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. 

These were just a few of the questions that motivated us at BioLogos to commission a survey of pastors on origins.  In 2012, the Barna Group conducted 743 telephone interviews with pastors from across the US, from churches big and small, and from all Christian denominations.  This comprehensive, in-depth survey provides a fascinating analysis of views held by clergy today.   In the coming month, we’ll be digging deeper into the survey results, but for now, here are some key highlights:

#1: Pastors hold a diversity of views on origins.

Overall, while a slight majority of the pastors surveyed fall under the label of Young Earth Creationism (54%), sizeable portions of clergy accept Progressive Creation (15%) and Theistic Evolution (18%).

The numbers varied widely based on a number of factors, however. Pastors of mainline churches were most likely to accept Theistic Evolution, while non-Mainline, Charismatic, and Southern Baptist pastors were overwhelmingly Young Earth Creationists. Pastors of larger churches were also more likely to accept Theistic Evolution.

Regionally, the highest percentage of YEC pastors was found in South, while the highest percentage of pastors accepting TE was in the Midwest. Pastors from the western states were the least likely to accept TE.

#2: Most pastors think science and faith questions are important.

Regardless of their views, the majority of pastors surveyed feel that the Church needs to look at how it handles issues of science. 72% of pastors with YEC views and 73% of pastors with TE views agree with the statement that “the Christian community needs to take a serious look at its understanding of science and human origins in order to maintain its witness in the world.” (The numbers are slightly lower for pastors who hold to Progressive Creation and who are uncertain).

Similarly, 66% of YEC pastors and 61% of both TE and Progressive Creation pastors agree that “younger adults today are more concerned than ever about whether faith and science are compatible.”

#3: Clergy think disagreements on science and faith harm our witness (but for different reasons).

Clergy across all three viewpoints feel that disagreements are harming the Church’s outreach, but they differ in how they view that harm.

YEC pastors overwhelming agreed (85%) that “Christian disagreement on matters of creation and evolution is compromising our witness to the world.” However, a majority of TE pastors disagreed with the statement (63%).

Conversely, a majority of TE pastors (63%) agreed that “The church’s posture toward science prevents many non-Christians from accepting Christianity,” while a majority of YEC and Progressive Creation leaning pastors disagreed (59%).

#4: Pastors aren’t avoiding science.

The majority of pastors think that addressing issues of science for their congregations is an important part of their work. Of those surveyed, 72% felt that addressing science issues in the local community was somewhat (51%) or very (21%) urgent. When asked about science on a national and global level, even more pastors felt that addressing science issues is important (43% somewhat and 46% very). Furthermore, 79% of pastors included scientific themes in at least one sermon in the past year, and 40% had included them in at least ten sermons.

The majority of clergy across all four viewpoints also agreed with the statement “Just as scripture should influence human interpretation of science, science should also inform our understanding of scripture.” The numbers were highest for TE pastors and those who are uncertain (81% and 72%, respectively), though over half of YEC and PC pastors also agreed (52% and 65%, respectively).

Finally, although YEC’s are more reluctant than other pastors to say “science should inform understanding of scripture, they strongly agree (84%) that “The Christian community needs a greater commitment to showing how young earth creationism is consistent with science.”

#5: However, they are concerned about evolution for biblical reasons.

Over half of pastors said they had “major concerns” about the idea that God used evolution. The main reasons for that concern were that the idea “undermines the authority of Scripture” (64%), “views portions of the Bible as non-literal, like Genesis” (62%), “raises doubts about a historical Adam and Eve” (61%), and “raises questions about how and when death and sin entered the world” (59%). However, 26% of pastors saw no concern with the idea that God used evolution.

#6: The majority of clergy accept parts of scripture as symbolic.

60% of the pastors surveyed felt that “some portions of the Bible are symbolic, but all that it teaches is authoritative.” Clergy whose views fall under theistic evolution and progressive creation were more likely to accept this statement (79% and 73% respectively), but a sizeable number of YEC pastors (40% among the core followers and 49% among those leaning towards YEC) also agreed with the statement.

#7: Clergy are concerned that changing their views on origins might compromise their ministry.

Over half of pastors (58%) who fell under the YEC category agreed that “If you publicly admitted your own doubts about human origins, you feel you would have a lot to lose in your ministry.” 41% of pastors in the Progressive Creation group also agreed with the statement. Pastors who were uncertain or who fell under the Theistic Evolution group were less concerned, with only 26% and 17% respectively agreeing with the statement.

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

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

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

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

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

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

Notes

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

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

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

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

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

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

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

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

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

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

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

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

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

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

ER: What qualifies as a “rare disease”?

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

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

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

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

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

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

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

ER: How did RGI get started?

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

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

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

Excerpts from Michael Hickerson Interview

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

JL: Medical and scientific doxologist.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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.

Conversations about science and faith can be like that. People hold clearly discordant points of view, and it would be dishonest to ignore the conflict. Yet some voices emphasize the dissonance without any note of harmony to put it in context. Too often, science and faith becomes a hostile battle of worldviews, sounding angry, dissonant chords even among fellow Christians. But civil, gracious dialogue is possible. On the BioLogos Forum, we invite authors from a range of positions, including some that don't agree with all our beliefs, but we strive to set these dialogues in a context of respect and civility. When authors are fellow Christians, we don’t shy away from disagreements, but remember the broader context of our unity as fellow believers, the harmony that binds us together.

My own story is more harmonious than dissonant. My interest in music was paralleled by my interest in math and science and my involvement in church. My family and teachers encouraged my interests in science, and I remember how fun it was to play math games with my dad and brother. And every week we were in church: twice on Sunday, plus Wednesday night club, youth group activities, and Bible quizzing. While my church accepted the young earth position, they didn’t emphasize it, and I was never told that a particular science view was essential to being a Christian. When I encountered the evidence for the age of the universe and the evolution of life, I also found Christian authors who showed me how this scientific evidence could fit with Christian beliefs.

But others have experienced more dissonance. Nearly four years ago, Dr. Francis Collins launched this website with the story of a young university student in the midst of a profound personal crisis, what Dr. Collins called “a wrenching crisis of worldviews shaking her deepest foundations.” Without a context of harmony, too many people – young and old – feel they have to choose between two incompatible positions, either Christian faith or the findings of science. BioLogos exists to show another way. We hold fast to the authority of the Bible and the core beliefs of Christianity, and at the same time, accept the rigorous conclusions of mainstream science.

It is with these chords of dissonance and resolution in mind that I come to this opportunity to lead BioLogos. I have long sensed God’s calling to serve the church as part of this dialogue. Some of you know of me from a book I wrote in 2007 with my husband Loren, called Origins. I’ve been speaking and writing on science and faith for many years, but I did this around the edges of my primary career of teaching and research in astronomy. While I thoroughly enjoy teaching students and doing research, over the last year I have recognized God’s hand in leading me to shift my fulltime work to the science and faith dialogue. Now I’m looking forward to using and developing my gifts in service of BioLogos.

Joining me as a new member of the leadership team is Dr. Jeff Schloss, who will serve as our Senior Scholar. Many of you are already familiar with his work, and know he brings not only a strong track record of scholarship in evolution and philosophy, but tremendous skill in communicating to lay audiences. Jeff and I share a deep commitment to the unity of the body of Christ and a desire to remove barriers for people to come to Christ. I am delighted to have him on board.

Jeff and I inherit a strong and vibrant organization from our outgoing President, Dr. Darrel Falk. Darrel brought his deep love and concern for the church, along with his considerable creativity and hard work, to this effort. We plan to continue and build on the excellent programs he established.

One of the pleasures of my first few weeks on the job has been getting to know the BioLogos staff. Kathryn, Lisa, Stephen, Mike, Laura J, and LeAnne each bring key skills to the organization, as well as energy and a passion for the mission of BioLogos. The team keeps BioLogos functioning behind the scenes, from finances to computer programming to event planning. Two team members, Mark Sprinkle and Tom Burnett, have decided to move on to other opportunities after a year of dedicated service to BioLogos. As web editors, Mark and Tom revamped the blog, making it a forum for rich scholarly dialogue and vibrant testimonies, and drawing in new authors to write on a great mix of topics. They also organized the archived material, so that the best of BioLogos is readily accessible. We wish them well in their new endeavors. Joining the BioLogos team is Emily Ruppel as Interim Web Editor. You may know Emily from her work to develop and edit the e-zine God & Nature for the American Scientific Affiliation; she will join us part time at BioLogos while she continues to work with ASA.

We believe God has great things in store for BioLogos. We will continue to focus on connecting with scholars, pastors, teachers, and lay people, but in the months ahead, we will also be sharpening our vision and engaging afresh in strategic planning. We’ll be considering new audiences, new programs, and new priorities. I invite your comments below on directions you’d like to see BioLogos take.

In just a few years, this organization has impacted the lives of thousands of Christians and brought an important voice to discussions taking place within the church. Thanks to the strong support from The John Templeton Foundation and many other generous donors, the vision of Francis Collins is thriving. BioLogos is on the cusp of enormous opportunities and huge potential. While transitions are times of risk and vulnerability, they are also times of great opportunity. My prayer is that God will give us wisdom and guidance to be good stewards of this opportunity. May God continue to use BioLogos to bring harmony to a conversation that has emphasized dissonance for far too long.

For more than a century, evangelicals and fundamentalists have typically rejected both evolution and higher biblical criticism. Sometimes there are good reasons: the claims of some biblical scholars are so outrageous and the claims of some scientists so anti-religious, that a strongly negative response is entirely appropriate. Too often, however, the evangelical encounter with modern science conforms to what historian Mark Noll has called “the scandal of the evangelical mind”—namely, “that there is not much of an evangelical mind.” Attitudes toward science have been crucial to this analysis. As Noll says, “since 1960 creationism has done more than any other issue except abortion to inflame the cultural warfare in American public life.” (p. 192)

Readers who want to know more about Noll’s book and its reception should go here and here. His conclusions about evangelicals and science are fully consistent with those I am about to present.

Evangelicals in Tension with Science

Evangelicals exhibit considerable tension and ambivalence when it comes to science, especially human evolution. On the one hand, evangelicals enthusiastically embrace the findings of science, when it comes to most applications in medicine and engineering. They also accept the experimental sciences, such as physics, chemistry, physiology, or thermodynamics. They have no problems with gravitation, the periodic table, the circulation of the blood, or the law of entropy. Here, their attitude is highly empirical: if it can be shown from repeatable experiments and observations, it’s true and presents no challenge whatsoever to religious belief.

On the other hand, evangelicals are quite hesitant to accept some conclusions of the so-called historical sciences, such as geology, cosmology, and evolutionary biology. Fundamentalists reject the very legitimacy of those sciences, and have created their own alternative explanation, “creation science,” which comports with their particular views of biblical authority and hermeneutics. Evangelicals are more ambivalent. As we’ve seen, many evangelicals accept the big bang and modern geology, with a 4.65 billion-year-old earth and the enormously long history of living things before humans arrived on the planet. But evolution–understood here to mean the common descent of humans and other organisms–presents very serious problems for many, perhaps most, evangelicals. This motivates them to look for alternative views.

The alternatives evangelicals embrace are precisely those we have studied in this series. Some eagerly support the YEC view. Others prefer one of the many varieties of the OEC view. Many like the strident tone of the ID movement, with its vigorous assault on biological and cultural “Darwinism” and its near-universal rejection of human evolution. For most evangelicals, however, TE is probably not a viable option at present, for biblical and theological reasons.

Reconciling Evolution with Scripture

Most evangelicals do not see any reasonable way to combine human evolution with the following beliefs:

• the uniqueness of humans, who alone bear the “image of God”
• the fall of Adam and Eve, the original parents of all humans, from a sinless state, by their own free choices to disobey God
• the responsibility of each person for their own actions and beliefs, within a universe that is not fully deterministic
• the redemption of individual persons by the atoning sacrifice of Christ.

Evangelicals cannot and must not be separated from these crucial beliefs about human dignity, freedom, responsibility, sin, and redemption. The 64-dollar question is: can these beliefs be maintained without simultaneously affirming the necessity of an historical, separately created first human pair? The answer is probably in the hands of evangelical academics, especially theologians and biblical scholars. Can they be persuaded that the scientific evidence for evolution is sufficiently strong to warrant a re-examination of the traditional view? Can a credible gospel and credible science be harmonized?

There exists an enormous gap between popular conceptions of science–conclusions, methods, and attitudes–and those of scientists themselves. This gap is not unique to science among practitioners of specialized knowledge, and it is not unique to evangelicals among the lay public. But it is real and very significant, and it affects theologians and biblical scholars no less than anyone else. Those who try to bridge this gap are mostly scientists (in their role as educators at colleges and universities and insofar as they write books for lay readers) and science journalists. Many influential members of those professional communities are skeptical or even strongly hostile toward Christian beliefs, and this can exacerbate an already difficult state of affairs. If ways can be found to popularize good science, while showing appropriate sensitivity to the concerns of evangelicals, it would be a very good thing.

Signs of Hope

Certainly there are reasons to hope. The conversation about science and religion is considerably broader now than it was at the time of the Scopes trial in 1925. Back then, many Protestants faced a very grim choice. On the one hand, they could follow politician William Jennings Bryan and the fundamentalists, rejecting modern science in the name of biblical authority and orthodox beliefs. On the other hand, they could follow theologian Shailer Mathews and the modernists, rejecting biblical authority and orthodox beliefs in the name of modern science. There was no one out there like John Polkinghorne, Francis Collins, Joan Centrella, Owen Gingerich, Simon Conway Morris, William Phillips, or Ian Hutchinson—to name just a few of the many top scientists today who accept evolution while affirming the divinity of Jesus, the bodily resurrection, and the actual divine creation of the universe. But they are all scientists, not theologians (except for Polkinghorne, who is both). In Galileo’s day, it was the scientists who eventually convinced the theologians and biblical scholars to accept Copernicus’ theory of the earth’s motion around the sun. But, it took a long time, and the process was difficult and often painful. Thus far, the biblical scholars and theologians who have tried to move the conversation forward have not been very well received, as Richard Ostling has so capably reported. I suspect we are in for more of the same.

It’s Your Turn to Talk

That’s what I think. What do you think? I’ll mainly be listening quietly, since I’ve now said all I wanted to say. Thank you all for hanging in there for ten months—far longer than I had originally anticipated. After a short respite I’ll return with a new series, but I’ll keep the topic under wraps for the time being.

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.

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.

The inevitable companion to the idea that the Church has held back scientific progress is that we must look outside Christendom to discover the origin of modern science. But this is also false. Modern science stands as one of the great achievements of Western civilization. And, despite what we have often heard, it is certainly an achievement of the West, not of Islam, China or even ancient Greece. Many historians of science are still reluctant to admit this. This may be because the fad of post-modernism bit them hard and has refused to let go. They have developed a habit of praising Arabic and ancient Greek science as successful on their own terms but they have lost sight of the fact that, viewed objectively, the theories advanced by early science were quite false.

Of course, we should have respect the Greek and Islamic natural philosophers who struggled to comprehend the world. But most of what they taught, through no fault of their own, was woefully inaccurate. This was because their aims for science were nothing like ours. They wanted to understand nature in terms that made sense of their ethical or religious beliefs, and formed their theories accordingly.

To take just one example, pre-modern medicine was an unmitigated disaster, far more likely to kill patients than cure them. Treatments such as bleeding and purging could only weaken the constitution of the sick, reducing their bodies’ capacity to fight off infection. It is no surprise to find that the most celebrated doctor of antiquity, Galen of Pergamum (left), considered himself as much a philosopher as a healer. Given the ineffectiveness of learned physicians, it’s little wonder that people put so much stock in miracles and magic. Perhaps the most surprising thing is that doctors were able to maintain their professional status through all the centuries that they could do little more that hasten their clients to the grave. Luckily for us, we can be much more confident that modern medicine really can cure us of many diseases. So the history of science should be the story of how we went from being fundamentally wrong about the natural world to being, in large part, right.

Science as we imagine it today, with laboratories, experiments and a professional culture, is a recent phenomenon that did not appear until the nineteenth century. But its origins can be found much earlier and we usually look for them in the period known as the ‘scientific revolution’. It is commonly believed that the recovery of Greek philosophy during the Renaissance gave Western civilization the inspiration it needed to launch this revolutionary way of looking at the world. In this view, hardly anything of consequence for science occurred between the fall of Rome and the era of Copernicus and Galileo. Carl Sagan produced a timeline of scientific progress in his book Cosmos (1980) showing nothing at all happening between AD415 and AD1543. But this is an illusion foisted on us by the same mentalité that declared science and religion must be in conflict. The truth is that to understand why modern science arose uniquely in the West, we have to travel all the way back to the Middle Ages.

Dispelling Myths

Before we do that, we should finally dispose of the two myths about scientific progress that we noted above. Firstly, as we have seen, the popular view remains that religion has held back science at every opportunity. Many people still believe that science has advanced by fighting superstition and making the world safe for rational enquiry. It is true that certain religious doctrines contradict some scientific discoveries. The creation/evolution controversy is a case in point, but such quarrels have been surprisingly rare. Even the infamous trial of Galileo, the other example of conflict most often cited, was an aberration in the Catholic Church’s usual supportive attitude towards science.

On the other hand, the problems with the thesis that science and faith are locked in a historical conflict are formidable. For a start, the so-called ‘scientific revolution’ in the seventeenth century coincided with the period when Christian belief in Europe was at its strongest. Only after science had triumphed did religion start to suffer any sort of decline. And, if Christianity really had tried to hold back scientific progress, the chances are that it would have succeeded. Modern science would not have arisen in Christian Europe at all.

As it happens, much of the evidence marshaled in favor of the conflict thesis turns out to be bogus. The Church never tried to outlaw zero or human dissection; no one was burnt at the stake for scientific ideas (not even Giordano Bruno); and no educated person in the Middle Ages thought that the world was flat, whatever the Bible might imply. Popes have had better things to do than banning vaccination or lightning conductors on churches. The thought of a pope excommunicating Halley’s Comet is absurd, but this has not prevented the tale of Calixtus III (right) doing just that from entering scientific folklore. It is remarkable that authors today, who consider themselves skeptics, can swallow some of these stories whole. Carl Sagan introduced his readers to a ‘baloney detector’ in his book, The Demon-Haunted World (1997). It is a great shame he never used it on his own writings. He presented a completely fictitious account of the murder of the pagan philosopher Hypatia in Cosmos and falsely blamed Christians for the destruction of the Alexandrian library.

Zealous Victorian historians did find occasional examples of ecclesiastical stupidity, such as the Boston pastor who warned that lightning strikes caused earthquakes. They rewrote history to make these marginal figures into leaders of opinion. Religious dissidents who paid the ultimate price for their faith were recast as champions of reason. Pope Boniface VIII issued a bull intended to stop crusaders sending their bones home for burial; he would have been most surprised to hear that, according to Andrew Dickson White, he had legislated against human dissection. Whenever a priest questioned a scientific theory, which they often did in their capacity as amateur scientists, this was held up as an example of religious obstruction. Historians have been debunking these legends for over a century now, but they continue to be recycled by each new generation.

The role of ancient Greek and Islamic thought

The other myth about the rise of science is that westerners only had to pick up the baton from the ancient Greeks, or, as has been more recently alleged, the Islamic caliphate. In reality, modern science is qualitatively different from the natural philosophy practiced by the likes of Aristotle or Avicenna. Aristotle started from the passive observation of nature and then built up a system based on rational argument. This had two enormous disadvantages: compared to controlled experiments, passive observation is usually misleading; and not even Aristotle’s powers of reason could prevent blunders in his arguments.

His discussion of motion is a case in point. He observed that everyday objects tend to stop when nothing was pushing them. From this observation, he deduced the principle that all moving objects must be moved by something else. He elevated this principle to the status of a logical certainty and then used it to explain other kinds of motion. He even thought that it successfully proved the existence of God. If the universe as a whole is full of movement, he argued, it requires an exterior unmoved mover,—that is, God—to keep it going. But of course, Aristotle’s initial observation was just a specific instance without any general applicability. We now know that objects do not stop when there is no force on them. They tend to keep going in a straight line: a principle enshrined as Newton’s First Law. Other observations led Aristotle to decree it certain that a vacuum can never exist; that heavy objects fall faster than light ones and that the earth must occupy the centre of the universe. All wrong. Aristotle, alas, was mistaken about almost everything. This was not because he was a fool but because he was practicing a natural philosophy that could never lead to true theories.

Alhazen

Islamic science suffered from similar drawbacks. Advances made by Muslim natural philosophers were significant, but rather more modest than we are usually led to believe. The importance of Alhazen’s investigations into the properties of light is indubitable. They were used by Roger Bacon in his own writings on perspectiva and thence were integrated into the modern theory of vision developed by Johannes Kepler. Even so, Alhazen’s experimental method was limited and not carried forward by his immediate successors. Similarly, the intuition of Ibn al-Nafis, in the thirteenth century, concerning the circulation of blood between the heart and the lungs is deeply impressive. But there is no evidence that he had any impact on the rediscovery of this phenomenon by Michael Servetus and Realdo Columbo three centuries later.

Consequently, we should be skeptical about some of the claims made for Islamic science in some recent television shows and books, not to mention in Wikipedia. That said, the misattribution of scientific advances to Islamic sources has sometimes been the fault of the pioneers who actually discovered them. Alchemy is a case in point. During the Middle Ages, it was customary for Christian alchemists to write their treatises under the name of the fabled Arab savant Geber. It is not surprising that later historians mistakenly assigned developments such as the first production of powerful acids as well as the isolation of alcohol to Geber himself. Alcohol was even assigned an Arabic name by Christian authors. We now know that he probably did not write any of the works attributed to him.

On the other hand, there was one towering exception to the rule that early science tended to be bunk: both the Greeks and Arabs excelled in mathematics. This was because pure rationalism works a treat when it is restricted to geometry and arithmetic. The imams had plenty of practical uses for math, as well: the Muslim calendar follows the moon and not the solar year, while mosques had to be orientated towards Mecca. Both these religious problems required mathematical solutions. It’s also said that the complicated rules of Islamic inheritance made algebra indispensable. Even our word algebra is a corruption of al-jabr, the name of an Arabic textbook widely used by Christians.

Despite these genuine contributions, it is nevertheless fair to say that neither Aristotelian rationality nor Islamic mathematics was the key to the developments that made the modern world possible. As we shall see in the second part of this essay tomorrow, the very different cultural situation in medieval Europe allowed for Aristotle’s faulty method to be criticised by the Catholic Church, meaning that previously forbidden ideas could flourish. The Church also made natural philosophy a compulsory part of the course that it required trainee theologians to follow. So, unlike in Islamic madrassas, science had a central place in Christian centers of learning. Indeed, it was a Christian worldview that proved especially compatible with—even necessary for—the rise of modern science.

Some implications and conclusions of Theistic Evolution

Bernard Ramm argued for just such a position in The Christian View of Science and Scripture, even though he was an OEC, not a TE. Denis Lamoureux takes it further in his recent book, I Love Jesus & I Accept Evolution. A glance at the table of contents shows that he emphasizes the presence of “ancient science in the Bible” and teaches us how to interpret the Bible in light of this. Just as we don’t take biblical astronomy “literally,” with its 3-tiered universe, we shouldn’t take biblical biology “literally,” with its fixed species and separate creations a few thousand years ago.

For a concise description of Complementarity, I borrow the words of Stanford physicist (now retired) Richard Bube, who wrote three books about science and Christianity, taught a course about it for decades, and edited the Journal of the American Scientific Affiliation (now called Perspectives on Science & Christian Faith) for many years. In his book, Putting It All Together, Bube presented seven “patterns” for relating science to faith (here and here), ending with his personal favorite, Complementarity, described as follows:

“Science and theology tell us different kinds of things about the same things. Each, when true to its own authentic capabilities, provides us with valid insights into the nature of reality from different perspectives. It is the task of individuals and communities of individuals to integrate these two types of insights to obtain an adequate and coherent view of reality.” (p. 166)

I’ll offer my own example to illustrate this model. Everyone reading this column originated in the union of two cells, one from each parent. Everyone reading this is also created in the image of God. Each of these two sentences is true, but the truths they proclaim are of a different order. The first neither implies nor negates the second. You can see where this is going: for TEs, the truth (in their view) that we are descended from other primates neither implies nor negates the truth that we are created in the image of God.

The Complementarity view, as I’ve briefly presented it, might seem quite shallow—nothing more than the simple, unsupported claim that science is about HOW and religion is about WHY. Readers who want a subtler account are invited to study Christopher Rios’ article about its development. Rios quite properly stresses the work of two important British scientists from the last century, quantum chemist Charles A. Coulson and his friend, brain theorist Donald M. MacKay, one of the most prolific and thoughtful Christian thinkers of his generation. If you don’t know MacKay, I unreservedly recommend that you get acquainted, but his work is so wide-ranging that I am hesitant to recommend a single starting place. Evolution was not one of his chief interests (I don’t offer him as a prime example of TE per se), but I can’t think of anyone who wrote more about the Complementarity model of science and Christian faith.

Physicist-theologian John Polkinghorne can also be understood as a proponent of Complementarity, though I would not characterize his position solely in those terms. His overall vision captures the essence of Complementarity: theology complements the limited picture of reality given to us by science; it goes beyond science, providing a larger metaphysical framework within which both nature and the science of nature are more intelligible (see below for more). Many of his books are conceptually deep, discouraging casual readers, but they are also eloquent and very creative, making the hard work of reading them time well spent. There simply is no good substitute for diving into them yourself. I’ve reviewed one of his recent books here.

(INVITATION: If you would like to take part in a full discussion of one of his books here at BioLogos, at some point down the road, please let me know, either in a comment below or privately (tdavisATmessiahDOTedu). Don’t make the commitment lightly—you would be expected to purchase and read the book—but please take the invitation seriously and respond accordingly.)

A theology of nature starts from the assumption that God exists and then seeks to understand the whole of nature in light of this. Polkinghorne does this in many of his books (see the review linked above for some specific examples). Natural theology, on the other hand, is the effort to demonstrate God’s existence (including some of God’s attributes, such as power, wisdom, and goodness) from reason or nature, without appealing to the Bible. Many Christian authors since the patristic period have done this, often citing the first chapter of Romans, though some of the most important have had doubts about the value of the whole enterprise; two prominent examples would be Blaise Pascal (see the article by George Murphy here) and John Henry Newman.

The golden age for natural theology lasted from the late 17th century (when Boyle and Newton were outspoken advocates of using science to argue for God’s existence) down through the mid-19th century, when Darwinian evolution provided a serious challenge to natural theological arguments based on “contrivances,” aspects of nature that appeared to be exquisitely crafted for a specific purpose by the Creator. Although it’s not true “That Darwin Destroyed Natural Theology,” (see the chapter by Jon Roberts here), it is true that TE authors no longer appeal to intricate biological “contrivances” to make their case. Prior to Darwin, a leading natural theologian, the great scholar William Whewell, had already made the case for a different type of natural theology in his famous contribution to the Bridgewater Treatises, a series of eight books on natural theology from the 1830s: “But with regard to the material world, we can at least go so far as this;—we can perceive that events are brought about, not by insulated interpositions of divine power, exerted in each particular case, but by the establishment of general laws” (Astronomy and General Physics Considered with Reference to Natural Theology, p. 356 in the fifth London edition of 1836). Ironically, Darwin placed this very passage directly opposite the title page in On the Origin of Species (1859).

Just a few years later, a Unitarian chemist from Harvard, Josiah Parsons Cooke, Jr., replied to Darwin in a book called Religion and Chemistry; or, Proofs of God’s Plan in the Atmosphere and Its Elements (1864). Cooke got around Darwin by inquiring into the basic properties of matter itself—the features of the physical universe that make biology possible at all. “There is abundant evidence of design in the properties of the chemical elements alone,” he argued, especially as they combine to make the unique substance we call water. Natural theology had found a more solid foundation, “which no theories of organic development can shake.”

Contemporary TEs do pretty much the same thing. They look for evidence of “design” or “purpose” in the nature of nature itself, not in biological “contrivances.” Discussions of the “fine tuning” of the universe are common in TE literature, including Francis Collins’ book, The Language of God and Ken Miller’s book, Finding Darwin’s God. Philosopher Robin Collins (who is writing a superb book about the fine tuning of the laws of nature) provides a helpful introduction to the terms and the issues here. Polkinghorne raises fundamental questions about the very intelligibility of nature in the wonderful title chapter in Belief in God in an Age of Science. Let’s pay careful attention to what he says about his overall approach:

“This new natural theology differs from the old-style natural theology of Anselm and Aquinas by refraining from talking about ‘proofs’ of God’s existence and by being content with the more modest role of offering theistic belief as an insightful account of what is going on. It differs from the old-style natural theology of William Paley and others by basing its arguments not upon particular occurrences (the coming-to-be of the eye or of life itself), but on the character of the physical fabric of the world, which is the necessary ground for the possibility of any occurrence (it appeals to cosmic rationality and the anthropic form of the laws of nature) ... [Consequently] the new-style natural theology in no way seeks to be a rival to scientific explanation but rather it aims to complement that explanation by setting it within a wider and more profound context of understanding. Science rejoices in the rational accessibility of the physical world and uses the laws of nature to explain particular occurrences in cosmic and terrestrial history, but it is unable of itself to offer any reason why these laws take the particular (anthropically fruitful) form that they do, or why we can discover them through mathematical insight.” (pp. 10-11)

Looking Ahead

Sorry to stop mid-stream, but this is enough for now. This discussion resumes in about two weeks with more implications and conclusions of TE. There should be enough here to keep us going until then!

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.