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

What you can expect

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

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

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

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

How you can help

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

Getting started

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

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

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

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

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

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

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

Notes

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

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

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

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

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

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

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

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

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

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

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

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

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

In concordist interpretations, God made the earth using the sequence of events described in Genesis 1. In non-concordist interpretations, God created the earth using a different timing and order of events than those described Genesis 1.

How should Christians go about choosing among all of these interpretations? Such a decision should be based on consistent principles and prayerful reflection, not just on “what sounds good.” Here are our own conclusions.

Weaknesses in Concordist and Non-Concordist Interpretations

Both concordist and non-concordist interpretations of Genesis 1 arise from good motives, a desire to show that the Bible does not conflict with nature’s testimony.  But both types of interpretations have their pitfalls.

For concordists, the temptation is to interpret every Bible verse to match the current scientific picture. The meanings of particular phrases can be bent out of shape to match a particular scientific finding. For example, Hebrew words that literally meant birds or plants to the original audience are redefined to meet some modern scientific category such as insects or single-celled organisms, just to make the order of events line up. By focusing on trying to match the details of the ancient text to twenty-first century knowledge, the concordist may miss meanings in the passage that were clear in the original cultural context, including important spiritual insights. Moreover, concordists can be forced to regularly change and update their interpretations as modern scientific knowledge grows and changes. For instance, the Gap Interpretation twisted the meaning of Genesis 1:2 outside its original intent; later it failed to match new scientific evidence.

For non-concordists the temptation is to interpret every Bible verse that appears to disagree with science as figurative without first studying the text. By interpreting a text that was intended tobe understood literally as metaphoric, they may bend the meanings of particular phrases to refer to purely spiritual ideas and ignore the historical meanings they had in the original cultural context. At one extreme non-concordists can apply the same strategy to all Bible passages and even interpret Jesus’ miracles and resurrection as spiritual symbols simply because they think that miracles are scientifically impossible.

For both concordists and non-concordists the temptation is to let science drive the interpretation of Scripture more than it should. When an apparent conflict arises between science and a biblical text, it can and should motivate us to consider a biblical passage more closely. The scientifically discerned testimony from God’s book of nature can even be a useful tool for deciding between two or more biblical interpretations that are otherwise equally valid. But the interpretations themselves are not determined by science; they must be driven by theological considerationsand be consistent with the rest of Scripture.

To avoid these risks we need to look at what the best biblical scholarship has to say about the passage rather than at how it fitswith science. Finally, we must take care that the desire to resolve conflicts does not distract us from the main message God has forus in the text. Our primary calling as Christians is to live our lives according to the clear messages of God’s Word; it is a lesser calling to debate the subtleties of interpretation of less clear passages.

Genesis 1 in Its Original Context

To choose among the various interpretations, we recommend using a consistent approach based on the principles of biblical interpretation discussed in chapter 4.  The first principle, that each passage should be interpreted in light of the rest of the Bible, provides some guidance. For instance, the Bible’s teaching on God’s truthfulness and his glory displayed in creation might lead us away from the Appearance of Age Interpretation.  The differences between the Genesis 1 and Genesis 2 accounts might point toward a non-concordist interpretation.

The second principle of interpretation gives more direction. It reminds us first to work out what the passage meant in its original literary, cultural, and historical context, and then figure out what meaning it has for us today. How do the various interpretations fit this principle? Of the four concordist interpretations discussed in chapter 5, the Young Earth Interpretation seems to come closest to what ancient peoples would have heard in the text. The Gap and Day-Age concordist views would have baffled the original audience, since these ancients would have had no concept of geological ages; if they could not fathom time periods of millions or billions of years, the text must have meant something different to them.

Of the four non-concordist interpretations of Genesis discussed in this chapter, the Proclamation Day Interpretation, while it has some basis in the text, seems least likely to be the meaning heard by the original audience. The proclamations are implemented as soon as God says them, and there is no reference to a different timing or sequence of events in terrestrial time. In our view a combination of the Ancient Near East Cosmology, Kingdom and Covenant, and Creation Poem Interpretations come closest to what the original audience would have heard. The differences between the Genesis text and the pagan stories highlight the sovereignty of God and the goodness of creation. The elegant poetic structure and inspired phrases reinforce the theological messages of the Kingdom and Temple interpretations.

Genesis 1 for Modern Readers

With a better understanding of what the original audience heard,we have insight into God’s message for them and thus for us. If God’s purposes in Genesis 1 did not include teaching scientific facts to the Israelites, then we should not look here for scientific information about the age or development of the world. For modern readers, as for the original audience, the message of Genesis 1 is its powerful theological truths. God does not use theBible to teach us the physical processes he uses to make the rainfall or the earth orbit the sun or to form the mountains. Instead, in a beautifully crafted and impressively short text, God teaches us all about

• his sovereignty.
• the goodness of creation.
• the honored status of humankind as his image bearers.

God has given us a text that speaks of the physical world in simple terms, based on how it appears, in order that all peoplemight understand it.  The common language of this text has made it accessible to people of many times and cultures, aiding the communication ofthe gospel around the world.

Does a non-concordist interpretation of Genesis 1 mean that we have sacrificed a literal understanding of the gospel? No. TheGospels were surely heard by their first audience as historical eyewitness accounts by the disciples, and everything about the emphasis and tone in those books indicates that Jesus’ resurrection and miracles are essential events in the story. That is how we should read the Gospel stories still today. In Genesis 1, on theother hand, the first listeners heard nothing new about the physical universe; all the emphasis was on who created the world and humanity and why they were created.

What does this mean for science? It means that Genesis 1 is not a science textbook. The text was never intended to teach scientificinformation about the structure, age, or natural history of the world. Thus, comparing Genesis 1 to modern science is likecomparing apples to oranges. Or perhaps more accurately, comparing Genesis 1 to modern science is like comparing Psalm 93:1 (“The world is firmly established; it cannot be moved”) to modern astronomy. Genesis is neither in agreement nor in conflict with the sequence of events found by astronomy and geology.

As scientific knowledge increases and changes over the centuries, its understanding of the physical structure and historyof the earth will change. But through all of those centuries the theological truths of Genesis 1 remain the same: there is one sovereign God who makes light from darkness, creates an ordered world from chaos, and fills an empty world with good creatures. Humans need not fear the capricious whims of a pantheon ofgods but can instead trust in the one true God who made us in his image and declares us “very good.”

For more discussion of Biblical interpretation, see chapters 4, 5, and 6 of Origins. Next week, we'll look at an excerpt on astronomy and the age of the universe.

Excerpt from Chapters 5 and 6 of Origins: Christian Perspectives on Creation, Evolution, and Intelligent Design (Grand Rapids, MI: Faith Alive Christian Resources), 2011. Reprinted with permission. To order purchase a copy of the book or e-book, please call 1-800-333-8300 or visit our website www.faithaliveresources.org.

Want a free copy of Origins?  For a limited time, donations of $50 or more will receive a  copy of the book! Plus, from now through April, your gift will be doubled thanks to a matching grant from a generous donor. You can learn more here.

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.

In this video Conversation, Denis Alexander addresses two prominent barriers for Christians to accept evolutionary creation. The first is Biblical interpretation. When contemporary Christians interpret the early chapters of Genesis literally, they do so out of a desire to take the text seriously. Yet the early church fathers saw these chapters as figurative—and that figurative interpretation did not lesson the important foundational truths taught in these passages. The contemporary literal reading is actually a modern approach to the text in that our scientific mindset inappropriately shapes the interpretation. Since science did not even exist at the time that Genesis was written, an overly literal interpretation can actually cause us to miss the inspired message that the Biblical authors were communicating.

The second barrier is the rhetoric of the New Atheists, who claim that it is impossible to accept evolution while still believing in God. Christians should challenge this. Traditional Christian views are not in conflict with modern science. Instead, they see nature as God's work, with St. Augustine writing that "nature is what God does." As humanity develops a scientific understanding of nature, we will only learn more about the handiwork of God. 

Genesis 8:1: But God remembered Noah and all the wild animals and all the domestic animals that were with him in the ark. And God made a wind blow over the earth, and the waters subsided; 2 the fountains of the deep and the windows of the heavens were closed, the rain from the heavens was restrained, 3 and the waters gradually receded from the earth.

The Flood narrative of Genesis 7-9 has played a prominent role in science and religion debates for over three hundred years and gave rise in earlier centuries to geological theories such as old earth catastrophism. While literary studies have uncovered the chiastic structure of the Flood story (see Gordon Wenham, “The Coherence of the Flood Narrative” Vetus Testamentum 28 (1978):336-48) and with it the theological pivot point of the entire narrative (Gen. 8:1 – “And God remembered Noah…), much of the popular attention remains on the questions regarding details (Is there THAT much water in the world to cover ALL the mountains to a depth of 15 cubits? Could you really fit two or seven of every animal species in an ark that size?)

Looking at a smaller matter, we find at the beginning and the middle of the narrative indications of an ancient Near Eastern worldview. As the story is told, the flood was not merely the result of excessive rain, but actually the convergence of the waters above the earth with the waters below the earth. It is, as one translation puts it, as if the sluice gates at the deep and of the heavens were thrown open and water poured in from above and below. This is a consistent picture from the Old Testament of a three-tiered universe—a dome above the earth holding back the heavenly waters, a flat earth with water on its surface, and water under an earth which is held up by pillars.

That the story is told using the cosmology of its time should not be unduly unsettling, nor that the story is reinterpreted as new understandings of the universe come into favor. By way of example, consider John Calvin and his understanding of the structure of the universe. Although committed to the principle of sola Scriptura, Calvin recognized that the Bible would have been written in terms its original recipients would have understood.

Calvin inherited the medieval cosmology of his time, a way of viewing the world heavily influenced by Greek thought and one which was about to receive shocks from astronomers such as Copernicus and Galileo. But not just yet. Calvin still subscribed to the common conception of his day in which the four elements—earth, air, fire, and water—comprised the earthly sphere and possessed unique characteristics. The nature of air and fire was to rise, while the nature of earth and water is to sink. Earth, being heavier than water, should sink to the center of the cosmos and water should compose the next layer. Both earth and water are spherical, i.e., naturally form spherically around the cosmic center. Thus the heavier spherical element of earth should be encased entirely within the lighter spherical element of water.

Notice what this does to the flood story. For Calvin, the amazing thing is that the world isn’t constantly under water and subject to flooding. In the cosmology of Calvin’s day, it does not take an act of God to cause a universal flood, but rather an actively present and restraining hand of God to keep the waters back in everyday circumstances and make inundation by water something other than universal.

Obviously, Calvin was wrong. Or perhaps we should say that medieval cosmology was flawed and justifiably gave way to new conceptions of the universe. The answer is not to return to an ancient Near Eastern cosmology, but to reinterpret cautiously within new and better cosmologies and to pay closest attention to the text and the theology of scripture.

The geological and planetary sciences bring their own unique contributions and are of more interest than the latest expedition to discover the ark on Mt. Ararat. Is the flood story a universalization of a catastrophic regional event that burned itself into the psyche of ancient cultures in the Mediterranean basin? Various theories regarding a Black Sea venue for a catastrophic flood event are still in process of being sorted out. It’s intriguing. Or the question where the water on Planet Earth comes from? Was it always here as an emanation of vapors from the earth’s crust in its early formation, or has it accumulated over eons through the steady bombardment of earth by small, icy comets? It’s an intriguing scientific question that is in the midst of determination through testing.

Preaching Suggestions

When preaching on the story of the Flood, it is easy to get lost in the debates over particulars. As mentioned elsewhere, to tackle all the peripheral issues threatens to turn a sermon into a geology lecture. Other settings are better suited to addressing those questions, and those are best addressed open-endedly.

A brief explanation of ancient Near Eastern cosmology can be helpful to contextualize the story. If there are those who are tempted to think that a cosmology embedded in the Bible must be inspired and definitive, one can note that cosmology has changed by the New Testament. The Bible itself isn’t wed to a particular structure of the universe.

What is important is to keep the theology of the text front and center, and in that theology there are at least three non-negotiables from the flood narrative. First, human sin and violence threatens to undo a good creation (the flood is a de-creation event, a return of the waters mentioned in Genesis 1:2). Second, God remembers Noah, and never forgets his promises. Third, the end of the flood is a covenant with the whole earth regarding the stability and endurance of the natural order.

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.

Augustine had a great deal to say about those chapters in Genesis that are especially controversial within Christianity today. In fact, Augustine dedicated about as much as any other Christian writer to the first few chapters of Genesis, so there is little guesswork we have to do in ascertaining what he believed Scripture to claim about creation. First of all, Augustine clearly rejected the notion that God had created the earth in six 24-hours periods. Instead, he believed that the universe was created instantaneously, and that the six days reported in Genesis were a metaphor for the various levels of dimensions of the created realm—something akin to what ancients referred to as the ‘Great Chain of Being’. But this is not to say that Augustine believed that the world was created as it is today in that instant. Rather, he affirmed that God created the world with inchoate potential for further development, like an acorn that will grow into a great tree when planted in the ground.

Augustine therefore affirmed that Creation has evolved and continues to evolve, though not driven by random natural processes, as affirmed by classical Darwinism. Instead, such evolution is governed providentially both via the inchoate potentialities present in the world from its beginning and by God’s ongoing governance of the universe.⁴ We should be careful not to turn Augustine too quickly into a modern advocate of theistic evolution, but the similarities are nevertheless significant. Augustine affirmed these ideas not on the basis of an attempt to accommodate Scripture to scientific discovery, but based upon his own reading of Scripture! Indeed, I think it fair to say that the great father of Western Christianity was something of a proto-evolutionary theist, and therefore one whose work deserves far more attention by those seeking to be faithful to both Scripture and Christian tradition while making sense of the claims of contemporary science.

Of course, we need to be careful not to push such claims too far. Augustine himself resists such a move by recognizing both the contingency of human interpretations of Scripture and the dangers of unintentionally imposing our own views on Scripture. A rather long, but significant quote from Augustine makes this point all too clear:

Let us suppose that in explaining the words, “And God said, ‘Let there be light,’ and light was made,” one man thinks that it was material light that was made, and another that it was spiritual. As to the actual existence of “spiritual light” in a spiritual creature, our faith leaves no doubt; as to the existence of material light, celestial or supercelestial, even existing before the heavens, a light which could have been followed by night, there will be nothing in such a supposition contrary to the faith until unerring truth gives the lie to it. And if that should happen, this teaching was never in Holy Scripture but was an opinion proposed by man in his ignorance.

On the other hand, if reason should prove that this opinion is unquestionably true, it will still be uncertain whether this sense was intended by the sacred writer when he used the words quoted above, or whether he meant something else no less true. And if the general drift of the passage shows that the sacred writer did not intend this teaching, the other, which he did intend, will not thereby be false; indeed, it will be true and more worth knowing. On the other hand, if the tenor of the words of Scripture does not militate against our taking this teaching as the mind of the writer, we shall still have to enquire whether he could not have meant something else besides. And if we find that he could have meant something else also, it will not be clear which of the two meanings he intended. And there is no difficulty if he is thought to have wished both interpretations if both are supported by clear indications in the context.

Usually, even a non-Christian knows something about the earth, the heavens, and the other elements of this world, about the motion and orbit of the stars and even their size and relative positions, about the predictable eclipses of the sun and moon, the cycles of the years and the seasons, about the kinds of animals, shrubs, stones, and so forth, and this knowledge he holds to as being certain from reason and experience. Now, it is a disgraceful and dangerous thing for an infidel to hear a Christian, presumably giving the meaning of Holy Scripture, talking nonsense on these topics; and we should take all means to prevent such an embarrassing situation, in which people show up vast ignorance in a Christian and laugh it to scorn. The shame is not so much that an ignorant individual is derided, but that people outside the household of the faith think our sacred writers held such opinions, and, to the great loss of those for whose salvation we toil, the writers of our Scripture are criticized and rejected as unlearned men.

If they find a Christian mistaken in a field which they themselves know well and hear him maintaining his foolish opinions about our books, how are they going to believe those books in matters concerning the resurrection of the dead, the hope of eternal life, and the kingdom of heaven, when they think their pages are full of falsehoods on facts which they themselves have learnt from experience and the light of reason?

Reckless and incompetent expounders of holy Scripture bring untold trouble and sorrow on their wiser brethren when they are caught in one of their mischievous false opinions and are taken to task by those who are not bound by the authority of our sacred books. For then, to defend their utterly foolish and obviously untrue statements, they will try to call upon Holy Scripture for proof and even recite from memory many passages which they think support their position, although they understand neither what they say nor the things about which they make assertion.⁵

I am tempted here to let Augustine have the final word, but I think there are three final points worth highlighting here as a way of connecting this quote to the two books theory and thereby concluding our discussion of Augustine:

1. The Book of Nature is clearly revelatory of God’s providential work in Christ, and even nonbelievers are capable of comprehending its complex order through the proper use of reason and experience (i.e. science properly understood).
2. The Book of Scripture is clearly revelatory of God’s providential work in Christ, and therefore is true and authoritative in all matters. The problem is that we often misinterpret Scripture by imposing our own preconceptions upon it rather than allowing it to speak for itself.
3. God’s two books can and should be read together in harmony when we are open to allowing them to speak for themselves on their own terms. Ultimately, they cannot contradict each other because the source of both is the same God and if they seem to be in contradiction it is because we have misread one or both of them, and we need to be willing therefore to allow ourselves to be open to thinking about either one in different ways, trusting that God will ultimately lead us to see the truth of the whole.

Notes

4. In truth, these two kinds of providence are one and the same for Augustine because God in some ‘stands’ outside of time as its eternal creator. So, for Augustine, eternality is not everlasting time, but the complete lack of temporality altogether. In this sense, all of creation at all times is eternally present to God, and there is ultimately no difference between God’s governance over creation at its beginning from God’s governance at any other moment in its history. In a way, God governs all of history all at once.
5. This quote is excerpted from St. Augustine, The Literal Meaning of Genesis, 2 vols., translated and annotated by John Hammond Taylor, SJ (Paulist Press, 1982), volume one of which can be read here.

A careful study of this chapter is important because it gives us a beautiful picture of the proper relationships we should have with God, the natural world, and each other. Numerous posts could be written on each of these relationships, but in this post I’d like to focus on how Genesis 2 describes our relationship to the rest of creation. These relationships are given deeper significance when we recognize that the garden is being described as a temple-like “sacred space,” not just an ordinary garden. There are numerous clues in the passage that this is the case. John Walton writes that the Garden/temple parallels “are givens that are simply assumed by the author and audience” ¹ of Genesis, but we completely miss them if we take fail to read the text the way the ancient author and audience would have.

Temples and Gardens

In the Ancient Near East (ANE), all sacred space was conceived of as something like a temple; it was a place where humans would serve God and experience their closest access to Him. Thus in ANE cultures, a temple complex was seen as being the apex and a microcosm of creation and the earthly abode of the god(s). Descriptions of temples often pictured a river flowing from under the temple and flowing out through an adjacent garden, symbolizing the fertile extravagance of the divine provision. A temple garden would be no mere backyard vegetable patch, but rather an elaborate, beautifully landscaped botanical park.

The same temple/river picture can be seen in the description of the eschatological temple in Ezekiel (ch. 47) and Revelation (chs. 21-22, where the final temple is God Himself). Sound familiar? In Genesis 2 we also have a river flowing “from Eden [‘Abundance’] to water the garden” (v. 10).² Not only is the Garden filled with “every beautiful tree with edible fruit” (v. 9), but the area itself is rich with gold, resins, and gemstones (sometimes translated “bdellium and onyx”), the same materials later used to decorate Israel’s tabernacle, temple, and priestly garments. Furthermore, many scholars are convinced that the design of temple’s Menorah (candlestick) deliberately echoes the Garden’s Tree of Life, and some also think that the Ark of the Covenant in the temple parallels the Tree of the Knowledge of Good and Evil.³

Made for Sacred Service

As inhabitants of this temple-garden, it comes as no surprise that Adam and Eve enjoyed a special closeness to God’s presence (Gen. 3:8 pictures God taking an evening walk through the Garden). But as inhabitants of the Garden, they had special responsibilities as well; they were told “to farm it and take care of it” (v. 15). The two Hebrew words used here have a broader range of meaning than their English translations suggest. As John Walton writes, the broader meaning of the word here translated “to farm” (particularly when used in a sacred context) “is often connected to religious service deemed as worship (e.g., Ex. 3:12) or of priestly functionaries serving in the temple precinct (e.g., Num. 3:7-10).” ⁴

The usage in Genesis 2 seems to have two layers of meaning: “farm/cultivate the Garden” (since it is an agricultural space) and “serve/worship God” (since the Garden is also a sacred space). The dual meanings are as intertwined in Hebrew grammar as they are intended to be in practice. The second Hebrew word (translated “take care of”) has a deeper religious meaning as well. The word can refer to protecting farmland from external threats, but in a danger-free sacred space like the Garden, the word more generally refers to “performing duties on the [temple] grounds,” that is, to “sacred service.”⁵

Walton therefore translates these two Hebrew words as “serve and preserve.” These same words appear again together several times in Numbers to describe the priest’s duties in the temple. Because of all this, Gordon Wenham describes Adam as “perhaps…an archetypal Levite” with a “quasi-priestly” role in the garden.⁸ Eve was created as Adam’s companion and “helper” in his work, a word which nowhere in the OT refers to a subordinate assistant, but rather to one who is at least equal to the one being helped.⁹

Genesis 2 should banish from our minds any idea that creation care is somehow “secular” work for a Christian, or that it is not even our responsibility. This was the first task given to humanity, to serve and worship God by cultivating and protecting the natural world. The centrality of our responsibility in this regard is even clearer when we back up to the beginning of the chapter. We know there was a river “flow[ing] from Eden to water the garden” (v. 10), symbolizing that “all fertility emanates from the presence of God.” ¹⁰ Nonetheless there could be no cultivated plants in the garden because “there was still no human being to farm the fertile land” (v. 5). With no gardener and no rain, the ground was watered indiscriminately; a human was needed to irrigate the waters and support a garden.¹¹ Therefore, God “formed the human from the topsoil” (Hebrew wordplay equivalent to “human from the humus”) before planting the garden. God certainly could have watered it another way without needing us, but He chose not to, and the resulting collaborative picture here is a beautiful one. All provision flows from God, but He has chosen to give us an essential part in further channeling his provisions in the natural world. Far from countering God’s creative work by destroying nature, we are intended to work with Him to preserve and further it.

Of course, though created primarily to glorify God, the world was also made to provide us abundantly with the food and resources that we need to live (Gen. 2:16). Yet we don’t need to look far to see that we have often failed in our responsibility to properly care for creation. We live in a fallen world, and sin has fractured the intended harmony of our relationships with God, creation, and each other (as described in Genesis 3:14-24).

I recently heard a striking crystallization of this fallen perspective in Spencer Tracy’s narration in the opening scene of the sprawling 1962 western film “How the West Was Won.” As the camera flies over majestic Western fields and mountains, the narrator tells us that “This land has a name today, and is marked on maps. But the names and the maps all had to be won, won from nature and from primitive man.” This is the fallen perspective – advancing our human purpose on earth is done through defeating nature and other people (derogatively labeled “primitive,” as well) apart from God. This perspective perfectly illustrates the conflict-based relationships that sin brings about, already described for us back in the first chapters of the Bible.

Are we doomed, then, to live helplessly in this way? If this is just the way the world is and the way we are, shouldn’t we just accept that? Apart from Christ the answer would be “yes,” but the New Testament makes it clear that though we are still fallen, the saving work of Christ has brought about a profound change in us. As N.T. Wright makes clear in his book Surprised by Hope, Jesus taught (and the Resurrection vindicated) that the Kingdom of God “was and is breaking in to the present world, to earth.” ¹² Christ’s Resurrection was the first act of the future new creation. If we are truly “born again” into this new reality, this new way of living, we must strive (in the Spirit’s power) to live lives of wholeness and right relationships, putting our sinful nature to death (Colossians 3). In doing so, we would be wise to include Genesis 2 as we seek to follow God’s will and God’s Kingdom, “on earth as it is in heaven” (Matt. 6:10).

In part 2 of this series, David describes how Genesis 1, Genesis 2, and modern scientific accounts offer complementary and mutually enriching perspectives in our understanding of God's creation.

Notes

1. John H. Walton, Ancient Near Eastern Thought and the Old Testament: Introducing the Conceptual World of the Hebrew Bible (Grand Rapids, MI: Baker Academic, 2006), 125.
2. Biblical quotations are from the Common English Bible unless otherwise noted.
3. Both symbolized divine wisdom that humans had to receive from God obediently, with the proper “fear of God” that the Old Testament wisdom literature stresses as a prerequisite. Disobediently eating the Tree’s fruit would lead to death and disobeying God would lead to expulsion from the Garden. Similarly, disobediently touching the Ark brought death (Num. 4:15, 2 Sam. 6:1-7) and disobeying God’s instruction led to Israel’s exile from their Eden, the land of Canaan.
4. John H. Walton, Genesis (Grand Rapids, MI: Zondervan, 2001), 172.
5. Ibid., 173.
6. Ibid., 192.
7. See Numbers 3:7-8, 8:26, 18:5-6.
8. Gordon J. Wenham, “Sanctuary Symbolism in the Garden of Eden Story,” in “I Studied Inscriptions from Before the Flood”: Ancient Near Eastern, Literary and Linguistic Approaches to Genesis 1-11, ed. Richard S. Hess and David Toshio Tsumura (Winona Lake, IN: Eisenbrauns, 1994), 401.
9. Walton, Genesis, 176.
10. Ibid., 170.
11. This follows Walton’s illuminating exegesis of this passage in Genesis, 164-65.
12. N.T. Wright, Surprised by Hope: Rethinking Heaven, the Resurrection, and the Mission of the Church (New York: HarperOne, 2008), 201.

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.

To say, “I believe in the Church” is to embrace and live into a reality that precedes us, encompasses us, and continues beyond us. Indeed, if we are to truly be the Church in the present, I believe that it is incumbent on us to listen to those who have gone before us, and recognize that our own “here and now” is not the whole of the Christian story. Moreover, paying attention to the voices in the history of the Church can reveal to us our own contemporary blindfolds and assumptions, and might even enable us to approach Scripture with fresh eyes.

As a case in point, over the next three posts I’d like to walk us through a number of what I call “pre-modern” church fathers’ readings of Genesis 1 so that we might hear how Christians have read this text across the last 1600 years. For, while exploring the history of interpretation of any biblical text can teach us several important things, the biblical account of creation in Genesis 1 is a particularly instructive case.

Many, many Christian readers interpreted Genesis 1 during the early, medieval and Reformation eras of the church, but my survey focuses on the accounts given by Origen, Augustine, Aquinas, Luther, and Calvin. Every one of these church fathers held to at least two strong, shared assumptions: first and foremost, they all believed Scripture is the inspired Word of God—an infallible revelation given by God to reveal God and God’s truths for the church. I will return to this point later to show that what these readers meant by “infallible” is not necessarily the same as what many modern readers mean today, but the fathers’ firm conviction in the absolute trustworthiness of the biblical text is something contemporary evangelicals have in common with our predecessors in the faith. Secondly, they all asserted that any good reading of Scripture has the ultimate goal of edifying the Church. A faithful reading is performed in, with and for the Church, for the Church’s strengthening and/or repentance.

Beyond these two essential points about the text itself, all five of these church fathers focused upon several shared theological teachings in their readings of Genesis 1:

• First, the world is created. In other words, the world is not eternal; it has a beginning and an end.
• Second, God created the world.
• Third, God created the world from nothing. This is the Christian doctrine of creation ex nihilo.
• Fourth, the Creator is also Trinity: Father, Son, and Holy Spirit.

The first three of these beliefs—the world is created, God created the world, and God created the world from nothing—set up a clear distinction between God the Creator and created creatures who depend upon God for their creation—that is, the supreme distinction between Creator and creature. This distinction is necessary to demonstrate that only God is God; there is no other God. There is no room for the world or anything else to claim existence outside of or beyond God. God is the beginning of all existence.

Finally, the church fathers’ agreement that Genesis 1 teaches us about God’s Trinitarian nature of Father, Son, and Holy Spirit gives us a sense of the complete and self-sufficient yet still relational quality of the Creator. In sum, Origen, Augustine, Aquinas, Luther, and Calvin agreed that the account of creation in Genesis 1 tells us in some kind of literal way how the world came to exist, but equally that Gen 1 is intended to teach us these key theological truths.

An infinite source of wisdom

One of the key issues debated amongst these early readers of Genesis 1 was a question of methodology: how should one read the text? The pre-modern Church held firmly to the belief of both the divine inspiration of Scripture and Scripture as an infinite source of God’s wisdom, revelation and teaching. This meant that the pre-modern Church believed that there was not just one singular correct meaning of a biblical text, but that there were many possible faithful readings of any given text.

Such an assertion involved the belief that since God is infinite, so also is God’s Word infinite. To assume that there is only one singular correct meaning of Scripture is in essence to “box God in” or offend the absolute sovereignty of God—namely, limiting what God may teach or say through God’s own very Word. Hence, from very early on in the Church’s history, the church held that Scripture has literal and spiritual meanings. The late-2nd / early 3rd-century church father Origen, for one, was a keen proponent of the spiritual reading of Scripture. He maintained that Genesis 1 has both a literal meaning and a spiritual or allegorical meaning. He wrote, “There is certainly no question about the literal meaning, for these things are clearly said to have been created by God,” but then he continued, “but it is also profitable to relate this text in a spiritual sense.”¹

The spiritual meaning of the text, according to Origen, is that the creation account is not simply about how the world was created, but it also sets forth the Christian’s journey in faith from infancy to maturity. Or, put another way, the days of creation are an illustration of the ethical journey of Christians toward righteousness. Thus according to Origen, for example, the separation of waters from the dry land (in verse 9) points to the call for the Christian to seek heavenly things rather than earthly things.² Though they may be literally the creation of the sun, moon and stars, the lights in verse 14’s “Let there be lights” spiritually signify Christ and his Church—Christ who is the “light of the world” and the church who has been called to reflect this light into the world (John 8:12).³ Hence, though Origen affirmed the literal reading of this text as teaching that God created the world, the weight of his focus fell upon reading Genesis 1 as a road map for the Christian’s journey in righteousness towards becoming more Christ-like.

The renowned late 4th/early 5th-century church father Augustine also believed in reading Genesis both literally and spiritually, though he placed more emphasis on the literal reading than did Origen. Augustine commented on Genesis 1 several times, including Against the Manichees and A Literal Interpretation of Genesis. In the both of these accounts, his primary intention was to set forth that the world is created by God out of nothing—hence light vs. dark or good vs. evil cannot be rightly believed to be dualistic entities. In fact, God is the only Supreme Being, and God created everything else out of nothing—not out of God’s self (which leads to pantheism or pan-entheism), nor out of something else existing alongside God (which would lead to dualism or the belief that there are two or more equal entities that can claim to be gods). All of these theological teachings were set forth to deliberately counter the heretical teachings of the Manicheans in Augustine’s day. Hence, one might argue that Augustine’s “literal” reading of Genesis was very much focused upon certain theological teachings of Genesis 1.⁴

But Augustine did not stop there. He also provided a number of ways in which the literal words of Genesis 1 may point to a spiritual meaning. For example, Augustine writes that the 7 days of creation represent the 7 ages of the world. Moreover, Augustine—much like Origen—also read the 7 days of creation in terms of the Christian’s spiritual journey in faith. Thus, Day 1 is the light of faith, day 2 is a time of learning and discernment; day 3 is the separation of heavenly and earthly things; day 4 is development in spiritual knowledge; day 5 involves good works; day 6 is being made in the image of God to gain mastery over carnal desires, and day 7 is a day of perpetual rest.⁵

Key theologians of the early church (such as Origen and Augustine, as we’ve discussed) read Scripture with multiple senses and meanings—with a literal sense and multiple spiritual senses. However, not all fully agreed with this methodology. Though most all would certainly hold to multiple senses of Scripture, some readers insisted upon a more profound attention to the literal sense, and the use of the literal sense to help restrain or hold in check the possible spiritual readings. Such 3rd- and 4th-century Church fathers, as St. Basil the Great, John Chrysostom, St. Ambrose, and Theodore of Mopsuestia insisted upon a much more restrained literal reading of Genesis 1.⁶

Yet even those who insist upon a more literal—or more historical—interpretation of Genesis 1 still contended that the primary purpose of any reading was to edify the Church, which entails setting forth the key theological teachings of Genesis 1, rather than focus on the material specifics. Again, such teachings include that the world is created, that God create the world out of nothing, and that the creation account demonstrates the great order and harmony of creation as a testimony of the God’s glory, beauty, and goodness.⁷

More than one thousand years later, 16th-century Protestant Reformers Martin Luther and John Calvin strongly argued for a literal reading of Genesis 1 over and against an allegorical one. Luther wrote, “God’s purpose is to teach us not about allegorical creatures and an allegorical world, but about real creatures and a visible world apprehended by the senses.”⁸ Calvin maintained, “For to my mind this is a certain principle, that what is here treated is the visible form of the world.”⁹

Yet Luther and Calvin also insisted that the central purpose of Genesis 1 is to set forth the theological teachings that the world is created, that God created the world out of nothing, and that creation demonstrates God’s providence, divine purpose, goodness and benevolence.¹⁰ While these historical readers do not all agree on whether Genesis 1 should be read allegorically, what becomes crystal clear is that for all of these interpreters, in one way or another, a “literal” reading of Genesis 1 retains as its focus the theological teachings of the text. In our next installment, we’ll look briefly at some of the difficulties our expositors perceived in Genesis 1 when they did attempt to read it literally.

Notes

1. Origen, Homilies on Genesis, 60.
2. Origen, 49, 50.
3. Origen, 53-55.
4. Augustine, Against the Manichees, 57, 58 and Genesi ad litteram, 145-46.
5. Augustine, Against the Manichees, 83-88, 89-90. The seven ages are the following: Day 1 = the infancy of the world that stretched from Adam to Noah; Day 2 = childhood, stretching from Noah to Abraham; Day 3 = adolescence, encompassing the biblical history from Abraham to David; Day 4 = the age of youth, from David to the Babylonian captivity; Day 5 = youth to old age, stretching from the Babylonian Exile to the first advent of Christ; Day 6 = old age, the coming of Christ until the 2nd coming; and Day 7 = on the even and including the 2nd coming of Christ.
6. St. Basil the Great, Hexameron 9.1.
7. Ibid, 7.6, 1.7-9, 1.2-4.
8. LW 1:5.
9. John Calvin, Commentary on Genesis, 79.
10. LW 1:3, 4, 10, 18, 36, 39, 47, 49. Calvin, Commentary on Genesis, 70, 89, 80-82, 88.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

The origins of human chromosome 2: a brief review

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

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

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

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

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

Enter the Denisovans

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

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

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

Implications for understanding our “becoming human”

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

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

No Football Coaches

When I explain this position to students, I like to start with a little puzzle. Many years ago, after attending an academic conference in a major city, I was driving through the rural countryside some distance away, en route to an historic house that wasn’t well marked. As I got closer to where I thought I might start seeing some signs directing me to the house, I noticed a fair-sized hotel, restaurant, and bar off to one side of the road. What really caught my attention was a sign, prominently displayed at the start of the driveway, warning off a certain clientele: NO FOOTBALL COACHES, it said. Unfortunately I’d forgotten my camera, but this is pretty much what I saw.

When I show it in class, I ask the students to guess what this was all about: why such a sign outside of such a place? The stories they come up with are pretty good. My favorite involves two neighboring high schools, arch rivals, with the football coach at one having an affair with the wife of his opposite number, resulting in fist-fights in that bar every fall, when friends of one man or the other would go at each other in the bar, which was on the highway connecting the two school districts. After a few students have tried their luck to no avail, someone asks, where did this take place? Was it maybe in England, where football means soccer and coach means bus? Give that student an A, I say. It was England, on a highway running between York and Manchester. Now, who can fill in the blanks? Almost right away, a student will explain that soccer fans in England can be pretty rambunctious, and that a busload of them might not make the best impression on the rest of the clientele at a respectable country inn and pub. Thus, the manager would rather not have their business.

The take-away message, of course, is that there is always a context in which the meaning of a text is embedded. Unless you know something about the time and place in which a text is composed, you aren’t going understand what it actually says. The same is true for any part of the Bible, including the opening verses of Genesis. That’s the bottom line for the Framework View: if you don’t know anything about literature and culture in the Ancient Near East, you won’t understand what Genesis is really saying.

Core Tenets or Assumptions of the Framework View

(1) The “days” in Genesis have nothing to do with historical time; they are literary devices, employed by God in order to communicate the story of the creation in terms that we can understand.

This sounds like an example of the principle of accommodation, and it should. The activities of the six days of creation are arranged into a “framework” of two triads (days 1-3 and days 4-6), with parallel types of activities in each triad.

Thus, light is created on the first “day,” and on the fourth “day” God makes the Sun and Moon, the two great lights in the firmament that produce light and “rule over” the day and the night. The air and sea appear on the second “day,” and on the fifth “day” God fills them with birds and fish, etc. In other words, the order of events seems to be more logical than chronological. The key element is the fourth day: as we noted in our discussion of Concordism, the Sun was not made until the fourth day, yet it was expressly given the task of producing the day and the night and we’ve had “evening and morning” since the first day. What’s going on here? How can this be taken “literally”? Advocates of the Framework view see a solution in the parallel triads.

Another way to see this focuses on the second verse in the Bible, which reads (in the American Standard Version, a translation that follows the Hebrew closely), “And the earth was waste and void; and darkness was upon the face of the deep: and the Spirit of God moved upon the face of the waters.” God is confronted by darkness, a watery abyss, and a formless earth—each of these features posing a problem for God, who deals with them in the subsequent six “days.” First, on “days” 1 to 3, God prepares the heavens and the Earth to be a home for the great creatures to come, by separating light from darkness, separating waters above the firmament from waters below the firmament, and causing the dry land to “appear” and to “put forth” vegetation. Then, on “days” 4 to 6, God makes the creatures and puts them in the places God has prepared—the Sun and Moon in the “firmament of heaven (day 4), birds in the air and fish in the seas (day 5), and finally “the beasts of the earth” and “man” on the land (day 6).

We emphasize that the Framework View is simply about the Bible, not about science. The Earth and the universe can be as “young” or “old” as anyone wishes to claim, because the literary form of early Genesis leaves this an open question. The “days” were probably meant to be understood “literally” as ordinary days, but only in the context of a literary form that was not meant to be understood literally, when taken as a whole.

What about the seventh “day”? Because it lacks a “morning” and an “evening” in the text (have you ever noticed this?), some authors interpret the seventh “day” as a prophetic reference to God’s own eternal rest, which has not yet begun and which we will share with God in the eschatological future. An OEC book I discussed in my column on Concordism, Robert Newman’s Genesis One and the Origin of the Earth (1977), advocates this interpretation (see pp. 65-66), and so do some advocates of the Framework View.

(2) When seen against the cultural and literary context of the Ancient Near East (ANE), it is clear that Genesis was written to combat the polytheism and pantheism of other creation stories. It was not written to provide a scientifically accurate account of the creation.

This is why the Sun and Moon are not even named on the fourth day: they were worshipped as divine beings by many people in the ANE, and the Hebrew author(s) of Genesis intentionally omit their names as an act of defiance against worshippers of those two false gods. (Remember: for the ancient Egyptians, the Sun was the chief god.) Furthermore, the stars are mentioned simply as an afterthought, at the end of verse 16: “And God made the two great lights; the greater light to rule the day, and the lesser light to rule the night: he made the stars also.” This was done deliberately, as a way of belittling the Babylonians and others who worshipped them. Indeed, the whole creation account stands in the face of polytheism, by affirming that the one true, invisible God has actually created all visible things, including the heavenly bodies. Nothing we see is divine: this is the essence of monotheism, stated bluntly and boldly.

(3) It is not possible to find a close match between what is proclaimed in Genesis—that God is the creator—and the details of natural history. We should not approach this text with inappropriate expectations.

For many readers, the crucial question awaits: according to the Framework View, is Genesis 1-3 historical in any meaningful sense? Here there is a division of the house, with authors falling into either of these two camps:

(1) Genesis 1-3 is an historical narrative (though not strictly chronological), not a creation myth. As Lee Irons and Meredith Kline emphasize in The G3N3S1S Debate, “The framework interpretation does not teach that creation was a nonhistorical event” (p. 220). The universe was actually created, Adam and Eve were the first humans, and the Fall was a real historical event. Some OECs like this approach, which can be seen as a looser type of Concordism than the day-age theory; Bernard Ramm’s “moderate concordism” might be understood as fitting into this category, even though he did not discuss the Framework View per se.

(2) Genesis 1-3 is not an historical narrative; it resembles some other, older ANE creation stories. Conrad Hyers advances this view in his book, The Meaning of Creation: Genesis and Modern Science ; see below. Some aspects of the story reflect this: the days, the progression from chaos to order, and the creation of humans from mud or clay. These are common to other ANE stories, and they are present in Genesis because that’s what hearers in the ANE expected such stories to include. Other aspects of Genesis, however, are profoundly unlike other ANE stories: the transcendence of God and the de-deification of nature. These constitute the crucial, timeless, substantive message that God has revealed to us. Theistic evolutionists tend to like this non-historical approach, which is not usually seen as a kind of Concordism.

Historical Comments

The Framework View is modern, but its attitude toward the Genesis “days” is similar to that held by Augustine. As I explained in an earlier column, he taught that God created all things at once and told us about it in the pattern of six days, in order that we could understand it. The days themselves, however, were “unknowable” and not meant as a “literal” description of the passage of time.

In the 19th century, the German scholar J. H. Kurtz put forth an interpretation that Ramm called the “pictorial day” view, which he considered to be a type of “Moderate Concordism,” the overall position that Ramm himself favored. Kurtz described the creation story as “prophetico-historical tableaux, [in] which are represented before the eye of the mind, scenes from the creative activity of God, each one of which represents some grand division of the great drama, some prominent phase of the development” (The Bible and Astronomy, 1861 Philadelphia edition, p. 110). His Scottish contemporary Hugh Miller, one of the most prolific and influential evangelical writers of his day, endorsed Kurtz’ interpretation, holding that “the form and nature of the revelation” in Genesis was “conveyed by a succession of sublime visions” (The Testimony of the Rocks, 1857 Boston edition, p. 180).

The Framework View itself, with the “days” arranged in parallel triads, was first proposed in 1924 by the Dutch scholar Arie Noordzij and made more widely known by another Dutch scholar, N. H. Ridderbos. His book—Is There a Conflict Between Genesis 1 and Natural Science?—was translated into English in 1957. Subsequently, Kline and the French theologian Henri Blocher have been its most prominent supporters.

An Assignment: It’s Your Turn to Read and Write

I’ve done most of the heavy lifting in this series, but now it’s your turn. As a way of getting into all three of the views we’ve studied thus far (not simply the Framework View), I’d like everyone to read an article by Conrad Hyers, “Dinosaur Religion: On Interpreting and Misinterpreting the Creation Texts,” Journal of the American Scientific Affiliation 36 (September 1984): 142-48. The questions below are intended as helpful suggestions; feel free to discuss other matters as well!

1. What does Hyers mean by “dinosaur religion”?

2. What is Hyers’ most basic objection to “creation science,” the YEC view?

3. What does Hyers believe to be the true message of Genesis One?

4. Overall, do you agree with what Hyers says? Why or why not? Whether or not you agree, do you have any critical comments?

NOTE: Hyers wrote a sequel, “The Narrative Form of Genesis 1: Cosmogonic, Yes; Scientific, No,” Journal of the American Scientific Affiliation 36 (December 1984): 208-15, in which he employs an interpretive scheme highly similar to the Framework View, although that term is not used. I encourage you to read this also, but our discussion will focus on the first article.

Looking Ahead

In our next column on August 14, we begin a lengthy discussion of Theistic Evolution. Although that is the view advocated (under an alternative name) by BioLogos, I will approach it no differently. After explaining its central tenets, we’ll examine them critically and outline its history. Between now and then, I’m keen to see your responses to the assigned reading. If you gotten this far, you’re more than just a casual reader. Tell us what you think of Hyers’ ideas.

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

This essay considers the meaning of another small word, but not one in Latin or Greek. This word appears in the Hebrew language in which the Old Testament was written. It is the word pronounced, mîn, that can be rhymed with “green.” In Modern Israeli Hebrew the word has taken on the meaning of “species.” This is also the traditional way in which is it translated in the Old Testament of Genesis 1. It appears in Genesis 1:11, 12, 21, 24, and 25. A survey of a variety of English translations (King James Version, New American Bible, New Revised Standard Version, English Standard Version, and New International Version) reveal that the translation “kind” or “kinds” is used.

Can we be more specific? Does the word imply a zoological classification such as the term “species” would in scientific discussions of the animal and vegetable kingdoms? It is always dangerous to apply modern concepts to ancient literature. The use of classificatory schemes provides a good example. The application of categories of knowledge in pre-Aristotelian writings invites misunderstanding as the means of viewing the world and its elements differed from the way we look at things today. This does not mean that communication is impossible; only that we need to remain especially cautious not to import our understanding of matters onto the ancient worldview of writers without approaching these questions carefully and critically.

In terms of ancient (or modern) literature, a word is best understood according to its usage in the writings in which it occurs. This suggests that context determines meaning. This is especially true where it appears multiple times in the same type of literature written from the same culture and general time period. The study of context is the primary determinant for understanding the definition of a word.

Secondarily, one may consider related words in the same literature. Because a Semitic language such as Hebrew is based on roots (usually of three consonants) that each generate verbs, nouns, and other particles of speech, words formed from the same root may provide additional understanding of the term we are considering.

The third area for study is where the same word occurs in comparative literature coming from similar, though not identical (which we consider in the first category), cultures and times. The Old Testament was written in Hebrew but we do not have much additional Hebrew writing preserved for us from the time when this part of the Bible was written. However, there are closely related Semitic languages that possess a wealth of literature and may contain our word in their writings. If so, it would be good to check this and see if there is a relationship there. At the same time, later Hebrew, written by Jewish scholars, may also use this word. It is of value to compare the usage here. This part of the study can confirm and refine our understanding of mîn, but it should not overturn clear contextual indications from the Old Testament usage itself.

Finally, we should note that, in the Old Testament, mîn does not appear by itself. Every one of its occurrences forms part of the same prepositional phrase. Thus our work is not complete when we have identified the contextual and comparative meaning of the word. Instead, we need to examine the usage of the term within this prepositional phrase. Such expressions can sometimes alter the meaning of the term. This is especially true in idioms, but also occurs in other common expressions.

Old Testament Context of mîn

The Hebrew term, mîn, occurs 31 times in the Old Testament. These occurrences are found in four contexts: the creation story of Genesis 1 (vv. 11, 12, 21, 24, and 25), the flood story (Genesis 6:20; 7:14), the lists of clean and unclean animals in Leviticus 11 (vv. 14, 15, 16, 19, 22, and 29) and Deuteronomy 14 (vv. 13, 14, 15, and 18), and the single occurrence in the prophet Ezekiel’s vision of the future river that will flow from the Jerusalem temple to the Dead Sea (Ezekiel 47:10).

The usage in Genesis 1:11 and 12 associates mîn with vegetation, especially those plants and trees that have seeds and bear fruit. These will form the basis for the food to be eaten by people, birds, and land animals in Genesis 1:29-30. There is no specification of mîn in terms of species or any more specific category than edible plants and fruit trees.

The same seems to be true in Genesis 1:21, where mîn appears alongside large and small sea creatures and birds with wings. The second and third days of creation in Genesis 1 describe God’s demarcation of three domains of the physical world: the sky, the seas, and the dry ground. On days five and six God fills these areas with life, with living creatures. For the sky and sea, the creatures are defined according to their general means of locomotion and not in any other way. Modern zoological classifications use criteria in addition to locomotion. Thus there are few clues that would connect mîn with any modern classification system.

The appearance of our term in Genesis 1:24 and 25 brings us to the fifth day when God fills the dry land with life. Here God creates three categories: livestock, wild animals, and creatures that crawl along the ground. In v. 24 the general category of all living animals on the ground is described with mîn; whereas in v. 25 each of these three categories receives this term. Thus the term can be used of more general and more specific “kinds” of animals within the same grouping.

The term recurs in Genesis 6:20 and 7:14, where it modifies individually the bird, the wild animal of the land, and the creature that crawls along the ground. In Genesis 7:14 livestock is added to those in the ark. It also is modified by mîn. Here the categories of animals resemble those in Genesis 1. From these “kinds” would come all the species that are found in nature. This confirms the broad usage of mîn but does not add new information.

The usage of mîn also occurs in the listing of unclean animals. It occurs in a list in Leviticus 11:14, 15, 16, 19, and 22; which closely follows the list in Deuteronomy 14:13, 14, 15, and 18. Only Leviticus 11:22 is separate. This list includes specific names of small wild animals, various birds, and insects (Leviticus 11:22). Although there is discussion and dispute regarding the specific identification of various of these animals, it is clear that they form subcategories of those types to whom the term mîn was applied in Genesis 1, 6, and 7. The resulting picture is thus that mîn applies to a variety of animal categories, both those more general and those more specific. While particular species may be described in Leviticus and Deuteronomy, that is certainly not the case in Genesis, where the categories of living creatures are much broader.

The remaining text with mîn is Ezekiel 47:10. Here the fresh water that will pour from the temple into the Dead Sea forms a natural habitat for fish that are mîn and are compared with those fish found in the Mediterranean Sea. As in Genesis 1:21, the picture is one of general creatures of the sea, rather than what anyone might identify as a particular species. Indeed, if the translation of the phrase in which mîn occurs is understood (following the New International Version) as, “The fish will be of many kinds,” then this could envision various species. However, such an interpretation is not explicit from the text itself.

Our survey of the usage of the term in biblical Hebrew suggests that it may describe all types of plants and animals, and this may include mîn in the broadest categories of living creatures: green plants with seed, fruit trees, birds, sea creatures, fish, wild land animals, domestic animals, and creatures that creep along the ground. It may also include specific categories as enumerated in Leviticus 11 and Deuteronomy 14. Thus mîn does refer to various kinds of living creatures without a predisposition as to how large a category is intended. Only context can tell us that. The term is applied only to living creatures as described in the Bible. It is never applied to people, abstract concepts, or nonliving objects.

In Part 2, Dr. Hess expands his analysis in by exploring closely related words in the Old Testament and by comparing how mîn is used in literature coming from similar cultures and times.

It is obvious to anyone with even a cursory interest in the topic of ‘origins’ that the Bible’s opening creation account (Gen. 1:1–2:3)¹ has been the subject of a very heated debate in recent years between so-called ‘six-day creationists’ and those branded ‘scientific materialists’. These labels are frequently used in a pejorative sense, so let me flag that my use of these epithets is one of convenience not criticism.

The six-day creationists insist, largely on the basis of Genesis 1, that the universe was created in just one week about 6000 years ago and that no other interpretation of the biblical material is possible for those seeking to be faithful to Scripture as divinely inspired. The scientific materialists retort, largely on the basis of the scientific data, that such a view is patently false and that the universe is close to 14 billion years old. Therefore, the Judeo-Christian account of our origins, they say, must be dismissed as irrelevant for our day. There are, of course, innumerable ‘middle-positions’ that are less relevant to the argument of this paper.

In what follows, I hope to demonstrate that both sides of the debate—as they typically present themselves—make a similar mistake. They form their conclusions about the biblical account of creation in isolation from the conclusions of many mainstream contemporary biblical historians. And it is as a historian that I wish to address this theme.

Six-day creationists and scientific materialists approach the opening chapter of the Bible in a ‘literalistic’ fashion. I use the word ‘literalistic’ deliberately, as I want to distinguish between literalistic and literal. A literalistic reading takes the words of a text at face value, interpreting them with minimal attention to literary genre and historical context. A literal reading such as my own, on the other hand, gives serious consideration to both the literary style and the historical setting of a text. It tries to understand not only what is said but what is meant—i.e. what the original author intended to convey. Sometimes in literature what is meant and what is said do not have a one to one correspondence. In metaphor, for example, what is meant is greater than what is said (‘The Lord is my shepherd’, Ps. 23:1). In hyperbole what is meant is less than what is said (‘If your right hand causes you to sin, cut it off and throw it away’, Mt. 5:30). One can read such literary devices literally—trying to discern what the literature intends to convey—without reading them literalistically.

Both six-day creationists and scientific materialists approach Genesis 1 as if the original author had intended to narrate the mechanics of creation in historical prose. I believe this is a mistaken, literalistic reading. For over a century now, a great many biblical historians have detected in the Bible’s opening words a style other than simple prose and a purpose other than to explain how the universe was made. These two issues, genre and purpose, are critical for understanding this foundational portion of the Jewish and Christian Bible. In what follows, then, I want to unpack what many modern scholars are saying about these issues and demonstrate that, properly understood, Genesis 1 teaches nothing scientifically problematic for the modern enquirer. I emphasize the adverb ‘scientifically’, since there is plenty in Genesis 1 that is theologically and existentially confronting. That is the aim of the text, as I understand it.

But, first, an important clarification: I must emphasize that this paper assumes no particular view of human origins. The questions explored are literary and historical, not scientific. My rejection of the literalistic reading of Genesis 1 offers no direct support for old-earth, progressive creationism (or ‘theistic evolution’, as it is sometimes called), nor is it intended to do so. In fact, the case made below is consistent with virtually any scientific account of origins. To put it starkly but no less accurately, even if science ended up proving that the universe was created in six days around 6000 year ago, this happy correspondence between the scientific data and the surface structure of Genesis 1 would not affect my interpretation of the text at all. I would still insist that the opening chapter of the Bible does not aim to teach a particular cosmic chronology and that to suggest otherwise misconstrues the author’s original intention.

An analogy may help. Suppose that some clear historical evidence were discovered that around AD 29 a certain fellow from Samaria was travelling along the Jerusalem-Jericho road and came upon a Jewish man stripped of his clothes and beaten half to death. The Samaritan promptly tended to his wounds and paid two denarii for his care at a nearby guesthouse. Would this chance discovery—perhaps in some passing report by Josephus or Philo—have any bearing on the actual point being made in Jesus’ famous parable of the Good Samaritan (Luke 10:30–37) where precisely such details are narrated? The answer is ‘No’. It would certainly be a happy coincidence if one of Jesus’ didactic illustrations turned out also to be a true story, but it would not alter the fact that the ‘parable’ itself—a well-known literary device of Jewish antiquity—was never intended to be heard as a historical narrative. Parables are narrative constructs with a moral or spiritual message. Whether they correspond to events in time is of no consequence.

The parable of the Good Samaritan, therefore, is (in theory) consistent with any view of the historicity of the story because factuality is not relevant to the genre. A person reading the text may, of course, believe that Jesus was telling a factual story—it may well be—but he or she could not argue that the story puts itself forward as such; it is obviously a parable (even though, interestingly, the story is not introduced as a parable in Luke’s Gospel). The point here is not that Genesis 1 is also a parable. Not at all. I am simply emphasizing that some parts of Scripture, rightly interpreted, commit us to no particular view of the factuality of what is described. I do not believe that Genesis 1 teaches a six-day creation but this is neither an endorsement of theistic evolution nor a denial of six-day creationism. It is simply a literary and historical statement. I am happy to leave the science to the scientists.

Interpretation of Genesis 1 in the pre-scientific era

Before I give an account of what contemporary scholars are saying about the genre and purpose of Genesis, I want to establish for readers that a non-literalistic interpretation of Genesis 1 is by no means a recent phenomenon. Sceptical friends have often put it to me that my interpretation of Genesis 1 is really just an act of acquiescence to the troubling conclusions of modern science: ‘It is now clear that life emerged over a period of billions of years’, they say, ‘so now you are trying to appear respectable by picking and choosing how you read the Bible.’ Richard Dawkins has echoed this criticism with great flair recently (Dawkins 2006 pp. 237–238). Interestingly, six-day creationists say the same thing. They insist that the non-literalistic reading of Genesis 1 is the result of biblical scholars losing their nerve or being taken captive to the Zeitgeist.

It is never wise to second-guess the motives of scholars on such questions but, more significantly, it is important to realize that the precedents for a non-literalistic reading of Genesis 1 can be found in the very distant past. What follows is not intended as a proof or validation of my interpretation; it is simply a counter-argument to the above suggestion. Genesis 1 was being interpreted in a non-literalistic fashion long before modern science became a ‘problem’ for some Christians.

The Jewish scholar Philo

The prolific Jewish scholar, Philo, who lived and worked in Alexandria in the first century (10 BC – AD 50), wrote a treatise titled On the Account of the World’s Creation Given by Moses. In this work, Philo says that God probably created everything simultaneously and that the reference to ‘six days’ in Genesis indicates not temporal sequence but divine orderliness (Philo 13, 28). In the introduction to the Loeb Classical Library edition of this work the translators, FH Colson and GH Whitaker summarize Philo’s rather complex and subtle view of things:

By ‘six days’ Moses does not indicate a space of time in which the world was made, but the principles of order and productivity which governed its making [original emphasis].

It is perhaps important to note that Philo was not marginal. He was the leading intellectual of the largest Jewish community outside of Palestine.² How widespread his views were we do not know, but his discussion of the topic reveals no hint of controversy.

The Greek ‘Fathers’

Philo is followed in this interpretation by the second century Christian theologian and evangelist, Clement of Alexandria (AD 150–215), for whom the six days are symbolic (Stromata VI, 16). A generation later, Origen (185-254), the most influential theologian of the third century—again, an Alexandrian—understood Days 2–6 of the Genesis account as days in time. However, he regarded Day 1 as a non-temporal day. He reasoned that without matter, which was created on the second day, there could be no time; hence, no true ‘day’.³ What is interesting here is that a leading Christian scholar of antiquity was comfortable mixing concrete and metaphorical approaches to Genesis 1 (Origen in Heine 1982).

The Latin Fathers and beyond

Moving to Latin-speaking scholars, the fourth century Bishop of Milan, Saint Ambrose (AD 339–397), taught a fully symbolic understanding of Genesis 1.⁴ Moreover, his greatest convert, and perhaps history’s most influential theologian, Saint Augustine, famously championed a quite sophisticated, non-literalistic reading of the text. Augustine understood the ‘days’ in Genesis 1 as successive epochs in which the substance of matter, which God had created in an instant in the distant past, was fashioned into the various forms we now recognise (Augustine 2002). Augustine’s view was endorsed by some of the biggest names in the medieval church, including the Venerable Bede in the 8th century (Hexaemeron 1, 1), St Albert the Great (Commentary on the Sentence 12, B, I) and the incomparable Thomas Aquinas (II Sentences 12, 3, I) in the 13th century.⁵

It must be said that such views were not the majority position during this period. The literalistic reading appears to have been the dominant one from the 5th-century through to today. In her review of the interpretations of Genesis 1-2 offered by the ancient Fathers, Elizabeth Clark argues that this concrete approach to the text developed in the 5th- century partly as a response to the ascetic, anti-creation heresies of the period. Only a literalistic understanding of the Bible’s creation account, it was thought, could preserve a truly biblical doctrine of the goodness of creation (Clark 1988 pp. 99-133).

Be that as it may, the larger point I wish to make is that a non-literalistic interpretation of Genesis 1 is not necessarily a nervous, modern reaction to the rise of contemporary science. It is a viewpoint (even if a minority one) with a long and venerable history in both Jewish and Christian traditions.

Having said this, there are aspects of the modern interpretation of Genesis 1 that only became possible in the 16th–19th centuries, at precisely the time of the scientific revolution. This is no coincidence. The Renaissance and Enlightenment periods precipitated a literary revolution in parallel with the scientific one. This was a time of increasing sophistication in the historical-critical analysis of ancient texts in their original languages. Out of such analyses have come particular conclusions about the genre and purpose of Genesis chapter 1.

Notes

1. Genesis 1:1–2:3 is the literary unit under discussion, even though I will frequently refer to it as ‘Genesis 1’ or the ‘opening chapter of the Bible’.
2. For a concise history of the Jewish community of the intellectual centre of Alexandria (and Philo’s place in it) see Binder 1999.
3. In this, Origen echoes Philo who argued similarly about Day 1 in On the creation (Philo 15, 26-27, 34-35).
4. For a history of interpretation of these sections of Genesis see Genesis 1-3 in the history of exegesis: intrigue in the garden (Robbins 1988). A detailed account of patristic (both Greek and Latin) interpretations of Genesis 1 is also found in Appendix 7 of St Thomas Aquinas Summa Theologiae (Aquinas 1967 pp. 202-210).
5. For Aquinas’ own careful and even comparison of Augustine’s view of creation with other ancient Fathers see Summa Theologiae Ia. 74. (Aquinas 1967 pp. 1-3) Excellent articles on the interpretation of the ‘Six Days’ (Hexaemeron) among medieval theologians are found in Appendices 8 and 9 in St Thomas Aquinas Summa Theologiae (Aquinas 1967 pp. 211-224).

In the next post, Dr. Dickson examines the genre of Genesis 1.

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.