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.

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

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

Grantees will benefit from in-person interaction through a series of summer workshops in 2013, 2014, and 2015. These meetings will not only foster a broader knowledge base, but will build a sustained network of scholars and church leaders, both young and seasoned, who are serious about addressing the concerns of the church about evolution. Also in 2015, in connection with the third summer workshop, BioLogos will host a large conference open to scientists, scholars, and church leaders from around the world.

ECF History

In January 2012, BioLogos was awarded a multi-million dollar grant from the John Templeton Foundation to fund the work of scholars and church leaders on evolution and Christian faith. In spring 2012 we worked hard to get the word out. You may have seen announcements on the BioLogos website, in our newsletters, on the Books & Culture, Leadership Journal, or First Things websites, on your professional society’s listserv, or perhaps on your friend’s blog.

The response was overwhelming: we received 225 letters of intent for a total request of $21 million—about seven times the amount we had to offer. We needed to invite the most promising applicants to submit a full proposal, but recognizing the projects with highest potential would require broad expertise. From the beginning, we envisioned that a panel of scientists, pastors, and scholars would oversee the application and review process as well as play key advisory roles throughout the project. A team of eight highly qualified individuals came on board in the early months of the project. They reviewed each proposal and together recommended that BioLogos invite 86 applicants to submit full applications.

The deadline for submissions was October 1, 2012. As in the previous round, the ECF panel evaluated each proposal. In addition, we asked 55 other experts to participate, so that each proposal received 3-4 scores. Criteria for the decision included significance of topic, project design, creativity and innovation, long-term impact potential, feasibility, and budget.

The panel then met together November 29-30, 2012, to make the final funding decisions. In the end, they recommended that BioLogos give 37 awards, ranging from $23,000 to $300,000. BioLogos staff notified applicants of their awards on December 14, 2013.

The Grantees

As part of our objective to create a network of scholars and leaders, we awarded grants to organizations across the U.S. and the world. Thirty of the 37 grantees are domestic; seven are international, hailing from Canada, France, Great Britain, Netherlands, and Spain.

Two-thirds of the accepted projects will be led by teams—some with three or more Project Leaders. We expect that the teamwork and time spent together at our summer workshops will be the start of a long-lasting network of people dedicated to helping the church think carefully about origins.

Applicants chose to apply under one of three program tracks: interdisciplinary scholarship (Track 1), intra-disciplinary scholarship (Track 2), and translational projects (Track 3). Track 1 projects focus on both the collaboration between individuals in different disciplines and the development of projects at the interface of different content areas. Track 2 projects focus on work done within a specific discipline. Track 3 focuses on projects that encourage Christians, especially those within more conservative traditions, to engage in meaningful and productive dialogue to reduce tensions between mainstream science and the Christian faith. The numbers of grantees in Tracks 1, 2, and 3 are 6, 8, and 23, respectively.

Many of the scholarly projects tackle questions about Adam and Eve, the Fall, human identity, and Original Sin—some of the most critical interpretive issues for evangelical theology.  Some examples: 

• Theologian Oliver Crisp of Fuller Seminary will take an analytic theology approach to ask to what extent a theological account of the origin of human sin depends upon the evolution of modern humans from one and only one ancestral pair—especially if that pair does not appear to correspond to what we would think of as modern human beings. 

• Pastor Michael Gulker and philosopher James Smith, leading a large team from The Colossian Forum, ask a related question: if humanity emerged from non-human primates—as genetic, biological, and archaeological evidence seems to suggest—then what are the implications for Christian theology’s traditional account of origins, including both the origin of humanity and the origin of sin? 

• Biologist Dennis Venema of Trinity Western University and New Testament scholar Scot McKnight of Northern Seminary will write a book on the evidence for evolution and population genetics, with informed theological reflection on how these issues interact with orthodox Christianity.

• Biologist David Wilcox of Eastern University will develop an updated model of human identity which reflects the complex recent scientific advances in genetics and paleoanthropology and yet is sensitive to theological concerns.  

These are just a few of the scholarly awards; check out the Grantees page for full descriptions of all Track 1 and Track 2 projects.

All projects have translational potential, but Track 3 projects are designed to meet the needs of a particular constituency within the evangelical church. These projects run the gamut from ethics to education to media production to ministry resources.  Some examples include:

• Theologian Lee Camp of Lipscomb University will produce “The Questions in Monkey Town,” an episode of Tokens, a live variety show that features musical performances, comedic sketches, brief interpretive monologues, and dialog with authors and scholars. The episode will be performed and filmed on the site of the famous Scopes Trial in Dayton, Tennessee.

• Chaplain Joshua Hayashi and Educator Diane Sweeney of the Punahou School in Hawaii will lead a team to produce multimedia curricula aimed at helping high school students connect with their biology curricula and, at the same time, deepen their Christian faith.

• Physics teacher and pastor Benoît Hébert of Science et Foi Chrétienne in France will lead an international, multi-denominational team of French speaking Evangelical scientists, pastors and church leaders to produce a large number of resources on evolutionary creation.

• Pastor Seung-Hwan Kim of Grace Truth Community Church, a Southern Baptist church in Cambridge, Massachusetts, will produce teaching and preaching materials about evolution for church leaders.

• President Gregory Wolfe and Director of Resource Development for IMAGE will gather artists and writers of faith whose work explores the dialogue between evolutionary science and faith practice, convening a conversation between them and scientists, theologians, and church leaders in private and public conferences.

Again, this is just a taste of the diversity of Track 3 projects. Read more about each project on the Grantees page. You can look forward to an incredible variety of resources coming out of the ECF program, many of which will be featured right here on the BioLogos Forum.

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.

For many American evangelicals it will come as a surprise to realize just how little Lewis thought was at stake in the scientific question of our biological origins. As we have seen, Lewis had no objection to the notion that “man is physically descended from animals.” Four years after admitting to being shaken by some of the writings from Bernard Acworth’s Evolution Protest Movement, Lewis could still write in a private letter, “I don’t mind whether God made man out of earth or whether ‘earth’ merely means ‘previous millennia of ancestral organisms.’ If the fossils make it probable that man’s physical ancestor’s ‘evolved,’ no matter.”¹ So far as we can tell, Lewis never took the view that belief in mere Evolution, “Evolution in the strict sense,”² “the Evolution of real biologists,” which he took to be “a genuine scientific hypothesis” and “a purely biological theorem”³ was necessarily at odds with a belief in mere Christianity.

Indeed, the final chapter of his classic book Mere Christianity, “The New Men,” assumes an evolutionary picture of life’s origins and development throughout.⁴ He writes,

Perhaps a modern man can understand the Christian idea best if he takes it in connection with Evolution. Everyone knows about Evolution…: everyone has been told that man has evolved from lower types of life.⁵

While Lewis acknowledges that “some educated people disbelieve [the theory of Evolution],” he gives no hint throughout the rest of the chapter that he is one of their number.⁶ In fact, throughout the rest of the chapter he seems to simply assume a broadly evolutionary picture of natural history (as he does in The Problem of Pain and elsewhere). So, for instance, he writes:

Thousands of centuries ago huge, very heavily armoured creatures were evolved.⁷

At the earlier stages living organisms have had either no choice or very little choice about taking the new step [of development]. Progress was, in the main, something that happened to them, not something that they did.

Century by century God has guided nature up to the point of producing creatures (humans) which can (if they will) be taken right out of nature, turned into “gods.”⁹

And he says much more in that vein. While it may be possible to read Lewis as invoking Evolution for purely illustrative purposes without actually believing in it, such a reading seems less than likely given his statements in this chapter and elsewhere. In fact, Lewis offers no hint anywhere in his public writings that he regards evolutionary theory as either untrue or conflicting with mere Christianity.

What Lewis did believe to conflict with Christian faith was what he called the great “Myth” of “Evolutionism” or “Developmentalism.” But this is not the same as evolutionary theory per se. “[We] must sharply distinguish between Evolution as a biological theorem and popular Evolutionism or Developmentalism which is certainly a Myth,” he writes in his essay “The Funeral of a Great Myth.”¹¹ Lewis believed that the great myth of “Evolutionism” conflicted not only with the Christian faith, but with Reason itself, undercutting the grounds for believing in human rationality and, therefore, in any human rationale that could be offered for believing in Evolutionism in the first place. According to Lewis,Evolutionism’s chief premise, namely, Naturalism, invalidates human reasoning itself, amounting to “an argument which proved that no argument was sound—a proof that there are no such things as proofs—which is nonsense.”¹² “All possible knowledge…depends on reasoning,” he writes in chapter III of Miracles.¹³ “We infer Evolution from fossils: we infer the existence of our own brains from what we find inside the skulls of other creatures like ourselves in the dissecting room.” All sciences, including evolutionary science, depend upon the validity of human inference for their own validity. “Unless human reasoning is valid no science can be true.”¹⁴ Naturalism, however, with its grand Myth of Evolutionism explains all of reality, including human reason, in terms of non-rational natural causes and effects, reducing all human reasoning to being no more than the accidental byproducts of chance, matter and time, and thereby undercutting the validity of reasoning itself.

However, if one allows, as Lewis apparently did, that God guided the evolution of humanity so as to make us reasonable creatures, then humanity’s descent from the animals in no way undermines the validity of human reasoning. By maintaining the distinction between Evolution as a scientific theory and Evolutionism as a popular Myth it becomes possible for one to be a full-blooded theistic evolutionist with both a robust belief in God and a robust belief in evolution. The distinction frees Christians to accept evolutionary science without knuckling under to reductionistic Scientism. Thus, in the very essay where Lewis most acerbically attacks Evolutionism, “The Funeral of a Great Myth,” Lewis also clearly allows for a form of theistic evolution. Lewis writes:

I am not in the least denying that organisms on this planet may have ‘evolved.’ But if we are to be guided by the analogy of Nature as we know her, it would be reasonable to suppose that this evolutionary process was the second half of a long pattern—that the crude beginnings of life on this planet have themselves been ‘dropped’ there by a full and perfect life.¹⁵

As Lewis makes clear in another piece, “Two Lectures,” the “full and perfect life” by which “this evolutionary process” was “dropped” exists outside of Nature, which is to say, exists outside of the purview of the natural sciences. “Is it not…reasonable to look outside Nature for the real Originator of the natural order?” he asks.¹⁶

Lewis, however, was no Deist. He clearly did not believe that the “crude beginnings of life” were simply “dropped” by God so that the “evolutionary process” would do what it would. Lewis seems to have thought that God at least superintended the evolution of humankind, particularly humanity’s cognitive capacities, in a rather hands-on manner:

For long centuries God perfected the animal form which was to become the vehicle of humanity and the image of Himself. He gave it hands whose thumb could be applied to each of the fingers, and jaws and teeth and throat capable of articulation, and a brain sufficiently complex to execute all the material motions whereby rational thought is incarnated. The creature may have existed for ages in this state before it became man: it may even have been clever enough to make things which a modern archaeologist would accept as proof of its humanity. But it was only an animal because all its physical and psychical processes were directed to purely material and natural ends. Then, in the fullness of time, God caused to descend upon this organism, both on its psychology and physiology, a new kind of consciousness which could say “I” and “me,” which could look upon itself as an object, which knew God, which could make judgments of truth, beauty, and goodness, and which was so far above time that it could perceive time flowing past.¹⁷

Whether this picture of hands-on divine guidance is friendlier towards present day Intelligent Design theory or towards theistic evolution, a la BioLogos, will be a matter for debate. Lewis does not draw the distinctions that are customary in contemporary debates surrounding evolution—macro- versus micro-evolution, Evolution qua mere common descent versus Evolution qua wholly unguided, random process, and so on—making it difficult to say with certainty what he would say if he were here today. It seems likely, however, that Lewis would not have expected the natural sciences to be able to detect God’s supernatural guidance of man’s evolutionary path any more than he expected the modern archaeologist to be able detect the moment when our ancestors crossed the threshold from beast to man, and that likelihood might count as a strike against the ID movement’s claim on Lewis. In any case, Lewis plainly outlines a view that is quite compatible with the standard evolutionary picture of common descent and that hardly amounts to Scientistic reductionism. In short, Lewis made it quite clear in his writings that he believed that there is no real conflict between mere evolution and mere Christianity.

Surprised by Jack

Whatever Lewis may have believed in private, as a spokesperson for the faith, Lewis consistently allowed that mere Christianity was compatible with mere evolutionary science, and he even took the trouble to articulate his understanding of the Fall in such a way as to harmonize it with his belief in human evolution. While some recent writers have attempted to wield Lewis as weapon in intra-Evangelical debates around Evolution, to wield a thinker is, as Martin Buber says, to treat that thinker as an ‘It’ rather than as a ‘Thou,’ to treat him as an object to be used rather than as person with the right and capacity to defy our expectations.¹⁸ We evangelicals have become so accustomed to inserting quotable quotes from Lewis’s corpus into our sermons, books, power-point presentations, Facebook walls, and Twitter feeds that we drowsily pass over the surprising elements of his thought—the elements not easily reconciled with our clean-cut theological shibboleths—without even noticing. This is an intellectual habit ripe to be broken, and it is high time we allowed the real Jack to shatter the cultural icon—indeed, the mirror—we have made out of him. At this watershed moment in the history of the Church, when so much seems to threaten to upend the faith once delivered—whether scientific or archaeological discoveries, cultural trends, or newfangled philosophies—there is doubtless much that the greatest modern exponent of mere Christianity can teach us to help us navigate these troubled times. But it is only by opening ourselves to being surprised by Jack that we will be capable of actually learning something from him.

Notes

1. C.S. Lewis to Joseph Cranfield, Feb. 28, 1955, unpublished letter, Wade Center Collection, Wheaton College, as cited in West, “Darwin in the Dock,” 113
2. Lewis, “Is Theology Poetry?,” in The Weight of Glory, 137
3. Lewis, “The Funeral of a Great Myth,” 85, 86
4. Lewis, Mere Christianity, 185-91
5. Ibid, 185
6. Ibid
7. Ibid, 186
8. Ibid, 187
9. Ibid, 188, my italics
10. Ibid
11. Ibid
12. Ibid, 24
13. Lewis, Miracles, 23
14. Ibid
15. Lewis, “The Funeral of a Great Myth,” in Christian Reflections, 91
16. Lewis, “Two Lectures,” in God in the Dock,
17. Lewis, The Problem of Pain, 68
18. Buber, I and Thou, (New York: Simon & Schuster, 1996)

Behe and IC

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

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

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

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

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

(Darwin’s Black Box, p. 39)

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

Behe and exaptation

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

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

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

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

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

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

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

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

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

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

For further reading:

Blount, Z.D., Barrick, J.E., Davidson, C.J. and Lenski, R.E. (2012). Genomic analysis of a key innovation in an experimental Escherichia coli population. Nature 489; 513- 518.

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

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

Michael J. Behe (2010). Experimental evolution, loss-of-function mutations, and “The first rule of adaptive evolution”. The Quarterly Review of Biology 85(4); 419-445.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

The origins of human chromosome 2: a brief review

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

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

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

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

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

Enter the Denisovans

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

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

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

Implications for understanding our “becoming human”

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

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

“Theistic evolution” has been discussed by that name since at least 1877, and one of the first to do so was the great Canadian geologist John W. Dawson, in his book, The Origin of the World, According to Revelation and Science (1877). In the midst of a lengthy discussion of the animals created on the fifth day of creation, he says:

The long time employed in the introduction of the lower animals, the use of the terms “make,” and “form,” instead of “create,” and the expression “let the waters bring forth,” may well be understood as countenancing some form of mediate creation, or of “creation by law,” or “theistic evolution,” as it has been termed; but they give no countenance to the idea either of the spontaneous evolution of living beings under the influence of merely physical causes and without creative intervention, or of the transmutation [evolution] of one kind of animal into another. (p. 225)

As the final part of this sentence implies, Dawson was (ironically) a staunch opponent of both human evolution and the common ancestry of other animals; in short, by no reasonable definition was he a theistic evolutionist, even though he thought that a great deal of change had taken place naturally, “within certain limits” that he associated with the created “kinds” spoken of in Genesis. Indeed, references to “theistic evolution” are probably no less common among opponents of the view (including William Jennings Bryan in the 1920s) than among proponents, but I won’t attempt to enumerate further examples.

In recent years, however, some proponents of TE have endorsed alternative labels for their position(s). The most prominent example is Francis Collins, the geneticist who started BioLogos. Collins uses the term “BioLogos” itself as the label for his overall position, which fits well within my TE category. The evangelical theologian Denis Lamoureux, one of the most qualified of all writers on this topic (he has earned doctorates in both theology and biology), strongly prefers the term, “Evolutionary Creation” (EC), precisely because he thinks the noun “creation” ought to have more emphasis than the adjective “evolutionary,” something that the term “theistic evolution” does not accomplish. I recommend his book of that title to anyone who wants an authoritative analysis of both biblical and scientific aspects of the origins controversy. The main ideas are clearly presented in his web lectures. Another highly qualified proponent of TE, George Murphy, also has reservations about the term, but he recognizes its wide recognition and agrees with the idea itself, that “Evolution is God’s way of creating”. I will have more to say about Murphy, a very important voice, in a subsequent post.

Despite these quite reasonable objections to the term, I continue to use the “TE” term, partly because it has historical continuity and I’m an historian, and partly because it’s easily recognized. If anyone wants to object, however, they won’t get objections from me, unless their own reasons aren’t reasonable. My only request: define your terms as clearly as I’ve defined mine.

Because the term is broad and a bit hazy, more should be said about it. When we talk about “Intelligent Design” next month, I’ll tell you that it’s a “big tent” (something proponents of that view also say), insofar as it glosses over the biblical and theological issues that have usually separated Christians into various “camps” (such as the various positions we are now studying) when it comes to origins. TE is also a “big tent,” in that adherents differ strongly amongst themselves on theological and biblical issues. Unlike ID, however, theology is openly discussed—and competing theologies of God, nature, and humanity are openly advocated, not left implicit. We’ll say more about this next time. This column presents one type of TE, a type favored by many evangelical scientists and scholars. For example, the people I will discuss all accept (as far as I can tell) the Incarnation and Resurrection—that is, they are Trinitarian Christians who believe that Jesus was fully divine (and fully human) and that the disciples went to the right tomb, only to find it empty, before encountering the risen Christ in diverse places. They also believe in creation ex nihilo, the classical view (illustrated at the start of this column) that God brought the universe into existence out of nothing. There are other types of TE, some of which are not (in my opinion) sufficiently biblical, or even sufficiently Christian, to be part of this series. Please keep that in mind as we proceed: don’t tar all TEs with the same brush—something that happens all too often elsewhere. Let knowledge, not ignorance, be our guide.

Core Tenets or Assumptions of Theistic Evolution

(1) The Bible is NOT a reliable source of scientific knowledge about the origin of the earth and the universe, including living things—because it was never intended to teach us about science.

This reflects not only modern scientific knowledge, but also (more importantly) modern biblical scholarship. Peter Enns and some other evangelical scholars have recently stressed this point, initiating a firestorm in the evangelical academic community that, so far, has confirmed my view that evangelicals in general are just not ready to deal with this, even though it is consistent with the classical notion of accommodation. My own comments about the magnitude of the problem, written before the firestorm started, can be found here.

(2) The Bible IS a reliable source of knowledge about God and spiritual things.

Remember the quip that Galileo attributed to Cesare, Cardinal Baronio, “The intention of the Holy Ghost is to teach us how one goes to heaven, not how heaven goes.” (We discussed this earlier in the series). Evolution was not an issue in Galileo’s day, but this platitude is frequently quoted by advocates of TE—and often without proper attribution to Baronio. Commonality obviously lies in the attitude, not the topic. Many critics of TE are willing to adopt Galileo’s approach when it comes to the Solar System, but not when it comes to evolution: they are anxious to keep Galileo out of the garden of Eden.

Portrait of Cesare, Cardinal Baronio,
attributed to Caravaggio (1602-3) (Source)

(3) Scientific evidence is irrelevant to the Bible—it is simply not a science book.

See above. This needs to be stated separately, since some believers look to science for “proof” of the Bible, just as some unbelievers look to science for “disproof.” Proponents of TE stress that science and the Bible aren’t like apples and oranges; rather, they are more like apples and rocks: you can hold one in each hand without tension, but they have very little in common. We wouldn’t look for God in the phone book, or in an automobile repair manual. Don’t look for science in the Bible. In principle, scientific theories neither support nor threaten the Bible.

(4) The creation story in Genesis 1 is a confession of faith in the true creator, intended to refute pantheism and polytheism, not to tell us how God actually created the world.

This is meant to echo what we said about the Framework View. It is not necessarily true that all TEs accept the Framework View or something like it, but many do. Most would probably say that the Bible is not contradicted by any specific scientific theory of biological diversity—unless that theory oversteps its philosophical boundaries and functions as a kind of religion, what Conrad Hyers called “dinosaur religion.”

(5) The Bible tells us THAT God created, not how God created

Again, this sounds like the Framework View—or, at least, it should. Belief in God the creator is consistent with science, and even supported by some aspects of science; but, it is not a substitute for scientific explanations.

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

Astronomer Owen Gingerich has written an eloquent little TE book, God’s Universe. A number of quotations have been compiled here. My review for First Things identifies some of the key theological and philosophical issues related to TE. Please follow these links, study what you find, and offer comments below. If anyone has actually read the book itself, your views would be particularly valuable to include.

Looking Ahead

In our next column in two weeks, we continue our discussion of Theistic Evolution, focusing on some crucial theological aspects of TE. In the meantime, please do the “assignment” and get back to us.

No Football Coaches

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

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

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

Core Tenets or Assumptions of the Framework View

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

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

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

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

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

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

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

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

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

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

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

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

Historical Comments

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

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

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

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

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

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

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

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

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

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

Looking Ahead

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

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

Review: gene structure and function

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

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

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

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

Comparing gene transcription across species at the genomic level

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

Old hypotheses, new technology

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

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

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

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

These results underscore a few important points:

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

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

For further reading:

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

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

In his book The Greatest Show on Earth (2009) on the first page of the second chapter, Dawkins raises the interesting question: “Why did it take so long for a Darwin to arrive on the scene?” After suggesting possible answers he approvingly quotes the late Ernest Mayr's suspicion as the most insightful answer to this question. According to Dawkins, Mayr’s suspicion is: “The culprit was the ancient philosophical doctrine of---to give it its modern name—essentialism. The discovery of evolution was held back by the dead hand of Plato [Dawkins' language].” Later in his book, Dawkins states boldly that evolution is anti-essentialist, a point Mayr made in other places. One can find the same argument, if not the same language, in the writings of Edward O. Wilson where the idea of nature trumps any idea of something existing above experience. Clearly, I am not the first one to consider this argument. I think, however, that further discussion regarding the implications of essentialism for evolutionary models remains important especially for theists in particular and humanity in general. At the heart of this discussion is the matter of ontology, the nature of being. While evolution speaks to the development of what is, it necessarily carries with it very strong ontological implications, implications that affect views on the nature of being. If the idea of essence has no currency in the discussion of reality, then the thing itself is all there is and, hence, quickly becomes the object complete in itself.

It seems that essentialism (I use this term with Christian emphasis), if true, would seriously challenge any form of evolution where different species evolve through common descent. The point that Mayr and others have made turns on the idea that essentialism provided the philosophical foundation for the idea of fixity of species from at least the time of Plato. If right, that would make evolution, in the sense of producing new species, suspicious if not impossible. Furthermore, it seems that essentialism cannot be easily dismissed simply because it is associated with Plato. One must consider the philosophical/theological legitimacy of essentialism based on the merits of its own claims within the discussion of the nature of reality. With that said, if Mayr and others are right about essentialism, then the question to be taken up is whether essentialism has any ground upon which to stand, especially within Christian theology.

Generally speaking, essentialism teaches there is more to reality of the thing than what is presented to the senses which, is to say there is more to reality than the biological dimension (we might say DNA). It is the material that provides a means of expression of the essence. A member belonging to a natural kind is so because of its essence and all members belonging to this natural kind must have this essence or it does not belong. In this way, natural kinds are distinct from others by virtue of their essence. While essence determines what natural kind to which a thing belongs, there are also non-essential or accidental properties. These help to distinguish one member from another within a natural kind, but these are not determinative for the natural kind itself as they are subject to change while essential properties are not. That is, what makes a cow a cow is the essence belonging to being a cow. Without that, the cow could not be a cow. In other words the idea of essence is what gives stability to natural kinds. If essentialism is true this would, as Dawkins points out, seriously challenge the idea of common ancestry.

Applied to human beings, the essential attributes of humanness are predicated of beings called human beings which distinguishes them from non-human beings –this is not an arbitrary naming. While human beings (a natural kind) share universally the same essence of humanness, they do differ in non-essential properties (short, tall, thin, fat, and so forth). So while the members differ in many non-essential ways, they belong to the same natural kind by their shared essential attributes of humanness.

If what has been called an essence (Plato referred to these as Forms and Augustine as Ideas in the mind of God or eternal reason) explains natural kinds, it is easy to see how this would logically lead to the idea of fixity of species (which may be very broad allowing for a wide range of adaptations and variations within natural kinds which allows for a very rich biological diversity). The suggestion here is that it is time to rethink the matter of essentialism in this discussion. Of course there must be some reason to think that essentialism has merit on its own terms.

The fact that a being is determined by its essence finds support in understanding who Jesus is. Consider what makes Jesus the God-Man. As argued by the early Church Councils, it was His nature (in Greek, OUISA). He had the nature of both---the essence of God and the essence of man. It was not that He had all the outward appearance and DNA function of a man that made him a man---it was more than that. He was a man, precisely because He possessed the nature (essence of a man) and He was God as He had the nature (essence of God). This at least supports the idea that a being is what it is, not by virtue of developmental issues, but because of its essence.

In thinking about essence, one might consider the matter of transubstantiation. One may discount transubstantiation on theological grounds, but it does say something interesting to the discussion of essentialism. It assumes that the bread is of one essence and the body is of another essence. In order for the wine to become blood (a different essence) it would take a miracle as one essence does not give way to a different essence in the process of nature. The idea of transubstantiation is discussed in Aristotelian categories; in this case substantive cause is what Aristotle meant by the whatness of a thing–that is, what makes it what it is. Additionally, Genesis 1:20 notes that living creatures were created according to their own kind (the whatness of the thing) supporting the idea of natural kinds, which is consistent with the idea of fixity of species.

Tomorrow in part 2, Dr. Little makes the case that modern science has unjustifiably marginalized essentialism because it does not fit within a purely physical understanding of reality.

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

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

(Click Image to Enlarge)

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

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

(Click Image to Enlarge)

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

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

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

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

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

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

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

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

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

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

Testing IC with new research

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

For further reading:

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

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

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

(Click Image for Full Resolution)

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

Instantly this prediction raises a host of uncomfortable questions: where did their hind limbs go? How did they acquire a blowhole on the top of their heads when other mammals have two nostrils on the front of their faces? How did they transition to giving birth in the water? What happened to the teeth of the baleen whales? What happened to the hair characteristic of mammals? and so on. In some ways, evolutionary thinking about whales creates more difficulties than it appears to solve.

And yet, these difficulties are the stuff of science. If indeed our “educated guess” of terrestrial, tetrapod ancestry for whales is correct, the evidence will show that these transitions, challenging though they may seem, did indeed occur on the road to becoming “truly cetacean”.

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

Evolution: A Theory with Bite

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

Independent Lines of Evidence, but Contradictory Stories?

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

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

Signature in the SINE

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

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

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

For further reading:

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

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

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