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. 

There’s a serious point in my playful invocation of Pilgrim’s Progress. Like many of the most complex human endeavors — parenting, farming, becoming a Christian — the life of a scientist is not just an “occupation,” something that occupies us for a while and might then be followed by something entirely different. Being a scientist is as much about being as doing, as much about a particular way of being formed as a person as it is a set of activities or even skills. Training in science is induction not so much into a particular worldview (though it includes absorbing plenty of the kind of cognitive presuppositions that that word suggests) as it is a kind of posture or stance toward the world, toward one’s work, and toward one’s fellow human beings, both scientists and non-scientists. And the life of a scientist is a journey, one freighted with ultimate concerns and laden with values. It is a journey into a set of virtues, the habits and dispositions that make one a person of a particular kind of character.

When we talk about faith and science, we tend to focus on the cognitive content of both endeavors, the truth claims and worldviews that animate these two crucial dimensions of modern human life. These are important matters, and I don’t at all mean to diminish them. At the same time, there are inevitable limits to what any pastor can do to constructively integrate the knowledge content of science — so vast and rapidly expanding that even scientists cannot pretend to be expert in anything but a tiny portion — with the content of Christian faith. But there is another way to approach faith and science which I believe might well be more within reach of most pastors, and more essential to their job description than being deeply literate in the latest scientific discoveries and theories — and that is simply to attend to, and prayerfully support and encourage, the scientific life itself as a vocation that can reflect the image of God and be a place for working out one’s own salvation.

So here is what I wish our pastors — and fellow Christians — knew about the life of a working scientist.

Delight and Wonder

If there is one personality characteristic of the vast majority of scientists I have met, it is delight. There is something about science that attracts people who are fascinated and thrilled by the world. To be sure, any given scientist is delighted by things that you and I may find odd or indeed incomprehensible — the intricacies of protein folding, the strata of Antarctic ice cores, or the properties of Lebesgue spaces (and no, I have no idea what that last phrase really means). But the specificity of their delights is one of delight’s secrets: like love, delight is always most potent when it is particular. It is certainly possible to find lawyers who are delighted by law (I have one friend who can go on at great length, with enthusiasm, about corporate bankruptcies), dairy farmers who are delighted by cows, or lumberjacks who are delighted by trees — but I dare say your chances are much better that when you meet a scientist you will find that they are delighted with the tiny part of the world they study day to day. (At least when they are not frustrated with it — which we’ll examine below.)

In many scientists, delight is matched by wonder — a sense of astonishment at the beautiful, ingenious complexity to be found in the world. This is not the “wonder” that comes from ignorance — “I wonder how a light bulb really works?” — but a wonder that comes from understanding. Indeed, as we progress further into humanity’s scientific era we have been able to disabuse ourselves of a mistaken early-modern notion: that the more the world became comprehensible, the less it would be wonderful. That turns out not to be true at all — ask a scientist. Wonder grows as understanding grows. Indeed, wonder only grows if understanding grows. If we replace our childhood awe of lightning with an explanation like, “It’s nothing but a transfer of voltage across a highly resistive material” (an example of what G. K. Chesterton wittily called “nothing-buttery”) perhaps the world will seem like a less wonderful place. But those who actually pursue knowledge of lightning — of electromagnetism or cloud formation or weather systems or climate — end up being more in awe of the world than they were as children. This is surely one of the remarkable features of our cosmos: the more we understand about it, the more we are in awe of its beautiful elegance and simplicity, and at the same time its humbling complexity.

To be sure, many if not most scientists do not see this wonderful world in the way that most Christians would hope for. For us, wonder is a stepping-stone to worship — ascribing our awe for the world to a Creator whose worth it reveals. For many scientists, wonder is less a stepping-stone than a substitute for worship. Yet they stop and wonder all the same.

Intellectual humility

I doubt that humility is among the first traits most people think of when they think of scientists. And indeed, some scientists (like some academics and intellectuals generally) exhibit a combination of confidence in their own intellect and limitations in their social skills that makes them seem abrasive if not arrogant. A few have made a public career of intellectual overreaching, not least in matters of science and faith. But in my experience (and certainly, let me stress, in the case of my own wife!) this is much more the exception than the rule. If intellectual humility is essentially a willingness to admit what you do not and cannot know, science cultivates humility like few other pursuits can — because in few other pursuits do you so often find out that you were wrong.

Even though we tell the story of science through its high points — the discoveries and confirmed theories that won Nobel Prizes and launched new eras in technology — the actual practice of science, for nearly every working scientist, involves far more failure than success. This is especially true for experimental science, the kind that requires the most direct interaction with recalcitrant reality. On most days, in most labs, the data do not add up, Matlab has an untraceable bug, the laser is on the fritz, and all the cultures have been contaminated when the undergraduate research assistant sneezed. And while each of these everyday setbacks requires immense amounts of patience and persistence to overcome, they are only the quotidian version of the perplexity that begins early in the study of science. Every scientist, in the process of their training, has had to repeatedly discover that their intuitions about the world are simply wrong, or at least incomplete. Even great scientists have come up against the sheer oddity and unpredictability of the world — Albert Einstein, for example, never fully accepted the uncertainty at the heart of quantum mechanics, something that is now universally accepted by physicists.

This regular confrontation with the limits of one’s own knowledge and skill is not to be taken for granted. The other divisions of the academy, the social sciences and the humanities, deal with matters of such variability and complexity that it is often difficult to say conclusively that anyone, or any theory, is entirely wrong. Marx’s and Freud’s grand theories may not seem nearly as plausible as they once were, but there are thousands of people following their lines of thought without losing the respect of their intellectual peers. But Ptolemaic cosmology or Lamarckian evolution now have, simply, no followers. They have been proved wrong beyond a reasonable doubt (although Lamarck’s ideas, interestingly, turn out to have a grain of truth in a way very different from what he expected). Who is likely to be more intellectually humble — someone who early in her training, and daily in her work, learns that her assumptions have been wrong, or someone who can always argue his way out of any intellectual predicament? It is perhaps no accident that “grade inflation,” in which undergraduates’ grades ratchet ever upwards in a nod to the consumer realities of the modern university, is much less pervasive in the sciences, where you can’t cajole your way into an A. The honest, and humbling, truth is that there is likely more intellectual humility in the average physics laboratory than in the average theology classroom.

For more from the "What I Wish My Pastor Knew" series, visit The Ministry Theorem.

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.

Motivated Belief

As we noted earlier [in this book], scientists are not inclined to subscribe to an a priori [i.e., knowledge that is not dependent on experience or empirical evidence] concept of what is reasonable. They have found the physical world to be too surprising, too resistant to prior expectation, for a simple trust in human powers of rational prevision [i.e., foresight] to be at all persuasive. Instead, the actual character of our encounter with reality has to be allowed to shape our knowledge and thought about the object of our enquiry. Different levels of reality may be expected to have their idiosyncratic characters, and there will not be a single epistemic [knowledge-based] rule for all. A physicist, aware of the counterintuitive natures of the quantum world and of cosmic curved spacetime, is not tempted to make commonsense the sole measure of rational expectation. Because of this, we have seen that the instinctive question for the scientist to ask is not “Is it reasonable?”, as if one knew beforehand the shape that rationality had to take, but “What makes you think that might be the case?” Radical revision of expectation cannot be ruled out, but it will only be accepted if evidence is presented in support of the new point of view that is being proposed. Science trades in motivated belief.

One of the difficulties that face a scientist wanting to speak to his colleagues about the Christian faith is to get across the fact that theology also trades in motivated belief. Many scientists are both wistful and wary in their attitude towards religion. They can see that science’s story is not sufficient by itself to give a satisfying account of the many-layered reality of the world. Those who acknowledge this are open to a search for wider and deeper understanding. Hence the wistful desire for something beyond science. Religion offers such a prospect, but many scientists fear that it does so on unacceptable terms. Their wariness arises from the mistaken idea that religious faith demands that those who embrace it should be willing to believe simply on the basis of submission to some unquestionable authority—the claimed utterances of a divine being, the unchallengeable assertions of a sacred book, the authoritative decrees of a controlling community, whatever it may be—simply declared to be unproblematic deliverances of infallible truth. [This describes the attitude that Polkinghorne likes to call “top-down thinking,” vis-à-vis “bottom-up thinking,” which is mentioned at the end of this excerpt.]

The picture that many scientists have of religious revelation is that it is a collection of non-negotiable propositions, presented to be accepted without further argument or attempt at justification. According to this view, faith is simply a matter of signing on the dotted line without taking too much care about the small print. These scientists fear that religious belief would demand of them an act of intellectual suicide. I believe this to be a quite disastrous misconception. If an uncritical fideism [reliance on faith alone] is what religious belief requires, then I would have the greatest difficulty in being a religious person.

What I am always trying to do in conversation with my not-yet-believing friends is to show them that I have motivations for my religious beliefs, just as I have motivations for scientific beliefs. They may not share my view of the adequacy of these motivations, but at least they should recognize that they are there on offer as matters for rational consideration and assessment. Theology conducted in the context of science must be prepared to be candid about the evidence for its beliefs. This task is one of great importance, since the difficulty of getting a hearing for Christian faith in contemporary society often seems to stem from the fact that many people have never given adequate adult consideration to the possibility of its being true, thinking that they “know” already that there can be no truth in claims so apparently at odds with notions of everyday secular expectation.

While science and religion share a common concern for motivated belief, the character of the motivating evidence is, of course, different in the two cases. [SNIP]  Theology lacks recourse to repeatable experimental confirmation (“Do not put the Lord your God to the test,” Deuteronomy 6:16), as in fact do most other non-scientific explorations of reality. Judgments such as that of the quality of a painting, or the beauty of a piece of music, or the character of a friend, depend upon powers of sympathetic discernment, rather than being open to empirical demonstration. Moreover, I have already said that I believe that no form of human truth-seeking enquiry can attain absolute certainty about its conclusions. The realistic aspiration is that of attaining the best explanation of complex phenomena, a goal to be achieved by searching for an understanding sufficiently comprehensive and well-motivated as to afford the basis for rational commitment.

Michael Polanyi (Source)

Neither science nor religion can entertain the hope of establishing logically coercive proof of the kind that only a fool could deny. No one can avoid some degree of intellectual precariousness, and there is a consequent need for a degree of cautious daring in the quest for truth. Experience and interpretation intertwine in an inescapable circularity. Even science cannot wholly escape this dilemma (theory interprets experiments; experiments confirm or disconfirm theories). We have seen [in another chapter] how considerations of this kind led Michael Polanyi to acknowledge the presence of a tacit dimension in scientific practice, depending on the exercise of skills of judgment, and to speak of science as necessarily being personal knowledge, not absolutely certain but still capable of eliciting justified belief. Recall that he said that he wrote Personal Knowledge to explain how he might commit himself to what he believed (scientifically) to be true, while knowing that it might be false. This stance recognizes what I believe to be the unavoidable epistemic condition of humanity.

When we turn to religious belief, it too cannot lay claim to certainty beyond a peradventure [uncertainty or doubt]—for believers live by faith and not by sight. Yet faith is by no means the irrational acceptance of unquestionable propositions. I believe my religious faith to be well motivated and that is why, for me, Christianity is worthy of acceptance and commitment. Religious people are content to bet their lives that this is so. If theology is to prove persuasive to enquirers in the context of science, it will have to set out the motivations for the assertions that it makes, expressed in as honest and careful a fashion as possible. I believe that the argument will need to have the character of bottom-up thinking, making appeal to specific forms of evidence.

Looking Ahead

In a couple of weeks we will continue exploring Polkinghorne’s approach to “motivated belief,” with further excerpts from this chapter.

References and Credits

Excerpts from John Polkinghorne, Theology in the Context of Science (2009), copyright Yale University Press, are reproduced by permission of Yale University Press. We gratefully acknowledge their cooperation in bringing this material to our readers.

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.

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.

Werner Heisenberg, in a letter to Albert Einstein¹

For many people, science invites awe and religion invites insight. When awe and insight engage, science-and-religion happens.

Ron Cole-Turner²

If we can understand the experiences of the people who work every day in the lab, our dialogues concerning science and religion will be far more fruitful than they would be otherwise. I realised this when someone recently asked me what the highlights had been during my own time as a biologist. I explained that what I appreciated most was the privilege of experiencing science first-hand. My horizons have been expanded, and I now have a better understanding of how vast and complex the natural world is. Appreciating the grandeur of the universe seems to be a universal for humankind, including research scientists in their own peculiar way. Everyone has something to add to a conversation about experiences of awe, as I discovered when I blogged on it recently and invited a number of friends and former colleagues to comment. This sense of awe is a perfect starting point for discussions of science and theology.

Life in the Laboratory

I had always loved finding out how things work, and that was one of the reasons why I chose biology, but actually working ‘at the coal face’ was an eye opener. Living organisms are extremely complicated, so one has to choose only a tiny part of an organism to study: maybe a single gene or a feature of its behaviour. It can take years to understand just one aspect of that tiny part in enough depth to be able to publish an academic paper about it. Experienced scientists describe how the sum of human knowledge is so small as to be insignificant in comparison to what is out there, and I can now appreciate that a little bit. I can also appreciate what fun it is to survey all that un-knowledge, grab a bit of it and try to figure it out.

In the world outside of the lab we hear the headlines about new discoveries, but we have no idea what is behind that one-liner. In reality the story of a discovery in biology may well have started with a graduate student who nervously began their new project, a more experienced scientist who sacrificed precious time to train and supervise them, and the lab head who looked over the data every now and then. There would have been long days and nights in the lab and many false turns before the first piece of promising data emerged. No doubt there were anxious re-runs of experiments to confirm the results, and moments of elation as things started to make sense. The work would have been presented to critical colleagues who suggested further experiments. Frustrating months would have been spent generating the final pieces of data, weeks bent over a computer writing a dense and meticulously referenced paper, submission to a journal, the referees’ criticisms, a few more experiments, resubmission, and a long wait. Finally the paper was accepted and the whole research group joined in the celebration. And this is only the simplest possible version of events – the process of producing successful research can involve large numbers of people over several years, international collaborations, promising leads that go stale, and surprising results from unexpected places.

The ‘real world’ of science is a million miles away from the debates on science and religion that happen in churches, universities and schools throughout the world. Behind every piece of research is a team of people representing different faiths and belief systems, a variety of cultures, social backgrounds and personality types. Perhaps scientists are all a little crazy (who would put in the hours otherwise?), but they’re definitely all motivated in different ways.

The factors that attract people to science are many, though inspiring and supportive parents or teachers can play a large part. The reasons why individuals decide to stick with research, despite all the demands and uncertainties that a life in science brings, are interesting and at times surprising. There is the fascination of understanding the natural world, the value of original research, the prospect of new technologies further down the line, and the privilege of making new discoveries. There is also the opportunity to ask new questions, and the immense satisfaction when things come together and begin to make sense. So far, so predictable. More unexpected drivers are the enjoyable process of tinkering with experimental systems, the opportunity to exercise great creativity, the beauty of scientific data, and a feeling of immense awe when one gets a rare insight into the way the world operates. The rewards for doing science range from the utilitarian to the downright spiritual.

Awe in Science

Awe is an important part of the experience of science – one could almost say it’s a universal. When a scientist feels awe it is usually in response to something complex, precise, ordered, powerful or beautiful. There is an element of unexpectedness and delight, maybe even respect, fear or reverence. Awe always involves the need for some sort of mental adjustment or accommodation: we need to make room in our internal map of the world for this new and amazing experience. The physicist Werner Heisenberg vividly described this process of taking on board a startling new concept when he wrote of his discovery of atomic energy levels:

“In the first moment I was deeply frightened. I had the feeling that, through the surface of atomic phenomena, I was looking at a deeply lying bottom of remarkable internal beauty. I felt almost giddy at the thought that I had now to probe this wealth of mathematical structures that nature down there had spread before me.”

Moments of awe are the rare high-points in science, both rationally and emotionally. Finally something is understood. That understanding and the new possibilities it opens up are wonderful, and the story is told and retold. Scientists, as you might expect, respond scientifically, with new questions and investigations. But they also respond in other ways depending on their personalities: aesthetically, using visual representations of the data in different ways; philosophically, as they discuss the ethical implications of the research or the surprising intelligibility of the universe; or spiritually, as they try to make sense of those feelings of awe and wonder at the immensity and beauty of the world.

When Elaine Howard Ecklund carried out some research into the beliefs of scientists in elite US universities, she discovered a surprising fact: 20% of the people that she and her research team spoke to were not members of any religious group, but considered themselves spiritual. For some of these scientists the experience of beauty, awe and wonder in their work led them to believe that there is something beyond science – one could perhaps call it ‘transcendent’ – an experience that motivated some of them in their research, their teaching, and their lives outside of the lab. I remember having a conversation with a colleague who had experienced something along these lines, so I’m not surprised to hear that many others feel the same.

According to the scientist-theologian Alister McGrath, experiences of the transcendent might involve a sense of the ‘numinous’ – a feeling that something ‘other’ might be behind what one is seeing. Or perhaps someone might encounter a deep truth about the unity of reality that strikes them in a particular way. Perhaps more common would be a moment of unexpected clarity – what some might call an epiphany – where suddenly things make sense. Experiences that might be called ‘transcendent’ are rare, but they leave a lasting impression.

The language used by many scientists when they describe the process of discovery is of a reality that was always there. Perhaps it’s not surprising that scientists are ‘realists’; they think that there is a real world outside of ourselves that waits to be discovered. Science does not answer the ultimate questions about the universe, but scientists are human beings so we just ask those questions anyway – sometimes looking for answers in unexpected places.

Spirituality in Science

At the beginning of this piece I mentioned my growing realisation of the size of the scientist’s task. The seeming inexhaustibility of the created order can be overwhelming, but many see this as something positive. There is so much more to explore. As the Jesuit philosopher Enrico Cantore has said, the mystery of the universe lies not in ignorance, but in dazzling intelligibility. Where do these thoughts of transcendence, reality and mystery lead? For Einstein, they were a religion. A Mind other than our own was somehow responsible for this world that we can make sense of using the language of mathematics. For others, the reality we see in the world leads to ideals that transcend differences of language, culture and religion.

We search for meaning, and we long for more. CS Lewis famously describes the world we live in as a pale reflection of the one to come.³ For those who already believe in God, what we see in science makes sense. We live in a world that operates according to principles that we can understand and describe mathematically. We can utilize what we find for good or evil (and everything in between), and what we discover is both beautiful and awe-inspiring. William Whewell, the nineteenth-century polymath and Master of Trinity College, Cambridge, said that ‘We must find the right thread on which to string the pearls of our observations, so that they disclose their true pattern.’

For me, what we see in science is not evidence for God, but works well as a thought experiment. What would you expect if God existed? In the context of faith, science increases my sense of awe and wonder and helps me to worship God in a more genuine way. The Christian songwriter Matt Redman said that we sometimes ‘take the extraordinary revelation of God and somehow manage to make Him sound completely ordinary’. Science has the power to expand our horizons and helps us to see how great God is. The dazzling intelligibility of the world increases our humility, as we realise that because we ourselves are a fragile and finite part of the universe, we will never be able to fully grasp what we see in an objective intellectual way.⁴ Our response to what we see in the world is rational, emotional and active: worship as well as systematic theology.

The highest mountain peaks and the deepest canyon depths are just tiny echoes of His proclaimed greatness. And the brightest stars above, only the faintest emblems of the full measure of His glory.⁵

Notes

The main sources for this piece are Enrico Cantore, Scientific Man: The Humanistic Significance of Science (New York: ISH Publications, 1977); Olaf Pedersen, “Christian belief and the fascination of science” in Physics, Philosophy and Theology: A Common Quest for Understanding, Eds. Robert John Russell, William R. Stoeger & George V. Coyne. (Vatican City State: Vatican Observatory, 1988), 125-140.; Alister McGrath, The Open Secret (Oxford: Blackwell, 2008).

1. From Enrico Cantore, Scientific Man: The Humanistic Significance of Science (New York: ISH Publications, 1977)

2. Ron Cole-Turner, ‘What Do You Find Most Interesting or Surprising About the S&R Discussion Today?’, Science & Religion Today, 21st May 2012, http://www.scienceandreligiontoday.com/2012/05/21/what-do-you-find-most-interesting-or-surprising-about-the-sr-discussion-today-ron-cole-turner-answers/

3. In C.S. Lewis, The Weight of Glory. SPCK, 1942

4. Jame Schaefer, Theological Foundations for Environmental Ethics: Reconstructing Patristic and Medieval Concepts (Washington, DC: Georgetown University Press, 2009), Chapter 1.

5. Matt Redman, Facedown (Eastbourne: Survivor, 2004).

Behe and IC

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

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

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

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

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

(Darwin’s Black Box, p. 39)

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

Behe and exaptation

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

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

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

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

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

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

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

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

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

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

For further reading:

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

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

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

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

The first video, “10 Questions with Katherine Hayhoe”, introduces the scientist in a brief and lighthearted interview. Hayhoe is presented with 10 questions concerning her personal life and beliefs. When asked, she explains that one thing people should know about Christianity is that having a relationship with the God of the universe is one of the most incredible experiences that a person can have. As the video unfolds, the viewer quickly begins to realize that, despite her unique profession of two seemingly incompatible beliefs, Hayhoe is a remarkably sane and “normal” individual. Her role model, she explains, is her father-- the person who first introduced her to science and showed her that it could be “really cool”. On a more serious note, the scientist admits that being both a scientist and a Christian can be difficult. The most frustrating thing about her position, she says, is the amount of disinformation which is targeted at her very own Christian community.

In the second video, “Climate Change Evangelist”, Katharine Hayhoe delves into deeper discussion of the perceived conflict between climate change and Christian faith. She explains that admitting her identity as a Christian scientist can be uncomfortable. Since evangelicals are the targets of much disinformation concerning science in general -- and specifically the science surrounding climate change -- many people in the church have a misguided view of the subject and do not look kindly at her career choice. One woman encountered by Hayhoe at a church in Texas, for example, believed that global warming was a lie taught in schools to mislead her children. In an effort to realign misguided views like these, Katharine Hayhoe and her husband wrote a book addressing the deep-rooted emotions often associated with climate change. People fear that addressing the climate issue will bring forth changes in the economy and uproot their way of life. However, Hayhoe encourages her viewers to act out of love, as the Bible calls us to do, rather than out of fear. Acting out of love inspires us to consider the poor and disadvantaged people around the globe when we respond to the reality of a changing climate.

In the final segment of this three part video montage, Hayhoe addresses the question of what climate change means. Specifically, she is concerned about how global warming affects people on a personal level. While global warming generally brings to mind melting ice caps and polar bears, its implications are far more widespread, affecting the lives of everyone around the world- from cotton farmers in Texas to public health workers in Chicago. If nothing is done to change current emission levels, the number of days per year which exceed 100 degrees Fahrenheit, for example, will begin to increase dramatically, and if emissions are increased, many areas will even develop extreme conditions like those seen currently in Death Valley. Hayhoe’s goal is to demonstrate clearly that the only way to preserve the world for future generations is to significantly reduce dependence on inefficient means of getting energy and instead transition to cleaner renewable energy sources.

Editor's Note: These videos first appeared on the Nova program "The Secret Life of Scientists & Engineers".

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.

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

Review: gene structure and function

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

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

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

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

Comparing gene transcription across species at the genomic level

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

Old hypotheses, new technology

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

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

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

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

These results underscore a few important points:

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

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

For further reading:

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

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

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

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

(Click Image to Enlarge)

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

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

(Click Image to Enlarge)

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

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

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

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

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

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

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

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

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

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

Testing IC with new research

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

For further reading:

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

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

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

Many people say that science and religion need to be even further apart. I disagree, however. And there are many scientists who agree with me.

I am a Christian. I believe that God is the ultimate reality and that the world, including me, was created by God. But this is not just an idle affirmation, a faith statement to be recited in church on Sunday. I find my experience of the world enriched in several ways by my belief in God.

For starters, my first contact with the world that God created is through its great beauty. I write these words from my desk in a sunroom on the back of my house. Outside my window a row of Newport plums is in bloom, their delicate pink flowers lighting up the landscape. My andromedas are also blooming. The dogwood, whose branches brush my window when the wind blows, is starting to bud. Directly in front of me the sun is coming up, visible through the forest. New spring foliage at the tops of the trees is becoming illuminated. In a few minutes I will have to pull my blind to keep the sun out of my eyes.

A choir of birds is singing, celebrating the arrival of the new day. I can tell from their joyous song that they must not be Red Sox fans. The sound of the birds is so welcome, in contrast to the traffic noise from the front of my house, which starts up shortly after the birds each morning.

Scientific explanations exist for all that I see and hear outside my window. And explanations can be proposed for why humans enjoy nature so much. But faith is God is not about explanations. We do not believe in God because we need to explain this or that feature of the world. That is what science is for. We believe in God because we see something deeper in the world, something that transcends the scientific explanations.

The experience of natural beauty is available to everyone, and only the flattest of souls cannot enjoy scenes like the one outside my window right now.

As a scientist, however, there are other layers to this experience. Underneath the artistic beauty of nature lies the deeper beauty of a system of natural laws. All the wonders in front of me are built from a few dozen different atoms -- hydrogen, oxygen, carbon, nitrogen. They combine and recombine to make life possible. Their molecular arrangements are the pixels of nature's most beautiful scenes.

These atoms are all built of protons, electrons, and neutrons. In all the atoms, electrons hum about tiny nuclear cores, following an amazing set of mathematical laws. I can still recall those giddy undergraduate days, decades ago, when I learned to solve the equations that specify what these electrons can do. The solutions were difficult and required the better part of a math degree to produce, but they were elegant beyond belief.

I remember working into the wee hours of the morning, losing track of time, hoping that I wasn't making mistakes along the way. And then finally a solution appeared on the paper in front of me that was so breathtakingly beautiful that I knew there was no way I had made a mistake. The solution was so simple. All you had to do was plug numbers into the final result -- simple integers like one, two, three -- and electronic arrangements would pop out. It was Sudoku on steroids.

The beauty of these mathematical patterns is a rich part of the scientific experience of nature. It is what draws people into physics and often turns them into detached and marginally functional mystics, like Newton and Einstein.

What seems the most remarkable of all, though, is the way that the whole system works together. That sun coming up in front of me is 93 million miles away. It takes eight minutes for the light generated by its fusion reactions to make the long trek to earth. Some of the light arriving outside my window is absorbed by chlorophyll molecules in the plants and becomes stored energy. Some of this energy was in the lettuce I ate last night in my salad. Now that energy is driving my metabolism, keeping me alive, letting me experience this new day, powering my fingers now on my keyboard. Some of the sunlight warms the ocean after a long New England winter, coaxing summer into existence. The light makes it possible to view the scenery outside my window. Everything I see becomes visible only when light strikes it.

I also note that this same multi-tasking sun provides the gravitational force that keeps the earth in its stable orbit, tracing out a mathematically perfect ellipse several billions times in a row.

The full experience of a new day is a complex mix of wonder and science, facts and beauty, mathematics and color. Science explains much of it, and what is left over is not so much in need of explanation as it is in need of celebration.

My belief in God provides a framework for this celebration. In some way that I cannot articulate, I praise God for each new day, dimly aware that I am sharing the experience with the artist who put it all in place and put me here to enjoy it.

This piece originally appeared April 21, 2010, on The Huffington Post.

Along the side of our patio in front of our family garden, I grow grapes. I was inspired to grow them from the tradition of my mother's homeland in Cyprus, where grapes, olives, figs and lemons adorn the patios of each house. I was challenged to grow them well by the words of Jesus in John 15: "I am the vine, you are the branches, I will prune you to produce much fruit." Pruning is the secret to successful grapes, but that's another story.

The point is that in tending that grape arbor and our family garden, and exploring the beautiful landscapes we are blessed with in Virginia, my wife Elizabeth and I, along with our three daughters, are in communion with the Creator and Sustainer of heaven and earth. That may sound like a lofty statement, but for me, nature, His created order, is where I find Him most personally. I have known and recognized this since I was a boy.

Though born in Richmond, I was raised in Portsmouth, Virginia, where my father and I would fish along the Elizabeth River and the Chesapeake Bay. With my friends, I hunted in the Great Dismal Swamp. My father grew up on my Grandpa's farm in Tennessee near Bristol and he took our family back there often. My grandfather was one of those vanishing breeds of men who had fidelity and love for the land. He was dependent on the land for his food and a few cash crops for income. He was intimately tied to the rhythms of the seasons and his work in the fields.

My grandfather and my aunts and uncles looked at this work as a partnership with the Lord. They taught me how to care for the land, as well as the names of plants that grew in the forests and along the streams that surrounded their farms. They also taught me skills that made me appreciate their way of life. Through these early experiences, I became fascinated with an essential question: What makes nature tick? I also developed an interest in the spiritual relationship between God and His creation. And so the journey began.

I took up the study of biology at Virginia Tech focusing on stream ecology, and then worked as a field biologist surveying rivers throughout the Southeast. Eventually, I returned to graduate school to study forest ecology in the Shenandoah National Park. My faith in the biblical account of creation was challenged by professors who taught evolution as the mode of creation of living things.

This challenge I brushed aside until I began teaching biology at a community college in Clifton Forge. The words in the textbooks and the words of Genesis took on new meaning. Did they contradict each other? Could all forms of life really evolve by chance? Weren't we created in His image? My students questioned me about this conflict and I started a search for the answers.

For several years I wrestled with these questions as an intellectual exercise. I began to make progress only when I started answering with my heart along with my head, aided by that other gift received from my parents, trust in the power of prayer. Looking back, this doubt and questioning, this need to have all the answers, made my faith real exactly as it taught me that I don't need to have all the answers: that is where faith comes in.

I do know with certainty that God created the heavens and the earth, and manages and sustains His creation even today. I cannot know with certainty how He did it with such precision and beauty. How God created is still a mystery that science, by its methods, tries to discover and cannot fully explain, and one that the Bible is mostly silent on.

To me, there should be no contradiction between science and the Bible. In the beginning, God was there and science cannot speak to that. It is by faith that I know that God created the world not by chance, but for his purposes and glory. The precision of natural order and its beauty have always focused me on the Creator, just as Paul states in Romans that all creation bears witness to God. The more I study nature and natural sciences, the more it drives me back to God who made all things.

In time, I was hired by The Nature Conservancy in Richmond as the ecologist and director of a new biological inventory for Virginia. Then another faith question came. Why did the Church not speak to the Christian practice of stewardship as it relates to creation? Why did many in my profession worship the creation and not the Creator?

I stumbled upon the work of Wendell Berry, who has since become one of my favorite authors. In a short essay he wrote in 1988 entitled God and Country, he said we must deal with the true meaning of Genesis 1:28 where God told Adam and Eve to "be fruitful and multiply and replenish the earth and subdue it." He was right. Berry noted that many people use the words "dominion" and "subdue" as "unconditional permission to use the world as they please." I came to realize, like many, that such an interpretation is contradicted by the rest of the Bible.

The ecological teaching of the Bible is clear. God made the world and it pleased Him. It is His and He loves it. He has never given up title to it. He wants us to take excellent care of it. In Genesis we see it in His instructions to Adam and Eve in the Garden; in Leviticus 20, we see it in the Sabbath year and the Jubilee—laws governing land use, land rest and God's ownership of the land; in Psalm 24 David affirms "the earth is the Lord's and everything in it"; Jesus, in Matthew 6, tells us not to worry, for if God cares for the birds and plants, he'll also care for you; and in Romans 8:19, Paul says the creation eagerly awaits freedom when right relationships will be restored.

Biblical ecology is really a moral understanding of what God expects of us in relation to the natural world, but also in relation to the other people with whom we share it. This kind of stewardship has only been recently talked about in the Church. It means careful management, not destruction and abuse. It is infinitely practical because a healthy planet is in our best interest (we depend on its fruitfulness, after all), but biblical stewardship is also an act of loving our neighbors as ourselves, of loving even our children and grandchildren, by leaving them a decent place to live.

Psalm 8 lays out a mystery that, with the rest of Scripture in mind, invites a response in action as well as praise: "When I consider the heavens, the work of your fingers, the moon and stars you have ordained, what is man that you are mindful of him?" After more than 20 years with The Nature Conservancy in Richmond, Elizabeth and I have made a home for our family and have a church home, as well—all places in which we can respond to that mystery by bearing fruit. And though my answering the call to use my talents and time in each of those realms branches in many directions, it is always rooted in my awe of God, who created and sustains the universe and seeks a relationship with us. It is a call I live out in my vocation of protecting and restoring the lands and waters in Virginia, and a call our family lives out in our garden, in our frequent excursions in the outdoors, our worship of the Lord in church and at home, and, yes, even in growing grapes.

Dr. Owen Gingerich is professor emeritus of astronomy and history of science at Harvard University. He grew up in a Christian home and attended a Christian college in northern Indiana that had a motto of “Culture for service”, something that was very important in thinking about what he might do with his life.

When it came time to go to graduate school, one of his science professors told him “If you feel a calling to go to astronomy, you should give it a try, because we shouldn’t let atheists take over any particular field.”

And so he went on to a career in astronomy. In the late 1980’s, Dr. Gingerich had a unique opportunity to give a lecture at the University of Pennsylvania on the topic of science and Christian faith. Since then, he’s been trying to help people better understand God’s creation. For example, God could have made the universe in many different ways, but given the particular way it appears, it suggests that we wouldn’t be here if the universe were not very, very old, because out of the big bang came hydrogen and helium, but not oxygen and the iron we need for our blood, for instance. Those things came from the interiors of giant stars and had to cook for long, long periods of time before we got those elements abundant enough for sustainable life. It’s a marvelous picture, and Dr. Gingerich is actively involved in telling people about it.

A member of a church that I was attending once told me that I was “giving bullets to the enemy” because I claimed to be a Christian and an Evolutionary Biologist. I responded (shamefully, with equally as little Christ-likeness) by saying that it was also possible to lead people astray by telling them that, to be a Christian, they had to dismiss scientific evidence in favor of something akin to fortune telling using sheep entrails—i.e. “Creation Science.” Understandably, this touched a nerve. Please don’t misunderstand me; I was not trying to be dismissive of his viewpoint, I was trying to be understanding, compassionate and loving. I confess to failing miserably at the attempt.

But you should not think that evolutionary biologist colleagues can be any less judgmental, or that I can be any more forgiving of their attitudes. That’s why when the evolutionary biologist accused me of having “no integrity” for saying that I could be both a Christian and an Evolutionary Biologist I responded that I was not the One he would have to answer to regarding his unbelief. I guess it isn’t surprising that that seemed to touch a nerve as well. For your information, I pray the same prayer for both my non-Christian, scientist colleague and my church acquaintance; that they both would come to the realization that we all need desperately God’s grace and forgiveness.

On the other hand, I must admit that in my least charitable moments I just pray that they would get a grip, start enjoying some hobby, or maybe a spouse or girlfriend/boyfriend, and in the process forget to accuse me, and others like me, of giving aid and comfort to those evil folks who stand on the other side of the philosophical fence. My prayer for myself is that my frustration over such interactions would leak quickly out the bottom of my left foot, never to return.

I really would like to be much kinder and gentler than the oft-times nasty, vindictive, hyperbolic tirades pulsating between the extreme elements of the so-named (by the other ‘side’) ‘spiteful, hell-bound evolutionists’ and the ‘brain-dead Christians.’ But it really is tempting to challenge the attitudes of the opposing evolutionist and creationist guerilla fighters mentioned above, and I suppose such an exposé could be both entertaining and enlightening. In fact, it might even cause my friends, who stand firmly in one camp or the other, to smile and maybe even take pity on us poor souls sitting on the razor wire fence between the warring factions.

That gives me an idea. Maybe my position is sort of like being a U.N. Peacekeeper in Lebanon. I mean you can’t get between the two opponents without getting shot at, you’re not supposed to shoot back, and you look somewhat silly in those powder blue helmets. In other words, no one takes you seriously, and your only useful role is as a negative example for parents to use: “Eat your broccoli and drink your milk, or you might grow up to be a U.N. Peacekeeper...or even a Christian Evolutionary Biologist.” The analogy of being a member of a mainly powerless peacekeeping force also illustrates how silly the “bullets to the enemy” accusation is. I mean why in the world would I prance (I am confident in my level of masculinity) into the camps of the vehemently-positive-of-their-correctness combatants, hand them ammunition and then prance (see above) back into no-man’s land all the while being shot at from both sides?

Hmmm. Maybe that is exactly what I am doing. I mean, look-it, very religious people who (at least according to my evolutionist friends) occupy the territory of mindless oafs see me as Satan’s Toady. To these religious adherents, I am Scut Farkus’ (a la A Christmas Story) right-hand man, Grover Dill: I have green teeth, dress in a James Dean-esque leather jacket, terrorize unsuspecting kids into submission (in my case, into believing the heresy of Evolutionary Biology), and am only brave when my enormous minder—made up of degrees, books, etc.—is starkly visible. As appealing as this image is to me, I really don’t fit the stereotype; my teeth are actually a shade of yellowy-brown due to my long-lasting love affair with espresso.

What about the opposing viewpoint of my hyper-enlightened, hyper-rational, hyper-intelligent, hyper-etc. evolutionist colleagues? Unfortunately, to them I am 1) suffering from a delusion – self-induced, or pathological, 2) a spy for those anti-evolution wackos, or 3) someone who just wants to be able to make loads of money from writing books and articles on how a person can be both a Christian and an Evolutionist. (O.K., so that last one is my idea.)

Some might conclude from the above that I, and others of my ilk, feel like a person from an ethnic minority at a skinhead convention—a bit vulnerable and a bit undervalued. Well then are Christian Evolutionary Biologists simultaneously heretical and ignorant? Realistically, if I am giving ammunition to each of two opposing factions, how then can I hope to be a card-carrying member of either? I guess my answer is that putting a bunch more cards into my wallet just increases the size of the lump I have to sit on. In other words, I either have to be content with a throbbing pain in my derriere, or I have to jettison trying to simultaneously please two groups of fairly discontented people. Christ talked about trying to serve God and the pursuit of money. I think that when I get depressed about not feeling a part of either of the groups that I truly like and understand—i.e., “Mindless Christians” and “Godless Evolutionary Biologists”—I am suffering from putting people ahead of God.

I intend this essay as a challenge to both myself, and anyone else interested enough to take the time to think about the various issues. The position of Christian Evolutionary Biologist continues to challenge me because I don’t see how all the pieces can possibly fit into a coherent picture. As someone who demands neat answers I find this frustrating and confusing. I do, however, believe that what I am outlining gives some sort of a platform for discussion, at least if we take Theodosius Dobzhansky’s words – quoted at the first of this essay – to heart. For this to happen, Christians need to refrain from using the Bible as a Biology/Geology/Chemistry/Physics textbook in order to prove to non-Christian Evolutionists that they (the Christians) are not unintelligent.

As an aside, Christians also need to quit trying to prove God’s existence through probability formulae. There is no danger of this outcome of course, but if we were able to prove God’s existence in this manner, then we would be God, and that would be a pretty disappointing turn of events. I really want to be careful here to not be ungracious, yet I have to say that misusing the Bible and attempting to prove God’s existence through cleverness tends to prove the non-Christian Evolutionists’ point...that some Christians—in their zeal to see themselves as triumphing over non-Christians—really can look pretty unintelligent.

In the same way, Evolutionists need to quit trying to convince people that understanding evolutionary processes is anywhere near as important as investigating the possibility of having a parent/child-type relationship with an omnipotent, omnipresent, omniscient God Who is able to judge people and send them to Heaven or Hell depending on whether or not they are members of His family. It flat won’t make a bit of difference if I work out the natural selection coefficients that were necessary to produce every species that ever existed if I end up denying God’s existence to my eternal regret.

The Apostle Paul wrote that Christians were people that should be pitied most if the basis of their religion (the resurrection of Christ) was found to be a hoax. In my weak humanity, I would have to disagree somewhat with this Pauline hyperbole. I would say that it is a whole lot better to have had a difficult time here on earth because you tried to live a “Christian life” and then die to realize that there is nothing on the other side (or actually not realize it because you aren’t there...well...you know what I mean) than it is to put your hope in your intellectual exercises and then die, come face-to-face with God, and thus discover that you weren’t nearly as clever as you supposed. I would suggest that the latter state would be infinitely and eternally worse than being a person from an ethnic minority at a skinhead convention.

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

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

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

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

Evolution: A Theory with Bite

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

Independent Lines of Evidence, but Contradictory Stories?

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

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

Signature in the SINE

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

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

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

For further reading:

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

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

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

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

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

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

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

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

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

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

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

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

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

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