pre-date any data we might come to possess that would lead us to judge them dangerous.  We are also repelled by them in ways that are independent of other aversive stimuli like smell (that is, you can’t explain this aversion by noting that people are scared off because of an unpleasant odor since studies show that the aversions are independent of that).

A second processor is our Agency Detection Device. Here, psychologists have identified a cognitive processor that seems to pre-dispose us to form beliefs in the reality and presence of (sometimes invisible!) agents under certain conditions. In these cases, when we look for the cause of certain events, motions, sounds, or structures, we are disposed to think that it was caused by a someone rather than by a something. Our ADD appears to be hypersensitive.  It is very good at detecting agency, and in fact is more likely to generate false positives than false negatives.  This is often referred to as our hypersensitive agency detection device (HADD), and may be reflected in manifold attributions of ghosts, fairies, forest spirits, and even personalities of machines!

In sum, psychologists have shown that our initial presumption about the contents of our mind was wrong. Our minds are not blank slates, but processing devices that come endowed with a complex operating system.

Many are quick to point out that this should not be surprising.  When we look across times and cultures and find very similar beliefs concerning the nature of physical, biological, and psychological reality, those similarities cry out for some explanation. Since these diverse individuals have a very wide range of experience, something other than, or in addition to, common experience would seem to account for the similarities of belief. And so it is natural to conclude that there is some fundamental similarity among human minds that explains it. And recent empirical evidence has in fact confirmed this conclusion.

One type of belief that is pervasive across times and cultures is religious belief.  One is thus led to wonder whether those sorts of beliefs are among those that we are naturally disposed to believe.  One New Zealand religion scholar, Joseph Bulbulia, argues that the emerging consensus is yes: “The view of mind expressed by Descartes as composed of innate understandings given in advance of any experience has been thoroughly vindicated after sixty years of cognitive psychology. It may be that Descartes will be shown correct on another score, namely that knowledge of the Divinity is imprinted on every mind [as well]”

Bulbulia’s remark invites us to entertain three key questions:

• Is there any evidence that we are naturally disposed to religion?
• How do we explain the origin of these dispositions?
• What are the implications of such explanations for belief itself?

These will be explored in the next post.

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

What you can expect

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

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

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

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

How you can help

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

Getting started

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

Antibody fine-tuning

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

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

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

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

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

Antibody production and evolution both involve mutation and selection

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

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

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

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

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

Though often neutral or destructive, mutations sometimes create new functionality

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

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

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

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

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

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

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.

1. We are a world that longs for goodness and beauty, whether we are believers or not.

2. The data from emerging neuroscience and attachment research points us to a world of goodness and beauty.

3. This same data reflects and energizes the biblical narrative. Creation itself points us to the very story God is telling.

4. One of the most integral processes—that helps us get to truth and beauty—involves the changing (and renewal) of our minds. The renewal of our minds is a subset of the renewal of everything. God is on a mission of complete renewal, albeit on his timetable.

In this mission for renewal, one of the most important aspects is the interpersonal experience of being known. We change primarily not by what we know, but by how we are known. We live in a culture that is really good at knowing things, but not so good at being known.

5. Our first reaction is likely to be, “How will knowing this stuff change me?” But the biblical narrative is not just about us as individuals, it is about a world of mercy and justice. In order for us to have mercy and justice, we don’t do it primarily as individuals, we do it as institutions. God’s renewal is not just about changing us, it is about changing everything.

See part 2 for the second half of Dr. Thompson's presentation

Let me be clear. I do not reject dualism on account of any kind of philosophical or other kind of argument. In fact, I find many arguments against dualism—philosophical and otherwise—to be pretty weak specimens. I’m what a friend calls an antecedent materialist. In other words, I come to the discussion assuming I am a physical object, since that is what I have always seemed to myself to be for as long as I can remember. A non-physical soul doesn’t explain anything about consciousness that cannot be explained without it, and it is furthermore a wholly unnecessary hypothesis for many religious doctrines, despite intuitions to the contrary by many religious believers. For example, belief in an afterlife, belief in the peculiarly Christian idea of the incarnation of Christ, as well as the belief that we human beings bear the image of God—none requires belief in a non-physical soul in order to be made sense of. So until I am confronted with some knock-down, drag-out argument to the contrary, or until I am presented with some phenomena that cannot be accounted for in naturalistic terms or, yet again, until I have something resembling a conversion experience that forces me to renounce my physicalism, I'm sticking with it.

To go a bit further, let’s consider several theological doctrines that seem to cut against a physicalist conception of human personhood. These constitute perhaps the three most common objections Christian physicalists receive to their physicalism. After I address these objections, I will say a little more about the content of my own physicalist conception of human persons, The Constitution View. Perhaps in a future post I can say a little bit about the science of consciousness itself and address some of the most common objections to physicalism based on that mysterious phenomenon.

Theological Objections to Physicalism about Humans

The Incarnation of Christ

The doctrine of the incarnation of Christ is a central tenet of Christianity, and it may seem that the doctrine is inconsistent with a physicalist conception of human personhood. Yet I believe a physicalist view of human persons—like my own—actually makes better sense of the incarnation than does dualism. Let me explain.

The putative problem for the physicalist is this: if God (or the second person of the Trinity in particular) is essentially a non-physical being, then how could such a being become purely physical without losing an essential property? And if the second person of the Trinity loses an essential property, then wouldn’t he not simply cease to be fully God but simply cease to exist? (An essential property is a property a thing has and can’t lack without ceasing to exist. For example, my dog has the property of being a canine. He can’t lose that property without ceasing to exist—he is essentially a canine.)

Well, according to the Chalcedonian formulation, the incarnate Christ is one Person with two natures, a fully divine nature (that of the Second Person of the Trinity) and a fully human nature (that of Jesus from Nazareth). The Constitution View I hold divides things just where one would expect—between the human nature and the divine nature of the single person. And keep in mind, by the way, that the person of Christ is not human; he is divine, being the second person of the Trinity. But this one person, in the incarnation, had two natures--human and divine. In this understanding of the dual natures, Christ is wholly non-physical in his divine nature and wholly physical in his human nature. Now consider the somewhat-awkward cleavage Substance Dualists must offer. According to Substance Dualism, Christ is wholly non-physical in his divine nature and partly physical and partly non-physical in his human nature. Not especially elegant. To my mind, far from being unable to accommodate the doctrine of the incarnation, my physicalist view of human persons is actually better able to explain the doctrine than is dualism.

Notice that if what I said above is true, the way this objection is often put contains an important mistake in assuming that the second person of the Trinity ceased to be something he was apart from the incarnation. Indeed, the second person of the Trinity did not become purely physical (or even partly physical!). The second person of the Trinity did not give up non-physicality in the incarnation. Remember: one person (Divine and non-physical) with not one but (in the incarnation) two natures—one non-physical, the other physical. How can that be? I don’t have the slightest idea; but, the mystery of the incarnation is not explained away by any account, be it dualist or physicalist.

The Imago Dei

Now, what of the imago Dei or image of God? If it’s true that we human persons are wholly physical beings—as any version of physicalism must claim—then what does it now mean to say that we have been created in God’s image? Doesn’t having been created in the image of God just mean having a non-physical soul and the features of intellect, will and emotion that characterize soul? I do not believe that our having been created in the image of God means that we are non-physical as God is non-physical. What then does it mean?

Well, there are many ways of understanding the claim that we human beings image God. One might mean that we image God when we care for Creation and contribute to the terrestrial flourishing of the Created order. This, after all, is what the Bible means when it speaks of our having been given “dominion”. We are God’s vice-regents, as it were. To have dominion is to care for others, including non-human “others” like oceans and streams, octopus and salamander; in other words to have dominion is tend to the well being of all the earth. Second, one might mean that we image God when we live in loving relation to other human beings and invest ourselves in their flourishing and well being. For we are essentially persons-in-relation. Since God is a Trinity, it is not surprising that we should image God in virtue of our essentially social nature. The tenor of the relation between the three persons of the trinity is one of a harmonious and free exchange of love and joy. So engaging in acts of mercy, hospitality, love, kindness, etc. is to act like God. In fact, we image God when we image Jesus, who welcomed the outcast, fed the hungry, clothed the naked, hated evil and delighted in doing the work of the Father. Finally, one might claim that we image God in our suffering. God is love. To love is to open oneself up to suffering. And suffering love is God-love.

Now of course none of these ways that I have mentioned that we image God rules out the possibility that we are wholly or partly non-physical beings; but it doesn’t imply it either. The fact that we have been created in the image of God is perfectly compatible with the claim that we are wholly physical beings. Indeed, there is nothing in the doctrine of the imago Dei, rightly understood, that entails a dualist view of human nature.

But even if neither the doctrine of the incarnation nor the doctrine of humanity as reflecting the imago Dei require that we be at least partially non-physical beings, what about the issue of life after death? I’ll address that third challenge to a Christian physicalism tomorrow.

Yet it doesn’t follow that we are mere animals, and our rationality is what sets us apart from the rest of the genus. Indeed, for Aristotle, and for Aquinas after him, rationality is unlike our other capacities in having an essentially immaterial and non-bodily aspect. The reason has to do with our capacity to form abstract concepts, which underlies all our other distinctively rational activities. It is because you can grasp what it is to be a man -- not just this particular man or that one, but any possible man, man as a universal -- that you can go on to form judgments like the judgment that all men are mortal, can reason from that judgment together with the judgment that Socrates is a man to the conclusion that Socrates is mortal, and so forth.

There are several arguments that establish that this capacity for abstract thought cannot in principle be reduced to or otherwise entirely explained in terms of brain activity, even if brain activity is part of the story. The arguments have their roots in Plato and Aristotle and have been defended in recent years by Aristotelian philosophers like Mortimer Adler, John Haldane, David Oderberg, and James Ross.¹ Answering the various objections to (and misunderstandings of) these arguments takes some work, but the basic idea can be set out fairly simply.²

Let us take as an example the thought that triangles have three sides. For that thought (or any other) plausibly to be material, it would have to be identifiable with something like a symbol or set of symbols encoded in the brain -- something analogous to the symbols encoded in the electronic circuitry of a computer. But there is no way a thought could be entirely reducible to that sort of thing. For no material symbol could possibly have the determinate or unambiguous content that at least many of our concepts have; and no material symbol could possibly have the universal reference that our concepts have.

Consider the most unambiguous symbol of triangularity there could be -- a picture of a triangle, such as the one to the right. Now, does this picture represent triangles in general? Or only isosceles triangles? Or only small isosceles triangles drawn in black ink? Or does it really even represent triangles in the first place? Why not take it instead to represent a dinner bell, or an arrowhead? There is nothing in the picture itself that can possibly tell you. Nor would any other picture be any better. Any picture would be susceptible of various interpretations, and so too would anything you might add to the picture in order to explain what the original picture was supposed to represent. In particular, there is nothing in the picture in question or in any other picture that entails any determinate, unambiguous content. And even in the best case there is nothing that could make it a representation of triangles in general as opposed to a representation merely of small, black, isosceles triangles specifically. For the picture, like all pictures, has certain particularizing features -- a specific size and location, black lines as opposed to blue or green ones, an isosceles as opposed to scalene or equilateral shape -- that other things do not have.

Now what is true of this “best case” sort of symbol is even more true of linguistic symbols. There is nothing in the word “triangle” that determines that it refers to all triangles or to any triangles at all. Its meaning is entirely conventional; that that particular set of shapes (or the sounds we associate with them) have the significance they do is an accident of the history of the English language. But something similar could be said of any material symbols whatever. Even if we regarded them as somehow having a built-in meaning or content, they would not have the universality or determinate content of our concepts, any more than the physical marks making up the word “triangle” or a picture of a triangle do. But then the having of a concept cannot merely be a matter of having a certain material symbol encoded in the brain, even if that is part of what it involves. Nor can it merely be a matter of having a set of material symbols, or a set of material symbols together with certain causal relations to objects and events in the world beyond the brain. For just as with any picture or set of pictures, any set of material elements will be susceptible in principle of alternative interpretations; while at least in many case, our thoughts are not indeterminate in this way.

We might understand the point by analogy with sentences. If you are going to use the English sentence “Snow is white,” you are typically going to have to express it via some material medium -- ink marks, pixels, sound waves, or what have you. All the same, the meaning of that sentence cannot be accounted for in terms of any of the physical properties of those media. There is nothing in the shapes of the letters that make up the words of the sentence, or the chemistry of the ink in which they are written, or the physics of the compression waves in the air that you generate when uttering them, that makes them refer to snow or to whiteness or indeed to anything at all. A sentence is a seamless unity of the material and the immaterial, and it is created by another seamless unity of the material and immaterial -- a human being.

At this point there will no doubt be those who object that positing ectoplasm or spook stuff is hardly a better explanation of thought than an appeal to brain activity is. And that is quite true. But then, I said nothing about ectoplasm or spook stuff in the first place. When a mathematician points out that it is just muddleheaded to speak of the square root of 25 as if it were a kind of physical object, it would be silly to accuse him of believing that the square root of 25 is made out of ectoplasm or spook stuff. If your picture of reality cannot accommodate numbers alongside physical objects, that is your problem, not his. Mathematics simply provides a powerful example of a body of truths that cannot be captured in the language of physics, chemistry, neuroscience, and the like.

Similarly, to point out that whatever a thought is, it cannot in principle be reduced to the physical properties of brain activity, is simply to provide another example of an aspect of reality that cannot be entirely captured in such language. Only if we assume that all of reality must be so captured will this sound odd, but that we should not assume this is, of course, precisely the point. And if we do assume it, we are doing so in the face of the evidence, and not on the basis of the evidence. For it is precisely what we know about thought from our everyday familiarity with it -- such as the fact that it sometimes has a determinate content, and a universal reference -- that tells us that it cannot be entirely material, just as it is what we know about numbers from our everyday familiarity with them that tells us that they cannot be physical objects.

But doesn’t neuroscience show that there is a tight correlation between our thoughts and brain activity? It does indeed. So what? If you smudge the ink you’ve used to write out a sentence or muffle the sounds you make when you speak it, it may be difficult or impossible for the reader or listener to grasp its meaning. It does not follow that the meaning is reducible to the physical or chemical properties of the sentence. Similarly, the fact that brain damage will seriously impair a person’s capacity for thought does not entail that his thoughts are entirely explicable in terms of brain activity.

Aristotle and Aquinas, though they regarded the human intellect as immaterial, would not have been surprised in the least by the findings of modern neuroscience. Indeed, they would have been surprised had neuroscience not turned up the correlations it has. This will sound surprising if you take Descartes as your paradigm of a philosopher who affirms the immateriality of the human mind. But defending Descartes is exactly the reverse of what I have been doing. For it was Descartes who substituted the real, concrete human being -- a seamless unity of the physical and the mental, the bodily and the immaterial -- with a bizarre patchwork of abstractions of his own devising. Materialists have followed him ever since. Materialism is just a riff on Cartesianism, not its opposite. Tomorrow, I’ll explain exactly what I mean.

Notes

1. See Mortimer Adler, Intellect: Mind Over Matter (New York: Collier Books, 1990); J. J. C. Smart and J. J. Haldane, Atheism and Theism, Second edition (Oxford: Blackwell, 2003), pp. 96-109; David S. Oderberg, “Hylemorphic Dualism,” Social Philosophy and Policy 22 (2005); and James Ross, “Immaterial Aspects of Thought,” Journal of Philosophy 89 (1992).
2. I provide an exposition and defense of such arguments in chapter 7 of my book Philosophy of Mind and chapter 4 of my book Aquinas. An especially detailed exposition and defense can be found in my article “Kripke, Ross, and the Immaterial Aspects of Thought,” forthcoming in the American Catholic Philosophical Quarterly.

What Is at Stake?

What does it mean to be human? In what ways, if any, is our essential humanity tied to body and soul, mind and brain? This is not the stuff of mere curiosity. A host of pressing issues are at stake:

• Is there anything about humans that our mechanical creations, our innovations in Artificial Intelligence, will be unable to duplicate?
• What view of the human person helps us to find what we want to know about ourselves theologically — about sin, for example, as well as moral responsibility, repentance, and growth in grace?
• Am I free to do what I want? Given what we have learned about brain functioning, how might we understand the “free” in “free will”?
• What portrait of the human person is capable of casting a canopy of sacred worth over human beings, so that we have what is necessary for discourse concerning morality and for ethical practices?
• If humans, like sheep, can be cloned, will the resulting life form be a “person”?
• How should we understand “salvation”? Does salvation entail a denial of the world and embodied life, focusing instead on my “inner person” and on the life to come?
• How ought the church to be extending itself in mission? Mission to what? The spiritual or soulish needs of persons? Society-at-large? The cosmos?
• What happens when we die? What view(s) of the human person is consistent with Christian belief in life-after-death?

For many, and not least for many Christians, what makes a human genuinely human is the identification of the human person with his or her soul. From the second century on, theologians debated the origin of the soul: Are souls created by God ex nihilo at the moment of their infusion into the body? Are body and soul formed together? Are souls preexistent? Indeed, in the late-second century it was clear to many, as the Letter to Diognetus puts it, that “the soul dwells in the body, yet is not of the body” (1.27). Traditionally, systematic theology has discussed the uniqueness of humanity in two theological loci: human creation in the divine image and the human possession of a soul. Often these two are reduced to one, with the soul understood as the particular consequence of creation in God’s image.

For persons of faith — Christians included, but many others besides — the idea of a soul separable from the body is not only intuitive but necessary. We have regularly appealed to the soul as proof that humans are not mere animals, and so as a foundation for our views of the sacredness of human life. Moreover, Christians generally have derived from belief in the existence of the soul their affirmation of the human capacity to choose between good and ill. Further, the existence of a nonphysical soul, distinct and separable from the body, is typically regarded as the means by which human identity can cross over the bridge from this life to the next. Indeed, traditional Christian thought has tended to regard the body as frail and finite, the soul as immortal.

But it is the human possession of a “soul” that science now questions. When, as neurobiology and evolutionary psychology increasingly urge, the attributes and capacities traditionally allocated to the human soul are conditioned at point after point by biological processes, on what basis can belief in a soul be maintained? If science is generating “a radically new understanding of what it means to be human,”³ then those of us in the church must prepare ourselves for searching questions about the propriety of Scripture and traditional Christian thought in our talk about humanity, salvation, the end time, and more.

Before we engage too much in worried hand-wringing, however, we should ask whether our situation is so dire. Do these innovations in our understanding of personhood in fact call into question our deepest beliefs as Christians? Interdisciplinary study — with contributions from neuroscience, but also from biblical studies, theological studies, ethics, and philosophy (see “Further Reading,” below) — are demonstrating that emerging scientific portraits of the human person are neither as novel as we might imagine, nor as threatening to the essential tenets of Christian faith.

Biblical Contributions

In the context of current discussion on the nature of the human person, the Christian Scriptures have two primary contributions. First, taken as a whole, the biblical witness is fully congruent with a view of the person that affirms the human being as bio-psycho-spiritual unity. Neurobiological evidence and/or philosophical arguments favoring some form of monism are not at all hostile to the witness of Scripture. Second, we must recognize that the Old and New Testaments do not define the human person in essentialist but above all in relational terms. Put differently, the Bible’s witness to the nature of human life is at once naive and profound. It is naive not in the sense of gullibility or primitiveness, but because it has not worked out in what we may regard as a philosophically satisfying way the nature of embodied existence in life, death, and afterlife. It is profound in its presentation of the human person fundamentally in relational terms, and its assessment of the human being as genuinely human and alive only within the family of humans brought into being by Yahweh and in relation to the God who gives life-giving breath. This non-negotiable biblical insight is being recovered by some scientists today — e.g., by J. Polkinghorne and W.S. Brown, each of whom has urged that the notion of “soul” be recast in relational terms.⁴

We can press further. First, Scripture outlines a series of qualities of the human person that contrast sharply with the “modern self” derived from dualistic portraits. In his Sources of the Self, C. Taylor finds that, for modern folk, personal identity has come to be shaped by such assumptions as self-sufficiency, self-determination, and self-referentiality (“I am who I am”); that persons have an inner self, which is the authentic self; and that self-autonomy and self-legislation are basic to authentic personhood (Harvard University Press, 1989). Without majoring on the notion of a metaphysical entity of the “soul,” Taylor’s analysis nonetheless intimates how modern, personal identity has been cultivated in the garden of anthropological dualism.

In Scripture, however, we find such emphases as the following: the construction of the self as deeply embedded in social relationships and thus the importance of dependence/interdependence for human identity; a premium on the integrity of the community and thus the contribution of individuals to that integrity; the assumption that a person is one’s behavior; an emphasis on external authority — that is, the call to holiness is a call to a human vocation drawn from a vision of Yahweh’s “difference”; and the reality of dualism vis-à-vis good/evil, resident in and manifest both outside and inside a person. The line from a substance dualism that locates personal essence in the “soul” to this vision of personal identity is not easily drawn.

The point is that the construction of personal identity that pervades modernity is at odds with biblical anthropology at almost every turn, while the witness of Scripture and the findings of neuroscience are converging at significant points.

Second, negatively, we err when we imagine that it is the “soul” that distinguishes humanity from non-human creatures. Aristotle is closer to the biblical tradition in his view that the soul is that in virtue of which an organism is alive (On the Soul 2.1 §§412a-413a10). Given this conceptualization, there is no particular reason to limit the idea of “soul” to the human person. Within the Old Testament, “soul” (Hebrew: nepheš) refers to life and vitality — not life in general, but life as instantiated in human persons and animals. Nepheš is not a thing to have but a way to be. To speak of loving God with all of one’s “soul,” then, is to elevate the intensity of involvement of one’s whole being. Accordingly, the Common English Bible gets it right when it translates “the first and greatest commandment” in this way: “You must love the Lord your God with all your heart, with all your being, and with all your mind” (Matthew 22:37). Morever, in the creation accounts of Genesis 1-2, the Hebrew term used of human beings in 2:7, nepheš, is also used with reference to all sorts of wildlife, to everything “in which there is life (nepheš)” (1:30). This demonstrates incontrovertibly that “soul” (nepheš) is not, under this accounting, a unique characteristic of the human person. Accordingly, one might better translate Genesis 2:7 with reference to the divine gift of life: “the human being became a living person” — or, to quote again from the Common English Bible: “The human came to life.”

Third, thinking still of Genesis 2, it is instructive that the same texts that are silent on the infusion of a human soul into a dust-created body nevertheless distinguish by their use of the term nepheš between a being that has life and lifelessness. This speaks against any dualism that deprecates the body in favor of the soul and against any conceptualization of disembodied human existence in this life or the next. It also contravenes the widely held view that the quality of human life is vested in some thing or quality intrinsic to the individual person and that, in order to speak meaningfully of an afterlife, this “thing” must survive death. The soul does not distinguish human life as human or of particular value, but the graciousness of God does. Scripture situates the human family within the grand narrative of God’s doing; this narrative places a premium on human relatedness to God, humanity, and the cosmos because it is determined by God’s own character; and it is precisely within this narrative that the human creature draws both its value and its reason for being.

Hence, from a vantage point within the biblical narrative, avenues determined by autonomous individualism, interior psychic and/or mental processes, or the behavior of a vast assembly of nerve cells are mistaken, however well-worn they may have become. Although each of these accounts might appear to support a workable portrait of the human person and of human health, none of these carry us far in our concern to address our deepest human questions about what it means to be fully human.

What does it mean to be human? From a perspective within the biblical narrative, the way forward is marked by an account that rejects the necessity of a separate, metaphysical entity such as a soul to account for human capacities and distinctives; that underscores the material location of the human person in relation to the created order; that refuses to reduce personal identity to our neural equipment but rather emphasizes the personal contribution and relatedness of human beings to the human family and the cosmos; and thus that has as its primary point of beginning and orientation the human in a partnering relationship with God.

Further Reading

• W.S. Brown et al., eds., Whatever Happened to the Soul? Scientific and Theological Portraits of Human Nature (Fortress, 1998)
• J.B. Green, Body, Soul, and Human Life: The Nature of Humanity in the Bible (Baker Academic, 2008)
• J.B. Green, ed., What about the Soul? Neuroscience and Christian Anthropology (Abingdon, 2004)
• M.A. Jeeves, ed., Rethinking Human Nature: A Multidisciplinary Approach (Eerdmans, 2011).

Notes

1. P. Churchland, Brain-Wise. MIT Press, 2002: 2
2. S. Blakeselee, “Humanity? Maybe It’s All in the Wiring,” New York Times, 9 December 2003, F1
3. T. Metzinger, “Consciousness Research at the End of the Twentieth Century,” in Neural Correlates of Consciousness: Empirical and Conceptual Questions. ed. T. Metzinger; MIT Press, 2000: p. 6
4. See J. Polkinghorne, “Eschatology: Some Questions and Some Insights from Science,” in The End of the World and the Ends of God. ed. J. Polkinghorne and M. Welker. Trinity Press International, 2000: 29-41 and W. S. Brown, “Cognitive Contributions to Soul,” in Whatever Happened to the Soul? ed. W.S. Brown et al.; Fortress, 1998: 99-125.

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

Sporadic extinction

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

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

Extinction, en masse

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

Speciation, en masse

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

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

Clearing the deck, and re-filling the niches

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

For further reading:

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

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

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

The Evolutionary Role of Death & Natural Evil

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

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

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

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

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

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

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

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

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

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

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

Notes

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

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

Review: gene structure and function

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

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

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

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

Comparing gene transcription across species at the genomic level

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

Old hypotheses, new technology

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

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

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

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

These results underscore a few important points:

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

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

For further reading:

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

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

I am glad to have the opportunity to dialogue with Dr. John Hammett. In addition to our shared Christian faith and our shared lack of expertise in evolutionary science, we have in common one of our teaching and scholarly foci: the nature of human persons. Dr. Hammett approaches this topic as a trained theologian, whereas I approach it as a philosopher. However, on a topic such as this one, those disciplinary boundaries can get smudged a bit when the discussants approach the matter from the standpoint of a biblically-rooted Christian faith. Indeed the issue is of such importance and complexity that I would welcome continued conversation with Dr. Hammett beyond this initial exchange.

The Christian Scriptures teach that we human beings have been created in God’s image. What does that mean? I am in substantial agreement with Dr. Hammett on this question. While I think that bearing God’s image involves our having or having a potentiality for certain basic psychological capacities that we associate with the term “person”, it has to do even more profoundly with our specific capacity for relationship with God. Indeed, I would go further and say that it is not just our having this capacity that makes us divine ikons, it is also the fact that God has activated this capacity—He has given the precious gift of His self-disclosure to us. Further still, it has an eschatological dimension, based on the revealed promise of a future development and perfection of each of us, and so by implication, of human nature itself, by almighty God. We are in the process of becoming fully human: beyond a descriptive biological or even psychological notion of human nature lies a teleological one—not a telos of nature but of God's loving purposes for us. Despite our unequally born deficits—physical, cognitive, emotional, and moral/spiritual—we are destined for a fuller, supernatural realization of our common nature.

That we are in these ways God’s image bearers is a (wonderful!) teaching of our faith. The Scriptures also speak in various places of the human “soul.” The idea of the soul seems clearly connected to the idea that we are divine ikons. But here we should tread carefully. It is of course not unique to the Hebrew and Christian Scriptures to use some such singular term to refer to that which is most distinctively human and that by virtue of which we are able to survive the death and decay of our bodies. But it is one thing to use the term as a kind of placeholder for whatever it is about us that enables us to be, feel, and act in distinctively human ways in this life and to survive death into the next; it is another thing to link the term to a specific metaphysical account of the matter, such as might say whether the soul is a kind of thing or substance, what kind of thing it is, and exactly how “it” relates to the human “body.”

It is (and always has been) very common for Christians to invest the term “soul” as it used in Scripture with such a metaphysical account. As these fellow Christians understand it, when the Bible speaks of my soul, it is referring to an immaterial substance that is, in the final analysis, the thing that I am. I have my body (by interacting directly with it and only with it among physical objects), but I am my soul. Many will add that, after my death and prior to the resurrection of the dead, I will exist in a completely disembodied state—a naked soul, as it were.

However, I believe it is a mistake to interpret Scripture as teaching or implying any such metaphysical account of the underpinnings of our distinctively human personal attributes or our capacity for surviving death. Now, after reflecting on the matter, we might conclude that the only way these Scriptural teachings could be true is for such a metaphysical account to be true, as well—an account in which we are immaterial substances, entirely separate from our bodies. Indeed, many have thought hard about it and have drawn just such a conclusion, and it is not hard to see why they find it tempting to do so. But to do so is to make a disputable philosophical inference; it is not a teaching of the faith.

The general perspective of BioLogos, which I embrace, is that theorizing about the underlying nature of the soul is best done by trying to read God’s Two Books (His Word and His Works) in tandem. Both Books have a great deal to say about us, and, as common products of an infinitely wise and loving Creator, what they say must ultimately be in harmony. As with any attempt to understand something deep and wondrous in God’s Creation, we should proceed with humility and carefulness and be prepared to rethink familiar and received ideas.

Spelling it out just a bit, the common Christian understanding of what it is to have a soul involves the yoking of two radically different things, a functioning human (wholly material) body and an immaterial mental thing that is the direct bearer of psychological properties such as self-awareness, emotions, and thoughts, and is that which chooses in accordance with desires and purposes. In short, a complex biological machine and a pure subject/purposive agent which interface in the brain. I want to acknowledge that this is a very natural perspective to have, quite apart from Christian revelation (hence its popularity among humans generally). It is very natural because our psychological abilities seem, introspectively, to be plainly something more than mere resultants of impersonal physical particle interactions, however numerous and complex these are within the human brain.

We can design highly sophisticated computers that process complex bodies of information with extraordinary speed, but no computer is a subject, or has a point of view. As philosophers of mind like to say, there is nothing “it is like” to be a computer in the way that there is something “it is like” to be a conscious subject. Put another way, no mere computer is a conscious, experiencing subject, having a point of view from which it regards and interacts with its environment. Neither do computers make autonomous choices in the face of competing moral and self-interested motivations, and so on. It seems but a short step from this observation to the conclusion that human persons (and thinking/desiring/choosing things more generally) must be fundamentally different sorts of things: fundamentally distinct capacities must reside in fundamentally distinct kinds of substances (mental and spiritual substances as opposed to physical substances, however complex).

I have just described how matters appear from the ‘first-person perspective’ of conscious experience and self-awareness. Let me be clear that I take such evidence very seriously: I know my own conscious thoughts and experiences better than I know any scientific theory,—even a very well-attested one—as all of our theories are at bottom built on information we derive from our experiences. So awareness of the distinctive character of conscious experience is part of what is given to us in the Book of God’s Works, since we are a part of that Book.

But alongside that ‘first-person’ data, we have had an explosion of relevant information coming from the ‘third-person’ perspective of the natural sciences, specifically evolutionary and developmental biology and cognitive neuroscience. This information, while still incomplete and only imperfectly understood, sheds light on the deep natural history of humans and present-day animals; the processes by which individual organisms of any species develop from inception to maturity; function-specific neural structures and processes that sustain and help regulate the unfolding first-person perspective of conscious agents; and finally, observed correlations between increasing complexity of neural structures and increased psychological complexity. This last correlation between structural and cognitive complexity is evident both when examining individuals as they develop, and when making comparisons across sentient species.

I suggest that this third-personal scientific information does not comport well with the two-substance or dualist metaphysical account of human persons. The fundamental problem is that our sciences point to continuous processes of increasing complexity, but the two-substance account requires the supposition of abrupt discontinuity. The “coming to be” at a particular point in time of a new substance with a suite of novel psychological capacities would seem to be a highly discontinuous development, both in large-scale bio-geological time and within the development of individual organisms.

Since souls as purely immaterial things would lack parts, we cannot make sense of the accumulation or diminishment of capacities by proposing increased or decreased structural complexity within the bearer of such capacities. And it just seems implausible to suppose that all the necessary basic capacities for, say, calculus problem-solving are there in the soul from the beginning, awaiting only physical maturation in the body in order to become activated, but still not directly dependent on that maturation. It seems rather that psychological capacities arise and develop in tandem with the development of the brain and nervous system.

Of course, it is possible for the soul-body dualist to retrench: we might offload to the brain ‘side’ of the divide some of the psychological functioning that, prior to the advent of neuroscience, we might have mistakenly thought belonged to the soul. But that tack risks (as neuroscience progresses) reducing the soul to a simple, immaterial object that is radically incomplete, merely a “bearer of consciousness” that enables personal identity over time and through death.

Despite the fact that such future retrenchment would seem to be required, this kind of dualism remains tempting for the Christian thinker. Why? The obvious answer is that it can seem to be the only way to accommodate our specifically Christian data that human beings are not mere machines: our thoughts, emotions, goals, and intentions are deep, not superficial features of ourselves; they confer a dignity upon us that makes us suitable bearers of the divine image such that human beings, after our skin has been destroyed, will yet see God. (Job 19:26). But is it true that the coherence of Christian theology requires this account? And if coherence of Christian theology does not require this account, which account might be the best one?

Tomorrow, in Part 2, I will address this question.

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.

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

Humanity is marked by the biological capacity for musicality. Every known culture has something like music. Understanding how we experience and create music in the present gives us clues to why and how music emerged as one of the defining features of human culture (and, therefore, of humanness itself) in the past. But thinking carefully about music and evolution can also help us reassess how we use music now: in the wider culture, collectively as the church, and even within our own homes. In a nutshell, then, this essay will examine how views on evolution impact how one assesses music’s effects and meaning. In many cases, problematic views about evolution and artistic creativity result in problematic views about music, but my argument is that an appropriate evolutionary view of music—one that looks at how music becomes meaningful within social relationships—is a view that actually enriches our appreciation of this most human endeavor, rather than trivializing it. In this first part I explore common discourses about the meaning of music and their relationship to ideas of creation. In part two next week, I suggest that understanding the role that music played in our biocultural evolution helps correct some of the myths that have made their way into popular discourse, especially with the growing popularity of trying to understand music via neuroscience.

Let’s begin by looking at a couple of popular ways of answering the question, “Where does musical meaning come from?” beginning with the idea that “music is in the ear of the beholder.” One thing that is clear from years of teaching classes of first-year university students is that they are musical relativists. They have ‘their’ music that they enjoy and even use to demark their identities, but are perfectly willing to allow others to like other music. After all, music is all about enjoyment, right? Historically, this cultural trope developed out of the post-Kantian argument of musical autonomy, the often-fashionable argument that music’s meaning is strictly musical and does not relate to other parts of the world. It is also reflected in Steven Pinker’s argument that music is ‘auditory cheesecake’. For Pinker, music used to be useful for things like attracting mates, but now we have evolved out of needing music: it’s not necessary, but is a nice extra. I might like cheesecake, but you might prefer ice cream. Either way, it won’t change the survival of the species, so we can enjoy what we like. This argument may have a harder time standing up when music is used as a means of torture at Guantanamo Bay, but it remains popular none-the-less. Like many ideas of creation and the arts, the idea of music as primarily pleasure (determined by individual taste) is a post-Enlightenment development.

This musical relativism takes a slightly more exacting form in another popular idea, that meaning is embedded within the ‘music itself’ not in the taste of the listener. This view of meaning is the starting point of Plato and Aristotle’s disagreement about the effect of certain modes, the disagreements in the early church about the usage of certain musical instruments, and the arguments of the detrimental moral impact of certain forms of popular music (which, by the way, is an argument not just limited to the 20th or now 21st centuries). It is also the foundation of the statement from one of my former conductors that if we played well enough, we would summon up the ‘spirit of Haydn’. In other words, ‘proper’ participation can reveal the meaning of the work—be that the composer’s meaning or another idealized meaning.

Musical autonomy in this case refers to the view that music stands apart and has no relations or meaning outside of itself. Many philosophers and musicologists rely on this view in an unreflective way, represented by Peter Kivy’s statement that music “is a quasi-syntactical structure of sound understandable solely in musical terms and having no semantic or representational content, no meaning, and making no reference to anything beyond itself”¹. For Kivy, the heart of the autonomy argument is that music is completely self-contained. Such a view is possible because of the historical development of ‘absolute music’, referring to music without a text or narrative, typified by the development of the symphonic form in the late 18th century. It is no accident that between 1750-1850, the form of the symphony developed, Kant theorized the idea of genius, and Schopenhauer claimed music to be “pure will.” In the 19th century, music came to be considered the highest of the arts, and even at the turn of the 20th century Kandinsky claimed that all art should try to achieve the autonomy and abstraction of music.

The idea of musical meaning somehow residing within the musical work is based on an assumption that the more one can isolate and analyze something, the more can be known about it. We can certainly learn much about a rock or plant by isolating it and putting it under a microscope, and those who take music to be autonomous believe that music can also be known most thoroughly by placing it ‘under the microscope’ through close analysis of a score or recording, or through close listening. It is through such pseudo-scientific analytical acts that knowledge about music is thought to be accessed. This is also the guiding ideology of ‘music appreciation.’ But while much can be gained by close examination of rocks or music, much more can be gained by studying how a rock or (especially) music is used by people—a central point to which we will return.

It is more than a little ironic, then, that a further example of the belief in an intrinsic musical meaning is the argument that music is ‘universal’; that is, that at least some music can cross cultural barriers and mean the same thing to all people. Often this view assumes a primacy of the Western canon, as it is believed that Mozart has a universal meaning but Chinese qin (zither) music does not. In a globalized world where many cultures listen to and value Mozart, people who do not share a common language or view of the world may find Mozart a common point of contact. But finding Mozart a point of contact is not caused by the music having a universal meaning. Rather, it is an example of the way music can become a shared space where people enter into a relationship via art. The West-Eastern Divan Orchestra (a project of Daniel Barenboim and the late Edward Said) is an example of music being a common ground where people from different views of the world can connect, not an example of universalized meanings of music.

Indeed, there are many situations when music’s meanings are not shared, showing that meaning is most definitely not universal. Martin Lodge recounts the encounter of Dutch explorers and the Maori people of New Zealand in 1642. When the parties got close enough to see (and hear) each other, each group signalled with trumpets. The Dutch, thinking they were successful in making contact, sent a boat of unarmed sailors to shore. The boat was met by Maori warriors who killed more than half of the sailors. This misunderstanding was caused by not sharing a musical meaning: “The Maori trumpeting in this case was the music of war, an invitation to fight. On the other hand the Dutch trumpets played a variety of tunes intended to be welcoming.”² Musical meanings are often shared, but are not universal or ‘in the music’.

As we have begun to see, considering music as culturally embedded lets us recognize something quite different from the arguments that musical meaning is either subjective or encoded within the music itself. Music does allow for subjective response, but not truly autonomous response—our experience of music occurs within the bounds of cultural norms. Since music’s significance cannot be abstracted from it’s embeddedness within social relationships, an attention to culture and human intentionality (not just a reductionist sense of biology) must inform the ways that music is studied, whether in contemporary culture, in neuroscience, and with reference to human evolution. Unfortunately even many Christian views of music have relied upon some of these problematic views of musical meaning, aligning ideas like individual artistic genius and the “meaning in the music” concept with theologies of creation ex nihilo. As Bruce Ellis Benson discusses in an essay in the journal Verge (and in a shortened version here at BioLogos), this combination or paralleling of genius and ex nihilo creation complicates the church’s understanding not only of music, but also about the Creator God, downplaying the essential element of community and interpersonal relationship inherent to both.

Next week, we’ll look at a similar tendency to abstract and quantify the way music makes meaning in the burgeoning field of neuroscience (from the “Mozart Effect” to fMRI scans), and return to the way that thinking about music within the evolution of human culture might give us a deeper appreciation of music—even of worship—within the church. In the meantime, here are some questions to consider:

How do my own assumptions of the way music is meaningful affect the ways I conceive of and use music?

Are there negative consequences stemming from these assumptions?

How have problematic views of musical meaning affected the use of music as personal identity? Or in the church? Or in the media? Or in popularized science?

Notes

1. Kivy, Peter (1990) Music Alone (Cornell University Press: Ithica, NY): p. 202.

2. Lodge, Martin (2009) 'Music Historiography in New Zealand' in ed. Zdravko Blazekovic, Music's Intellectual History (RILM: New York): p. 627.

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?