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. 

Such remnants are also found in our genomes.  Humans, unlike most mammals, cannot synthesize (make) our own vitamin C, but we carry the genes for synthesizing vitamin C.  One of these genes encodes the GLO (L-gulonolactone oxidase) enzyme, and this gene in humans contains inactivating mutations and is therefore a “pseudogene.”  This pseudogene and the genes that encode the enzymes of the vitamin C biosynthetic pathway are the remnants of our own evolutionary lineage from an ancestor that was able to synthesize its own vitamin C.⁴ Furthermore, the GLO pseudogene is just one of a graveyard of inactivated genes, transposons, retroviruses and other non-functional sequences that litter our genome.  While some of these sequences have been co-opted for particular functions, many of them have no known function.⁵ We share many of these non-functional sequences with chimpanzees.  The very presence of these genomic and anatomical flotsam and jetsam only makes sense if evolution has occurred.⁶

A third piece of evidence for evolution comes from biogeography.⁷ The flora and fauna of islands such as those of the Galápagos and Hawaii are radically unbalanced in that they lack many types of plants and animals but contain a profusion of clusters of similar species.  Hawaii, for example, has no native mammals, reptiles, or amphibians, but a profusion of fruit flies and silversword plants.⁸ One third of the 2,000 species of fruit flies are found on the Hawaiian Islands, which only covers 2 percent of the land on earth.  These islands were never connected to the continents and arose as a result of volcanic activity and were, at least initially, completely uncolonized.  The colonization of these islands occurred by means of occasional introduction of creatures from the mainland that then rapidly speciated on these islands to fill every available ecological niche.  Thus, the organisms most closely related to island species come from the closest mainland areas, and often include those creatures most likely to find their way to islands, such as birds and flying insects. 

The Galápagos Islands provide an excellent example of how biogeography provides evidence for evolution. The Galápagos have fourteen species of finch whose closest relative is probably the South American grassquit (Tiaris), yet only four of these finch species feed on seeds as finches normally do, while two others feed on cacti, seven eat insects, and another eats almost exclusively leaves.⁹ Darwin, while visiting the Galápagos, still thought that species only varied within a particular kind (though he would not have used that terminology) but could adapt to various local environments and become particular subspecies. Therefore, he originally listed the warbler finch (Certhidea olivacea) as a wren and listed the small cactus finch (Geospiza scandens) as a member of the Icteridae or the family of meadowlarks and orioles.  Only after Darwin had deposited his Galápagos specimens with the British ornithologist John Gould did Darwin discover (in a meeting with Gould that occurred during March, 1877), that his finch collection included thirteen or fourteen species of unusual finches that were all so closely related, Gould classified them in a single group all their own.  This meeting showed Darwin that the immutable barrier between kinds of species did not exist.  The Galápagos Islands were not a distinct “center of creation,” but a workshop for evolution in which an ancestral species made it to the yet uncolonized island and underwent a massive degree of speciation to adapt to the environment of the island.¹⁰ This is precisely what one would expect if the species of islands had arisen by evolution. 

A scientific theory also allows scientists to make predictions, and good theories provide accurate predictions.  Can the theory of evolution allow accurate predictions?  The answer, once again, is yes.  Darwin himself predicted that the earth must be very old for evolution to occur.  He did not know the age of the earth, but further research has shown that the earth is 4.55 billion years old, which is plenty of time for evolution to occur.  Darwin also predicted that since plants on islands were most closely related to certain mainland plant species, the seeds of these plants should be able to withstand immersion in sea water for long periods of time, and again, Darwin was shown to be right.¹¹ Many decades after Darwin, we now know that variation in organisms is due to mutations in DNA and that these mutations are inherited, just as Darwin predicted.¹² Also, Darwin’s principle of natural selection predicts that particular sequences of DNA should behave in a manner that benefits only themselves and not their carriers, which modern research has thoroughly confirmed with the discovery of transposons and other types of “selfish DNA.”¹³

Is evolutionary theory a good scientific theory?  It has been repeatedly tested for over 150 years since its inception, and it has passed those tests successfully.  The theory has been modified in response to new data, but the outlines of the theory have remained largely intact.  It has existed at risk from new data.  During the molecular biology revolution that began with the discovery of the structure of DNA by Franklin, Watson and Crick in 1953, the explosion of new data could have shown contemporary evolutionary theory to be wrong.  However, some of the most powerful evidence for the theory of evolution has come from a field of science that did not even exist during Darwin’s time.  The ability of a theory to withstand such intense scrutiny is a clear sign it is robust and enduring.  As shown, the theory of evolution has predictive power, and it also integrates and makes sense of data from several fields of science, including ecology, paleontology, genetics, historical geology, paleoclimatology, and comparative anatomy and biochemistry.  The highly integrative nature of evolutionary theory makes it a fine theory by any measure. 

In conclusion, when measured against the standards of a good scientific theory, modern evolutionary biology clearly qualifies as good science.  Ongoing debates within evolutionary biology exist about mechanism, rates, and causes, but not over whether evolution occurred.  Such a question has been largely settled by the last 150 years’ worth of research.  The future certainly looks bright for this field of science and I cannot imagine a more exciting topic to study. 

Notes

1. Davit-Béal, Tiphaine,Abigail S. Tucker, and Jean-Yves Sire. “Loss of Teeth and Enamel in Tetrapods: Fossil Record, Genetic Data and Morphological Adaptations.” Journal of Anatomy 214, no. 4 (2009): 477–501. 

2. Tian, Natasha M. M.-L., and David J. Price. “Why Cavefish are Blind.” BioEssays 27 (2005): 235–38; Yamamoto Y, Stock DW, and Jeffery WR (2004) Hedgehog Signalling Controls Eye Degeneration in Blind Cavefish. Nature 431:844–7; Jeffery, W. R. “Adaptive Evolution of Eye Degeneration in the Mexican Blind Cavefish.” Journal of Heredity 96, no. 3 (2005): 185–196. 

3. Bejder, L., and B. K. Hall. “Limbs in Whales and Limblessness in Other Vertebrates: Mechanisms of Evolutionary and Developmental Transformation and Loss.” Evolution and Development 4, no. 6 (2002): 445–58. 

4. Lachapelle, M. Y., and G. Drouin. “Inactivation Dates of the Human and Guinea Pig Vitamin C Genes.” Genetica 139, no. 2 (2011): 199–207.

5. Avise, John C. Inside the Human Genome: A Case for Non-Intelligent Design. New York: Oxford University Press, 2010.   Romano, C. M., F. L. Melo, M. A. Corsini, E. C. Homes, and P. M. Zanotto.  “Demographic Histories of ERV-K in Humans, Chimpanzees and Rhesus Monkeys.” PLoS One 2, no. 10 (2007): e1026. http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0001026. 

6. Max, “Plagiarized Errors and Molecular Genetics,” http://www.talkorigins.org/faqs/molgen.

7. Coyne, Jerry A. “Intelligent Design: The Faith that Dare Not Peak Its Name.” In Intelligent Thought: Science Versus the Intelligent Design Movement, edited by John Brockman, 3–23. New York: Vintage, 2006. 

8. Kricher, John. Galápagos: A Natural History. Princeton, NJ:  Princeton University Press, 2006. 

9. Grant, Peter R., and Rosemary B. Grant. How and Why Species Multiply: The Radiation of Darwin’s Finches. Princeton, NJ: Princeton University Press, 2011. 

10. Sulloway, Frank J. “Why Darwin Rejected Intelligent Design.” In Intelligent Thought: Science Versus the Intelligent Design Movement, edited by John Brockman, 107–25. New York: Vintage, 2006. 

11. Darwin, Charles. “On the action of sea-water on the germination of seeds.” Journal of Proceedings of the Linnean Society of London (Botany). 1 (1857): 130–140.

12. Futuyma, Douglas J. Evolution. 3rd ed. Sundbury, MA: Sinauer Associates, 2013. 

13. Dawkins, Richard. The Selfish Gene. New York: Oxford University Press, 2006.

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

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

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

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

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

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

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

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

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

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

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

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

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

JIMMY LIN: Currently I’m on faculty at Washington University at St. Louis, where I am a research instructor in the pathology department. Also, a year and a half ago, I founded the Rare Genomics Institute (RGI)—a nonprofit that helps find cures for people with rare diseases.

ER: What qualifies as a “rare disease”?

JL: These are diseases like cystic fibrosis and Huntingdon’s disease—diseases that affect less than 200,000 Americans each year. There are over 7000 different rare diseases, and less than 5% of them have any therapy. Altogether, they affect about 25-30 million people.

This creates what we call a “long tail problem”—it’s hard for a top-down research system to create research programs for all 7000 rare diseases. So instead, we are creating a bottom-up platform from which the patients themselves can create research projects and help fund them. We connect patients with physicians and researchers, customize a research program with top medical universities, design the experiment, and then use an online fundraising platform to fund the study through [mostly] friends and family of the patient.

Basically, we create a “foundation in a box.” By partnering with the Rare Genomics Institute, patients and their friends and families who want to study rare diseases don’t have to go through the hoops of creating their own nonprofit or lab—we do that for them. So, instead of creating 7000 different nonprofits, we create a generalized platform from which studies can be conducted.

ER: Who qualifies for care through the Rare Genomics Institute?

JL: Anyone with a rare disease can come to us. The main thing we’re doing right now is diagnosis. When families come to us, they either don’t know the disease that’s affecting them or their child, or they don’t know the gene that’s wrong.

For instance, if a child had a condition that doctors couldn’t identify, his or her parents might come to us for help. What we’d do then is sequence the genes of the mother, father, and child, and compare them to reference genome to determine what mutations each of the parents have. Depending on what the disease is and what the gene causing it is, we can filter out mutations that don’t mean anything using the parents’ genomes—then, after filtering, we can potentially pinpoint the genes that fit the genetic pattern of the disease. This is the first step.

After that, we are building infrastructure to determine the effect of these changes and a way to help. For example, after looking at the literature, we can perhaps design experiments using cells extracted from the patient; this part of the process is different for every disease. Then, if we can determine that there is, for instance, a pathway missing a specific enzyme, we can try using drugs, a bone marrow transplant, or gene therapy to try to put healthy cells into the child… But there’s a variety of diseases, of course, so there’s a variety of different approaches—and we’re just starting to explore these aspects.

ER: How did RGI get started?

JL: It really started when I was in medical school at Johns Hopkins—there was this boy that came to our clinic to be seen. My research was in cancer genome sequencing, and the family had come to our department looking for answers about what was wrong with their son. At that point, the family was almost hopeless—they had gone to so many doctors, run so many tests—I decided I wanted to try to help children like this. That’s when my friends and I decided to start the Rare Genomics Institute.

Currently, there are about 50 researchers associated with the organization, and we are all volunteers. It’s growing much, much faster and been more amazing than we’ve ever imagined—we’re already making an impact. In May of last year, we were able to discover a new disease using the world’s first crowd-sourced, crowd-funded genome. Working with researchers at Yale, we delineated a disease of which our patient was the first identified.

Right now, we’re in the middle of raising funding and hiring staff to make this organization one that is self-sustaining, and to increase its impact even more.

Excerpts from Michael Hickerson Interview

MH: …you call yourself a doxologist. What’s the full term you used in your Jubilee bio?

JL: Medical and scientific doxologist.

MH: How did you decide on that term and what does it mean to you?

JL: I listen to a bunch of teaching by J.I. Packer , who teaches theology at Regent College and is one of the leading thinkers on these things. Interestingly, before any one of his classes, he says “Theology is for doxology,” and then the whole class sings the Doxology together out loud in class. I thought, “Wow, that is so great,” because everybody sometimes learns theology just for intellectual things [instead of for worship].

That’s not just true for theology, it’s for everything: biology is for doxology; chemistry is for doxology. That’s when I started to think, I should consider myself, first and foremost, as a person who praises God in what I do. And then no longer make “Christian” the adjective, right? “Doxologist” is the noun. But then what kind of doxologist am I? So I call myself a medical and scientist doxologist. I would call someone, for example, in the marketplace, a business doxologist. Or, someone who does art, an artistic doxologist. To really have the noun as our identity, and then our vocation as just a descriptor of how we do that.

MH: That’s a great point. A noun is always stronger than the adjective. So, you want that to be the focus, rather than the add-on.

JL: In our current culture, we’re defined by our jobs. It’s having a vocation. I wanted to shift away from that. I didn’t want to be a doctor first and foremost, or a scientist, but one who praises God. And evidently, within science you don’t want to call yourself a Christian Scientist. That’s another religion, so . . .

MH: [laughs] That’s right. I run into that, as well, when I’m teaching or talking about science to Christians. You always run into that stumbling block.

JL: With “scientific doxologist,” people don’t confuse them. You do have to explain what it means. And that gets in a little story actually, on what it means about vocation. It’s a small lesson — a teaching point when you do talk to people about vocation and calling. That’s why I use it.

MH: I guess my final question would be what spiritual practices help sustain you? What helps you stay in contact with God and keep a good foundation?

JL: First, I am interested in many, many different things. I sort of mix it up in terms of spiritual practices. Besides the fundamentals, of course, of quiet time, devotional reading, and scriptural reading, I do theological study because I have to do that academically. I find a lot of time with God through the spiritual disciplines, such as times of solitude — which is very interesting for someone who is in academics to no longer think about ideas but just to be quiet before God — how silence, time to think by yourself, or sitting in silence is also something you should foster.

In terms of spiritual formation, what you really need is definitely a good community of people. I have a very supportive community at my church. I’m the deacon of devotions, so that of course keeps me on track. It encourages me as I, in my own spiritual walk, encourage other people. Fundamentally, I think for all Christians, whether you are academic or no matter your vocation or calling, being in the Word and prayer are the most important things. Doing that and being spiritually fed is what is important.

Understanding John Polkinghorne: Theology of Nature

John Polkinghorne’s interest in natural theology is important, but what really sets him apart from most others is that he combines it with an equally strong interest in theology of nature, which is not the same thing. Where natural theology involves, “metaquestions about the pattern and structure of the physical world,” theology of nature involves, “metaquestions about how its historical process is to be understood.” Rather than “looking to the physical world for hints of God’s existence,” we look “to God’s existence as an aid for understanding why things have developed in the physical world in the manner that they have.” (Belief in God in an Age of Science, p. 13)

On this front, Polkinghorne advances a strongly Christocentric theology of creation, stressing Jürgen Moltmann’s notion of The Crucified God . In the context of Polkinghorne’s theology of nature, the point is that the Creator is the crucified and resurrected second person of the Trinity. Since I devoted a column to this before, I won’t say more here, except to alert readers to the singular importance this particular idea has for him—especially when facing the problem of suffering. “The insight of the Crucified God lies at the very heart of my own Christian belief, indeed of the possibility of such belief in the face of the way the world is.” (Belief in God in an Age of Science, p. 44)

Situating John Polkinghorne: The Resurrection of Jesus

Many Christians today see science as posing dangerous threats to their faith, challenging their understanding of the Bible and undermining core tenets such as the bodily Resurrection of Jesus, the historical basis on which the Christian faith stands or falls. “Evolution” is often identified as the problem, but the real danger is unbridled naturalism. A commitment to naturalistic methods, known as “methodological naturalism,” (MN) has been an integral part of science and medicine since the ancient Greeks. Those methods have been highly successful at producing a coherent, often very convincing picture of nature and the history of nature.

Advocates of Intelligent Design and some other Christians reject MN, but many Christians who work in the sciences and related fields (such as engineering, medicine, or the history and philosophy science) support MN as a properly grounded and properly limited way of understanding reality. In their view, a robust Christian faith is consistent with a commitment to MN, provided that the limits of scientific inquiry are not simply equated with the limits of rationally grounded belief. Polkinghorne fits squarely in this category.

To understand more clearly where Polkinghorne lies on the larger landscape of science and religion, let’s consider his approach to the Resurrection. Many contemporary thinkers, including some theologians and clergy, believe that “science” has somehow made it impossible to believe in the Resurrection, the deity of Jesus, and even belief in the transcendent God of the Bible.

A prime example is John Shelby Spong, a retired Episcopalian bishop whose books have sold more than one million copies. Spong sees the bodily Resurrection as a figment of the disciples’ imaginations, a vestige of a theism that now we must throw away like a threadbare suit of clothes. For Spong, Christians today need to go "beyond theism" throwing out the baby of divine transcendence—the fundamental truth of monotheism—along with the bath water of the credulity and mythology of the pre-modern authors of the Bible and the ecumenical creeds. Spong’s message is that “Christianity must change or die,” and all in the name of “science.”

As Spong likes to say, his work is very controversial, and not just among rank-and-file Christians. Scholars have also railed against him. “I have been attacked in books from the religious right by such people as Alistair MacGrath [whose surname is actually spelled McGrath], N.T. Wright, and Luke Timothy Johnson,” he complains (Why Christianity Must Change or Die, p. xvi).

I understand (with much sadness) that we live in a highly polarized age. Nevertheless, it’s difficult for me to grant much credibility to an author who identifies McGrath, Wright, and Johnson as representatives of the “religious right.” Indeed, if anyone here is distorting the news it is Spong, not they. As the (late) great Catholic biblical scholar Raymond Brown once observed, “I do not think that a single NT [New Testament] author would recognize Spong’s Jesus as the figure being proclaimed or written about.” (Birth of the Messiah, note 321 on p. 704)

Matthias Grünewald, The Resurrection (a wing of the
Isenheim Altarpiece, ca. 1515), Unterlinden Museum,
Colmar, France

Polkinghorne certainly understands science far more than Spong does, and his conclusions about the implications of science for Christian beliefs are markedly different. With respect to the Resurrection, he is basically on the same page with his friend Wright, whose profound book, The Resurrection of the Son of God, he cites with appreciation. Belief in the Resurrection is well supported by the evidence, and the Resurrection, itself, is “the pivot on which the claim of a unique and transcendent significance for Jesus must turn.” Considering authors like Spong (although he does not explicitly name him), he adds, “it would be a serious apologetic mistake if Christian theology thought that operating in the context of science should somehow discourage it from laying proper emphasis on the essential centrality of Christ’s Resurrection, however counterintuitive that belief may seem in the light of mundane expectation.” (Theology in the Context of Science, pp. 135-6)

Amen.

Looking Ahead

This is the Easter season, and I’ll return in a couple of weeks to begin examining Polkinghorne’s approach to the Resurrection more fully, using excerpts from the chapter on “Motivated Belief” from his recent book, Theology in the Context of Science.

References

Raymond E. Brown, Birth of the Messiah: A Commentary on the Infancy Narratives in the Gospels of Matthew and Luke. (1992).

John Polkinghorne, Belief in God in an Age of Science (1998).

John Polkinghorne, Theology in the Context of Science (2009). My review for First Things online is here.

John Shelby Spong, Why Christianity Must Change or Die (1998).

DOUG LAUFFENBURGER: It could look like a lot of things. One way to envision what I mean is to put yourself back a hundred years. For instance, in 1913, an electronic computer was unimaginable. But using physics, quantum physics, leading to semiconductors and devices like that, people figured out over the next 20 to 30 years how you could build a machine to do calculations and so forth. And then, of course, all sorts of thing happened…

We’re roughly at that stage with biology, even though it seems like things are more imaginable because—and we don’t have to go strictly century by century here—because we can already guess the way some things might change, whereas in 1913 there was no inkling, really, as to what would happen in the computer revolution.

So, to enumerate some of the things that are conceivable—let’s just start with computers, because we were just there.

There’s a notion that computers get faster and cheaper by making their logic gates smaller, and how you improve a design with physics keeps bumping up against how you make these little units smaller. Well, using biology, the solution seems self-evident—you just line up the pieces of DNA, and if you put the right pieces of DNA in the right places, the resulting parts are so much smaller than the things we can do with physics. You can imagine, even though it’s just a theory now, computers continuing to become many times smaller and cheaper—and be made via environmentally benign manufacturing processes—through biomolecular construction.

Now that’s exciting from one point of view, but from another, it’s not that revolutionary, because you’re just using DNA as a piece of physics. It’s not really biology—it’s merely a biological molecule being used to make better physics.

For a different example, if you think about the way we make things, the way we manufacture plastics, gasoline, energy—we have to do all that using chemistry, and to make that chemistry happen, we have to input a lot of energy—in fact, one of the most costly industries in terms of energy usage is the energy industry. You have to put in so much energy to refine petroleum and things like that. And to make plastics, ceramics—things of that nature—is also very energy intensive, and it’s also where a lot of pollution comes from, because you’re mixing together all these chemicals that really didn’t want to be mixed together. You get what you want, but you get a lot of byproducts, toxins, etc.

Well, people have started to realize that a lot of this work can be redone through the use of biology. You can turn corn into fuel or plastic, and you can make magnetic or electrical storage devices out of biological units (viruses can pattern the crystals, so instead of using mixtures of toxic chemicals, you just pull the viruses with the right properties together). Right on this tabletop, you could make materials that by current manufacturing processes would otherwise cause a great amount of environmental hazard.

As for another exciting development—well, to preface, one of the problematic things about modern agriculture is the necessity of using fertilizers (there are insecticides to be concerned about, too), but fertilizer manufacturing is terrible for the environment. You have to make fertilizer out of ammonia and that’s a horribly polluting and energy-intensive manufacturing process. What you could potentially do, instead, is program into bacteria the genes that take nitrogen out of air, turning it into organic nitrogen then just scatter the bacteria onto the field—and you wouldn’t need to make ammonium using the current very caustic processes.

These are the sorts of things I mean—and we haven’t even touched on medicine, yet. People tend to think about medicinal advances, first, but before you even get to medicine, you can think about energy, manufacturing, materials, and agriculture. In 50 years, we should be able to do things in ways we don’t do them now, that will be cheaper, less toxic, less polluting, more efficient, and so forth.

ER: A lot of people are nervous about the idea of “programming” life. Can you respond to this fear as a Christian?

DL: As a Christian, I would say that God gave humankind dominion over the earth, to do good things—he gave us minds, a passion for understanding how things work, and then he put in this world all these fascinating processes, which, if we figured them out, we could do good things, could feed more people—could feed more people without causing extensive damage to the environment. And cure disease and injury. And the list goes on. I think all that is good, and that God would be pleased that we would be using His creation to live better—I’m not saying more luxuriously, but more happily, contentedly, with each other.

ER: But back to the topic—advances using biology in the next century. You had just mentioned medicine…

DL: So, yes, there’s also medicine. Now, obviously, in thinking about this, the use of stem cells comes to immediately the fore. There are a lot of diseases out there that you really do need to correct using cellular processes. Right now, we try to make these corrections through chemistry. For instance, we give you a pill, and that pill should interfere with something that’s going wrong in your body—and yet it’s really never adequate to just interfere with something that goes wrong in the body, because you don’t really set it right just by getting in the way of it.

The opportunity with stem cells is that you can say, “I’ll replace the cells in the body that are doing something wrong with cells that are actually doing it right again.” If you program cells to be neurons, heart cells, or bone cells, you can regenerate properly functioning physiology. Rather than, say, replacing a hip with a metal part, you could regenerate the bone, itself, or you could regenerate neurons in Alzheimer’s patients. Never in the past has medicine been able to regenerate a proper physiology; it’s only tried to replace it with an inadequate surrogate, or minimize how much damage a disease is doing. With the use of stem cells, you can actually imagine returning the body to its proper physiology.

A different use of stem cells is to generate human tissue in the laboratory for better studies of human physiology and pathology and improved testing of drug effectiveness and toxicity.  This will be a major advance over animal models, because of the significant disparities between animal physiology and human physiology.

A key point to emphasize is that there are different kinds of stem cells, which involve big differences in potential concerns. For Christians, clearly, stem cells derived from embryos present a tremendous ethical issue. Fortunately, a good proportion of stem cell technologies can be pursued using stem cells from adult tissue. These cells can be stimulated to develop into certain tissue-specific physiological behavior, or can now even be “re-programmed” to become quite similar to the more broadly flexible stem cells derived from embryos but now not requiring the embryonic source. Happily, the days of reliance on embryo-derived stem cells appear to be over for purposes of beneficial technologies.

We also should consider genomic medicine, and what’s attractive about that field is that with the way we do medicine now, which is chemistry-based—say you have a disease, and we might give you a pill to correct it—well, the biggest problem with that is that while I think this pill will help ameliorate your condition, maybe it won’t. Maybe that drug only works in ten percent of the patients and not ninety percent.

For example, consider cancer. You’ve got a particular kind of cancer, and we prescribe a certain treatment… well, hopefully you’re among the lucky ten percent, and you’ll be in much better shape in two or three years. If you’re not, then we’ve wasted your time. In fact, we’ve probably hurt you rather than helped you, because we’re using chemistry to interfere with things, and even though we might be reducing the damage of some things, we’re probably causing toxicity elsewhere in the system, because that same chemistry is also interfering over there.

So the value of genomic medicine is to get enough information about you through sequencing your genome that we can say, “Ah, for you this particular pill is not a good idea; it will actually do more damage than good. But for your brother, it’s likely to work, and the ratio of benefit to harm is much better.” This is the reason genomic medicine is more imminent—it’s what’s closest on the horizon to being realized—because we can use the same drugs we have now, we’ll just be using them more effectively. At the moment, we can sequence genomes, and we do have these treatments that help, and it’s just a matter of matching up these two technologies.

Now, on the other hand, when you think about genome sequencing, you can find out all sorts of things, and you have to decide, “What if I learn something negative?”

EDITOR’S NOTE: Join us next week as we continue the conversation about genomic medicine, bioengineering, and being a Christian in science.

About a year ago I posted the first article in this series, asking whether recent advances in genomics made any difference to the Judeo-Christian notion of humanity being made in the 'image of God'. That article focused on DNA sequencing data from our closest relatives. This article will focus on the issue of genetic determinism.

Theologians have spent many centuries mining the rich vein of the 'image of God' metaphor. Central to the idea is humanity with spiritual capabilities and responsibilities, equipped for moral decision-making and a relationally rich life in community. Historically, the idea has contributed to the conviction that each human individual has an absolute value, independent of their ethnicity, educational level, health status or income.

Do recent advances in genomics threaten or support such a view of humankind, or are they just neutral? Irrespective of one's belief in God, or not, this is of more than passing interest. Imagine the poor person wrestling for years with the great questions of life and finally deciding to become an atheist, only to then be informed that a cognitive bias derived from his particular set of genetic variants made that decision pretty much inevitable anyway. Such news might be equally unsettling for the person who had just struggled to faith following years of agnosticism. Our deepest human feelings are closely connected with the idea that we choose our own path through life.

The flourishing of genomics in the early part of the 21st century has certainly conveyed the message to many that one's destiny is written into one's genome. Whereas scientists are generally scrupulously careful not to give the impression that there is any such entity as a "gene for" some human trait, by the time the latest discovery appears in the media, such caution is often thrown to the winds. The past year has seen the trumpeting of a "gene for happiness," a "kindness gene" and a "believer gene." It is not even a question of education, but "genes are to decide" if you are a "caring person." Genetic testing websites assure us that "your genes are a road-map to better health," and we all know that road-maps are fixed. Small wonder that there is a creeping genetic fatalism around that subverts the idea of personal responsibility.

Fatalism in itself impacts on human behavior. Studies have shown that subjects exposed to the writings of authority figures doubting free-will are then more likely to cheat. Conversely, workers convinced of the reality of free-will are rated higher in the work-place than those whose beliefs tend more towards determinism.

The reality is that recent genetics research has continued to move steadily away from any notion of genetic fatalism, highlighting the sheer complexity of the genome, and providing some fascinating examples of the ways in which our choices impact upon our own genomes. There is no gene "for" any complex human trait because in fact genes encode proteins or other types of information-containing molecules, and thousands of genes collaborate together during human development in interaction with the environment to generate the unique human individual that each person represents. Those requiring an introduction for the non-specialist are referred to "The Language of Genetics."

Epigenetics adds further layers of variation and complexity. This refers to the chemical modifications of the DNA that cause genes to be switched on or off. It is such epigenetic modifications that generate the 220 specialized tissues of our bodies. Such acquired changes can even be inherited across several generations, certainly in plants and animals, and maybe in humans as well. In choosing to smoke, drink in excess, or take drugs, we also choose to modify our genomes.

So it turns out that even identical twins are not really genetically identical, developing different profiles of epigenetic modification as they go through life. This no doubt contributes to the otherwise surprising result that the age of death of identical twins, who share identical genomes, is comparable with that observed in non-identical twins, whose genomes are as different from each other as any two sibs. In one study of 184 pairs of twins in Spain, the difference in the age of death between the identical twin pairs was seven years on average, but such averages hide the fact that the age differences ranged from a couple of weeks to eighteen years. In the case of the non-identical twins, the difference in age at time of death was nine years, and the range was three to nineteen years. So there was really not that much in it.

What would happen if there was a genetic marker that identified nearly everyone in prison, marking them out as genetically distinct from half the world's population? What would that do to our ideas about genetic fatalism and convictions about moral responsibility? As it happens that marker already exists. Out of 131 countries worldwide, an average of 96 percent of the prisoners are male and, in this case, no complicated genetic studies are needed to know that the genetic marker that identifies this population is the Y chromosome. So universal is the correlation between the Y chromosome and criminality that we can safely say that no other genetic correlation will ever be found between a variant genome and criminality that surpasses this one. And yet we still hold nearly all males responsible for their criminal actions and put them in jail as soon as they're convicted. Furthermore, we note that most people who possess a Y chromosome go through life without committing a crime. So having a Y chromosome, with its unique set of genes, does not "determine" human criminality, although clearly we cannot go to the opposite extreme and say that it is completely irrelevant for patterns of human behavior.

The point in citing such examples is not to suggest that our genomes have nothing to do with our lives. They certainly do, not least in their significant contributions to our personality differences. The point rather is that the latest results in genetics provide no grounds for fatalism, instead highlighting the richness and diversity of the human population, and our own moral responsibilities, including the challenge to be good stewards of our genomes.

An argument for the existence of God this is not. But for those of us whose world-view is shaped by the conviction that we humanity are made in God's image, it is good to know that the latest genetics is consistent with such a perspective.

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

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

Creator of the Stars at Night

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

Behe and IC

Since we have previously explored Behe’s idea of irreducible complexity in an entire series, we will not revisit it here in great detail. It is important, however, to reemphasize how Behe defines irreducible complexity (IC). As we noted in the first part of that series, Behe frames his ideas on IC as a counter to Darwin’s ideas of gradualism.

For Behe, the argument for IC is a critique of gradual evolutionary processes, of the kind that Darwin saw as necessary for his theory to hold. When Behe introduces and defines IC in his book Darwin’s Black Box, he has a key quote from Darwin on gradualism explicitly in view:

Darwin knew that his theory of gradual evolution by natural selection carried a heavy burden: "If it could be demonstrated that any complex organ existed which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down."

It is safe to say the most of the scientific skepticism about Darwinism in the past century has centered on this requirement… critics of Darwin have suspected that his criterion of failure had been met. But how can we be confident? What type of biological system could not be formed by “numerous, successive, slight modifications”?

Well, for starters, a system that is irreducibly complex. By irreducibly complex I mean a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning. An irreducibly complex system cannot be produced directly (that is, by continuously improving the initial function, which continues to work by the same mechanism) by slight, successive modifications of a precursor system, because any precursor to an irreducibly complex system that is missing a part is by definition nonfunctional. An irreducibly complex biological system, if there is such a thing, would be a powerful challenge to Darwinian evolution.

(Darwin’s Black Box, p. 39)

The definition of an IC system is thus straightforward: it is a matched group of components, where all the components are necessary for the function of the system. The necessity of each component can be demonstrated by attempting to remove it – if the system no longer works if even one component is removed, it is by definition IC.

Behe and exaptation

The standard response to Behe’s argument from IC is to discuss the evolutionary concept of exaptation: that new systems and functions are cobbled together from components that have functional roles in other systems already present in the cell. Behe discusses, and ultimately dismisses this idea in Darwin’s Black Box as follows:

In Chapter 2 I noted that one couldn’t take specialized parts of other complex systems (such as the spring from a grandfather clock) and use them directly as specialized parts of a second irreducible system (like a mousetrap) unless the parts were first extensively modified. Analogous parts playing roles in other systems cannot relieve the irreducible complexity of a new system; the focus simply shifts from “making” the components to “modifying” them. In either case, there is no new function unless an intelligent agent guides the setup.

So for Behe, two points are clear: parts selected for function in one system cannot be exapted for use in other systems since they would require too many modifications; and the emergence of a new function is the indication that an intelligent agent is guiding the process.

Behe has responded to my previous posts to claim that the tandem duplication event that brought about the Cit+ actualization event should not be considered a gain-of-FCT mutation under his criteria:

The gene duplication which brought an oxygen-tolerant promoter near to the citT gene did not make any new functional element. Rather, it simply duplicated existing features. The two FCTs comprising the oxygen tolerant citrate transporter locus -- the promoter and the gene -- were functional before the duplication and functional after. I had written in my review that one type of mutation that could be categorized as a gain-of-FCT was gene duplication with subsequent sequence modification, to allow the gene to specialize in some task. Venema thinks the mutation observed by Lenski is such an event. He has overlooked the fact that there was no subsequent sequence modification; a segment of DNA simply tandemly duplicated, bringing together two pre-existing FCTs.

As an aside, quibbling over whether this mutation constitutes a “genuine gain-of-FCT” mutation is not my purpose here, since the definition is Behe’s to define, and I am not aware of anyone else in the scientific literature who uses Behe’s definitions. That said, I consider it passing strange to claim that a series of events that produced a gene that has a new sequence and functional properties distinct from either of its component parts does not constitute the production of a new “functional coded element.” If nothing else, it is a functional coded element that has not previously existed, cobbled together from parts of other functional coded elements, displaying new, adaptive properties. If according to Behe’s definition that’s not “new” or a “gain” then I guess it’s not, but that seems to me to torture the words “new” and “gain” beyond recognition. But I digress.

The important point for our purposes, however, lies elsewhere. Note carefully how Behe describes the Cit+ actualization event. By dividing the new aerobic citrate transporter gene into two previously existing FCTs, Behe is describing an exaptation event. The one FCT (the aerobic promoter) starts off as a necessary component of a gene transcribed when oxygen is present. As such it is under selection for that function, which has nothing to do with expressing a citrate transporter. The second FCT (the citrate transporter amino acid coding sequence) is under selection to be a citrate transporter, which has nothing to do with the function of the gene the promoter comes from. The Cit+ actualization event, then, exapts these two FCTs by placing them together to create a new function (which Behe does not mention).

And here’s the kicker: the new system (expression of the citrate transporter when oxygen is present) requires both FCTs in order to work. It has become a system of “well matched, interacting parts that contribute to the basic function” (i.e. transporting citrate in the presence of oxygen) “wherein the removal of any one of the parts causes the system to effectively cease functioning.”

In other words, it is a new IC system – a small and relatively simple system, yes, but nonetheless IC. Now, I’m fairly sure that Behe would not define this system as IC, since the documentation of an IC system evolving would seriously undermine his thesis. I am interested, however, in how he will handle this development, on two fronts. First, he would need to explain specifically why two exapted FCTs that are required together for a basic function does not constitute an IC system (if indeed he wishes to preserve his definition). Secondly, given that he allows for exaptation in this case, he needs to explain how exaptation is not a threat to IC in general. In Darwin’s Black Box he disallows exaptation altogether, but that option is no longer on the table.

In the next post in this series, we’ll continue to explore the evidence for exaptation as a means to build new FCTs, and go on to examine the implications of this evidence for Douglas Axe’s proposed limit to evolutionary mechanisms.

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, Darwin’s Black Box: The Search for the Limits of Darwinism (New York: Free Press, 2006).

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.

With the complete genome sequence in hand, we knew the sequence and location of our genes, but what we didn’t know was how all those genes are regulated: how do the trillions of cells in our bodies know when to turn on or off all those genes? How do the hundreds of distinct cell types develop and function together, when they are all running on the same DNA “operating system?”

That’s where the ENCODE (short for Encyclopedia of DNA Elements) project comes in. Launched in September 2003, shortly after the announced completion of the Human Genome Project, the goal of the ENCODE project is “to build a comprehensive parts list of functional elements in the human genome, including elements that act at the protein and RNA levels, and regulatory elements that control cells and circumstances in which a gene is active.” In other words, the project seeks to understand how the genome “works.”

Early this month, researchers from ENCODE released more than thirty papers presenting their findings. During a Science magazine online chat, the project’s data coordinator, Ewan Birney, explained the outcome:

The ENCODE project aimed to start our understanding of how the human genome works. We know that (nearly) all the information that determines a human is in the genome, as we all start off as single cell with this DNA. However, we had a patchy understanding of how it works, in particular away from protein coding genes.

To work out how the genome works, we used the fact there are many tiny machines (proteins and RNA - RNA is very like DNA) in each of our cells which know how to "read" parts of the genome. By monitoring where these little molecular machines are on the genome, or how parts of the DNA are copied into RNA (there are quite a few different types of RNA as well), we start to gain some insight into the genome.

We did many such experiments, across different cell types (eg, one cell type was very similar to a liver cell type; another was very similar to a white blood cell). This way not only can we see what is similar, we can also see differences between these cell types.

There is a lot more to get to know and understand here - this is definitely closer to the start than the end. But it is a substantial amount of data, and analysis, to start on this journey.

According to the abstract of one of the lead papers from Nature, this extraordinary glut of data “enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions.” Only 2% of the genome codes for proteins, but 80% or more has some biochemical function. As a Science news article put it, these 30 papers “sound the death knell for the idea that our DNA is mostly littered with useless bases.”

The pro-Intelligent Design organization The Discovery Institute has heralded the discovery as the “demise of junk DNA.” Casey Luskin writes for their blog Evolution News:

Let's simply observe that it provides a stunning vindication of the prediction of intelligent design that the genome will turn out to have mass functionality for so-called "junk" DNA. ENCODE researchers use words like "surprising" or "unprecedented." They talk about of how "human DNA is a lot more active than we expected." But under an intelligent design paradigm, none of this is surprising. In fact, it is exactly what ID predicted.

The extent to which the ENCODE project been able to identify function has been surprising—even exhilarating—though scientists have for some time been getting glimpses of the many ways in which segments of DNA can be “active.” Even in 1970 biologists knew that some non-coding DNA had function, and by 2003 there was a large body of work demonstrating that many non-coding elements acted as promoters, enhancers, insulators, and so on. Indeed, in recent years many have come to appreciate the fact that “junk” was never really an appropriate metaphor in the first place. Still, because sequencing of multiple genomes has shed such extraordinary light on key evolutionary mechanisms, many geneticists have focused on function primarily in terms of which regions do or do not contribute to the evolutionary fitness of their host, rather than whether they were merely "doing something" biochemically. What the impressive ENCODE project has done is open a treasure trove of new information that can only accelerate the pace at which researchers are able to explore the incredible subtlety and complexity of DNA, and refine the very concept of “functionality.”

So with all this in mind, is ENCODE a stunning victory for ID, as Luskin believes? Bryan College biologist Todd Wood thinks not. He writes, “I don't think that function equates to design, nor do I think that design requires or predicts function. They're not the same thing… my understanding of function does not require me to hypothesize God (or an anonymous designer, if you must) as the proximal cause.”

We agree. Indeed we would go on to say that evolution and design are not mutually exclusive. So while finding function is not sufficient to prove design, recognizing that function has arisen by way of evolution does not indicate that God was not at work. We at BioLogos believe God providentially works out his purposes—his designs—through the elegant processes of evolution, not in opposition to them.

Amazing as the new data are, it only strengthens and enhances our evidence for evolution. While much of the genome is “doing something” biochemically, it is still likely that the majority of the sequence is evolutionarily neutral (Senior Fellow Dennis Venema discusses the evidence for this “neutrality” in a post on our site, including a striking comparison between 29 different mammal genomes and the human genome). In fact, another ENCODE researcher participating in the Science magazine chat, John A. Stamatoyannopoulos of the University of Washington School of Medicine, thinks the findings align beautifully with evolutionary theory:

ENCODE's data provide a unique and powerful window through which to view evolutionary change. We can see those changes directly by lining up the genome sequences of many different organisms -- these line-ups have revealed millions of regions where all the genomes agree, indicating sequences that have been specially preserved by evolution while others have decayed away (ie freely changed their letter codes). We now see that a large proportion of these 'conserved' regions are lighted up by ENCODE annotations, indicating that they are marking spots in the genome that contain important instructions for cell function.

We’ve discussed “junk” DNA previously, including a multi-part series by Dennis Venema, and we’ve received many emails over the past few days asking for our comments on the ENCODE findings. On Monday and Tuesday, Dr. Venema will begin to offer his own thoughts on ENCODE.

A special thanks goes to Darrel Falk, Mark Sprinkle, Kathryn Applegate, Dennis Venema, and Tom Burnett for their contributions to this post.

The Denisovans, an extinct hominid group that interbred with modern humans, made the news again lately with the publication of a more detailed study of their genome. One of the many interesting findings was that the Denisovans share the same chromosome 2 fusion that modern humans have. In this post, I review what we know about the origins of human chromosome 2, and then discuss the new Denisovan findings and their implications.

The origins of human chromosome 2: a brief review

Though I have discussed the evidence for a fusion event leading to human chromosome 2 before, perhaps a brief review of the evidence is in order. The human genome is made up of 23 pairs of chromosomes (for a total of 46 chromosomes). This makes us something of an oddity among living great apes, all the rest of whom have 24 pairs of chromosomes (for a total of 48). Given that there are many independent lines of evidence that support the conclusion that we share a common ancestor with other great apes, this poses something of a conundrum: how is it that our species arrived at this specific chromosome number? If we were to represent this “problem” on a phylogeny, or tree of relatedness, it would look something like this (not to scale):

Our closest living relatives, chimpanzees and bonobos, both have 48 chromosomes, as do all other great apes such as gorillas and orangutans. This pattern has one of two explanations, one of which is much more likely than the other. Either the common ancestor to these species had 48 chromosomes, and there was an event that reduced that number to 46 specifically on the lineage leading to humans (option A), or the common ancestor species had 46 chromosomes, and there were independent, repeated events that increased chromosome number in all other great ape species (option B). We can compare these options by placing the required event(s) on the phylogeny (again, not to scale):

It should be obvious that the option that requires the fewest events is the more likely one – in this case option A with an event that reduces chromosome number in the lineage leading to humans. The other option, that of repeated, independent events to increase chromosome number, remains a formal, but unlikely, possibility. Events that reduce chromosome number are not frequent occurrences, so Option A is more likely than Option B.

We can also find further support for Option A, because it predicts a specific type of event, namely one that reduces chromosome number. Since loss of a large amount of chromosomal material is almost always detrimental, we need an event that reduces chromosome number without losing information. One way for this to happen is for two chromosomes to fuse together and become one. Initially, this event would produce an individual with 47 chromosomes, where two different chromosomes get stuck together. Contrary to what is often assumed, this individual would be fertile and able to interbreed with the others in his or her population (who continue to have 48 chromosomes). In a small population, over time, two relatives who both have one copy of the fusion chromosome may mate and produce some progeny with two copies of the fused chromosome, or the first individuals with 46 chromosomes. Since either a 48-pair set or a 46-pair set is preferable for ease of cell division, this population will either eventually get rid of the fusion variant (the most likely outcome), or by chance will switch over completely to the “new” form, with everyone bearing 46 chromosome pairs. While not overly likely, this type of event is not especially rare in mammals, and we have observed this sort of thing happening within recorded human history in other species. Some mammalian species even maintain distinct populations in the wild with differing chromosome numbers due to fusions, and these populations retain the ability to interbreed.

Further evidence for a fusion event in the lineage leading to modern humans comes from comparing synteny, or gene locations and orders on chromosomes within modern great apes – an issue we have discussed here before. In brief, what we see in human chromosome 2 is exactly what we would predict for a fusion event. When compared to other great apes, we see the genes on human chromosome 2 match up, in order, with two smaller ape chromosomes. We also see that sequences used at the tips of chromosomes are present at the proposed fusion site, and that human chromosome 2 has not one but two sites for the cell cytoskeleton to attach to for cell division – but that one of the sites is mutated and not functional, though it lines up precisely with the location of this site on the appropriate ape chromosome. Together, this evidence consistently supports both common ancestry for humans and great apes, and specifically that the difference we see in our chromosome numbers arose due to a single fusion event. I briefly discussed this evidence in my last post where I describe how I teach some of this material and the compelling impact it has on students exploring the evolution question for the first time.

Enter the Denisovans

With that as background, we are now prepared to appreciate a new finding that comes from genomics work done on the Denisovan hominids, an archaic species that is more closely related to Neanderthals than to us, but that nonetheless interbred with some anatomically modern humans as they migrated out of Africa and populated the globe. (For those not familiar with the Denisovans, or the evidence for our interbreeding with them, both Darrel Falk and I have written on this previously, here and here). Recently, a more detailed understanding of the Denisovan genome was published, and nested in the new information is the discovery that the Denisovans share the 46 chromosome set with the same fusion that we have. This strongly supports the hypothesis that the fusion event predates the separation of our species. If we were to represent this on a phylogeny, we can now place this event with more accuracy than before (as before, the phylogeny is not to scale):

Despite this new information, one obvious question remains. Did the Neanderthals also have the 46-pair set? From looking at the phylogeny above, we can see that the most likely answer is that they did, since the fact that the Denisovans had it strongly implies that the last common ancestor of humans and Neanderthals / Denisovans had it as well, and the Neanderthal-Denisovan split comes later. While the Denisovan DNA samples are of high enough quality to make this assessment, we do not yet have Neanderthal DNA of high enough quality to do the same analysis with current methods (though one additional feature of the new work on the Denisovan genome is developing more sensitive DNA sequencing techniques that may resolve this question in the future).

In other words, this fusion seems to be an ancient one, predating our species by several hundred thousand years. Present estimates of the last common ancestor between humans and Neanderthals / Denisovans range at about 800,000 years ago.

Implications for understanding our “becoming human”

The main implication from this work is that it places the fusion event well before the advent of our species. I’ve often chatted informally with Christians about evolution, and at times some have thought that this fusion event was what “started” our species, or made our species unable to interbreed with other groups. Some have even suggested that perhaps the fusion event was what produced the first human (i.e. Adam).

Note that thinking this way suggests a misunderstanding of how chromosome fusions occur and what effect they have on their hosts. A fusion does not precipitate a speciation event, but rather the individual with the fusion remains a part of his or her population, and able to interbreed, even if with reduced fertility. Also, there is no necessary biological effect or change that the fusion produces on the appearance of the organism. These misunderstandings aside, however,what this new evidence shows is that this fusion event took place long before modern humans arose at around 200,000 years ago. Indeed, the 800,000 years ago date for the last human - Denisovan common ancestor means that this is the most recent date possible for the fusion. While it is an interesting piece of our evolutionary history, it doesn’t seem to have much to do with how we came to acquire the traits that set us apart from, and ultimately outcompete, other similar species.

Keeping History Safe

In the cold morning air with the sun not yet over the ridge, the place to begin preparation for summiting Mount Darwin is to ponder the reasonableness of miracles. Many Totalizers would like to ban miracles from university consideration and inquiry. Trouble is: human history is awash with credible people reporting miracles.

Modern academic tradition tends to try and maintain order. For historians it behooves us professionally to avoid accounts of alleged spiritual events. We find comfort in a little logical gymnastics that keeps history safe for us to wander in, a deceptively formulaic avoidance method that helps us avoid what people are telling us about extraordinary events in the past.

David Hume popularly articulated this logical gymnastics in an essay titled “Of Miracles” that was eventually printed in Enquires Concerning Human Understanding (1748). “I flatter myself,” Hume triumphantly proclaimed, “that I have discovered an argument . . . which, if just, will, with the wise and learned, be an everlasting check to all kinds of superstitious delusion, and consequently, will be useful as long as the world endures.”

His everlasting check on superstition begins with a circular argument that because miracles can’t happen, a reasonable person should not even listen to reports of them. Hume taught that though the normal job of a historian was to listen to the testimony that comes down to us from the past, there is a point at which you can close your ears. Hume knew that historical testimony can get wild, so he came up with a way to domesticate the wildness, a way to make history a zoo rather than allow it to be a jungle. His “Of Miracles” has been tremendously influential in the discipline of human history over the last two hundred and fifty years, not because his ideas are strong, but because his ideas are useful. Get rid of “superstitious delusions,” and the discipline of history can be turned from a safari into a form of home economics. Hume’s domestication of history is seductively simple. Instead of following the Aristotelian tradition of linking the credibility of hard-to-believe testimony to the credibility of the testifier, Hume recommended disregarding the testifier and focusing only on the testimony. This effectively removed the persuasive power from hard-to-believe testimony. Miracles need the credibility of an eyewitness in order to have persuasive power. Hume cut the power source from the unwanted testimony.

Essentially, Hume adopted the modeling technique that Darwin later used and is best seen in Global Positioning System (GPS) units. Hume recommended gathering testimony from the past and every region to create a general model of what humans generally experience. Using this mass of information, one should generalize standards of common experience. Now if anyone reports a miracle, the alleged event can’t be true because it does not conform to the generalized standards of common experience. (Of course, Hume had already refused to allow that any reports of miracles could be used even to generalize common experience.) It’s tricky. Its logic is circular. But it works to weed out awkward, quirky information. It is as if a domineering GPS unit created a sphere to serve as an abstraction for the earth, then insisted that the earth can’t have wobbling poles and flattening in the upper latitudes because the sphere in the GPS shows it can’t be true. Given a useful and trustworthy GPS, don’t listen to a scientist who might tell you something different than what the GPS tells you.

The circularity of this argument has been noted ever since Hume first proposed it, but Hume was a good writer and said what a lot of people wanted to hear. Miracles are impossible so miracle reports can’t be true. Don’t even listen to reports of them.

Balancing Likelihoods

Also embedded in Hume’s essay is the awkward “rule of logic,” most often called “Balancing Likelihoods.” By combining math and logic in an odd way, Hume’s “Of Miracles “ offered another way for historians to avoid thinking about miracles. Balancing Likelihoods has many names but is probably best stated by David Hackett Fischer, in his Historians’ Fallacies: Toward a Logic of Historical Thought, as “the rule of probability:”

“[A]ll inferences from empirical evidence are probabilistic. It is not, therefore, sufficient to demonstrate merely that A was possibly the case. A historian must determine, as best he can, the probability of A in relation to the probability of alternatives. In the same fashion he cannot disprove A by demonstrating that not-A was possible, but only by demonstrating that not-A was more probable than A. This is the rule of probability.”

This seems to be practical but is impossible. Balancing Likelihoods, in the way described by Fischer, cannot be used by historians in any normal practice. It is a talisman to keep history mentally safe from the wildness that is reported to exist. Logicians, especially mathematicians, have long criticized intellectual constructions like this. The “probability” that Fischer writes about is seemingly mathematical, but the math is simply implied to give a sense of strength to human feelings.

Before Hume wrote “Of Miracles” probabilistic logic had been advancing rapidly and there was a great hope that mathematical analogies would strengthen human thinking—even Christian apologetics. “Pascal’s Wager,” the most famous mathematical apologetic from the seventeenth century, equated eternal salvation with mathematical infinity and then applied it to a gambling formula. Antoine Arnauld, in The Port-Royal Logic (1662), and John Locke, in his Essay Concerning Human Understanding (1690) and Discourse on Miracles (1706), carried probabilistic math and logic into the handling of reported miracles. A half-century later, however, Hume reacted against Arnauld and Locke’s teachings that mathematical analogies could help in the discussion of the credibility of miracles. Hume insisted that to handle a reported miracle, a historian had to create two separate ratios, pro and con, for believability. The ratios were then to be weighed against each other. This is Fischer’s “rule of probability” quoted above. In the language of Hume’s era, this was proclaimed as the “calculus of good sense.”

Lorraine Daston, in Classical Probability in the Enlightenment (1988), offers an excellent study of Hume and the many eighteenth-century mathematicians who wanted to help bring rigorous quantitative thinking to what today would be called the humanities. Daston writes that by the 1840s, mathematicians realized that “the ‘calculus of good sense’ had become antithetical to good sense,” and that today most of what these early probabilists were trying to do is considered “patently absurd.”

In 1901, one of America’s preeminent philosopher-mathematician-logicians, Charles Sanders Peirce, wrote three essays attacking the way historians had adopted Hume’s bad logic: “A Preliminary Chapter, Toward an Examination of Hume’s Argument Against Miracles, in its Logic and in its History,” “Hume’s Arguments Against Miracles, and the Idea of Natural Law,” and “On the Logic of Drawing History from Ancient Documents especially from Testimonies.” Peirce showed that historians are in error when they talk of judging testimony by balancing probabilities because “in a scientific sense, there are no ‘probabilities’ to be judged.”

Probability, Peirce wrote, “is the ratio of the frequency of occurrence of a specific event to a generic event.” A testimony “is neither a specific event, nor a generic event, but an individual event.” Peirce further pointed out that what people were justifying by claiming Balancing Likelihoods was really simply relating “what they prefer to do” to what they don’t prefer. “Likelihood is merely a reflection of our preconceived ideas.”

Historians like me who teach in universities about the reasonable credibility of Jesus’ resurrection need to be students of Peirce not Hume on the subject of assessing the credibility of reports that come down to us from ancient history. Dealing wisely with reports of events verging on the incredible is just part of the normal job of being grounded in the social study of our complex human past.

“Come to history as a doubter,” Richard Marius advises in a historical methods manual. “Skepticism is one of the historian’s finest qualities. Historians don’t trust their sources. . . . Nothing is quite so destructive to a historian’s reputation as to present conclusions that prove gullibility.”

But Marius is wrong. In practice, historians have to trust more than doubt. In practice, historians, especially ancient historians, can’t rely on doubting. Historians have to be close listeners, discerning listeners, wise listeners, who sometimes have to make harmonies and stretch for belief.

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

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

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

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

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

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

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

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

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

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

Another theologian who agrees is John Macquarrie, who says,

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

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

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

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

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

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

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

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

Ernst W. Mayr

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

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

A Christian at the forefront of evolutionary biology

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

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

David Lack at the International Ornithological Congress, 1962.

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

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

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

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

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

Blind Chance or Divine Plan?

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

David Lack responded,

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

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

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

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

Death in Nature

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

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

Image courtesy John Marsh Photography via Flikr

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

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

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

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

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

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

Miracles

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

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

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

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

Conclusion

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

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

Notes

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

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

Review: gene structure and function

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

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

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

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

Comparing gene transcription across species at the genomic level

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

Old hypotheses, new technology

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

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

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

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

These results underscore a few important points:

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

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

For further reading:

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

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

In the last post in this series, we introduced a paper by Chen and colleagues that sought to identify new genes in various Drosophila (fruit fly) species. The youngest (i.e. the most recently evolved) gene they found is one specific to Drosophila melanogaster, the species of fruit fly beloved by geneticists as a model organism. The gene is named “p24-2” (not the most imaginative name, but it serves its purpose) and the gene it is duplicated from is called “Éclair”. The Éclair gene is found in a number of Drosophila species. A simplified “family tree” of three Drosophila species (D. melanogaster, D. simulans and D. erecta) is shown below. The duplication event that generated the p24-2 gene happened within the lineage leading to D. melanogaster, but after D. melanogaster and D. simulans separated as distinct species:

Since the entire genomes of these species are now sequenced and available online, it is possible to look at the chromosome region where the Éclair gene is found in all three. By looking at this region in D. melanogaster, we see that the brand-new p24-2 gene is almost right next door to its “parent” gene, Éclair. Below is a screen shot taken when looking at this region using a Drosophila “genome browser” that is freely available online. The red arrow indicates the Éclair gene, and we can see p24-2 is just one gene over, and seems to be nested within another gene called “Unc-115b”. The green arrows are pointing to two different “versions” of how p24-2 is made into an mRNA working copy. The Unc-115b gene (blue arrow) has five different mRNA versions. (One of the p24-2 mRNA versions has a lot of Unc-115b sequence that is not used when the p24-2 protein is made).

(Click Image to Enlarge)

Finding a duplicated gene next door to the sequence it is copied from is pretty common in genomes – when chromosomes are copied or recombined during cell division, side-by-side copies of parts of chromosomes show up every now and then. It’s also not surprising to see a new gene cobbled together with another gene. In this case, Unc-115b and p24-2 are overlapping but separate functional entities: they each have their own protein sequences, but each includes the code of the other as a sequence that does not actually translate into protein. The details of how this “cobbling” happens aren’t important for this discussion, other than to note that the mechanisms are known and not rare. In the chart above, then, the orange sections indicate the active parts of the transcribed sequence, while the gray are sections that are included in the RNA molecule, but do not get used directly to code for the new protein.

When we look at this same chromosome region in D. simulans and D. erecta, however, p24-2 is missing. Éclair and Unc-115b are there, but p24-2 is not, since it arose after D. melanogaster separated from its common ancestors with the other species. (Note: this entire region is a mirror image in D. simulans and D. erecta when compared to D. melanogaster due to a large scale chromosome inversion that covers this whole area. So, while it looks “backwards” compared to the image above, that is not surprising, it’s expected):

(Click Image to Enlarge)

So, with the p24-2 gene in D. melanogaster, we have a bona-fide, recent gene duplication event. This gene is brand new, evolutionarily speaking (less than 3 million years old, given the calculated speciation times of D. melanogaster and D. simulans). Not only is it brand new, it is also essential for survival in D. melanogaster: if you remove it, the fly dies. Obviously, since every other Drosophila species lacks p24-2, this gene is not essential for survival for any other species. It’s new, and now it’s necessary.

Do new, essential genes refute the Intelligent Design (ID) argument from Irreducible Complexity (IC)?

So far, nothing we have discussed explicitly threatens the ID argument from IC, though it does threaten the ID argument that new information cannot arise through evolution, a topic we have discussed in detail before. Michael Behe, the main ID proponent of the argument from IC, has commented on this research by Chen and colleagues (thanks to commenter “Bilbo” for pointing this out). Behe’s rejoinder was to a blog post by biologist and atheist blogger Jerry Coyne, who used the paper by Chen and colleagues to attack Behe’s ideas. Since Behe’s reply deals with his understanding of how gene duplication relates to his argument from IC, I will quote it here at length:

I have never stated, nor do I think, that gene duplication and diversification cannot happen by Darwinian mechanisms, or that “they play almost no role at all” in the unfolding of life. (As a matter of fact, I discussed several examples of that in my 2007 book The Edge of Evolution. That would be silly — why would anyone with knowledge of basic biochemical mechanisms deny that, say, the two gamma-globin coding regions on human chromosome 11 resulted from the duplication of a single gamma-globin gene and then the alteration of a single codon? What I don’t think can happen is that duplication/ divergence by Darwinian mechanisms can build new, complex interactive molecular machines or pathways. Assuming (since he is in fact critiquing them) Professor Coyne has been attentive to my arguments, one background assumption that he may have left unexpressed is that he thinks the newer duplicated genes discovered by Professor Long’s excellent work represent such complex entities, or parts of them.

There is no reason to think so. A gene can duplicate and diversify without building a new machine or network, or even changing function much. The above example of the two gamma-globin genes shows that duplication does not necessarily result in change in function. The examples of delta- and epsilon-globin, which, like gamma-globin, presumably also resulted from the duplication of an ancestral beta-like globin gene, show that sequence can diversify further, but function remain very similar. Even myoglobin, which shares rather little sequence homology with the other globins, has not diverged much in biochemical function.

In his recent work Professor Long discovered that many of the new genes were essential for the viability of the organism — without the gene product, the fruitflies would die before maturity. Perhaps Professor Coyne thinks that that means the genes necessarily are parts of complex systems, or at least do something fundamentally new. Again, however, there is no reason to think so. The notion of “essential” genes is at best ambiguous. We know of examples of proteins that surely appear necessary, but whose genes are dispensable. The classic example is myoglobin. It is also easy to conceive of a simple route to an “essential” duplicate gene that does little new. Suppose, for example, that some gene was duplicated. Although the duplication caused the organism to express more of the protein than was optimum, subsequent mutations in the promoter or protein sequence of one or both of the copies decreased the total activity of the protein to pre-duplication levels. Now, however, if one of the copies is deleted, there is not enough residual protein activity for the organism to survive. The new copy is now “essential”, although it does nothing that the original did not do.

The main points of Behe’s reply can be summarized as follows:

1. Gene duplications and subsequent changes to the copies (diversification) can and do happen, but the results are nothing really “new”— no new molecular machines or pathways (nor parts of such pathways), nor much in the way of new functions.
2. Duplicated genes can become essential simply by “sharing” the original function, and then reducing their share to a minimum, perhaps through the amount of protein that each copy makes. Again, this is not anything really new, since the copy doesn’t do anything that the original didn’t do already. So, the finding that some gene copies are essential genes is not a threat to the IC argument.

Note that Behe’s reply makes predictions that can be tested with further research. These predictions might be summarized in this way:

1. If IC is correct, duplicated genes will not be part of new, complex molecular pathways or machines.
2. If IC is correct, duplicated genes that are both essential should “share” the original function.

Testing IC with new research

Behe’s reply to the Chen paper is of course hypothetical and speculative – as demonstrated by his own comment that “there is no reason to think” that the duplicated genes are components of new complex pathways or systems. Accordingly, the validity of Behe’s reply depends on its ability to hold up over time as more work is done. Of note, the functions of p24-2 and its parent gene Éclair have been studied intensively since 2010. These studies, as we shall see in the next post in this series, shed quite a bit of light on these questions.

For further reading:

Behe, M.J. Darwin’s Black Box: the Biochemical Challenge to Evolution. Free Press, New York, 1996.

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

Chen, S., Zhang, Y, and Long, M (2010). New genes in Drosophila quickly become essential. Science 330; 1682-1685.

(Written by the BioLogos editorial team)

In a recent lecture in Washington, D.C., Intelligent Design advocate Stephen Meyer noted that scientists and theologians are generally uncomfortable with the idea of "supernatural intervention" in natural processes such as evolution. He then posed the question, “What's so bad about supernatural intervention?” Meyer’s comment touches on a point of particular tension among Christians engaged in understanding how our science and our theology interact: the nature of divine action.

Much of the confusion in this area, however, stems from the inexact meaning of intervention, which—like evolution or Darwinism—implies different things to different people. All Christians affirm that God works powerfully in the world, doing extraordinary acts of creation and salvation. In common conversation, then, intervention tends to mean simply “acts that are recognizably or obviously God’s,” whether as dramatic as the parting of the Red Sea or as subtle as an individual believer hearing a clear call to repentance or to mission from the Lord. Even in this most casual sense, intervention tends to mean special occasions of God’s providential care, rather than his ordinary sustaining work.

But to Christian scientists and philosophers trying to understand God’s action in creation—especially how he might go about his sustaining role—intervention has another connotation: namely, that recognizing something as “divine action” requires it to be in violation of the natural laws which God himself established. Put another way, many Christian thinkers associate the word intervention with the idea that to act in the world God “must” act from outside the world. That view is a central tenet of deism, not Christianity. One response to Meyer’s comment, then, is to ask whether intervention is the only (or even a helpful) way of thinking about God’s work in biological creation. Is there another way of talking about “divine action” that does not restrict God's work to only extraordinary events? Can we conceive of divine action in a way God is never absent, distant, or in any way removed from the creation he sustains at every moment?

Finding such an alternative vocabulary to talk about the different ways God acts in his creation is the purpose of this short series introducing the work of theologian and physicist Robert John Russell. Russell’s book Cosmology: From Alpha to Omega explores the history of Christian thinking about divine action and proposes one model for how we might understand it in light of Scripture, the traditions of the church, and contemporary scientific explorations of the material world.

To be clear, Russell argues that God does unmistakably act in the world. He singles out the bodily resurrection of Jesus not only as a prime example, but as a truly unique event distinct even from Christ’s other miraculous acts during his ministry on earth. That is, the resurrection was an in-breaking of God’s new reality into the present one, something “beyond miraculous.” This series, though, offers his perspective on the more basic issue of how God might be at work in what we have called the “ordinary processes” of his world.

We begin our three-part series below with Professor Russell’s description of how views of divine action have changed throughout history (excerpted from Chapter 4 of Cosmology: From Alpha to Omega).

Historical background to the problem of divine action

The notion of God’s acting in the world is central to the biblical witness. From the call of Abraham and the Exodus from Egypt to the birth, ministry, death and raising of Jesus and the founding of the church at Pentecost, God is represented as making new things happen. Through these “mighty acts,” God creates and saves. Rather than seeing divine acts as occasional events in what are otherwise entirely natural and historical processes, both the Hebrews and the early Christians conceived of God as the creator of the world and of divine action as the continuing basis of all that happens in nature and in history.

The view that God works in and through all the processes of the world continued throughout Patristic and Medieval times. For example, God was understood as the first or primary cause of all events—where all natural causes are instrumental or secondary causes through which God works. The conviction that God acts universally in all events, and that we act together with God in specific events, was maintained by the Reformers and the ensuing Protestant orthodoxy. John Calvin (1509-1564) argued that God is in absolute control over the world and at the same time maintained that people are responsible for evil deeds. Questions about human freedom and the reality of evil were seen more as problems requiring serious theological attention than as reasons for abandoning belief in God’s universal agency.

Moreover, faith in God the creator was articulated through two distinct but interwoven doctrines: creation and providence. The doctrine of creation asserts that the ultimate source and absolute ground of the universe is God. Without God, the universe would not exist, nor would it exist as “universe.” Creation theology, in turn, has often included three related but distinct claims: 1) the universe had a beginning; 2) the universe depends absolutely and at every moment on God for its sheer existence; and 3) the universe is the locus of God’s continuing activity as Creator. The first two have traditionally been grouped in terms of creatio ex nihilo(creation from nothing), and the third in terms of creatio continua (continuing creation).

The doctrine of providence presupposes a doctrine of creation, but adds significantly to it. While creation stresses that God is the cause of all existence, providence stresses that God is the cause of the meaning and purpose of all that is. God not only creates but guides and directs the universe towards the fulfilling of God’s purposes. These purposes are mostly hidden to us, though they may be partially seen after the fact in the course of natural and historical events. The way God achieves them is hidden, too. Only in the eschatological future will God’s action throughout the history of the universe be fully revealed and our faith in it confirmed. General providence refers to God’s universal action in guiding all events; special providence refers to God’s particular acts in specific moments, whether found in personal life or in history.

Divine intervention arises in the Enlightenment

The rise of modern science in the seventeenth century and Enlightenment philosophy in the eighteenth, however, led many to reject the traditional views of divine action. Although Isaac Newton (1643-1727) argued for the essential role of God in relation to the metaphysical underpinnings of his mechanical system, and in this way defended the sovereignty of God in relation to nature, Newtonian mechanics depicted a causally closed universe with little, if any, room for God’s special action in specific events—and then only by intervention: that is, by acting as from outside that closed system. A century later, Pierre Simon Laplace (1749-1827, pictured left) combined the determinism of Newton’s equations with epistemological reductionism (the properties and behavior of the whole are reducible to those of the parts) and metaphysical reductionism (the whole is simply composed of its parts), to portray all of nature as a causally closed, impersonal mechanism. This in turn led to the concept of interventionism: if God were really to act in specific events in nature, God would apparently have to break the remorseless lock-step of natural cause and effect by intervening in the sequence and violating the laws of nature in the process.

The eighteenth century also saw the rise and fall of deism, in which the scope of divine agency was limited to an initial act of creation. According to deism, the universe was like a clock which, once built and set in place, proceeded to run on its own. David Hume (1711-1776) challenged the deistic (and theistic) arguments for God as first cause and as designer. In response, Immanuel Kant (1724-1804, pictured right) constructed a new metaphysical system which emphasized the mind’s role in organizing sense-data through universal categories of intuition and forms of sensibility. According to Kant, the sphere of religion lies not in our knowing (the activity of pure reason) but in our sense of moral obligation (the activity of practical reason). It is our ethical system, not our knowledge of nature, that requires us to postulate God, freedom and the immortality of the soul. The consequence of Kant’s thought for the West was the philosophical separation of the domains of science and religion into “two worlds”—a move which was to have an immeasurable effect on Christian theology up to the present.

Theology splits into conservative and liberal interpretations of divine action

As a consequence of the philosophical division of science and religion, theology in the nineteenth century was faced with a fundamental challenge not only to its contents and structure, but even to its method. The variety of responses to this challenge tend to fall into two groups: “liberals” largely accepted and worked within the terms of the discussion that modernity dictated while “conservatives” upheld traditional formulations and tended to reject “modernity.” The earliest and most influential figure among liberals was Friedrich Schleiermacher (1768-1834), who responded to Kant by locating religion as neither a knowing nor a doing. Instead religion is grounded in personal piety—the feeling of absolute dependence.

Schleiermacher held that theological assertions emerge from the immediacy of the religious self-consciousness. He understood God’s relation to the world in terms of “universal divine immanence” [the idea that God is present to the entire cosmos at all times], and he blurred the distinction between creation and providence by collapsing the later into the former. In a famous move he defined miracle as “. . . simply the religious name for event. Every event, even the most natural and usual, becomes a miracle, as soon as the religious view of it can be the dominant.” Schleiermacher’s arguments became characteristic of liberal Protestant theology throughout the nineteenth century and continued into much of twentieth century theological work.

The second half of the nineteenth century saw the rise of Darwinian evolution, which combined random variation and natural selection to explain biological complexity. To some in the nineteenth and twentieth centuries, the fundamental role of chance in nature seemed to undercut any notion of divine action in the world; to others, such as the Anglo-Catholic liberal movement in Britain and America, Darwinian evolution could be accommodated and even integrated into theology without interventionism, since God works immanently in and through the very processes of nature. In contrast, religious conservatives tended either to reject evolution as a whole or give it a limited acceptance with the proviso that the objective acts of special providence constitute divine interventions in nature.

The rise of neo-orthodoxy in the twentieth century

Protestant theology in the first half of the twentieth century was largely shaped by Karl Barth. In his rejection of nineteenth-century liberal theology, Barth returned theology to its biblical roots and focused it on the God who is “wholly other.” Recognizing that a religion founded exclusively on subjective experience is vulnerable to the critiques of Feuerbach and Freud, Barth and his followers held fast to the objective action of God in creating and redeeming the world. “The Gospel is . . . not an event, nor an experience, nor an emotion—however delicate! ... It is a communication which presumes faith in the living God, and which creates that which it presumes.” The ‘God who acts’ became a hallmark of the ensuing “biblical theology” movement which arose in the 1940s and 1950s. To many this movement seemed to offer a tertium quid between liberal and conservative theologies.

But do Barthian neo-orthodoxy and the biblical theology movement actually produce a credible account of divine action? On the one hand neo-orthodoxy attempts to distance itself from liberal theology by retaining biblical language about God acting through wondrous events and by viewing revelation as including an objective act. Yet on the other hand, it, like liberalism, accepts the modern premise that nature is a closed causal system, as depicted by classical physics. The result is that neo-orthodoxy seems to assert a contradiction: God does act objectively in nature (as conservatives believe) and God does so without intervening, violating, suspending or obstructing the ordinary processes of nature understood as a closed causal system (as liberals believe).

A third way between liberal and conservative theologies

Any purported “third option” will require an intelligible concept of objectively special providence which does not entail divine intervention. Such a concept could serve as a genuine tertium quid to conservative and liberal notions of special providence, combining strengths borrowed from each. Specifically, we will seek to speak about special divine acts in which God acts objectively in an unusual and particularly meaningful way in, with, and through events which serve to mediate God’s action. We will seek to do so without entertaining—in fact by refusing—the additional claim that God must intervene in, or at least suspend, the laws of nature. Those laws are themselves the result of and description of God’s continuous creation, after all. I call this type of divine action Non-Interventionist Objective Divine Action (NIODA).

In part 2 of this series, Tom Burnett will explore in more depth what Russell takes to be wrong with the Enlightenment concept of “supernatural intervention.” Part 3 will explain and clarify Russell’s theory of NIODA.

From Chapter 4, “Does ‘The God Who Acts’ Really Act? New Approaches to Divine Action In Light Of Contemporary Science,” in Cosmology: From Alpha to Omega by Robert John Russell, copyright © 2008 Fortress Press. Reproduced by permission of Augsburg Fortress Publishers. All rights reserved. No further reproduction allowed without the written permission of the publisher.

This ongoing series grew out of a conversation that Kenneth Keathley, the Senior Vice President for Academic Administration at Southeastern Baptist Theological Seminary and I had last year. We agreed that he would solicit a set of essays from scholars at Southern Baptist Seminaries who would specifically identify their concerns about what they perceive to be the BioLogos view of creation. In response to this request, Dr. William Dembski of Southwestern Baptist Seminary submitted the essay “Is Darwinism Theologically Neutral?” Although I do not consider my view Darwinian, I am sure that my view and that of others associated with BioLogos is perceived that way by some, so this gives me an opportunity not only to respond to his analysis, but to clarify my position on creation and how I think it is distinct from what Dembski calls “Darwinism."

God’s Activity in Creation

I will begin by summarizing my view of the nature of God’s activity in creation. I think that God created all living organisms, including humans, through the evolutionary process. Acceptance of creation through evolution does not mean that I reject the notion of a miracle-working God. On the contrary, I believe in the miracles of Scripture, and I believe that we’ve experienced God’s supernatural activity in our own lives. I stand in awe of a personal God whose activity is not constrained by natural laws, but also includes supernatural acts.

But what are the natural laws? Are not the the laws of nature simply a description of God’s ongoing and non-ceasing activity in the universe? The Law of Gravity, for example, is not something that God set up in the beginning, thereafter recusing himself from further involvement and exiting from the scene. Instead, the Law of Gravity works as it does because of the ongoing activity of God’s Spirit in the universe. So consistent is that activity that it can be described mathematically through scientific analysis. If God ceased to be active, however, then not only would the matter of this universe no longer function in a way which enables a mathematical description of gravity, matter itself would cease to exist. Paul, referring to Christ, writes “All things are created by him and through him.” Continuing, he goes on to state that “He himself is before all things and in him all things hold together” (Colossians 1:17). So he created in the beginning and, indeed, “…without him not one thing came into being.” (John 1:3) But it doesn’t end there: his ongoing activity is necessary for the universe to function. As the writer to the Hebrews declares “He sustains all things by his powerful word.” (Hebrews 1:4) The laws of nature, then, are simply a description of the ongoing activity of God which—because it is so consistent, dependable, and pervasive—points to the trustworthiness of God. Put another way, the activity of God is not restricted to that which we call the supernatural; it is all God’s activity. It is just that some aspects of God’s activity are so consistently repeatable that we can develop laws which describe the regularity of the divine activity which “holds” and “sustains” the universe. This latter type of activity is no less magnificent just because God does it continuously. Indeed, the Psalmist marveled at God’s natural activity and worshipfully reflected upon it.

On the other hand, the God we know through Scripture and personal experience also works in ways that are not mathematically predictable. We call this aspect of God’s action supernatural, and we seem to think of this facet of God’s work—this law-defying activity—as being more God-like. Indeed calling it super-natural suggests we think of it as God’s “turbo-charged” activity. But are not miracles simply a reflection of God choosing to work in a unique, non-customary manner to accomplish God’s purposes in God’s time? (See here for more detail.) When God works in this way, Scripture generally presents such activity in the context and purpose of God’s desire to enter into or renew a relationship with an individual or with a community of people. For example, God’s miraculous involvement in the lives of the elderly couple, Abraham and Sarah, led to the birth of their son, Isaac, and marks the beginning of God’s very special relationship with their descendents. God’s interaction with Moses through the burning bush initiated a new phase of God’s relationship with the Hebrew people as they moved out of slavery and back into the Promised Land. And of course, the supreme examples of miraculous activity are the incarnation, the empty tomb, and the resurrected Body. We worship a personal God whose desire for an ongoing loving relationship with humankind is first laid out in the early chapters of Genesis, but does not end there. In all divine activity—supernatural and natural—God is just being who God is: Creator, Sustainer, and loving Father. There are not two sets of activities, even though we label them “super” and “ordinary.” All are “super,” because all describe the activity of our supernatural God. Some are regular, predictable and ongoing, while other activities of God are not, for reasons often based in the fact that God is lovingly responsive and relational.

The Genesis narrative gives us no details about the mechanism by which God brought the universe and life into existence. God gave the charge: “Let there be lights in the dome of the sky..., “ “Let the waters bring forth…,” “Let the land bring forth…,” “Let the birds multiply…,” and, in response, we are told, it happened. Scripture does not explain how it happened, although as we read God’s other book—the book of nature—we see that God’s work extended over a long period of time. In these details, the Bible does not say whether the “bringing forth” was fulfilled through God’s natural activity (that which is regular, ongoing, and can be described by science) or God’s supernatural activity (that which is not regular and predictable). Given the many examples of supernatural activity in Scripture, we human beings tend to expect that for something as special as creation of stars or new species, supernatural activity would have been required. But we cannot derive this from the scriptural account and, therefore, it is wise not to second-guess how God might have worked based on the Scriptures.

Indeed, the distinction is softened by Scripture itself, which often speaks of God’s natural activity in ways that sound supernatural. For example, the Psalmist writes of God opening his hand to feed the living creatures (Psalm 104:28). We know how God does this and so did the Psalmist—he did it through natural means—but it was still God’s process and God’s provisions. Job speaks of thunder as being the voice of God (Job 40:9). We know God’s natural activity produces thunder and we can describe the laws that are responsible for it, but the fact that we know how it works certainly doesn’t negate the point being made in the book of Job. When the Psalmist describes the heavens as being the work of his fingers (Psalm 8:3), this does not negate astronomy’s description of the regular and ongoing processes that give rise to stars in God’s universe. Those processes are natural, but they are every bit as much God’s activity as if he were to take huge balls of matter and miraculously fashion sparkling stars with his hands.

Still, given that there is extensive supernatural activity exhibited in God’s interaction with Israel and in the life of Jesus, it is entirely possible that he did work supernaturally in fulfilling the creation command, as well. Even though the miracles described in the Bible primarily serve some theological or pastoral purpose that stems from God’s earnest desire to make his presence known and to deepen his relationship with humankind, we should reserve judgment about whether only God’s natural activity was responsible. It is not clear though, that supernatural activity would often be God’s chosen mode of action millions of years before humans had arrived. Thus, we should not assume with certainty that God would choose to use supernatural flurries of activity if his ongoing regular activity—that described through natural laws—would accomplish the same end, albeit over a longer period of time. For all we know, God may prefer slowness, even though we seem to be inclined to think that faster is better. After all, in the history of Israel and the church, God gave no new prophecy for 400 years before the coming of Christ, and it took the early church five centuries to come to a clear—albeit mysterious—understanding of the Trinity. Even now, two thousand years after Christ, we wait for his return.

In the next part, Darrel responds to Dembski’s lists of non-negotiables and clarifies how he sees BioLogos as different from “Darwinism”.

In the previous post in this series, we explored how evolution can force science into making predictions that seem counter-intuitive. For cetacean (whale) evolution, we saw that the preliminary lines of evidence (the fact that whales are vertebrates, and mammals, for instance) pointed to the prediction that modern whales are descended from four-limbed, land-dwelling ancestors. As we then noted:

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”.

We have already discussed hind limb and hair loss in whales, citing evidence from embryonic development in modern whales that shows how hair and hind limbs develop early in their embryogenesis, but then are lost at later stages. We now turn to one of the remaining questions: tooth loss in the lineage leading to modern toothless whales (order Mysticeti). To obtain their food these whales pass seawater through a baleen, a large sieve-like structure that filters out plankton, small fish and other food items. Some recent genetics sleuthing has investigated a portion of this riddle, and adds further details to the story of how the baleen whales came to be.

Evolution: A Theory with Bite

If indeed modern whales are descended from ancestral, four-limbed, terrestrial ancestors, then those ancestors, like mammals in general, had teeth. Modern toothed whales (order Odontoceti) have retained those teeth to the present day, but baleen whales have adopted a new way of life as filter-feeders. Researchers were curious to see if traces of a “toothed past” could be found in the genomes of modern baleen whales, so they went hunting for remnants of genes devoted to making teeth. Such defective gene remnants would be examples of pseudogenes, and we have discussed pseudogenes previously in this series. While pseudogenes in and of themselves are powerful evidence for evolution, pseudogenes that are “out of place” are especially so. One such example we have seen before is the human vitellogenin pseudogene, the remains of a gene used for yolk production in egg-laying organisms found in the exact location in the genome that evolution would predict for it. As mammals that receive embryonic nourishment through a placenta, we have no need of egg-yolk genes. Similarly, baleen whales have no need for genes responsible for making teeth, and finding the remnants of such genes would make a strong case for an evolutionary origin of baleen whales as the modified descendents of toothed whale ancestors.

Independent Lines of Evidence, but Contradictory Stories?

Some of the genes known to be used in all mammals for tooth formation were the obvious candidate genes to start with: the products of the ameloblastin, amelogenin, and enamelin genes are all used in the formation of tooth enamel, the hardest structure in the vertebrate skeleton. Researchers went looking for these genes in several Mysticete (i.e. toothless whale) species. The results showed that all the species studied did indeed have these three genes present as pseudogenes (and more specifically, as unitary pseudogenes, a special class of pseudogene we have discussed in detail previously). Finding these genes as pseudogenes in toothless whales was exactly what evolution predicted, but there was a catch: none of the mutations that removed the functions of these three genes were shared between different species, suggesting that these genes lost their function independently in the species studied. This finding was at odds with data from the fossil record, which suggested that teeth were lost only once, and early in the lineage leading to all modern toothless whales. So, the researchers seemed to have two lines of evidence that at face value contradicted each other. The fossil record suggested that tooth loss occurred once in the common ancestor of all toothless whales, but these three genes seemed to have been inactivated independently, several times over, suggesting that loss of teeth should be happening later in Mysticete evolution, and more than once.

One proposed explanation for the apparent discrepancy (among several put forward) was to predict that a fourth gene required for enamel formation was lost early in Mysticete evolution. The loss of any one gene necessary for forming enamel would be enough to prevent the process altogether. In this case, the loss of this fourth gene would prevent tooth enamel from forming, even though the genetic sequences of the other three enamel genes would still be intact. Once enamel function was lost, random mutations in the remaining enamel genes could then accumulate later in Mysticete evolution after speciation in this group was already underway. To test this hypothesis, the research group went hunting for other enamel genes in toothless whales.

Signature in the SINE

The smoking gun for tooth loss in Mysticetes turned out to be exactly what was predicted: a fourth gene, necessary for enamel production, and mutated with the same inactivating mutation in all modern toothless whales. The gene in question, named enamelysin, was destroyed when a mobile genetic element called a SINE transposon inserted into it, breaking it into two halves and removing its function:

The fact that the same SINE insertion mutation at an identical location is found in all modern Mysticete species indicates that this mutation happened once in a common ancestor and then was inherited by the entire group. Since this must have occurred early in the evolution of toothless whales in order to happen in the common ancestor of the entire group, the picture from the genetics and the fossil record match. Once again, findings in one discipline (in this case, paleontology) can be used to make very detailed predictions about what another, unrelated discipline (comparative genomics) should reveal. These results are also entirely consistent with the observation, made in the 1920s, that toothless whales form tooth buds during embryogenesis that are later reabsorbed prior to the point when the deposition of enamel would begin. As with the hind limb story in whale evolution, lines of evidence from genetics, paleontology and embryology converge to support the hypothesis that modern toothless whales descend, through modification, from toothed ancestors.

In the next post in this series, we’ll examine a few more lines of evidence for whale evolution, and extend our discussion to converging lines of evidence for the evolution of our own species.

For further reading:

Meredith, R.W., Gatesy, J., Cjeng, J., and Springer, M.S. (2011). Pseudogenization of the tooth gene enamelysin (MMP20) in the common ancestor of extant baleen whales. Proceedings of the Royal Society B: 278 (1708); 993 – 1002. Available online: http://rspb.royalsocietypublishing.org/content/early/2010/09/16/rspb.2010.1280.full.pdf

Ridewood, W.G. (1923). Observations on the skull in foetal specimens of whales of the genera Megaptera and Balaenoptera. Philosophical Transactions of the Royal Society of London B: 211; 209 - 272. Available online: http://rstb.royalsocietypublishing.org/content/211/382-390/209.full.pdf

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