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. 

More Than One Christian View

Many parents and pastors are wondering what to tell their children about creation and evolution. While Sunday school classes often cover Genesis 1 around kindergarten (with kids coloring pictures of what God created on each day), most curricula do not address science again before kids leave for college. Yet issues of creation and evolution can be addressed in age-appropriate ways throughout Sunday school. Elementary school children already learn about idol worship from other Old Testament stories, so teachers have an opportunity to contrast Genesis 1 with the idol-rich creation stories of other cultures. Middle school students can be given basic tools for considering creation and evolution such as the contrast between the “how” questions answered by their science lessons in school and the “who” and “why” questions answered in Scripture. Middle and high school students can find role models by reading the testimonies of scientist Christians.

Youth need to be encouraged to discuss their questions and doubts, while affirming core beliefs. When asked why they left the faith, scientists often mention that the church was not open to their questions and told them to “just believe.” Churches can demonstrate openness to questions by teaching youth about multiple Christian views on an issue. Students need to hear that some Christians accept the science of evolution and others do not, and have a conversation about the reasons why. Too many young people have struggled when they felt they had to choose between clear scientific evidence and the beliefs they grew up with. Even when parents and leaders are unsure about evolution, they can help students by saying, “While I have concerns about evolution, I’ve heard that some Christians accept the science of evolution while still believing in the God of the Bible.”

Difficult issues like origins cannot be addressed in a single event. People need time to ponder the issues, and spaces to talk it through. One church did a six-week sermon series, with parallel curricula for all ages in Sunday school, so that families could work through it together. Another church did a sermon series and discussion group for adults for four weeks, to prepare parents before a four-week series for the youth group. Other churches encourage small groups to read a book on science and faith and discuss a chapter a week. (Since all authors have their favorite view, I recommend discussing at least two books from different authors to learn about multiple Christian positions.)

More Than Evolution

In our science-saturated culture, evolution is not the only science topic the church should be considering, and not even the most important. With church members encountering the latest medical advances as patients and family members, a discussion on bioethics would be very relevant. Since young people are usually the first to use hot new gadgets, they should be considering the appropriate Christian use of technology . As the issue of climate change becomes more pressing every year, churches need to talk about it, and not avoid it because it is so political. The Evangelical Environmental Network offers many resources for churches, emphasizing ways that creation care benefits the poor and the unborn. One group of churches, with the help of Calvin College, joined together to clean up the local creek that drains the watershed in which the parishioners live, work, and worship. Many of the congregants were not even aware of the size of the watershed or the pollution level in their own creek. This was a hands-on opportunity for all ages, directly caring for their own corner of God’s green Earth.

More Than Controversy

With so many issues to discuss, Christians can easily get the feeling that science is always attacking the faith. It is essential to balance such conversations with positive responses to God’s creation. After all, the primary response to the natural world in the Bible is to praise the God who made it. The first time I led an adult Sunday school class on creation and evolution, I was amazed how much the participants appreciated simply ending each session with a Psalm reading or creation hymn. Thoughtful frowns turned into relaxed smiles as the group remembered our unity in Christ and the centrality of God as the Creator.

Creation themes can be incorporated throughout worship. One church asked the congregation to submit their favorite creation photos at the end of the summer (from backyard flowers to National Parks), then wove the images into a worship service with creation songs and readings from the Psalms. In addition to flowers and mountains, modern science has revealed incredible glories that can inspire our praise and reflection. Several contemporary Christian musicians have begun to artfully incorporate the wonders of the natural world into their music; Chris Rice sings of “cratered moon and Saturn’s rings,” and Third Day praises the “God of wonders beyond our galaxy.” In one church, an elder brought in modern science when leading the congregation in prayer with these words: “Creator God, out of nothing you created all that is. You hurled the galaxies through time and space. . . . The universe is your hourglass, the continental drift your minute hand, the Grand Canyon your second hand. You are infinite.”

Preachers can incorporate science in the same way they make references to movies, current events, or best-selling books in sermons. To notice these connections, take some time to encounter science: read the science section of the New York Times, visit a local science museum, or ask scientists in the congregation about their work. A visit to a planetarium might give a new appreciation for the vastness of the universe, which could illuminate a sermon on the vastness of God’s forgiveness in Psalm 103:11–12. Pastor John Van Sloten learned about the neural networks in the brain and incorporated it into a sermon on the vine and the branches of John 15.

Preachers are understandably concerned about avoiding scientific errors when preaching, but this should not prevent engagement with science. Some pastors do their own research to get the details right because they enjoy digging into a science topic. Other pastors bring in a scientist (live or by video) so that they do not have to explain the technical material themselves. Others play to their strengths by choosing topics with fewer technical details, such as the Christian motivation for doing science or exposition of Bible passages relevant for scientific questions. Many of the questions Christians have are really about biblical interpretation and Christian theology, areas where the pastor is an expert. Minor technical errors made in good faith are forgivable, but a sermon that argues that mainstream science is wrong on some point can be devastating for the faith life of teenagers who are learning the correct science in school.

Beyond Sunday morning worship and preaching, science can show up in many areas of church life. During a youth camping trip or church picnic, include a nature walk concluded with praise. After a winter evening worship service, invite a local amateur astronomer to set up a telescope in the parking lot to show people the moon and planets. Convert a vacant lot near church into a community garden, so kids can experience firsthand how God provides food from the Earth.

More Than Programs

In all these activities, remember that views on science are “caught” more than “taught.” Congregants will naturally pick up on the attitude of the pastor or ministry leader, whether skeptical of science or celebrating science as the study of God’s creation. Visitors will pick up on this too, so these attitudes are part of being a church that welcomes and ministers to scientist Christians . Recently I was invited to speak at a church on the expansion of the universe and the possibility of a multiverse. Several enthusiastic young people in attendance had clearly caught the love of science from the church leaders who planned the event. One girl came up afterward with her dad, both of them marveling at God’s creation. They were amazed not just with the particular things I had discussed, but with the way in which God has embedded wonders at every level of understanding. Everyone can marvel at the starry skies, school kids can learn about the planets and asteroids, and scientists with PhDs can study dark matter and string theory. No matter how deep we look, we keep discovering more and more ways that creation declares the glory of God.

For Further Reading

For more resources on a full range of science topics, visit the The Ministry Theorem collection at http://ministrytheorem.calvinseminary.edu/. You will find sample sermons, curricula for children and adults, worship resources, essays by a dozen scientist Christians, and much more.

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.

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.

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.

By Luci Shaw

Blessed be God for thaw, for the clear drops
that fall, one by one, like clocks ticking, from
the icicles along the eaves. For shift and shrinkage,
including the soggy gray mess on the deck
like an abandoned mattress that has
lost its inner spring. For the gurgle
of gutters, for snow melting underfoot when I
step off the porch. For slush. For the glisten
on the sidewalk that only wets the foot sole
and doesn’t send me slithering. Everything
is alert to this melting, the slow flow of it,
the declaration of intent, the liquidation.

Glory be to God for changes. For bulbs
breaking the darkness with their green beaks.
For moles and moths and velvet green moss
waiting to fill the driveway cracks. For the way
the sun pierces the window minutes earlier each day.
For earthquakes and tectonic plates—earth’s bump
and grind—and new mountains pushing up
like teeth in a one-year-old. For melodrama—
lightning on the sky stage, and the burst of applause
that follows. Praise him for day and night, and light
switches by the door. For seasons, for cycles
and bicycles, for whales and waterspouts,
for watersheds and waterfalls and waking
and the letter W, for the waxing and waning
of weather so that we never get complacent. For all
the world, and for the way it twirls on its axis
like an exotic dancer. For the north pole and the
south pole and the equator and everything between.

Editor's Note: If you'd like to see other great posts like this, go to the BioLogos Navigator topic Worship & Arts.

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.

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.

We tend to think of creativity in terms of flashes of insight and brilliance, of novelty, and especially of unexpected things bursting upon the scene. But creativity is no less creative and no less remarkable when it proceeds step by step, according to discipline, according to rule. We notice significant ruptures in the flow of things and upheavals of the regularity and predictability of life, faith, or science, precisely because such revolutions happen against a background of the ordinary. Even when the rules are interrupted and disturbed, they are usually not obliterated but modified. We and the rest of creation begin again by applying them anew and continuing on in light of what has changed.

Artist Linnéa Spransy makes this paradoxical ‘rules and rupture’ quality of life the method, not just the subject of her art, bringing a fascination with the mathematical underpinnings of the natural world together with her commitment to the kind of renewal-through-brokenness that comes with following Christ. As she says, “the boundaries between art, worship and natural sciences are fluid. I go [to that place of intersection] to be more amazed by the strangeness of existence, to experience awe and wonder.”

Confronted with the scriptural assertion that “eternity is written in [our] hearts,” Spransy wondered how we even begin to understand what that means. What might visual corollaries for such a statement be? How do we represent the tension between freedom and constraint, that dynamic dance of continuity and change, of predictability and surprise, that exists at every level of our experience and study of the world—from quantum physics to genetics to geology—and that seems fundamental to the ways of the Lord with us, as well? Her answer began to form around the study of fractals, mathematical rules whose reiteration in nature leads to endlessly new things. In her own work, a similar fractal sensibility leads to visual representations of something eternal.

Spransy says that every painting she completes “is the manifestation of a predetermined scheme – a system of small limits, with a clear beginning and end. These scripted pieces of visual choreography are allowed to accrue to show me their beauties and surprises, allowing discovery in the midst of certainty.” In other words, images like Frenetic Sequence, 2011, above, are not pictures of natural systems or objects, but representations and results of the processes and relationships by which natural systems and objects come to be. They are built from the inside out, as it were.

To begin a piece, Spransy assembles a library of “research drawings” that play out the various rules and rule sets she intends to use—essentially a kind of preliminary modeling of the visual system she wants to explore. Sometimes these are based on fairly simple mathematical or geometric rules that tell her when a line or shape will turn or divide or end. Other times she uses several different sets of rules at the same time—whether mathematical or derived from biological relationships such as those between base pairs on the DNA strand, or the way bacteria will move towards available sources of food in a Petri dish. But though these rules are established at the outset of a new piece, when she begins a new large-scale work, the outcome is anything but mechanistically predetermined, for several reasons.

First, the physical context in which she’ll be exploring each basic “module” or set of rules is different from that of her research drawings, having moved from a sheet of paper onto large prepared canvases that are five or six feet on a side. She does not transfer the small drawing from the paper to canvas, but regards that earlier work as preparation and practice of the process out of which the final work will emerge. Second, because the works are hand-drawn, there is always the element of her own agency and engagement with both the materials and the rules. There is an inescapably subjective quality to the way she responds to both materials and means. There is also subjectivity to the way she engages with the lines and shapes she has already laid down. Put another way, the abstraction of the rules is always mediated by and expressed through specific, very concrete and physical circumstances.

Finally, Spransy’s process includes what she thinks of as cataclysmic events or moments of chaos: intentional ruptures of the emergent system by gestures that overwhelm and obliterate sections of what she’s already done. Often she will shield sections of the existing system from the coming trauma either by masking them off or by subtly manipulating the flood of color—tilting the canvas to preserve sections of what was there. Afterwards, she will continue scribing and painting lines from the original system on top of or adjacent to the new areas of color, but in ways that respond and adapt to the new visual ecosystem. In this way, layers of work are built up, obliterated, and built up again.

Again, there is an inescapable agency at work in what—from the imagined standpoint of the system itself—must seem a randomly destructive occurrence, but Spransy’s point in breaking into the system is to test the limits of its creative, integrative capacity. By creating “environmental pressure” in this way, then coaxing the fragments and remnant information to multiply and reassert their orderly identities again, she asks, “How flexible are the rules?” The finished paintings are not rote recitations of fractal or statistical formulae, then, but objects with both a physical and a relational history. They are records of a thoughtful, physically engaged, but also humble exploration of how the confluence of order and chaos creates meaning.

Though Spransy denies that there can be such a thing as a “perfect analogy,” her artistic practice has spiritual underpinnings and spiritual implications, as well as visual results. Like many working scientists, she is seeking a way of understanding how the creator engages with His creation, and a better grasp on how we creatures should make our way in response. On one hand, her attentiveness to the basic orderliness of the material creation has a corollary in the familiar disciplines of faith, including reading the scriptures, prayer, and responding with mercy to ruptures in human lives and communities. But on the other hand, her embrace of surprise and chaos is, as she says, an “invitation to the otherness of God,” and a recognition that radically “dissimilar things sometimes occupy the same space.” In combination, those divergent elements help Spransy’s works hover at the boundary between knowing and un-knowing, between control and accident, between freedom and determinism.

Spransy notes that “even in the aftermath of great destruction, life is given great opportunity. In science we’re actually happy and excited when there’s a break in the rules.” This insight, clarified and lived out in her life as well as her artistic practice, directs us to consider not only the necessity and goodness of diligent pursuit of the rules, but also to reconsider the goodness of what we are otherwise inclined to see as calamity and chaos. Indeed, Spransy’s work points us back to the central paradox of the Christian faith: that the most radical disruption of the natural systems of the world occurred two thousand years ago in Palestine with the coming of Christ—singular proof that rupture does not necessarily end in destruction, but may be our means to redemption.

Linnéa Gabriela Spransy grew up in rural Oregon in a community attentive to Christ’s call to live in community with one’s neighbors, but was herself equally aware of God’s presence in the natural world around her. She received her BFA in Drawing from the Milwaukee Institute of Art and Design, and her MFA from the Yale University School of Art. In the midst of exhibiting in solo and group shows in university and commercial galleries, she moved to Milwaukee to study the Bible and consider how it might re-frame her sense of self and her career as an artist. In 2005 she relocated to Kansas City to help found the Boiler Room, a prayer-focused intentional community where she lives and in which she is the artist in residence. She continues to show her work widely, has pieces in pubic and private collections, and was the subject of a recent film-making project: Linnéa: Freedom Through Limits. More of her art can be seen on her website.

Originally posted February 4, 2012

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.

Photo credit: Jan Bacon

Singer/songwriter Andy Zipf’s “Stumble on the Line” is built around the image of a river flowing through a canyon it has sculpted—an image that can easily be played out as a picture of the way that the Lord has been at work preparing a path for us in the material world, complete with signposts to his former and present activity. Zipf’s imagery of flowing water as a powerful (even dangerous) but also refreshing force echoes the similarly-complicated place of springs and rivers and seas in the scriptures; his description of his own path through the canyon calls to mind the Psalmist’s affirmation that his help comes not from the idols erected on the heights, but from the maker who has crafted both heaven and earth. Here, the river has literally made the canyon, carving it through the “years and layers,” and leaving the evidence of that long work as a sign to all who journey through.

But though Zipf’s canyon provides shelter, a good measure of necessary constraint, and even encouragement to keep moving along the river-course, the thrust of the song is that seeking God is a complicated, sometimes difficult endeavor, whether we are looking for Him through what He has made or through what He has said. The lyrics suggest that walking with the Lord is a path of halting discovery and intrigue, of our learning to notice the way God’s actions in the past are written subtly into the world around us. But Zipf also implies that this is a path that requires obedience, since we are also confronted with the fact that He sometimes speaks to us directly and unequivocally, saying, “follow me.” The song does not take its name and refrain from the river itself, then, but from how we tend to navigate and respond to the terrain it has carved: we “stumble on the line.”

Though pursuing the text’s geologic conceit a bit further is possible, what is more poignant for all of us engaged in the science and faith dialogue is that “Stumble On the Line” is at its heart a love song addressed to the “you” that is the river—the one who has carved the path and along whose banks the singer and we pick our way. Our attentiveness to this terrain of faith does not come first from our desire to analyze and categorize the “evidence” of how it came to look as it does, or even to demystify the mechanism by which a message might be written “in a line of stones.” Rather, what leads us on is the desire to know how to relate to the water itself. The song describes not just a physical path, then, but one of the heart and will.

Indeed, the personal address of the song focuses our attention on the fact that the subtlety or obviousness of the signs along our way have much less to do with whether or not we heed them than does the basic dividedness of our hearts. As Zipf says, we alternate between “trying to reach” and “trying to leave” the One we love. Put another way, we do not reject how God has written his past activity into the layers and years of the earth, or spelled out his intentions for us in the future because they are not obvious, but for the same reason we reject any and all of His claims on us at one time or another: because we wish to be the ones who forge the path, write the story, and sing the song. Our pride—whether in our science or our righteousness—is what keeps us blind and deaf to His leading in our daily path. And yet, even—perhaps especially—in response to our pride, God makes a way for us to gain a better perspective, and leads us on towards Him through whatever means we need.

To return to the language of the song, there is a beautiful ambivalence to the word “stumble,” that contains reminders that following the Lord involves being ever surprised by His ways (we “stumble on” his truth as an unexpected discovery), and ever broken by our own ways (we “stumble on” our pride as an impediment to seeing and following). Yet in both cases, our stumbling leaves us in the same position: on our knees before the one who is both maker and guide. In the last few repeated lines of the piece Zipf affirms that we must and will continue to stumble on in this path of love, whether we come to each stumbling place through surprise and joy, or pride and brokenness. From that position of humility and worship we have the proper perspective to see and affirm that the God who creates is the God who speaks is the God who redeems—the Lord who meets us on our knees, lifts us up, and guides us into the steps of His righteousness.

“Stumble On the Line”

© 2009 by Andy Zipf

I walk a weathered canyon
you're the rapids, running through it
years and layers start to show
in the soil, there is a swelling, beating rhythm to it
earnest prayer I used to know

on the one side, I reach you
on the other, try to leave you
in between the faults of my youth
I stumble on the line to love you

came upon a message,
hidden in some shallow water,
written in a line of stones
telling me to go on down the canyon, follow after. . .
so I keep on. . .

on the one side, I reach you
on the other, try to leave you
in between the faults of my youth
I stumble on the line to love you

I walk a weathered canyon
you're the rapids, running through it
years and layers start to show
in the soil, there is a swelling, beating rhythm to it
earnest prayer I come to know

on the one side, I reach you
on the other, try to leave you
in between the faults of my youth
I stumble on the line to love you.

Though now based in Washington, DC, Andy Zipf began life in the Midwest (Indiana, Illinois, Iowa), but moved to Pennsylania and then New Jersey before his family settled in northern Virginia. He began his career as a professional singer and songwriter shortly after high school, and has performed over 400 times in the last four years—in living rooms, coffee houses, churches, concert halls, and bars. Though “Stumble on the Line” comes from Andy’s 2009 ep “Our Voice Is a Weapon,” his third full-length album and seventh studio release, “Jealous Hands,” became available in July, 2011. More details on Andy and downloads of his music may be found on his website.

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.

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

One thing I ask from the LORD,
this only do I seek:
that I may dwell in the house of the LORD
All the days of my life,
to gaze on the beauty of the LORD
and to seek him in his temple.

Psalm 27: 4

I belong in the ranks of those who have cultivated the beauty that is the distinctive feature of scientific research.

Marie Curie¹

All of the biologists I know are undeniable lovers of their objects of study...

Konrad Lorenz²

Beauty in Science

As a biologist, I am fascinated by the fluorescent-on-black images of cells, 3D rotations of protein structures, and cross-sections of colourful tissue samples that grace the covers of scientific journals. I have spent whole weeks staring down a microscope at the beautifully transparent bodies of developing fish embryos, and whenever possible I illustrate my written work with photographs of the natural world. I’m not alone. In the institute where I did my PhD we had a basement full of microscopes and imaging technology, and it was considered important to have beautiful images in your presentations—movies were even better. The journal Nature: Cell Biology always features striking images on its covers, and in an editorial these photographs were described as works of art in their own right. In fact, ‘scientific art’ has become a recognised genre, and displays of science-related images are increasingly popular in research institutes, museums, science festivals and other public spaces.

Indeed, a number of practicing scientists have devoted their time outside the lab to communicating the beauty and wonder of science to the general public. (See sidebar.) One of these is Dr. Lynne Quarmby, a cell biologist who’s passionate about explaining her work to people outside of the scientific community. She writes a regular column, a ‘nexus of mystery, art, literature, beauty and science,’ for the online literary magazine Numéro Cinq.

If we can recognize and acknowledge that our direct biological senses, as wonderful as they are, give us only a tightly pinched and cloudy view of the world, then we open ourselves to unimagined beauty.

Lynne Quarmby, Numero Cinq, 2011³

Biologists often label themselves according to the ‘model organism’ that they work on. I was a zebrafish person, and Quarmby is a Chlamydomonas person. Chlamydomonas is not an STD (you’re thinking of Chlamydia), but a gentle single-celled algae that is in all likelihood swimming around the standing water in your garden as you read. This microscopic creature is easy to grow in the lab (a jam jar on a sunny windowsill will do), its genome has been sequenced, and it is a surprisingly powerful tool for studying human disease.

Chlamydomonas was not an obvious choice for medical research, but the secret is in the cilia. Cilia are hair-thin appendages that wave around in a coordinated fashion to move their owner from A to B. But these algae don’t spend their whole lives swimming around. When they reproduce, their cilia are absorbed back into the cell body (scroll to the 4th video here). When conditions are stressful, the cilia simply drop off. Quarmby and her students studied Chlamydomonas mutants that hold on to their cilia, and discovered a family of proteins involved in the regulation of both cilia and cell division.

At the same time as Quarmby was studying the behaviour of cilia in Chlamydomonas, medical researchers were identifying genes that are mutated in humans. The same proteins involved in cilia and cell cycle control in Chlamydomonas were affected in some patients with polycystic kidney disease. What’s the connection? Cell biologists knew that most of our cells have cilia on them, but assumed that they were not important. Our cells generally do not swim around, unless they’re sperm. It turns out that these tiny appendages are involved in a whole range of vital cell functions. The cilia on kidney cells are important for sensing the flow of urine, and without these the kidney cannot function properly.

Perhaps beauty is in the eye of the beholder when it comes to unicellular flagellates, but what I appreciate is the detail. To see the minutiae of cell structure is stunning, particularly when you know how difficult it is to achieve images like the ones in this article in the journal Cytoskeleton, or even the image of an adult rat head, below. And little Chlamydomonas, a microscopic pond dweller, has advanced our understanding of a devastating human disease. This combination of aesthetic experience and elegant scientific explanation is what I find beautiful. ⁴

Adult rat head MRI © Gavin Merrifield, University of Edinburgh.

It appears to be a universal experience for scientists to find beauty in their experimental systems. Perhaps this is because the daily discipline of examining anything in detail brings an appreciation of its finer points. Or maybe the process of choosing something to study and then spending the greater part of one’s waking hours staring at it provokes something akin to the loyalty of the mother who thinks her child is beautiful, despite the large pimple on its nose. But even bearing in mind the fascination and devotion of the true professional, there seems to be something more in the scientist’s experience of beauty.⁵ Most, I think, simply delight in the beauty of creation. For some, this gives a sense of the transcendent: a sort of natural spirituality. For a Christian, this encounter with beauty draws them nearer to God.

Christian Appreciation of Beauty in Science

One of the driving forces behind the work of many of the early scientists was their Christian faith. The astronomer Johannes Kepler (1571-1630) initially hoped to pursue theology, but was eventually satisfied that science was also a way to glorify God.⁶ Many others, including the famous naturalist John Ray (1627-1705), were ordained clergy in addition to their academic studies, so their science and theology were naturally interwoven. Others, like James Clark Maxwell (1831-1879), examined Christianity as rigorously as their scientific experiments.

These pioneering scientists (or ‘natural philosophers’, as they called themselves back then) were encouraged by a rich tradition of theology that wholeheartedly encouraged their exploration of creation. The Hebrew Scriptures tell how creation reveals the glory, generosity and faithfulness of God who created and sustains everything.⁷ The beauty of the land and everything in it is celebrated: mountains and trees, plants and animals, men and women.⁸ A number of the earliest Christian theologians, the Church Fathers, often expressed their delight in the details of animal and plant life, and what we now understand as ecosystems.

Diversity of beauty in sky and earth and sea…the dark shades of woods, the colour and fragrance of flowers; the countless different species of living creatures of all shapes and sizes…the mighty spectacle of the sea itself, putting on its changing colours like different garments, now green, with all the many varied shades, now purple, now blue.

Augustine, The City of God

Theologian Jame Schaefer has surveyed the writings of many of the Church Fathers and Medieval theologians, and found five broad themes in their contemplation of creation.⁹

• Affective appreciation: Simply delighting in what is seen.
• Affective-cognitive appreciation: A deeper, scientific study of creation leads to even greater joy for the beholder.
• Cognitive appreciation: Thinking in more abstract ways about the beauty of the interconnected universe. Each part plays its unique role for the greater good of the whole.
• Incomprehensibility: Being overwhelmed by the magnitude and complexity of the universe and everything in it.
• The sacramental quality of the physical world: The world God has created mediates something of God’s presence and character to us.

One of my favourites among the theologians covered in Schaefer’s work was an unnamed Cistercian who in the twelfth century wrote extensively about the grounds of the abbey in which he lived, and the surrounding countryside. He was obviously very happy with his vocation, and had a good understanding of the interconnectedness of the different factors: water, weather and crops - an early ecology. Basil of Caesarea (ca. 329-379) spent time observing animals and plants, noting similarities and differences, and encouraged others to do the same, giving glory to God for everything he saw. Hugh of Saint Victor (1096-1144) delighted in what his senses could tell him about creation, so enabling him to praise the Creator all the more, and lamented that others might pass such an opportunity by.

An important Medieval figure in the early development of science is Albert the Great (ca. 1200-1280), teacher of Aquinas, who wrote on “the importance of observation and experimentation in field and laboratory studies of animals, plants, metals, and inorganic elements”. He carried out field studies, and “legitimised the study of the natural world as a science within the Christian tradition.” For him, appreciation of creation had both cognitive and emotional aspects.

For all of these early scholars, to study creation and enjoy its beauty was an activity that everyone should engage in using their God-given intellect. Their detailed exploration of the wonders of the universe was fuelled by faith in a benevolent creator God, and this deep intellectual study led to heartfelt praise for the one who made it. Is this something we can share?

Protein structure model © Dr Neville Cobbe

The series continues tomorrow with Part 2: Understanding Beauty in Science.

Notes

1. Bersanelli, M. & Gargantini, M. Galileo to Gell-Mann: The Wonder that Inspired the Greatest Scientists of all Time. Templeton Press, Philadelphia, 2009. Page 9.
2.Ibid., Page 10.
3. I should highlight that as far as I know Lynn Quarmby is not religious and has not in any way endorsed this blog.
4. Further reading: http://quarmby.ca/, http://blog.quarmby.ca/, http://www.ncbi.nlm.nih.gov/pubmed?term=Lynne%20Quarmby, http://www.ciliopathyalliance.org/
5. I try to avoid using the words ‘nature’ or ‘the natural world’ as much as possible because of the ambiguity of the word nature, which is often wrongly used to create a divide between natural and supernatural worlds. This is ancient Greek philosophy and has nothing to do with the God of the Bible. When addressing Christians I usually use the word ‘creation’ in its traditional theological sense, meaning ‘everything that exists apart from God’, without connection to any one particular interpretation of Genesis 1-3.
6. Frankenberry, N.K. The Faith of Scientists, Princeton University Press, 2008.
7. For example, Psalm 29, 104, 148; Job 38-41; Joel 2: 18-32, Isaiah 41:17-20, Hosea 14:5-8.
8. Young’s Analytical Concordance to the Holy Bible.
9. Schaefer, J. Appreciating the Beauty of the Earth, Theological Studies 62 (2001), p23-52 & Schaefer, J. Theological Foundations for Environmental Ethics: Reconstructing Patristic & Medieval Concepts, Georgetown University Press, Washington, DC, 2009.

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.

“The heavens,” wrote the psalmist “declare the glory of God.” (Ps 19:1 NIV)

The universe that inspired the psalmist three thousand years ago grows grander as each new generation of astronomers adds yet another layer of understanding. Each new discovery pushes back the boundary that separates the known universe from the vast terra incognita that beckons and teases us to keep going, to sail ever further from familiar shores.

A few centuries ago the great philosopher Immanuel Kant repeated the psalmist’s declaration: “Two things fill the mind with ever new and increasing admiration and awe, the more often and steady reflection is occupied with them: the starry heaven above me and the moral law within me. Neither of them need I seek and merely suspect as if shrouded in obscurity or rapture beyond my own horizon; I see them before me and connect them immediately with my existence."

The night sky still beckons us, as it once did the psalmist. I spend time each summer at a rustic family cottage in the wilderness of my native New Brunswick, Canada. There, miles from electricity, the night sky does not compete with artificial light. Smog does not obscure it. Planes do not draw white trails on it. It does not compete with cable television or even cell phones, silenced by the absence of signals. The night sky is simply there, quietly declaring the glory of God. Its many lights reflect off the ripples of the lake, and are accompanied by the rustling of leaves and the voices of the many creatures that call this wilderness home. Only a jaded soul could sit by that lake and not wonder if there wasn’t some larger meaning to the experience.

I can see what the psalmist saw and rejoice as he did. But I watch the night sky through the eyes of a twenty-first century scientist. I have the benefit of centuries of scientific advancement and can see, in my mind’s eye, so much more. Those visible stars are just the advance guard of an almost infinite army of stars going back almost forever. The stars are not attached to a dome that one might reach with an ambitiously tall tower or puncture with a long-range missile. They are so far away that their light has been traveling at unimaginable speed for years, centuries, milennia and longer. The light from the stars in the Hyades Cluster began its journey to the earth at about the time that my ancestors—Loyalists from Pennsylvania—began their journey to this part of North America in the eighteenth century. The light from the closest stars, the trio that make up Alpha Centauri, takes over four years to reach earth. The most distant star ever detected from the earth is a “gamma ray burster” that launched its signal almost 13 billion years ago, when the universe was young. The powerful gamma ray signal from this star began its journey before our planet was even formed, reaching the earth in April 2009.

The psalmist did not know that the stars were made of hydrogen and helium. He did not know they generated their energy through nuclear fusion or that many of them explode at the end of their lives. He knew nothing of galaxies and the layers of structure in the cosmos. He did not understand how fast light travels or that the light from our sun powers photosynthesis and many other processes here on the earth.

The universe brought into view by science is like a collection of Russian matryoshka dolls nestled one inside the other. With the psalmist we can see the outer layer—and it is grand. But inside are additional layers, each one with a new type of grandeur. And at the very end of the unpacking lie the remarkable laws of physics that keep the earth orbiting about the sun, the sun shining reliably, and the sunlight providing energy to sustain life on our planet.

The universe as we understand it today inspires awe. And for those open to its message—from the psalmists of yesteryear to the believers and even the thoughtful skeptics of today—it speaks of a Creator. Our universe does not look like a cosmic accident, where lots of stuff just happened. It looks like the expression of a grand plan—a cosmic architecture capable of both supporting life such as ours and of inspiring observers like us to seek out the Creator.

This is why Antony Flew—“world’s most notorious atheist”—changed his mind and started believing in God.

Despite a common desire among Christians to find evidence for the activity of the creator God in the natural world, the Scriptures themselves more often give us images and analogies of God’s providence rather than “proof” that would be admissible in peer reviewed journals, much less in court. In his final climactic week in Jerusalem, Jesus used image after image, parable after parable to convey the urgency of his message that the Kingdom of God was coming to pass through his own coming Passion.

Though His disciples did not understand them at first, it was by new pictures (the lost coin, lost sheep and lost sons) and reinterpreted old ones (like the vineyard), that they came to understand the “facts” of His healing miracles and, ultimately, His death and resurrection. By reframing concrete happenings and material relationships, stories and images opened up possibilities rather than limiting them—and they still invite us to enter into them, rather than leaving us dispassionate and disconnected.

As we remember the narrative that takes us from Good Friday through Easter morning, the image of a buried grain of wheat invites us into the story rather than just describing what happens in it. Certainly this is an image for Christ Himself, but as I’ve written elsewhere, the seed isn’t just a symbol of His death and rebirth from the grave, but a promise of future abundance, lavish reproduction, and a pointer to the coming harvest: Jesus Himself is the “first fruits” of the new creation. We are called not only to be workers for that harvest, but to be, like Him, the harvested grains. As Christ entered into His glory through self-sacrifice, so we, too, give ourselves in order to share in and contribute to the shalom—the comprehensive flourishing—promised as the marker of God’s Kingdom now and in the future.

This combined image of death and renewal, single seed to field, is the heart of John Crumb’s hymn “Now the Green Blade Rises,” first published in 1928 in the Oxford Book of Carols and originally set to an old French Christmas carol (“Noel Nouvelet”). By clicking the image above you can hear a new version as revised and re-arranged by contemporary hymnist Alex Mejias. We offer it as a meditation on the sacrifice and victory of Jesus, the glorious promise of resurrection, and the call upon us all to join in God’s story of redemption and renewal.

“Now the Green Blade Riseth”

John MacLeod Campbell Crum (1872-1958),
© Oxford University Press
adapted and arranged by Alex Mejias

Now the green blade riseth from the buried grain,
Wheat that in dark earth many days has lain.
Love lives again, that with the dead has been:
Love is come again, like wheat that springeth green.

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. More details on these projects and music may be found at High Street Hymns.

My curiosity immediately led me to see what he had cut out. All of the miracles and the Resurrection passages were gone, and the Gospels were rearranged in a linear fashion, edited and pasted together as a single narrative. Then I looked particularly to see what Jefferson did with John 11.

Why John 11? For the past several seasons of Lent, I have been meditating upon this account of three siblings: Martha, Mary and Lazarus of Bethany. In particular, John 11:35 has become a central passage for me to consider in self-reflection, because an artist learns very early that creativity demands boundaries and limits to thrive. When I began on my recent journey to illuminate the Four Holy Gospels for Crossway publishing's celebration of the 400th anniversary of the King James Bible, I needed to find a thematic boundary. I was so overwhelmed with the grand scale of the project that I chose this shortest passage in the Bible—“Jesus Wept”—and that decision has led to many discoveries along the way.

"Jesus Wept" is, to me, the most profound passage in the Bible. After I gave a recent lecture on this verse at Duke University, Richard Hays commented on my reflections: "The Incarnate Word of God stood wordless at Bethany." Indeed, Jesus' tears make no logical sense, as he came to Bethany with the specific mission to raise Lazarus from the grave. He told the disciples his mission (and why he intentionally delayed his arrival, knowing that Lazarus lay dying) and revealed to Martha that he was and is the "Resurrection and the Life." So why did he, upon seeing the tears of Mary, waste his time weeping, when he could have shown his power as the Son of God by wiping away every tear, telling people like her, "Ye of little faith, believe in me!"?

In my reflections, this "irrational," emotional response from Jesus became a central means to understand the role and even the necessity of art in the midst of suffering—what I have began to call our "Ground Zero" conditions. Art, like the tears of Christ, may seem useless, ephemeral and ultimately wasteful. But even though they evaporate into our atmosphere, the extravagant tears of God dropped on the hardened, dry soils of Bethany, or onto the ashes of our Ground Zero conditions, are still present with us. Because tears are ephemeral, they can be enduring and even permanent, as with “Jesus wept.” In the same way, perhaps our art can be so as well. What seems, at first, to be an irrational response to suffering may turn out, upon deep reflection, to be the most rational response of all.

Predictably, "Jesus Wept" did not make into the Jefferson Bible. John 11 was cut out entirely, falling onto the floor of his Monticello home and discarded, along with Martha's confession. Jefferson's rationalism allowed only a distant deity that made sense in reference to objective ‘scientific’ calibrations, not ephemeral marks of compassion. Yet, when this attitude is actually applied to the sciences, they also become, like Jefferson's Bible, a “cut and paste” product, based on a limited viewpoint.

Even with my rudimentary understanding of the early phonetic and acoustic research my father was part of at Bell Labs in the 1970s, I know that the optimism of many scientists there was based on reductionistic assumptions. I described my father’s wrestling with the basic theses of linguistic research in a previous essay:

In the 1980s, [while in his] early 50’s, my father began to send a series of notes to his colleagues questioning the basic tenets of acoustics research, as he found them flawed and inadequate for the goals pursued. . . .[W]hat the early research assumed was that by segmenting speech patterns, you could have enough data to rebuild speech. It would be a bit like dissecting a frog, and stitching it back together, only to expect it to jump again -- A typical reductionist/modernist assumption. (Refractions 24: "The Resonance of Being")

My father began to challenge these underlying but over-simplified assumptions and as a result, came under criticism for abandoning many of the positions held by his peers. I continue:

My father’s Converter/Distributor theory (C/ D theory) assumes that computer technology is now capable of anticipating contextual patterns of speech, and is able to simulate an architectural structure to account for the morphing of speech production. Rather than the segmental approach, he calls his new thinking prosodic, as it accounts for the complexity of speech and language. But it would take years of research to get to a point of presenting his new ideas to the linguistics/phonetics community.

My father, who had rarely had problems finding support for his research before, was in for a battle. . . . He could not find funding, and found himself fighting the establishment of the research world—the very establishment he had helped to build. After my father’s many futile attempts to secure funding for his new research, my brother, a successful entrepreneur in Silicon Valley, stepped in to fund a post for a graduate student at Ohio State, to help my father compile enough data to be able to begin his research.

To my father, the integrity of the scientific process demanded such a course. He never considered that his challenge to reductionism would be seen as a threat by many of his colleagues. He simply was seeking after Truth.

Even in the objective rigor of the research process, then, human factors intervene—sometimes for better, sometimes for worse. Our presuppositions surface eventually, and it becomes clear where we place our "faith. " My father's C/D theory is an intuitive leap, arising from his love for synthesis and beauty, but pulled up by hard data and a stubborn commitment to the truth of matter. It is an example of the way intuitive, subjective insight can connect the ephemeral with the rational, objective and concrete. Should we seek, then, to make the sciences a Jeffersonian cut-and-paste re-narration of our reality? Are we so inflexible in how we will understand the great mystery of our being? If so, the gap between that reduced ‘reality’ and what is truly human is the very gap into which Jesus' tears still fall.

Jesus wept for Lazarus, but also, perhaps, for Jefferson as he snipped out John 11 with his own hands; for to dismiss Jesus’ tears as irrational and unnecessary is to miss Jesus entirely. Jefferson sought to cut out the Deity, but also lost the Man. Without Jesus' full humanity, coupled with his Divinity, we do not have a Savior. Without this fullness of humanity—concrete and ephemeral, intuitive and objective—we lose perspective on why we are doing our research to begin with. If we assent to the fragmenting, segmental assumptions of modernity, we will have stitched the frog back together only to bury him anyway. If the dead are to live, we will require a Miracle Worker to show us that the world that is cohesive, and rational, but only when seen through a veil of tears.

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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When astrophysicist Dr. Jennifer Wiseman first published the following posts as a paper in the BioLogos Scholarly Essay series, the essay’s subtitle asked the question, “Can Recent Scientific Discovery Inform and Inspire Our Worship and Service?” Over the next few weeks, we will look at Dr. Wiseman's answer to that query—an emphatic “Yes!”. But in this first installment we begin by describing some of the reasons such a posture of worship through science is not more common in the contemporary church than it already is.

Oh Lord My God, when I in awesome wonder, Consider all the worlds Thy hands have made; I see the stars, I hear the rolling thunder, Thy power throughout the universe displayed.
Then sings my soul, my Savior God, to Thee; How great Thou art, how great Thou art

(Carl Boberg, 1885; Trans. Stuart Hine 1949)

The words of this great hymn convey the proper overwhelming sense in which the wondrous Creation of God should translate directly into a response of awe and praise from mind, body, and spirit. The writer sees and hears the wonders of nature with his body, considers with his mind what all this implies, and responds with songs from his soul.

But is this worshipful response happening in our Christian congregations today? I believe this kind of response to the Creation can and should happen within the hearts of God’s people and wherever congregations of believers are gathered. Such power can even unify believers who differ on lesser matters as we all look up outside of ourselves at the same wonders and respond with the same praise. As an astronomer, I have felt the sense of being “blown away” by seeing images of countless distant galaxies, or even by just looking up at the array of stars overhead on a dark moonless night and sensing something of the “big-ness” of God.

There are impediments to realizing the fullness of this kind of worship experience for many Christian congregations today. I believe four of the main culprits are ignorance, distraction, controversy, and uncertainty.

Let me start with the first, and clarify up front that by ignorance I am simply referring to being uninformed, rather than the sometimes more negative connotations of the word. How up-to-date is the scientific knowledge of average, educated, committed evangelical church members and pastors?Americans, both adults and schoolchildren, are not ranking favorably compared to the rest of the world’s developed nations in science knowledge these days. We enjoy our technological achievements and resulting gadgets, but true comprehension of scientific principles and recent discoveries is not a strong part of our culture and national conversation these days.

This is reflected directly in what kinds of things are (and are not) discussed in church. In my own generally very good church experience growing up in mainstream America, I can only remember science and nature being discussed in a general way (e.g., we should look at the beauty of flowers and mountains and animals and thank God), except for once in a specific way in a children’s sermon (where we were told we should not believe we came from monkeys!). That was a while ago, but how are science issues handled today? Do pastors speak about the evidence from cosmic background light for a spectacular beginning to the universe? Are the genetic codes being mapped out for animals and humans resulting in praise for God’s amazing “blueprint”? Are the advancements in nanotechnology and biotechnology and medicine subjects for discussion of good and poor uses of technology in church? The answer to these is, of course, “no”, for the most part, yet even issues seemingly more relevant to the daily lives of parishioners are often driven by current technology and scientific advancement, and an informed congregation can better understand how to praise, pray, discern, dialogue, and serve.

Related to being uninformed is the condition of distraction for many evangelical Christians today. The distractions of overloaded schedules, pressured jobs, divided families, and even church environments of entertainment-based worship and activities can impede a lifetime of quiet listening, learning, and contemplation. If there is no encouragement from church leaders to learn and incorporate nature and current scientific discovery into contemplation and praise and service, then there will be no space available in the lives and activities of congregants for what should be the resulting awe and praise.

But what does it mean to be informed about science in today’s evangelical congregations? Too often this has implied a direct relation to controversy, the third reason science is not often inspiring worship these days. There are many voices trying to “inform” Christians about science, and for the average evangelical congregant, discernment about which authority figure to believe can be difficult. Many times Christians are presented with a clear and strong implication that scientific conclusions, especially on issues related to origins of the universe and of life, are part of the secular “World” camp rather than the camp of “God’s Truth”. And Christians “know” that they must be on one side or the other of this stark line of worldliness. Often in more conservative churches a teaching will come from the pulpit that goes something like this: “Scientists tell us that *...+, but they cannot give a reason how *...+ happened; but WE know how: God is responsible!” Therefore any serious consideration of a scientific understanding of the development of the universe and life implies that one is “compromising” the teaching of the Word of God, rather than studying the details of how God works. In Scripture, however, never is the study and experience of nature seen as somehow antithetical to knowing and following the Lord; just the opposite in fact!

This often boils down to the correct interpretation of Scripture. Through sermons, radio spots, television shows, and literature, evangelical Christians are hearing adamant messages conflating the acceptance of modern scientific discovery with worldly compromise, or else providing alternative ideas that are not entirely satisfying. From Young-Earth Creationists, they hear that a literal reading of the Biblical creation account is the only correct one, so all scientific discovery must be reinterpreted to fit a recent Creation. But this robs them of the sense of awe we glean from the magnitude of space and time revealed by astronomy, geology, and fossils. From the Intelligent Design community, they hear the message that life (and perhaps the entire universe) is too complicated to develop through natural processes alone, and therefore that God’s work requires miraculous inputs of information into the natural world. This implies that somehow natural processes must not be fully God’s processes, or that God’s work through them is somehow inadequate. They also hear the message to “teach the controversy,” so that somehow by proclaiming that there is a controversy about natural processes as an adequate explanatory tool for natural history, the controversy will in fact become real. They are then surprised to find out from either advanced scientific study or from the Evolutionary Creation voices that in fact there is no great controversy in the scientific community about the basic structure and timeline of the natural history of the universe and life; that in fact there need be no theological debate about how God brought (and is bringing) the universe and life into being, rather, the issue is whether God is in fact real and responsible for all we know and are. And yet even this unifying message can sometimes seem to gloss over the central theological issues of suffering and death and fallen-ness in Creation. So every approach to origins and evolution evokes some difficulties and challenges with which the Christian congregant must grapple.

Next week, Part 2 concludes Dr. Wiseman's discussion of the stumbling blocks that can stand between the church and its appreciation of science as a means of worship, and turns to the ways that the pursuit of God through study of the created world can help overcome those difficulties by pointing us directly to the Lord.