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

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

Evangelicals in Tension with Science

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

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

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

Reconciling Evolution with Scripture

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

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

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

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

Signs of Hope

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

It’s Your Turn to Talk

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

According to Merriam Webster, the term “intelligent design” has been used since at least 1847, in reference to “the theory that matter, the various forms of life, and the world were created by a designing intelligence.” That’s a decent definition, also consistent with those offered by today’s proponents of intelligent design (ID). For example, the leading ID think tank, The Discovery Institute (Seattle), has this:

Intelligent design refers to a scientific research program as well as a community of scientists, philosophers and other scholars who seek evidence of design in nature. The theory of intelligent design holds that certain features of the universe and of living things are best explained by an intelligent cause, not an undirected process such as natural selection.

And in the opening sentence of a book he edited with philosopher Michael Ruse, ID theorist William Dembski said, “Intelligent Design is the hypothesis that in order to explain life it is necessary to suppose the action of an unevolved intelligence.” (Debating Design, p. 3)

On the other hand, while a recent contest on a prominent intelligent design (ID) website uncovered several other early uses of the term, it is important to note that it does not always mean exactly the same thing in each reference. The term itself has an interesting history, and while ID authors obviously did not invent the term “intelligent design,” they have given it specific content in recent years. Indeed, they have even removed content in some cases: a point I will return to later is that, though it seems the only viable candidate for such an “unevolved intelligence” is God, ID proponents sometimes seem to do cartwheels to avoid saying as much. When a term has such a complicated past, there simply is no substitute for looking at specific references in their own contexts as we move to seeing how ID plays out today as one of the 5 ways of relating science and the Bible.

Interestingly, many Protestant “modernist” scientists and theologians from William Jennings Bryan’s day (see my previous column) unhesitatingly endorsed the idea that a designing intelligence lay behind nature. At least one such person, Nobel prize-winning physicist Arthur Holly Compton, even used the very term “intelligent design” in an address he gave at a Unitarian church in 1940: “The chance of a world such as ours occurring without intelligent design becomes more and more remote as we learn of its wonders.” (Quoting his pamphlet from 1940, The Idea of God as Affected by Modern Knowledge, p. 13. For more about this aspect of Compton’s views, click here.) However, Compton regarded design as a philosophical and theological inference from science, not an explanation within science to be invoked when other explanations fail. He also accepted the common ancestry of humans and other organisms. This is a significant difference from the ID movement today, which offers ID as a scientific alternative to Darwinian evolution and (at least in many cases) seeks to undermine public confidence in common ancestry (even though ID per se is not actually opposed to it).

If any ID proponents are sympathetic to the type of religious modernism that Compton and his friends embraced, I cannot tell you who they are. In a curious, ironic twist, ID is often used by conservative Christian apologists partly to defend a cluster of traditional theological and hermeneutical positions that none of the modernists would have defended. A further irony: the intellectual descendants of the modernists—those scientists and theologians who occupy the left wing of the modern “dialogue” of science and religion—exhibit a studied avoidance of the term “design,” disconnecting them on that score from the modernists of the 1920s.

Many other contemporary writers, including some evangelical TEs, are also reluctant to use the word “design,” precisely because in their view it has been co-opted by ID proponents and they do not want readers to misunderstand their position(s). They may agree with ID proponents that certain features of the universe reflect divine design, but because they do not see design as a scientific explanation they employ other language. (Likewise, the YECs have co-opted the word “creationism” to mean just one specific understanding of God’s creative activity, leading most advocates of other views either to provide their own definitions of the word or else to avoid using it altogether. Politics dogs this conversation at every turn.)

Core Tenets or Assumptions of Intelligent Design

With that bit of historical context for the term “Intelligent Design,” let’s now look at the first of the Core Tenets of this perspective in its current state, and as it is most often used by those associated with the Intelligent Design movement.

(1) The Bible is NOT to be mentioned (at least for now); ditto for “God” and “theology” as far as possible.

This is a deliberate strategy, adopted for political reasons to keep arguments at the level of philosophy and science. Here, “political” refers to the American political system, with its constitutional disestablishment of religion, not to partisan politics. Since the 1980s, federal courts have consistently ruled that “creationism” (which was specifically of the YEC variety in the relevant cases) is sectarian religion, not science, and therefore it cannot be taught in public school science classes. Anxious to avoid a similar fate, proponents of ID always want to ensure that they are not perceived as advocates of “creationism.” The less they mention God and the Bible, the reasoning goes, the less likely they are to fall afoul of those decisions.

The First Amendment to the U.S. Constitution, pertaining to the freedom of religion and the freedom of the press.
Source: http://www.rochester.edu/college/psc/images/Courses/Spring2008/FirstAmendment.png

Phillip Johnson, the former law professor who effectively began the ID movement some twenty years ago, has put it bluntly: “To put things on a more rational basis, the first thing that has to be done is to get the Bible out of the discussion.” He quickly adds, “This is not to say that the biblical issues are unimportant; the point is rather that the time to address them will be after we have separated materialist prejudice from scientific fact.” (“The Wedge: Breaking the Modernist Monopoly on Science,” Touchstone: A Journal of Mere Christianity, July/August 1999, p. 22.)

If God and the Bible are really to be left out for the time being, then why am I discussing ID in a series on “Science and the Bible”? It’s a fair question. I simply don’t see any way meaningfully to avoid talking about ID apart from the culture wars in which it is embedded (I’ll say more about this in a subsequent column), and the Bible is never far from the surface when the battle being fought involves origins. Conservative Christians sense that ID really is about God—Dembski’s “unevolved intelligence”. As Dembski himself has said, “no intelligent agent who is strictly physical could have presided over the origin of the universe or the origin of life”, and there aren’t a lot of candidates for that job. Many Christians also identify strongly with the ways in which ID seeks to confront the secular establishment, in an explicitly-stated effort to combat what Johnson calls “the modernist scientific and intellectual world, with its materialist assumptions.” (“The Wedge,” p. 23.) They see it as a way of getting traditional theistic perspectives and Christian values back into the academy, once “design” has become an acceptable academic talking point—and it isn’t very far from there to conversations about “science and the Bible.” If this were not so, then why would so much ID literature be published by Christian presses? Indeed, when I tell church audiences with a straight face that ID purports not to be about the Bible at all, I’m usually met with considerable skepticism.

When I’m back in about two weeks, we’ll look at further Core Tenets of ID—the ones that have even less to do with the Bible, explicitly, and more to do with the way we approach the study of the natural world.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Surprised by Jack

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

Notes

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

Introduction

One of the reasons that some of us are hesitant to accept evolutionary creation is that it seems to make God responsible for the suffering and death of innumerable creatures over millions of years—before humans ever existed or sinned against their creator. Since we believe in and worship a God who is loving, benevolent, and all-powerful, it sounds quite implausible that our God would have created a world like that; therefore, any scientific evidence for evolution must be incorrect.

Other people look at the scientific evidence for evolution and find a compelling case that it has taken place during our earth's history. On this basis they may conclude that if evolution is true, then the belief in an all-powerful, perfectly good God must be false!

The trouble with both of these views is that they tend to invoke a completely abstract, philosophical god, not the living God of the Bible—the God who became a human being, experienced unimaginable suffering, and died in a grotesque and humiliating public display. The death of Jesus completely defied the expectations (and common sense) of his followers, as well as the expectations of any “rational” understanding of the way the Creator of the universe should act in the world. On the cross, in the person of Jesus, God took upon himself far more suffering than any creature has ever experienced.

If God himself is willing to die, particularly in such a gruesome way, then perhaps we should at least consider the possibility of God allowing the death of other creatures, too. But would this really be compatible with what we know of God through Scripture? In this essay, we will explore this quandary through a “theology of the cross”, a concept articulated by pastor George Murphy in his book Cosmos in the Light of the Cross.¹

Theology of the cross

Before we jump into the theological problems associated with evolution, let’s take a look at how we understand Christian theology itself. For the reformer Martin Luther, any theology (or science) that tries to reach knowledge of God apart from the cross is bad theology.² Instead, Luther pointed to a theologia crucis, in which the true God is seen first and foremost “through suffering and the cross”. To make his point even clearer, Luther insisted that “the CROSS alone is our theology”.³ It is the lens through which we view everything.

Of course Martin Luther, having lived in the 16th century, was not aware of the vast history of life on our planet (or any other aspect of modern science, for that matter), but George Murphy draws from Luther’s teachings the foundation that all human knowledge begins with the Word made flesh and crucified.⁴ With the cross of Christ as the ultimate framework through which we view reality, we are bound to view the processes of nature quite differently. As Murphy explains it,

A theology of the cross is an explication of belief in a God who becomes a participant in the history of the universe and thereby shares in the suffering, loss, and death that are part of worldly experience.⁵

God does not sit idly by and watch unaffected as his creatures suffer, but neither does he swoop in and make everything completely effortless and easy. Instead he chose another way, the crucifixion of Jesus—certainly not the approach that we would have preferred! The apostle Peter went so far as to try to talk Jesus out of it, but he was met with a stern rebuke (Matthew 16:21-23).

Why is evolution so disconcerting to Christians?

The problem of suffering throughout all of human history is troubling enough for us to reconcile with a loving, personal God. But in addition to that, the discovery of vast numbers of fossils reveals that death has taken place on a far greater scale than we had ever imagined. Both the wide variety of extinct creatures and their sheer numbers is quite staggering, and it raises questions about our Creator:

The picture of a God who is immune from suffering and death but who forces organisms through millions of generations and extinction is disturbing to those who believe in a God of love.⁷

The mass extinction of life on earth was already well established by the early 19th century—decades before Darwin’s research—and extinction can be empirically verified independent of any theory of evolution.⁸ The fact that the earth’s crust is a veritable graveyard of long-lost creatures is deeply troubling, and as late as the 1790’s, distinguished intellectuals such as Thomas Jefferson denied the very possibility of extinction.⁹

But in addition to the reality of species extinction, the theory of evolution by natural selection proposes that new species also arise in an environment containing widespread pain and death. Both the creatures that are now living and those that are gone are tainted by an “acrid smell of death”.¹⁰ It makes us wonder, if our Creator is not the God of the dead, but of the living (Mk. 12:27), where is God’s presence in the evolutionary picture?

In all honesty, creation through evolution is not what we would expect from God, but Scripture is full of examples in which God acts in unexpected ways. After all, God’s choosing to undergo an agonizing death on a cross is not what we would expect from the all-powerful Creator of the universe, either. In both cases, new life comes about through pain, suffering, and death. As George Murphy puts it,

A priori ideas about God have to be overcome, and God's character has to be learned from God's self-revelation.¹¹

God’s fullest self-expression is in Jesus Christ himself, one who is intimately familiar with and personally endured creaturely pain and death. The theology of the cross reveals that God's self-revelation takes place in situations of suffering, loss, and apparent hopelessness, much like situations that occur through natural selection.¹²

The crucifixion is disconcerting too

Not only is creation through evolution an unexpected and unsettling process, but so is the crucifixion of Jesus! Killing someone by hanging them on a cross is an unbearably painful, prolonged, humiliating form of death. It was such a horrific type of public execution that it wasn't until after the Roman Empire stopped the practice of crucifixion—and people no longer witnessed it personally—did the cross become a visual object of devotion.¹³ Our culture is sufficiently removed from crucifixion that we are desensitized to its original significance, but to connect it to our current context, imagine the reaction you would get by wearing jewelry designed to look like an electric chair.¹⁴

Once we are more attuned to the brutality of crucifixion, it seems all the more striking that the cross is the sign of God’s work, what George Murphy calls “the trademark of God”.¹⁵ The suffering and death of Jesus is featured prominently in the Gospels, but the crucifixion-resurrection pattern is strongly resonant within the Old Testament, too. Israel suffered and toiled as slaves in Egypt for centuries before they were rescued in the Exodus, bringing life to a people who were spiritually dead. Centuries later, the nation of Israel would experience death again when the Babylonians destroyed the Davidic monarchy, burned their Temple, killed their people, and sent many into exile.¹⁶ Neither Israel (God’s chosen people) nor Jesus (God’s own son) were spared from death and suffering; rather, suffering seems to have been the way in which God re-forms and renews humanity to fully bear His own image.

Redemption extends to all of creation

Fortunately, God’s story does not end with death. God gives new life after his creatures have been subjected to terrible circumstances. Redemption was promised to Israel itself—Ezekiel’s vision of the valley of dry bones describes how God would renew His chosen people (Ezek 37:1-14). Later, the astonishing resurrection of Jesus made salvation possible not only for Jews, but for all people in Christ (Gal 3:26-29). Ultimately, the New Testament makes it clear that God’s renewal will encompass the entire Creation:

For God was pleased to have all his fullness dwell in him, and through him to reconcile to himself all things, whether things on earth or things in heaven, by making peace through his blood, shed on the cross. (Colossians 1:19-20)

With all wisdom and understanding, he made known to us the mystery of his will according to his good pleasure, which he purposed in Christ, to be put into effect when the times reach their fulfillment—to bring unity to all things in heaven and on earth under Christ. (Ephesians 1:8-10)

Christians are accustomed to thinking of the death of Christ in regard to humans, but our culture rarely acknowledges God plan for the redemption of His entire creation. This is partly attributable to the fact that discussions of creation and origins are often separated from the topic of salvation.¹⁷ In doing so we tend to marginalize Jesus as we argue about Genesis. Rather than fall into this trap, if we view nature through a theology of the cross, we will see Christ as both the alpha and the omega point in discussions of life’s history and life’s future. With this perspective, we are more apt to sense our solidarity with the rest of creation as we wait in eager anticipation of a glorious future:

The creation waits in eager expectation for the children of God to be revealed. For the creation was subjected to frustration, not by its own choice, but by the will of the one who subjected it, in hope that the creation itself will be liberated from its bondage to decay and brought into the freedom and glory of the children of God. (Romans 8:19-21)

Conclusion

As part of the Church’s conversation about the problem of natural evil, this essay is meant to be a brief introduction to a “theology of the cross”. One can explore this concept in greater detail in Murphy’s book The Cosmos in the Light of the Cross. While there is a lot more to be said, let me conclude with the following observation: though evolution may not be compatible with some interpretations of Christianity, evolutionary creation is certainly compatible with the crucified Christ and the theology of the cross. In the person of Jesus, God suffers with the world and ultimately redeems it. As George Murphy puts in, “The world's pains are God's stigmata.”¹⁸

Explore this Topic Further

• Miller, Keith. “And God saw that it was good”: Death and Pain in the Created Order. BioLogos series
• Murphy, George L. The Cosmos in the Light of the Cross. Harrisburg, PA: Trinity Press, 2003.
• Murphy, George L. “Cross, Evolution, and Theodicy: Telling It Like It Is”. In The Evolution of Evil. Edited by G. Bennett, M.J. Hewlett, T. Peters, and R.J. Russell. Göttingen: Vandenhoeck & Ruprecht, 2008.
• Southgate, Christopher. The Groaning of Creation: God, Evolution, and the Problem of Evil. Louisville, KY: Westminister John Knox Press, 2008.

Notes

1. Murphy, George L. The Cosmos in the Light of the Cross. Harrisburg, PA: Trinity Press, 2003.
2. Murphy, p34
3. “CRUX Sola Est Nostra Theologia,” in D. Martin Luthers Werke, Kritische Gesammtausgabe (Weimar: Hermann Boehlau, 1892), 5:172. The captitalization is in the original. Cited in Murphy, p26.
4. Murphy, p108
5. Murphy, p4
6. Murphy, p43
7. Murphy, p3
8. Some Christians ascribe animal death to some combination of Adam’s fall and Noah’s flood, but this does not resolve the problem that the animals are still suffering and dying through no fault of their own. See Keith Miller’s BioLogos series Death and Pain in the Created Order for the limitations inherent in a fall-based theodicy.
9. Rudwick, Martin. The meaning of fossils: Episodes in the history of paleontology. Chicago, University of Chicago Press, 1985.
10. See Jeff Schloss’ BioLogos essay Evolution, Creation, and the Sting of Death
11. Murphy, p63
12. Murphy, p122
13. Murphy, p27
14. This example is drawn from an evangelical outreach event held by a Christian student group in Innsbruck, Austria. On campus one day, they started conversations with their classmates by asking the question, “Would you wear an electric chair on your neck?”
15. Murphy, George L. The Trademark of God: A Christian Course in Creation, Evolution, and Salvation. Wilton, Conn.: Morehouse-Barlow, 1986.
16. Murphy, Cosmos in the Light of the Cross, p 31-32.
17. Murphy, p35
18. Murphy, p87

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.

Genesis is one of my favorite books of the Bible. I read through it probably once every few months and repeatedly grind my Hebrew language skills on its opening chapters. Unlike Leviticus (at least in the opinion of most people I know), the Genesis narrative is exciting and adventurous. Some of our favorite stories come out of the book: Noah and the Ark, The Tower of Babel, Abraham and Isaac, Joseph and the Coat of Many Colors, and so on.

But no story is perhaps as infamous and well known as the creation account (or accounts) as presented in Genesis 1-2. Almost every Christian or Jew, even those less than devout, know the opening words to the tale: “In the beginning, God created the heavens and the earth.” We know that God created the earth in six days. We know Eve was taken from Adam's rib for a companion. We know that God called the general creation “good”, the special creation of man “very good” and, at the very end of it all, took a day of rest (which I'm sure most of us would call “very good.”)

Of course, we know all of this. Yet we challenge it (and are challenged by it), continually, when we consider the variety of interpretations of how this story intersects the world as described by science. With Genesis, are we dealing with a literal scientific account, where “day” means 24-hours; are we dealing with metaphorical “days” in which epochs or periods of time or even processes are being described; or are we readers of a creation mythology from the Ancient Near East that doesn’t have anything directly to do with material origins? Interpretations go on and on, as anyone who has spent any time at all studying the creation debate knows. By and large, however, we can probably categorize Genesis interpreters into three camps: the Young Earth Creationists, the Old Earth Creationists, and the Theistic Evolutionists.

Now, I have the unique benefit of falling into all of these individual camps at one point or another in my life, sometimes even mixing them up. I have made a strong transition from being a die-hard Young Earth Creationist to being convinced that the evolutionary story is, in fact, the more substantiated and evidenced position. I say this with no pride, since my own transition involved many agonizing questions, a whole lot of reading, and a significant internal spiritual battle: what I believed about when and how the earth was created would not only change the way I read Scripture, it would also change certain aspects of how I viewed the Creator.

While I've certainly learned a lot of information on my journey, it was not an accumulation of facts that has kept me following Christ through all the ups and downs, but Jesus himself, and the knowledge that truth is not something which the Christian should find spiritually threatening. Nevertheless, those same ups and downs—and my internalization of each of these views on creation in turn—has provided me with one simple realization about the debate over scripture and evolution: most of us are not so committed to finding the truth about Genesis and creation as we are to sustaining and maintaining our own interpretive boundaries and the boundaries of the communities which influence us. In other words, the debate is often not so much over Genesis—or even over whether we can all follow the same God when we believe different things about how he created—it's over our own ability to be right. I know this because admitting that I was wrong was the most difficult part of my own transition.

Interpretive communities

While I am pretty convinced of the truth of an evolutionary portrait of reality and an ANE reading of Genesis similar to that espoused by scholars like Peter Enns or Bruce Waltke, I can still make this claim about interpretive communities because my intention is not to dissuade others from debating the issues involved, but to ask that we simply recognize our own limits and check them as often as possible. This is part of following Jesus, is it not? Unfortunately, vigorous debate often deteriorates quickly into screaming matches where proponents of one position or another simply are talking heads, speaking past each other and forgetting our fellowship in Christ. We play into the same interpretive competition that the Pharisee and Sadducee scribes were well known for, each claiming to have a proper interpretation of the Scriptures, but all the while forgetting that interpretive arguments matter exceptionally little if a genuine search for God is not at the forefront. This is certainly not to insist that the discussions cease, but rather, to insist that these discussions can only be propelled forward if individuals—of whatever stripe—step outside of their own interpretive boundaries and communities and humbly present themselves before God, seeking His truth alone. It is to insist that “system maintenance” must die along with the self, because only then can we allow Scripture to interpret itself. Unfortunately (and this is an issue that goes way beyond the Genesis text), too many of us are more committed to a specific model than we are committed to seeking God’s truth, whatever inconvenience to us that truth proves to be.

In 2006, for instance, I heard a popular and well-trained Young Earth paleontologist make the following statement: “If all the evidence turns against young earth creationism, I will still believe it because that's what the Bible says.” I followed up with him in a conversation a year later over lunch and quickly realized that I did not misunderstand his statement. For him, the parameters of his convictions were set in concrete and the truth of the overarching story of Christianity rested on these parameters not being crossed. In his view, the Bible absolutely and fundamentally teaches a universe which came into existence 6,000-10,000 years ago; to deny that is to deny Scripture, and if evidence turned up to the contrary one must not alter those parameters but, instead, search (perhaps in vain) for counter-evidence or be willing to live in blind faith. For this paleontologist, confident Christianity hinged on the stability of those borders of interpretation. Transition wasn't allowed.

But I have heard and read statements coming out of the two other camps of thought that share this kind of certainty over interpretation, too. There is a sense of doing injustice to scripture, thereby doing an injustice to Christianity, and, thereby again, doing an injustice to God if one strays from the preferred reading. One Old Earth Creationist remarked in a popular book that an interpretation of Genesis that allows for evolution is a “contradiction in terms” and it's an unfortunate thing to “blame God for it.” Genesis, in the mind of this thinker, specifically precludes any interpretation which leads to the sort of story evolution tells. To think otherwise is to “blame” God for something which he intentionally tells us is otherwise against his nature.

I have equally heard some theistic evolutionists deride—in a very spiritually shallow and personally offensive way—those who do not accept an evolutionary viewpoint. As one who went through an interpretive evolution on biological evolution, I can say confidently that I believe my own transition would have been much easier both intellectually and spiritually if not for feeling as if certain theistic evolutionists accused me of intentionally lying or being mentally ignorant. It seems that all three camps are at least sometimes plagued by the issue of pride—especially in the cases of a few strong advocates. But pride is nothing less than the cement by which interpretive barriers are built, helping them become unmovable walls that protect the interpretive communities within.¹

On the other hand, one of the great benefits of the fall of positivism (or verificationism) and the rise of postmodernism was the realization that total objectivity among individuals is a false conception. And, since individuals make up communities, neither are camps of thought above error and immune from being wrong. Yet way too many Christians continue to approach Genesis as if we can interpret it on its own terms, completely and totally, without reference to our own location in history and culture. We're still functionally positivists. But it is an illusion that we’re above the interpretive fray, and we must realize time and again that we are subjective individuals, affected by a number of factors and people. We are deeply influenced by those that speak into us, those that we trust, and those that we find credible. As W. Randolph Tate writes,

Interpretations...must be consistent with the established interpretive framework of the interpretive community. The worldview of the interpretive community sets the parameters within which interpretations are accepted or rejected.²

The Bible takes a slightly different angle and puts it this way: “for all have sinned and fall short of the glory of God.” In other words, we are not objective data-interpreting individuals but fallen men and women, even as followers of Jesus.

So it’s when groups of folks line up on either side of an issue and make their positions part of their identity that the debate over interpreting Genesis reaches a near stalemate. It's communities against communities, PhDs against PhDs, experts against experts, and—perhaps more internally—interpretive parameters against interpretive parameters. The truth is that as long as we are first and foremost committed to maintaining the community in which we are involved, there will be very little chance of us getting at the real issues and the best conclusions, much less giving an adequate witness to our God, both Creator and Redeemer.

New eyes, fresh air

I mentioned earlier that I spent time in all three major camps of thought on this issue. I was a hard-lined Young Earth Creationist, debating on forums and writing creationist papers in college. I argued for the existence of modern-day dinosaurs, major flood geology, and so on. I was convinced I was right, that defending the truth meant digging my heels deeper into the sand. But two questions plagued my thoughts: first, I asked whether Christianity fell to pieces if I was wrong. Second, I asked whether I was committed to Christ or, rather, to myself and my interpretations. With that as my first major paradigm shift, I eventually came to accept an Old Earth view. I sat comfortably within the Old Earth view for several years, but the Lord was still at work in me, and, once again, brought those two questions to my mind. Back to the books I went, back to the Bible I went, and back to prayer I went.

Through months of extremely difficult and heart-rending transition, I found myself considering a particular reading of Genesis that I would have regarded as unacceptable as a YEC. But then I was confronted with this even more important point about Christianity: often God finds what is unacceptable to us very acceptable to Him! That included me, personally, and I felt the warmth of God’s grace flow over me. In the wake of that change of heart, people accused me of rejecting my background, my Christian education, and my interpretive communities. And, yet—whether I was right or wrong—I knew God accepted my path towards this new reading of Creation as a genuine search for Him. My spiritual struggle—contrary to what I thought while it was happening—was not a struggle to reject bad data and exegesis, it was a struggle to reject myself.

While the “facts” were important, that spiritual struggle was even more so for me. What was God showing me in the midst of it all? Was thinking differently about the creation making me appreciate the Creator less, or more? Did reading Genesis differently mean only that I had been wrong, or that it was somehow less true? What did any of this have to do with my sense of calling to love and serve God and my fellow men? In a way, I’m still figuring this out. But I can absolutely testify that the struggle transformed every single one of these questions. Indeed, for the first time, I believe I saw God as much this-worldly as other-worldly. I saw nature as intimately intertwined with itself, still being woven together by God’s hand. I saw Scripture as a beautiful expression of God’s desire that man should participate in creation. I saw that my fellow men and my fellow Christians were all on a journey, much the way I was. And I saw myself as a flawed, stubborn, and prideful man, yet forgiven for the times I’ve pitted myself and my presuppositions about Scripture against God, its author.

As settled as I am now, I have not forgotten that the common ribbon which ties together all of these transitions is my commitment to keep asking questions within my own circle, too—realizing that God still has much to teach all of us. I have learned the continuing importance of stepping outside of my camp and making sure I haven’t become merely a product of or a willing prisoner to thinking a certain way, unwilling to consider that it and I might be incorrect. I came to realize that everyone (including myself, of course) has stories and life experiences that become the framework in which they read Genesis 1-2. And if I stopped pretending that I, myself, could be perfectly objective, then I also had to stop pretending that those in the community that I trusted were necessarily objective, themselves.

Ultimately, I had to be willing to be wrong and to see that my friends might be wrong, too. That’s not something that any of us are “naturally” very good at, but it is possible when we realize that the world does not depend on us being right, but upon Jesus being right. For me, seeking truth rather than presupposition requires that we all be able to approach the communities that have influenced us deeply, and ask not just “what” they say but “why” they say it. We all have to guard our hearts even more than our heads. Frequently reminding myself to walk back to the edge of my own camp—to follow Jesus’ example and withdraw to a solitary place—has shown me that there is room to breathe outside our familiar interpretive parameters. At certain times, I have found it to be the most refreshing air I've ever tasted.

Notes

1. Though, admittedly, the theistic evolutionists tend to have a greater sense of leeway when it comes to how the claims of Genesis 1-2 affect Christianity as a whole. It would be an odd thing to say that to not interpret Genesis 1-2 as an evolutionary metaphor is to reject Christianity. As far as I know, most Christian evolutionists are very much willing to acknowledge that Young and Old Earth Creationists are still within appropriate spiritual bounds, even if not scientific ones. It seems to me that if individual theistic evolutionists choose an issue about which to be rigid, it’s the Fall and the existence of Adam.
2. Tate, W. Randolpy. Biblical Interpretation: An Integrated Approach. Peabody, MA: Hendrickson, 2008, p 222.

One of the challenges for my students learning biology is summed up in one of my favorite sayings (that I’m sure some students are tired of hearing from me): “All the good concepts are fuzzy.” Take a basic concept like “living” versus “non-living,” for example. Obviously this is a fundamental concept for a biologist, since “biology” means the study of living things. Even here, though, we find that a precise definition of what is “alive” is a hard thing to nail down. While things like humans, dogs and cats obviously qualify (though some days with early lectures I might have my doubts for humans), there are other entities out there that blur the boundary between life and non-life. Viruses, for example, have many of the features of living things, but lack some others. Transposons are less life-like even than viruses, and there are even transposon-like entities that parasitize viruses. Life and non-life are useful concepts, but the precise boundary between them is fuzzy.

More technology = greater fuzz

Often, an increase in technological ability exacerbates the “fuzziness” issue. One example in genetics (that we will later see to be highly relevant to understanding the results of ENCODE) is the concept of “dominant” versus “recessive” for different versions of a given gene. If you recall anything at all about genetics from high school, you might remember learning about Gregor Mendel crossing pea plants that differed in certain characteristics (purple versus white flowers, for example). Mendel deduced that the “particles” that controlled a certain trait (what we would later call “genes”) came in pairs, and that the presence of one type of particle (e.g. the one for purple flowers) could mask the presence of another (in this case the one for white flowers). He deduced that one gene version (what we now call an allele) was dominant over the other one, which in turn was recessive. For Mendel, one determined a dominant / recessive relationship by examining the appearance of a plant with both alleles: whichever allele determined the appearance was the dominant one.

Advances in technology would later do two things to Mendel’s model. First, they would provide deeper insights to what was actually going on at the biochemical level. Secondly, those deeper insights would cause the concept of “dominant” or “recessive” to become more fuzzy. I’ll illustrate what I mean with a (hypothetical, but representative) example.

When Mendel did his work he was limited to what he could observe with the naked eye. Now we have the ability to examine the effects of alleles at much deeper levels than Mendel could. Let’s say, for the sake of the discussion, that the gene Mendel was working with made an enzyme that produced purple pigment. The “purple” allele of the gene (let’s represent it with the symbol “P”) made a fully functioning enzyme: its DNA is copied into mRNA, and that mRNA is used to code for the protein enzyme that does the work of making pigment. The “white” allele (let’s call it “p”), on the other hand, turns out to have a mutation in the protein coding portion of the gene. This single mutation has two effects: it stops translation early, resulting in a protein that is too short and cannot work as an enzyme. The mutation also has an effect on the stability of the mRNA: the mRNA produced by the white allele degrades more readily, resulting in a lower steady-state amount of the mRNA in the cell.

With this background in mind, suppose a scientist performs a series of different tests on a plant that has one purple allele and one white allele (i.e. is “Pp”):

If the scientist looks at the flower color of the Pp plant, she would conclude (as did Mendel) that the p allele is recessive to the P allele, since the Pp plant is as purple as a plant with two purple alleles (PP). This arises because one P allele can produce enough enzyme for complete flower pigmentation.

If the scientist compares the amount of mRNA for this gene between PP, Pp and pp plants, she would notice three different outcomes. PP would have the most, Pp would have less, and pp would have the least. For this test the Pp plant is intermediate between the PP and pp plants. The scientist would conclude that neither the P nor p allele is completely dominant over / recessive to the other (an effect known as “incomplete dominance”).

If the scientist did a test to compare the physical size of the protein enzyme in PP, Pp and pp plants, she would again notice three outcomes. PP plants would have only full-sized enzymes, pp plants would have only small enzyme fragments, and Pp plants would have both distinct sizes, full-sized and small. In this case, the Pp plant shows both character traits (full-sized and small) at the same time. The scientist would conclude that the P and p alleles are both dominant, since both alleles display their version of the trait with neither masking the other in any way (an effect known as “co-dominance”.)

So, is the P allele dominant, incompletely dominant, or co-dominant with respect to the p allele? The answer is “yes” – all three apply, but it depends specifically on the details that the new technology is revealing. Which answer is the most meaningful one? Well, it depends on the specific question the researcher is asking. Now that we have the ability to sequence DNA, we can directly observe the nature of all alleles in any given organism, and the presence of other alleles does not interfere with this observation. In effect, modern molecular biology has made all alleles “co-dominant” since all alleles display their “version of the trait” (i.e. their sequence) when they are sequenced. If one was so inclined, one could argue that “recessiveness” is an outdated concept, and that eventually we will determine through sequencing technology that all alleles are co-dominant. While this would be technically true, it would be very misleading. The p allele remains “recessive” in biologically meaningful ways: it is a loss of an enzyme function, and its complete loss has an effect on the appearance of the organism. Plants that have one of each allele (Pp) have the same enzyme content as PP plants. Anyone who would argue that “recessiveness” was no longer a feature of alleles in light of the new sequencing technology would have to address these issues in a meaningful way, since the evidence for “recessiveness” did not simply evaporate when we learned how to sequence genomes. By any measure, Mendel’s ideas of dominance and recessiveness are still useful concepts.

The relevance to ENCODE

So, how does this all relate to the ENCODE project? It hinges on another very useful, and therefore fuzzy term: “function.” Like “life” and “dominant”, “function” is a useful idea in biology, but much hinges on precisely how it is defined, and the technology used to assess its presence or absence.

The ENCODE definition of “function” is a useful one for the purposes of the large undertaking that this project represents. Specifically, ENCODE was seeking for biochemical activity in the genome: the interaction of chromatin proteins with DNA, regions of DNA that are made into RNA, and so on. This is all well and good, for we now have new tools available that allow us to test for these effects – we have new technology that can shed new insights on what is going on in the genome.

What these results don’t do, however, is cause the prior lines of evidence relating to non-functional DNA to suddenly disappear. As we saw with the dominance issue, the results from new techniques will need to be integrated into a more complete understanding of the data. We must also have a wider understanding of the strengths and weaknesses of various techniques to answer certain specific kinds of questions.

As a way to illustrate these issues for the ENCODE project, let’s consider the hypothetical example we used to explore the dominance issue. The ENCODE definition of “function” includes any detectable biological activity such as the presence of an mRNA transcript. In our example, both the “P” allele (that produces a working protein enzyme) and the “p” allele (which does not) both produce an mRNA transcript. As such, the ENCODE project would indentify both alleles as equally functional. In fact, the ENCODE definition of “detectable biological activity” as “function” would not be able to distinguish between these two alleles in any meaningful way, despite the fact that they have real, biological, and obviously functional differences. This is not to criticize the working definition of function adopted by ENCODE, but merely to demonstrate that this definition, while useful in some contexts, has limitations.

These limitations should stand as a caution to any group that wishes to adopt the ENCODE definition as the only viable definition of biological function. To consider our example again, I suspect that many of those opposed to evolution would bristle at the suggestion that the p allele was equally functional to the P allele, given than it represents a clear loss of function in keeping with common Young Earth Creationist, Old Earth Creationist, and Intelligent Design definitions of loss-of-function alleles, and the propensity of these groups to insist that such mutations destroy functional information. Yet what we have seen from these groups, by and large, is a robust embrace of ENCODE and its view of function. I suspect that these groups, in their excitement over the media frenzy declaring the idea of “junk DNA” to be dead, have not yet had time to carefully think through the implications of that embrace.

In Part 2 of this series on Wednesday, we’ll explore other working definitions of “function,” look at other lines of evidence that are better suited to distinguishing between biologically functional and non-functional sequences, and revisit some examples from my previous series on “junk DNA” in light of ENCODE.

In Tennessee and across the country, many others weighed in on the subject over the next few weeks, including two essays (here and here) on the BioLogos Forum. But soon after that, other issues crowded that story off the front page. Now, though, teachers and students across my state are returning to science classrooms, and we will all get to see what effect the law has in practice. Again speaking as a Christian, a biologist, and educator and drawing on all three of those perspectives, I’d like to offer my own reflections on the bill’s likely effect on Tennessee teachers and students, beginning with this excerpt from the bill itself:

The teaching of some scientific subjects, including, but not limited to, biological evolution, the chemical origins of life, global warming, and human cloning, can cause controversy . . . The state board of education, public elementary and secondary school governing authorities, directors of schools, school system administrators, and public elementary and secondary school principals and administrators shall endeavor to assist teachers to find effective ways to present the science curriculum as it addresses scientific controversies. (Tennessee HB368 / SB893)

As an evangelical, I think this bill could be more detrimental than helpful to Christian teenagers’ faith. Many students who are particularly interested in the sciences and theory of evolution are already in the uncomfortable position of hearing pro-Intelligent Design doctrine from the pulpit on Sunday and then listening to their science teacher’s evolution instruction on Monday. I was one of those students—sitting in more than one congregation under pastors who were particularly antagonistic to the theory of evolution, and who made not-so-subtle comments that it cannot co-exist with authentic Christian faith. Having a keen interest in the sciences and wanting to explore the data so widely accepted by the scientific community, I felt confused and ostracized in my church. I wondered if I would have to choose between my faith and intellectual integrity. The church family I trusted clashed with the science that I also trusted, causing a near catastrophe for my faith. I am thankful to the few people who offered me grace, allowing for my questioning of some of what I heard in church without labeling me a heretic.

Though the conservative Christian community may view this bill as a “win for the faith,” it is actually a loss if it reinforces the idea that this is simply an issue of science vs. scripture. Evolution is central to modern biology; trust in the authority of the Scriptures is central to Christian faith. But this fight mentality between the two established communities is detrimental to our young teenagers who are seeking to grow in faith, but who cannot seem to reconcile scripture and scientific data. We need them to seek after that reconciliation, not be told it can’t be done. Whatever they are hearing from the pulpit, the science classroom should be the one place that students can learn science. Students may well emerge with bitterness towards the church for dismissing the evidence of evolution not only so quickly, but in what is so often a haughty and condescending manner. Worse yet, students may emerge with bitterness that they were forced to choose between faith and intellectual integrity. Is this really an all or nothing argument? Are the two truly diametrically opposed?

In my world, these two have reconciled, and they now co-exist in peace. It has been a very long road to get there and I could not have done it without both access to good data and the freedom to explore it. Having taught teenagers in an evangelical church for years and having observed in many biology classrooms as well, I know that many students are still struggling for this same reconciliation. That reconciliation is perhaps most easily attained when the seeking student is able investigate evolution in the science classroom without harassment from opposing religious forces. With this freedom, the student may very well realize that the fear that he/she may have regarding evolution is really just a fear of the unknown, and that it is possible to have intellectual integrity and to praise God for initiating and sustaining the evolutionary process.

In Tennessee’s science classrooms there are surely many teachers who begrudge being told that they must teach evolution, and who are relieved that they can now present it as a controversy and/or allow Intelligent Design as an alternative. They, too, will likely see this law as a “win.” But isn’t public science education is about giving students an accurate picture of the state of science, not about teachers’ philosophical opinions? As has been pointed out before, most Tennessee science teachers have not had the training to teach about religion or philosophy; they have been trained to teach about the basic principles of the biological world.

This bill may be particularly frustrating, then, to teachers who do simply want to teach science. From the many hours I’ve spent in secondary biology classrooms this year, I can say for sure that time is of the essence. Tennessee teachers have barely enough instructional time to cover what students must know to pass the end-of-course biology test required for graduation; they do not have extra time to spend covering material that is not science. I have seen classroom arguments over evolution’s feasibility that ate away precious instruction time and only left a greater rift between the two camps and no doubt, a frustrated teacher. News of the Intelligent Design movement’s success in creating political and legal controversy is misplaced content in the secondary biology classroom.

Furthermore, as it allows teachers to frame biological evolution in terms of “controversy”— something that is a topic for debate—this law will likely not result in students who are more engaged in understanding science, but instead, only in more confusion (and possibly antagonism) in the classroom. Educators welcome debate in many cases because debate encourages critical thinking that leads to “formal thought,” the Holy Grail of Piaget’s Theory of Cognitive Development. But the practice of science is about proposing hypotheses and testing the data, not primarily argumentation. And if the science community is not “debating” evolution, why should high school science students be debating evolution as part of their biology curriculum?

The bill is correct in stating that the purpose of science education is to “inform students about scientific evidence” and “help students develop critical thinking skills necessary to becoming intelligent, productive, and scientifically informed citizens.” I certainly agree, though I question whether it needed to be legislated. Rather, my answer is: “Let’s actually do it!” Before bringing “debate” and “controversy” about scientific theories into the classroom, let’s instead teach our students about sound scientific practice; let’s give them opportunities to learn how to research and to employ the scientific method in everyday life. Let’s focus on teaching them about observing the indicators of climate change, the intricacies of DNA, conservation of ecosystems, and the principles of molecular and cell biology. Let’s give them the tools—specific to science— that help them think critically and work out problems, rather than undermining faith in those very practices and the community of people that uses them every day. Let’s not teach them to live in denial of the ordinary dependability of science, let’s not teach them to distrust scientists who have no interest in “debate,” but want to understand the world God made.

In Tennessee and elsewhere, let’s give both our students and those scientists the grace and support they need to merge authentic faith and intellectual integrity.

Asa Gray

If Thomas Huxley earned the title of "Darwin's bulldog," then Asa Gray should be remembered as "Darwin's dove." Whereas Huxley enjoyed a good fight in his defense of Darwin's theory, Gray sought to mediate and bring sides together around a common understanding of "good science." As Darwin's strongest and most vocal scientific ally in the United States, Gray recognized the scientific importance of Darwin's efforts for the growing professionalism of biological researchers.

But as an orthodox Christian, a Presbyterian firmly devoted to the faith expressed in the Nicene Creed, Gray saw in Darwin's theory both evidence for his philosophical commitment to natural theology and support for his opposition to the idealism advocated by Louis Agassiz and the Naturphilosophen in both Europe and America. Indeed, Agassiz's advocacy of Platonic forms as a basis of biological understanding (e.g., "A species is a thought of the creator")¹ would be a major source of American opposition to Darwin's theory.

Professor of botany at Harvard during most of the middle half of the nineteenth century, Gray was one of the few members of the scientific community to whom Darwin revealed his theory before the publication of On the Origin of Species, and, from what I can tell, the only American. Gray and Darwin met briefly in January 1839 during one of Gray's visits to England. Later, during the 1850s, Darwin wrote Gray on several occasions requesting information--a practice that Darwin frequently employed. In 1854, Darwin's friend and confidant, Joseph Hooker, showed Darwin Gray's review of Hooker's Flora of New Zealand, in which Gray had argued strongly against Louis Agassiz's idealism and had raised questions from his own work on the stability of species. Gray was not yet ready to deny their permanence, but hybrids and other observations were beginning to trouble him.

The next year Gray wrote a lucid and penetrating positive evaluation of Alphonse De Candolle's two-volume Géographie botanique raisonnée, a pioneering work dealing with plant geography and distribution from a statistical perspective. Hooker had sneeringly dismissed the work. In A. Hunter Dupree's authoritative biography of Gray, he describes Gray's puzzlement at Hooker's response in these terms:

Although in the long view Gray's evaluation of the epoch-making nature of De Candolle's book was more justified than Hooker's sneers, [Gray was confused by his response, for] Hooker seemed to be talking with a more comprehensive theory definitely in mind, some reason for taking his position, which he did not divulge and which his friend [Gray] did not possess.²

Darwin, however, saw in both Gray's review of Hooker's book and in his comments on De Candolle's tome that Gray was troubled by some of the same empirical data that had been bothering him. In April 1855, Darwin wrote Gray to urge that Gray update his Manual of the Botany of the Northern United States first published in 1848, and especially to address the issue of the range of Alpine plants in the United States. Specifically, he said: "Now I would say it is your duty to generalise as far as you safely can from your as yet completed work."³

Behind this request was Darwin's desire to test his impression that Gray could make a good ally. Gray passed the test, and finally, in July 1857, Darwin let Gray in on his theory of the transmutation of species. Gray was never an uncritical supporter, and there are many evidences in the correspondence between these two scientists that Gray was willing to challenge Darwin and disagree with some of his conclusions. Nevertheless, Gray saw the importance of Darwin's work and the ways in which it provided answers to the troublesome issues that he had confronted in his own botanical efforts.

Gray responds to Darwin's theory

After considerable interchange--one might even say debate--among Gray, Darwin, and Hooker, Gray wrote to Hooker in October 1859 (one month before the publication of On the Origin of Species) saying that he had absolutely no problem with cognate species arising by variation. He did, however, raise a concern that would be the source of much future discussion. He wondered about Darwin's "carry[ing] out this view to its ultimate and legitimate results,--how [do] you connect the philosophy of religion with the philosophy of your science." He added: "I should feel uneasy if I could not connect them into a consistent whole--i.e., fundamental principles of science should not be in conflict."⁴

When Origins was published, Gray wrote a clear, positive, yet critical review in The American Journal of Science. Aware of mounting religious opposition, he ended his review by arguing that whereas one could use Darwin's theory in support of an atheistic view of Nature, one could use any scientific theory in that way. He wrote: "The theory of gravitation and ... the nebular hypothesis assume a universal and ultimate physical cause, from which the effects in nature must necessarily have resulted."⁵ He did not see the physicists and astronomers who adopted Newton's theories as atheists or pantheists, though Leibniz earlier had raised such reservations. And a similar situation existed with the origin of species by natural selection. Darwin, Gray continued: "merely takes up a particular, proximate cause, or set of such causes, from which, it is argued, the present diversity of species has or may have contingently resulted. The author does not say necessarily resulted."⁶

This far Gray could go with Darwin. But there was a point at which he parted company, and that was the fortuitous randomness of the process that Darwin's theory seemed to imply.

In part 2, Dr. Miles describes Darwin's struggle with the problem of natural evil and design in nature.

Notes

1. Cited in A. Hunter Dupree, Asa Gray: American Botanist, Friend of Darwin (Baltimore: The Johns Hopkins Press, 1959), 151. 2. Ibid., 236.
3. Charles Darwin, More Letters of Charles Darwin, ed. Francis Darwin, (New York: D. Appleton and Company, 1903), 252.
4. Dupree, Asa Gray, 266.
5. Asa Gray, "The Origin of Species" in Darwiniana (Cambridge, MA: The Belknap Press of Harvard University, 1963), 44.
6. Ibid.

But it is also important that we engage believers who disagree with us (on human origins, especially) with charity and humility as a witness to our common identity in Christ—that we may be known by our love for each other in tandem with our demonstrated love for the secular world that does not yet claim Christ as Lord and Savior.

While the BioLogos Foundation is committed to both of these aspects, we are especially pleased that our desire to engage in gracious dialogue with fellow believers who reject biological evolution has been receiving increased and very favorable attention in both the Christian and secular press. More importantly, we are being joined in that reconciling project by those who have often been defined primarily as our “opponents,” rather than as brothers and sisters in Christ.

First, A Tale of Two Scientists, the cover story of Christianity Today’s July-August 2012 issue, featured the accounts of BioLogos Foundation President Darrel Falk and Todd Wood, Director of the Center for Creation Research at Bryan University. Though Wood does not accept biological evolution on theological grounds, both men recognize its strength and explanatory power. But more importantly, both reject the warfare model between science and faith (and between Christians who think differently) as being, in Wood’s words, “detrimental to the Church.”

Second, our Southern Baptist Voices series has become a model for how such dialogue can be pursued, even in the sometimes no-holds-barred context of the web. Several installments in our ongoing dialogue with Southern Baptist theologians have been covered by the Erin Roach of the Baptist Press (on May 25th , June 6th, and July 3rd) and on on July 19th by Lillian Kwan of the Christian Post. And just this past week, Associated Press reporter Travis Loller highlighted the series in an article picked up by the Huffington Post, the Washington Post, and many other news outlets across the country.

To make it easier for readers to find the entire Southern Baptist Voices series and join in the conversation themselves, we’ve launched a new landing page here: Southern Baptist Voices. It is our hope and prayer that this initiative will set the stage for future dialogue between evolutionary creationists and those who hold other perspectives, as well.

Since this post, and those that will follow it, depend on an accurate representation of the argument for irreducible complexity (IC), I will take some time to clarify exactly how Michael Behe, the biochemist and Intelligent Design (ID) proponent who has most extensively developed the IC argument, uses the term. 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. Since an IC system requires all the components to be present for its function, it is not possible for the system, in its current state, to have been produced directly from a non-functional precursor. If one grants this premise, it leaves two options: that the IC system was derived indirectly, from a system that is not IC, or that the system was assembled by fiat and thus represents the actions of a designer. Behe’s criterion for distinguishing between these choices is based on evaluating the probabilities of these competing options:

Even if a system is irreducibly complex (and thus cannot have been produced directly), however, one can not definitively rule out the possibility of an indirect, circuitous route. As the complexity of an interacting system increases, though, the likelihood of such an indirect route drops precipitously. And as the number of unexplained, irreducibly complex biological systems increases, our confidence that Darwin's criterion of failure has been met skyrockets toward the maximum that science allows. (Darwin’s Black Box, p. 40)

As we will examine in an upcoming post, Behe attempts to determine the precise limit of what evolutionary processes can (and cannot) achieve in a second book, The Edge of Evolution. For our present purposes, however, it is enough to note that the strength of the argument from IC depends on the perceived implausibility of the opposing explanation – that of an indirect evolutionary route that produces an IC system from a non-IC precursor system.

Building IC, one step at a time?

The presence of IC systems in biology as Behe has defined them is not contentious: there are many biological systems that cease to function when parts are removed. Indeed, the success of classical genetics in “dissecting” which genes are needed for certain functions largely rests on the ability to see some effect on function when a gene is removed from a system by mutation. What scientists dispute, however, is Behe’s claim that identifying IC systems is a hallmark of design. The evolutionary model for building IC is quite simple, and Behe has set it out as an option: an indirect route where non-essential parts are added to a system, and then over time the system comes to depend on those parts. We can diagram this model as follows:

The key to the model is that new parts can be added to a system, and that these parts are not essential when they are added. The resulting system is thus not IC, since it has parts that are not essential to its function, even if the new parts are advantageous in some way. If the new component is taken away at this stage, the system merely reverts to the precursor system. The second part of the model is that these intermediate, non-IC systems then may become IC if small changes make the new parts essential.

The addition of new, non-essential parts can be accomplished in several ways, such as a change in an existing protein that allows it to bind to a “precursor system”. More extreme would be the generation of a new protein that then adds to a precursor system as a non-essential component. Brand new genes, by definition, cannot be essential when they arise, since they arise in an organism that, up to that point, had no need of them. Looking to see if new genes then later become essential would be very good experimental support for the evolutionary model for how IC systems arise.

In practice, it takes a lot of scientific effort to tease out changes to an existing protein that allow it to become part of an intermediate system and then progress to an IC system, though we have examined one such example in a previous post. Looking for brand new genes, however, is much easier – and some recent work in several fruit fly species (Drosophila) has done just that.

The Young and the Restless

So, how to go about finding genes that are new? We have already discussed, in the context of duplicating an entire genome, how duplication of genes may lead to the two copies picking up new functions over time. While duplication may happen rarely at a whole-genome scale, small-scale duplication of small numbers of genes happens quite frequently as an error during cell division. At the time of the duplication, the two copies are the same, and therefore functionally equivalent. Over time, however, the two copies may become different and acquire distinct functions.

One way to look for genes that have arisen due to a recent duplication event is to compare the genomes of closely related species and look for genes that are present in one species but not another, or in a subset of related species. Duplicated genes will show up in a nested hierarchy, much like how pseudogenes appear in the same nested pattern, as we have discussed previously here.

The complete genome sequences for a number of fruit fly species are available, so researchers used this method of comparison to look for new genes that mostly arose “recently” (over the last 35 million years) within flies. Since the speciation times for the various fly species are known to a good approximation, the time of the various duplication events can be estimated as well.

Putting the argument for IC to the test

Using this method, researchers identified 195 recent, “young” genes that arose through duplication events. (Note: this finding, in and of itself, is problematic for the ID argument that significant amounts of new information cannot arise through evolutionary mechanisms). More problematic for the argument from IC, however, is that just less than one third of these new genes are now essential for development in the species that carry them. This fraction is approximately the same for “old” genes – about one third are essential for development.

The implications are easily grasped: many new genes have arisen through duplication, and a sizeable fraction are now part of IC systems. When they arose, they could not have been essential, but now they are emphatically so. As such, they must have been added to previous systems, and become IC over time. Moreover, this effect is not a rare, one-off event, but rather has been repeated time and again in recent evolutionary history.

In the next post in this series, we’ll delve into some of the details about how these new genes arose, and what sort of functions they have.

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.

I ask the question, “Why is the universe so special?” Now scientists don’t like things to be special; we like things to be general, and our natural anticipation would have been that the universe is just a common or garden specimen of what a universe might be like.

But we’ve come to understand a lot about the history of the universe. We know that our universe started 13.7 billion years ago, and it started extremely simple, just an almost uniformly expanding ball of energy, about the simplest physical system you could possibly think about. But a world that started so simple has of course become rich and complex. With you and me, in fact, the most remarkable and complex consequences are its history, at least of which we are aware. The human brain is far and away the most complicated physical system we have ever encountered anywhere in our exploration of the universe.

That fact itself might suggest that something has been going on in cosmic history rather than just one thing after another. But we’ve also come to understand many of the processes by which this rich fruitfulness has come to birth. As we’ve come to understand these, we’ve come to see that though these processes are of course evolving processes, they took long periods of time – the universe was 10 billion years old before any form of life appeared in it, at least as far as we know anyway – and life of our complexity only appeared yesterday.

Nevertheless, the universe is pregnant with life, pregnant with the possibility of life, essentially from the beginning onwards. By which I mean the given laws of nature had to take a very specific, very finely tuned form, if the universe was to have so fruitful a history.

That’s a very remarkable discovery, and let me give you some examples of why we believe that. If you’re going to have a fruitful universe, one of the first things you have to get right is that you have to have the right stars in the universe. The stars are going to have a very important role to play. First of all, you must have some stars that are going to be very long lived, live for billions of years, steadily burning, steadily producing energy which will enable the development of life on one of the encircling planets. We understand what makes stars burn in that sort of way very well, and it depends on a delicate balance between the strength of gravity and the strength of electromagnetism. Electromagnetism is the force that holds matter together. The seats on which you are sitting are held together by electromagnetism and in fact you are held together by electromagnetism.

If you alter that balance a little bit in one direction the stars will begin to burn intensely, furiously, just pouring out energy and they will only live a few million years rather than a few billion years. If you move it a little bit in the other direction they will burn so slowly they will be brown stars and they will not produce enough energy to fuel the development of life. So you have to have a very delicate finely tuned balance between the strength of gravity and the strength of electromagnetic forces in a fruitful universe.

Remember, science takes the laws of nature, takes the given strengths of gravity, the given strength of electromagnetism, uses that to explain processes in the world, how things happen, but it doesn’t explain where those laws of nature come from. They are just brute facts as far as science is concerned.

And the stars have another absolutely indispensible role to play. The stars are the place where the heavier elements essential for life are made in the interior nuclear furnaces. There are many elements that are necessary for life, of which carbon is perhaps the most essential. Carbon is the basis of the long chain molecules, which are the biochemical basis of life. The early universe only makes the simplest elements; it makes hydrogen and helium and it makes no carbon at all. Carbon only begins to be made when the universe, which started uniform, begins to condense and become lumpy and grainy with stars and galaxies. As the stars condense they heat up, nuclear processes begin again in their interiors. And it’s those nuclear processes in the stars that make carbon and the heavier elements. Every atom of carbon in your body was once inside a star. We are people of stardust made in the ashes of dead stars.

And that’s a very beautiful process that takes place in that sort of way. And one of the great triumphs of astrophysics and the second half of the 20th century was to unravel that process. One of the people who did some of the most important work on that was a senior colleague of mine in Cambridge called Fred Hoyle. And they were trying to figure out how to make carbon. They got helium, and if you can make three helium nuclei stick together that will produce carbon, but when you have something as small as a nucleus it is impossible to get three to stick together at one time, they’re just too small.

Ok, so let’s do it step by step. Stick two together gives you berylium. Helium 4 gives you beryllium-8, hope it stays around for a bit, another helium comes along, attaches itself, and bingo, you’ve got carbon-12. That’s the obvious thing to think about but it doesn’t work in the obvious way, and the reason it doesn’t work in the obvious way is that beryllium-8 is terribly unstable. It doesn’t oblige you by staying around long enough to catch that third helium, at least in an ordinary, straightforward way.

But Fred realized that it would be just possible for this to happen if there was a very large enhancement effect, in the trade we call it resonance, occurring in carbon at just the right energy, it has to be the right energy, which would enable that attachment process to catch that third helium much much more quickly that you might have thought, in fact so quickly that some of them would get caught before the beryllium-8 disappeared. It was a very good idea, and he must have felt pretty pleased with himself and he went off to just check in the nuclear data tables of this particular resonance’s energy levels, and it wasn’t in the tables, but he knew it must be there, he’s carbon based life like you and me.

So he rang up some friends in the States, a father and son team who were good experimentalists and he said, “Look, you missed something. There’s a resonance and energy level in carbon that you haven’t spotted, and I’ll tell you exactly where to look for it. I know exactly where this energy has got to be. You go look for it.” And they said, “No, no, we don’t want to do that, we have more interesting things to do.” But Fred was very determined and he bullied them into looking for it and they found it.

Now that’s a wonderful achievement, to predict an energy level in carbon on the basis of how it might have been made in the stars is a fantastic scientific achievement. But it’s more than that. Fred had a lifetime conviction of atheism, realized of course that if the laws of physics had been just a little bit different that resonance wouldn’t have been there, and the possibility of carbon-based life is too significant for it just to be a happy accident in his view, so he says in a Yorkshire accent that is beyond my power to imitate, he said that the universe is a put-up job. Fred didn’t like the word God, and so he said some Intelligent, capital “I” Intelligence, must have monkied with the laws of nature to make carbon production possible. What that could possibly be I don’t know, but the more sensible thing to say is that creation is ordained, that the laws of nature would be such, as to enable the fruitfulness of carbon-based life.

We’ll come back to evaluating that possibility in a minute, but before we do, let me give you two other examples of how specific, how special, our universe has to be for us to be able to be here today to think about. We live in a universe that is immensely big, beyond our powers to imagine really. There are a hundred thousand million stars in our galaxy in the Milky Way, of which our sun is just a common or garden specimen, and there are about a hundred thousand million galaxies in the observable universe, of which our Milky Way is a pretty common or garden specimen. So we live in a world that is unimaginably vast, and sometimes we might feel upset by that and think, “What could be the significance of us who are simply inhabitants of a speck of cosmic dust, as you might say, in this vast, vast universe?”

Nevertheless, if all those stars were not there, we would not be here to be upset at the thought of them. Because there is a direct connection between how big a universe is and how long it lasts, and a universe that is significantly smaller than our universe would not have been able to last the 14 billion years, which is the necessary time to produce beings of our complexity. So that’s another condition of the world that has to be right for human beings, or something like human beings, to be a possibility.

One final example, which is the finest tuning of all: quantum theory suggests that there should be an energy attached to space itself. In quantum theory the vacuum, so called empty space, is not just a void. There are things called vacuum fluctuations which occur in a continual sort of seething mass of things coming into being and going out of being all the time. So while there is nothing there that doesn’t mean there is nothing happening. That may sound strange and paradoxical but believe me that’s what quantum theory implies. And of course these happenings, these fluctuations, generate a certain amount of energy, we call it “zero point energy”, and that energy is spread out over the whole of space. So we expect there to be energy associated with space.

And just recently the astronomers have discovered something called dark energy which is driving the expansion of the universe, which is just such an energy associated with space. Well that’s very good, you might say. However, when we estimate, just from thinking about quantum theory, how much energy there should be in space it turns out to be a fantastically large amount, and when we see the amount of energy there actually is per volume in space, it turns out to be very, very small in relation to that expected size. In fact, it turns out to be smaller by a factor of 10^-120. That means by a factor of 1 over 1 followed by 120 zeros. You don’t have to be a great mathematician to see that’s a fantastically small number. So some fantastic cancellation has taken place to turn that big number into the tiny number that we actually observe, and if it hadn’t taken place we wouldn’t be here to observe it because significantly higher energy would simply have blown the whole show apart too fast for anything interesting to happen. That’s the finest tuning that we know in the universe: one part in 10¹²⁰.

So we live in a world that is very remarkably finely tuned, and we have to consider that. And all scientists would agree about what I have been telling you; this is non-contentious. Where the contention comes in is what we might make of that, what is the further significance of it.

In the conclusion to Dr. Polkinghorne’s lecture, he looks at two explanations for the "fine-tuning" principle -- the multiverse theory and the existence of a divine intelligence -- and explains why natural theology alone is not sufficient to make the case for a God who interacts and cares for his creation. To make the case for theism, he argues, we need revelation, God's self-disclosure. This is manifest in various ways, including that which we experience personally, including ethics and aesthetics.

Jeff, who identifies himself as a Christian home-schooling father wrote in comment #69363:

. . . contrary to the modern model of education which isolates academic subjects by assigning to each one a separate teacher and classroom, it should be stressed that the pursuit of knowledge in general is greatly served by teaching students about the important relationships that exists between the various academic subjects in the real world. Thus, to include in a discussion of the theory of evolution some exposure to the theological and philosophical assumptions upon which that theory is based [emphasis added] is not only appropriate, but of great value in exploring the full scope of the theory as it has developed in our world and much of the controversy that surrounds it.

As another home-schooling father (of three boys) I concur wholeheartedly with Jeff’s assessment of the modern educational system—not just in public schools, but in far too many private and Christian schools, and in not a few home-schooling communities, as well. The breadth and depth of human knowledge is now so great that we must, in fact, have specialists who devote their lives to particular areas of study; but this makes the need for a broad and integrated education in the primary and secondary levels more important, rather than less. Beyond that, we need conversation between fields of knowledge as much as we need such dialogue within them. Indeed, part of our goal at BioLogos is to demonstrate that we in the Christian community can and must think deeply but also broadly about these issues if we want to do justice to the complexity of biological life, but also to the complexity of our lives of faith: to the complex redemptive mission God has called us to in Christ, through the Holy Spirit.

But two things strike me as off in the quoted paragraph. The first issue is that it seems to attribute the most problematic philosophical issues of Evolutionism to the theory of evolution itself, as if those are foundational to the science rather than being philosophical add-ons. The very thrust of the statement included above is that an integrated learning is necessary in order to tease apart the philosophy from the evidential science—or, as I would describe it, to tease apart secular ideology and atheism from the powerful and beautiful descriptive and predictive account of biology that evolutionary theory provides—but that laudable strategy is abandoned at the outset when the two are inextricably linked together.

Again, BioLogos exists in part to show that the science of evolution (though always being refined) is sound in spite of the grandiose philosophical claims made “on its behalf” by those who despise faith and the faithful. Our own Senior Fellow in Biology, Dennis Venema, posts regularly on the compelling scientific evidence for evolution, and we also offer both brief and longer-form resources on our website to help readers distinguish between the science of evolution and the philosophical worldview that is Evolutionism.

But it should be noted that the “philosophical assumptions” that are rightly considered foundational to evolutionary theory—like a commitment to methodological naturalism—are seen by the majority of Christian and non-Christian scientists alike as foundational to all science. Furthermore, those basic assumptions came out of a Christian intellectual tradition that affirmed God’s trustworthiness as much as an Enlightenment belief in the power of reason. But perhaps more to the point, to read the history of evolutionary theory in more than a selective and superficial way is also to see that—from the beginning—many orthodox, evangelical Christians have seen it as consistent with their faith, and have given good theological reasons for thinking so.

The second issue, though, is more practical and bears on our life together as the church as much as it does on current educational strategies. Since generations of teachers have now been trained to teach in specific areas of knowledge, and covering state-mandated materials while also attending to classroom management is no small feat, I doubt that there are many elementary and secondary-school science teachers in Tennessee (or anywhere else) that feel adequately equipped to provide that level of integrated knowledge and instruction about that these subjects deserve, combining hard science, social and church history, the history of philosophy, and even theology. This is no slur against teachers.

The kind of discussion that really ought to be had—one that engages the philosophical and spiritual components of our knowledge—should happen (and can really only happen) in churches, not public schools. In church settings, our ability to discuss the relationship between science and Christian faith and doctrine will always be more robust than the anemic versions that would be permissible in public schools, even under this new law. But more importantly, churches may be the only place to find the level of civility, charity, and love that is necessary to understand, much less work through our differences. Or at least they ought to be safe places where that kind of conversation can happen—even with atheists.

But here’s the more troubling point: that “speaking truth in love” mentality is often not in evidence within the Body of Christ. Instead, many Christians seem convinced not only of the correctness of their own interpretation of scriptures, but also that those who hold different views are worthy of contempt—and that they have nothing worth hearing to bring to the conversation. A priori distrust of the Christian identity of those who see evolution as God-given, for instance, makes dialogue difficult, at best. If we can not muster the humility and charity to disagree with our brothers and sisters in Christ in a way that still honors their basic integrity and faith, how can we hope to have proper humility before God’s Word or world, admitting the possibility that we have not plumbed the ultimate depths of what they have to tell us? It therefore seems folly to advocate—much less legislate—that our elementary middle- and high-school teachers “teach the controversy” when we, as the church, do such a poor job of telling the whole story ourselves.

Finally, and perhaps most importantly, it seems dishonest to claim that we want to “teach the controversy” in public schools without any reference to our Christian commitments. Rather than hide our belief that Jesus is Lord of all (including cosmology, geology, biology and history), let us make that claim forthrightly—let us reject atheistic accretions to evolutionary science, yes, but never deny that love of our Lord and Savior is what motivates us to wrestle with the mystery of God’s creative and saving work in the world.

Within hours of the bill’s becoming law, numerous news stories, blog entries, and web sites issued warnings of the “anti-evolution law” that will “allow creationism back into the classroom.” Yet it is important to note that the bill itself does not use this language; rather, I believe that such terminology regarding this bill is derived in no small part from sentiments about Tennessee’s past. Specifically, the Butler Act of 1925 prohibited the teaching of biological evolution in all public schools of Tennessee, and the Scopes Trial brought this act—and Tennessee’s educational policies—into the national spotlight. The bitter aftertaste still lingers for many. While it may be tempting to look at the current law in light of Tennessee’s colorful history on science education, I will intentionally avoid doing so in this essay. This will allow us to focus entirely on the content of the bill, rather than the perceived motivations or purported agendas of the bill’s authors.

The bill begins by stating the importance of students receiving a rigorous science education, developing critical thinking skills, and becoming generally informed and knowledgeable citizens. This declaration is to be welcomed by all who believe that science is not only a noble pursuit, but accessible and relevant even to those who are not scientists. The text goes on to state that many educators are unclear about how to teach certain subjects, including biological evolution. Indeed, we must agree that there is substantive confusion amidst the nation’s public on the topic of biological evolution.

I have two major concerns about this section. First—without any substantiation—it erroneously proposes that biological evolution is controversial within the scientific community. Quite to the contrary, biological evolution is hardly contentious among scientists. Various polls over the years have consistently demonstrated that over 95% of scientists (and 99% of earth and life scientists) believe in biological evolution. This is underscored by the fact that some of these scientists are notable luminaries who are also committed Christians in the public sphere: Francis S. Collins (Director, National Institutes of Health); Jennifer Wiseman (Chief, Laboratory for Exoplanets and Stellar Astrophysics at NASA); and John Polkinghorne (Particle physicist and winner of the 2002 Templeton Prize).

In the past few years, BioLogos has performed the tremendously important work of gathering scientists, theologians, and evangelical pastors around the country to initiate a dialogue, grounded in mutual respect and honesty, on the topic of biological evolution and creation. While not all theological questions have been answered, and some certainly require more study, there is broad agreement on the following: (1) that there is little-to-no controversy about biological evolution within the scientific community, (2) that the preponderance of evidence—particularly from the field of genetics/genomics—is overwhelming, and most importantly, (3) that when biological evolution is rightly separated from ideological evolution (or Evolutionism), it is harmonious with the Christian’s faith in God as the magnificent Creator of the world.¹ This bill clearly disregards all of these, and in so doing, represents a major step backward in the national dialogue. Specifically, the bill’s implication that biological evolution is scientifically controversial and just one among many equally-likely speculative hypotheses to explain today’s diversity of life represents a gross mischaracterization of the position of the scientific community and many in the faith community.

Second, as it is written, the primary purpose of this law seems to be providing educators with almost unmitigated latitude when “helping students…critique [biological evolution and other ‘controversial’ topics]…in an objective manner.” But objectivity can only be pursued in a context where a common standard of truth is upheld. In a science classroom, this standard should be set by the overwhelming scientific consensus; however, in this bill, it appears that teachers are given the right to set their own standards of truth as they see fit, even though the law does not formally alter the curriculum. While at first glance this appears to be a bill about empowering teachers, it is ultimately one that could confuse students, given that their scientific education will be tailored by their teachers’ varying personal opinions. It is true that science changes, and that questioning is always a critical component of the pursuit of learning and truth. But, in science, questioning must be motivated by (and result in) empirical data, not by how well the evidence fits into our personal comfort zones. As stated previously, there is overwhelming agreement on biological evolution within the scientific community, and it is not legitimate to teach students otherwise.

To be clear, I do believe it is important to “teach the controversy,” in the sense that students should be informed and knowledgeable about the current national dialogue on a variety of topics, including biological evolution. However, this is not best done in the science classroom, because doing so gives the impression that the controversy is based in the science, when in fact it is largely based on a number of other factors. Thankfully, the bill does not support the promotion of any specific religious doctrine, but it does appear to sacrifice the integrity of science education at the altar of the educators’ and students’ comfort.

Influential Christian leaders like Bruce Waltke² and Tim Keller have modeled what it looks like to be intellectually honest students of both the Bible and the world around us; they do not necessarily agree on everything with regard to biological evolution, but they have exhibited a refreshing willingness to meaningfully engage the real science behind it. It is my sincere hope that those of us in the Christian community—particularly educators—who are unsure about how to navigate subjects such as biological evolution will take our cue from such models, resisting the temptation to pursue our own more comfortable versions of reality. Scientific and faith-based communities are often talking past each other, and I am eager to see us spend more time talking to each other. As is often the case, we might find we have more in common than we thought.

Notes

1. D.R. Alexander, Creation or evolution – do we have to choose? (Monarch, 2008).
2. B.K. Waltke, An Old Testament Theology: An Exegetical, Canonical, and Thematic Approach (Zondervan, 2007)

In our previous post, we examined processed pseudogenes – transcribed gene copies that randomly insert into genomes. Unitary pseudogenes, however, are different: unlike processed pseudogenes, they are unique sequences in genomes, and not copies. They have the features one expects of “real” genes: regulatory sequences, introns, and protein coding sections – but with mutations that prevent them from being transcribed or translated. Like buildings in various states of repair, there is a similar range for unitary pseudogenes. If they have only been recently inactivated, they will be largely intact – like a recently abandoned building with a few broken windows. Others are further along in their degradation, like a stone building without a roof and grass growing up through the floor. Some are so far gone that one needs to peel back the turf to search for what remains of the foundation. Despite their various states of disrepair, they remain recognizable – in some cases, they can persist for millions of years before they slowly mutate beyond recognition.

The reason for these defective genes is straightforward: the organism that had the original mutation that removed the function of the gene was not significantly impacted by the loss. One example I have previously discussed is the human GLO pseudogene. The functional GLO gene is part of the biochemical pathway for making vitamin C, something that humans and other primates are not able to do: if we don’t get enough in our diet, we get scurvy. In an environment with adequate dietary vitamin C, however, the loss of the GLO gene is no big deal – and mutations that remove its function would not have been a disadvantage. The mutations that remove GLO function in humans are the same mutations we see in other species – they are an example of mutations in a nested hierarchy, the type of pattern that relatedness produces. This indicates that the mutations happened once, in a common ancestral species, and have been inherited by several species that descend from that ancestor, ours included.

So, what’s a defective gene like you doing in a species like this?

While it makes sense that mammals ought to be able to make vitamin C (even if humans and other primates cannot), in some cases pseudogenes seem much more “out of place.” One example from the human genome that we have discussed in the past, is the vitellogenin gene, a gene required for egg yolk formation in egg-laying organisms. This gene is present in the human genome as a pseudogene, even though humans are placental mammals – human embryos are nourished through a placenta, not egg yolk. This pseudogene was located in the human genome by predicting that its genomic location relative to its neighboring genes would be retained for a long time, even after its inactivation. Accordingly, researchers found a functional vitellogenin gene in the chicken genome, and noted the genes on either side of it (let’s just call them “Gene A and Gene B” for convenience). Gene A and Gene B are also side by side in the human genome, so the researchers looked between them for the signs of vitellogenin gene remains – and found them in that precise spot, still visible despite approximately 300 million years since we last shared a common ancestor with chickens:

Other examples like this abound: whales, for example, have unitary pseudogene remnants of genes devoted to an air-based sense of smell, even in cases where the whale species in question does not have an olfactory organ. A second example from whales are pseudogene remnants of visual pigments adapted for wavelengths of light found in terrestrial settings, not aquatic environments. These examples make perfect sense in light of the terrestrial ancestry of whales, but are challenging to account for from an antievolutionary perspective.

Pseudogenes: evolution’s silver bullet?

Unitary pseudogenes with shared mutations in nested hierarchies among related species are far from the only evidence for evolution, and are not even necessarily the line of evidence most convincing to specialists. Specialists can see the broad pattern of multiple lines of converging evidence that support common ancestry to an extent non-specialists cannot easily appreciate. Unitary pseudogenes, however, are valuable tools for demonstrating a sampling of those lines of evidence, and providing a window into the world of comparative genomics that, to paraphrase Dobzhansky’s famous quote, would make absolutely no sense except in the light of evolution.

Yes, the implications of unitary pseudogenes such as these are easy for even non-specialists to grasp: whales have the defective remnants of genes adapted to terrestrial vision and air-based smelling because they descend from terrestrial ancestors. Placental mammals, including humans, have a defective remnant of a gene used to make egg yolk because they descend from egg-laying ancestors. Unitary pseudogenes share identical mutations across related species because they were inactivated in a common ancestor, and were inherited by every species that descended from that ancestral species.

No special training in genetics is required to appreciate the strength of the evidence that these examples provide. Nor does it require special insight to see that attempts made by antievolutionary groups to refute this evidence face an uphill battle. Its daunting nature notwithstanding, some have undertaken just that task, since the evidence is too compelling to ignore, and too risky to leave unanswered.

Bringing it together: antievolutionary approaches to pseudogenes, unitary and otherwise, miss the mark

Now that we have covered significant ground with respect to what various classes of pseudogenes are and how they arise, we are now able to properly evaluate antievolutionary arguments put forward in an attempt to discredit these lines of evidence for evolution. Attempts to discredit unitary pseudogene evidence generally have one or both of the following two approaches, which we will evaluate in turn:

Approach 1: Discuss rare examples of processed pseudogenes that have acquired function, and imply that all pseudogenes, including unitary pseudogenes, will similarly be shown to have function.

This approach is a fairly common one in the antievolutionary literature, and examples abound. We have examined previously how processed pseudogenes may, in rare cases, acquire a function and come under selection. Note well: the vast, vast majority of processed pseudogenes are not functional and are slowly mutating beyond recognition as DNA not under selection. While rare examples that have acquired function are very interesting from a scientific perspective, they do not “confer functionality” on the remainder of processed pseudogenes, let alone on unitary pseudogenes.

The other issue with this argument is that in many cases we know what the function of the unitary pseudogene once was. We know what the function of vitellogenin is, for example – and we can find this gene in modern-day egg-laying animals. When we see the remnants of this sequence in the human genome it is a stretch to argue that it has another, as of yet unknown function. When we see the human pseudogene sitting between two other genes in the human genome the same order as we observe in the chicken genome, it stretches credibility well past the breaking point.

Approach 2: Claim that unitary pseudogenes with mutations shared across species are the result of non-random mutations that occurred independently in the two species, and are not inherited from a common ancestor.

This argument, though having an appearance of validity, is similarly doomed to frustration. While mutations are not entirely random (certain regions of the genome mutate more readily than others) there is no known mechanism that could create the precise, repeated pattern of shared mutations we observe between related species. The most significant attempt to mount this type of argument against unitary pseudogenes in general was directed at the GLO pseudogene, and I have already discussed the specific details of why that attempt was inadequate. No refinement of that argument, to my knowledge, has been put forward since.

In summary, pseudogenes in general, and unitary pseudogenes in particular, remain a significant thorn in the side of antievolutionary groups. In the next post in this series, we’ll cast our net wider and explore an example of how multiple, convergent lines of evidence support evolution, often in unexpected ways.

For further reading:

http://biologos.org/blog/signature-in-the-pseudogenes-part-1
http://biologos.org/blog/signature-in-the-pseudogenes-part-2
http://biologos.org/blog/a-tale-of-three-creationists-part-3

It is easy to be confused about what science is and what scientists do. In part, this is because scientists do so many different things in so many different ways. By way of illustration, I was a Junior Fellow in the Harvard Society of Fellows in the 1980s. I shared this pleasure with many other young scientists who were also launching their careers within the Society.

One member of my cohort was Gary Belovsky, now a professor of biology at Notre Dame. He was interested in how animals search for food, how this search relates to competition between species, and how nutrients were recycled in the ecosystem. To a layperson, however, Gary traveled in Montana chasing moose and analyzing their droppings.

Another Junior Fellow was Lawrence Krauss, a cosmologist interested in the birth and death of the universe. Lawrence, who later wrote The Physics of Star Trek, recently assumed leadership of the Origins program at Arizona State University. As he did his science, Lawrence mostly sat in his office working with equations.

I was a chemist. I was interested in how the phenomenon of life could be understood in terms of the interactions between its constituent molecules, and how this understanding might help diagnose and treat human disease. What I did all day was make molecules, doing something that looked much like what chefs do when they are cooking in a restaurant kitchen.

Each of us called ourselves "scientist". And yet there was scarcely more similarity in what we did in our daily lives than there is between (for example) an auto mechanic and a symphony conductor. Field work, equations, and cooking sample quite broadly all of human activity.

This notwithstanding, each of us belonged to a traditional field of science having a traditional name, biology, physics, and chemistry (in our cases). These sciences are well respected in modern culture. Further, the views of their practitioners are often accorded special standing in the public square, especially when compared with the views of lawyers, advertising executives and politicians, to mention practitioners of a few other noble professions.

This respect is not irrational. Nearly everyone recognizes that biology, physics, and chemistry have empowered society, in the material and manipulative senses of this term. Empowerment by physics is evident from nuclear power plants, spacecraft that land on the Moon, and television sets, inter alia. Empowerment by chemistry is illustrated by the colorful fabrics that we wear, the materials used in our hybrid cars, and the medicines that we take to cure our diseases. Biology has identified genes that cause cancer, viruses that cause AIDS, and vaccines that have all but eliminated small pox, polio, tetanus and diphtheria.

We may not agree that these fields of science have produced "knowledge". We may not know what "knowledge" is. Nevertheless, we must agree that science has produced something that behaves like knowledge should behave. Whatever knowledge is, it should confer manipulative control and predictive power upon those who possess it. Physics, chemistry, and biology have done just that.

In this sense, science seems to be special among other intellectual activities that have engaged the human mind over the millennia, including religion, philosophy and art. Many religions, philosophies, and artistic forms claim to confer "knowledge" of some kind. Yet they do not credibly claim the predictive and manipulative empowerment that the sciences claim, even though they might claim other things, such as aesthetic transformation and personal fulfillment.

It shows no disrespect of transformation and fulfillment as human goals to note that the product of the "knowledge" proffered by religious, philosophical, or artistic thinkers cannot be universally recognized, and therefore does not command universal assent, at least not in the same way that scientific knowledge does.

That seems to be largely because religious, philosophical, or artistic "knowledge" does not generate the manipulative empowerment that science does. You may believe that your faith in the virgin birth has empowered you to do good works. An observer might observe those works and choose not to dispute your claim that your faith has been motivating. But the details lie obscured within your psyche. This is not the case when a scientist tells you that water is H2O, even though you have never seen either an H or an O.

So what is special about science that allows it to create the empowerment that is expected from actual knowledge? Certainly, historians, philosophers, and religious thinkers have been no less interested in understanding reality than Galileo, Newton, and Einstein. We all try to state our propositions in language that makes semantic sense. We all use logic in our arguments. We all refer to the natural world. What we teach in middle school is that scientists apply something called "the scientific method".

No doubt.

But a century of effort has had difficulty defining what that "method" is. This difficulty is illustrated in the context of a suggestion made by Karl Popper, Michael Polanyi and others. These philosophers suggested that scientific propositions could be distinguished from nonscientific propositions by their being "falsifiable".

This "demarcation criterion", as philosophers call it, is widely accepted, even among scientists. Most scientists believe that it is a good idea to make their propositions falsifiable. Yet this cultural belief immediately creates a new debate around a new question: exactly when is a proposition falsifiable?

For example, a few years ago Karl Giberson, discussed Intelligent Design (ID) with Francis Collins, now Director of the National Institutes of Health. In that discussion, Collins wondered what an Institute of Intelligent Design might study, as "ID doesn’t actually propose any falsifiable hypotheses." A clear application of the demarcation criterion, it would seem.

The blogged retort from Casey Luskin from the Intelligent Design community was simple enough. Luskin went to Collins' recent book and found passages where the NIH director had contradicted ID by citing evidence from the structure of the human genome. Collins cannot have it both ways, said Luskin. ID must be falsifiable if observations from the human genome can falsify it. Therefore, ID must be scientific. And so the dispute was not resolved by the demarcation criterion; it simply moved to a new dispute.

In my next post, we’ll continue to examine why simple concepts, like falsifiability, do not adequately explain whether a given activity is scientific in nature.

This blog was first posted in April 2010.

Discussion:What new insights does Benner’s post provide to the discussion? Is Intelligent Design falsifiable? If so, is that enough to make it science?

Populations and genetic diversity

One consequence of speciation being a population event is that populations have genetic diversity – not all members of the population are genetically identical. For any particular gene, then, a population may have several slightly different forms present within it. These different forms are called alleles. An example in humans that is fairly well-known is the different alleles that control blood types: one allele gives rise to the A type, another to the B type, and a third allele the O type. Individuals may be either blood type A (either two A alleles or A + O); blood type B (either two B alleles or B + O); type AB (one A allele + one B allele) or type O (two O alleles). Any one individual can have only two alleles of this gene (one from mom, the other from dad), but as a population we collectively maintain all three. Other human genes have many more alleles than three (for example, some genes of the immune system have hundreds of alleles) despite the fact that any given individual can have at most two. The larger a population is, the more alleles of a given gene it can maintain. Smaller populations are more at risk of losing alleles due to chance (something called genetic drift).

Genetic diversity and speciation

The fact that populations maintain genetic diversity is important to remember when considering speciation. Speciation events are commonly represented with branching tree diagrams (“phylogenies”, or “species trees”) such as this one:

Here we see that Species 1 and Species 2 are more closely related to each other than they are to Species 3. What this says is that Species 1 and Species 2 shared a common ancestral population more recently with each other than either did with Species 3. So far, so good – but what this doesn’t mean, however, is that comparing gene sequences between these species will always group 1 & 2 together as more similar to each other than to 3. While this will be true most of the time, it is expected that some of the time this pattern will not hold. The reason is due to something called incomplete lineage sorting, and it has to do with the fact that populations going their separate ways carry genetic diversity with them. Let’s try to explain what is going on here.

Imagine that the ancestral population of all three species (the 1,2,3 common ancestor) has four alleles of a certain gene (represented by different colors in the diagram). These alleles originally arose due to a single mutational difference during DNA copying. Once there is a difference in place, two alleles can go on to acquire other differences over time, again, through copying errors. As a result, alleles can be compared to each other, just like species. Alleles that are recently separated will have more similarities in common, and alleles that have been separate for longer will have acquired more differences. In this example, the blue and green alleles are more similar to each other than either is to red or orange, and vice versa. The blue and green alleles arose from a common ancestral allele, and the red and orange alleles arose from a common ancestral allele. Further back in time, these two ancestral alleles themselves arose from one common starting allele. All four alleles will have a great deal in common (nucleotide sequences inherited from the single ancestral allele), as well as differences (for example, the red and orange alleles will share all changes that occurred between the time they split off from the blue/green lineage and when they themselves separated into two distinct alleles).

Now consider the time when the (1,2,3 common ancestor) population divides to become the (1,2 common ancestor) species and the Species 3 ancestor (the first branch in the diagram). As this population divides into two species, it is not guaranteed that all four alleles will be present in the founding population of each new species, simply by chance. Each founding population is a sample of the original population, but any given sample may omit certain alleles:

In the example above, we see that the red allele has been lost from the (1,2 common ancestor) species, and that the Species 3 ancestor has lost the blue and orange alleles. What this means is that the founding population of the (1,2 common ancestor) species didn’t have any individuals that carried the red allele, and that the Species 3 ancestor founding population didn’t have any individuals that had the blue or orange alleles. Both events happened simply by chance, because the founding populations are not representative samples of the original population.

Later, as the (1,2 common ancestor) species separates again into Species 1 and Species 2, the same issues arise. The two founding populations may not transmit all of the genetic diversity of the (1,2 common ancestor) population:

In this case, the founding population leading to Species 1 did not include a member with the green allele, and the founding population leading to Species 2 did not include any members with either blue or orange alleles. Also, the green allele has been lost in the lineage leading to Species 3 (it became rare and was eventually not passed on due to chance).

In the present day, examining the alleles of the three modern species will reveal different levels of similarity. The blue allele is now only found in Species 1, and it is most similar to the green allele in Species 2, and less similar to the red allele in Species 3. This pattern matches the overall “species tree” pattern for these three species:

The orange allele in Species 1, however, tells a different story: it is most similar to the red allele in Species 3, and less similar to the green and blue alleles. If we knew only about the orange allele in Species 1, we might conclude that Species 1 and Species 3 are the closest relatives. This is because the “gene tree” for these alleles places orange closest with red, even though the true “species tree” reveals an overall pattern of speciation that is different:

The orange allele thus has a gene phylogeny that is said to be “discordant” with the overall species phylogeny.

How do biologists assemble species trees if gene trees can be discordant?

It might seem from the above discussion that assembling a species phylogeny from gene phylogenies is a hopeless task: after all, if any individual gene tree might be misleading, how can we be certain we have the correct species tree?

The solution is to realize that while any individual gene tree might be discordant, gene trees that match the species tree will be the most common category. In our example above, Species 1 and Species 2 share a common ancestral population for some time after the (1,2 common ancestor) and the Species 3 common ancestor populations diverge. This means that any event that happens to this population (loss of an allele, for example) will be reflected in all descendant species (in our example, Species 1 and Species 2). This common history favors gene trees that match the species tree. For a discordant tree, the ancestral (1,2) population needs to maintain two alleles, and these alleles cannot sort equally into Species 1 and 2. This can happen, but it is less likely.

What this means in practice is that biologists expect a certain pattern of gene trees when comparing related organisms. Using our three species as an example, most gene trees should match the species tree. The less likely outcome is a gene tree where an allele from Species 1 is more similar to the allele in Species 3. We can be confident we have the correct species tree because the majority of the gene trees favor one species tree over the alternatives.

A problem for common descent?

The fact that gene phylogenies/trees and species phylogenies/trees don’t always match is not something that surprises scientists, since it is a well-known phenomenon and the mechanisms underlying it are understood: species arise from genetically diverse populations and that diversity does not always sort completely down to every descendant species. Discordant phylogenies, however, are commonly used among Christians as a means to cast doubt on to common ancestry and/or evolutionary biology as a whole. One example from the Intelligent Design movement will serve as an illustration. In a blog post discussing discordant trees found when comparing the human genome to that of other primates, Casey Luskin argues

Since humans are typically said to be most closely related to chimps, this data conflicts with the standard supposed tree … the basic problem is that one gene (or portion of the genome) gives you one version of the tree, while another gene (or portion of the genome) gives you a very different version of the tree. This leads to discrepancies between molecule-based trees, wherein DNA data fails to provide a consistent picture of common ancestry.

In the end, molecular trees are based upon the sheer assumption that the degree of genetic similarity reflects the degree of evolutionary relatedness … Clearly this assumption fails when different genes paint contradictory pictures of evolutionary relationships.

As we have seen, these differences are the natural, expected consequence of genetic diversity from an ancestral population sorting itself incompletely into different descendant species. The data set Casey is concerned about is primate evolution, where the species tree for humans, chimpanzees, gorillas and orangutans is as follows:

In the article linked above, Casey is discussing a recent comparison of the newly-completed orangutan genome with the human genome. The availability of the orangutan genome allowed researchers to scan the human genome for locations where humans are more similar to orangutans than to chimps. These regions are rare in the human genome, and very short in length. Indeed, the researchers found a pattern: chromosome segments in humans most often match chimpanzees, and do so for thousands of nucleotide base pairs at a time, on average. Those regions that match orangutans are tiny (on average less than 100 base pairs) and rare. This is exactly what one expects from the species tree: humans and chimps are much more likely to have gene trees in common, since they more recently shared a common ancestral population (around 4-5 million years ago). Humans and orangutans, on the other hand, haven’t shared a common ancestral population in about 10 million years or more, meaning that it is much less likely for any given human allele to more closely match an orangutan allele. It is certainly possible, however, and in scanning over the entire genome rare sites that have this pattern can be found. Indeed, the authors of the paper above used previously-determined speciation times and population size estimates to predict what fraction of the human genome would be expected to match more closely with orangutans. Based on these parameters obtained in other studies, they predicted 0.9% of the human genome would have a human : orangutan gene tree. Their observed value was 0.8% - a result that provides additional support for the population size estimates and speciation times from other studies.

Why is this data interesting?

Aside from its misinterpretation by the ID movement, this sort of data actually provides us with information about the population size of the species that went on to give rise to orangutans, gorillas, chimpanzees and humans, as well as times for the various speciation events. I have discussed similar data for the (gorilla/chimpanzee/human) and (chimpanzee/human) common ancestor populations elsewhere; this new data merely confirms previous estimates of the population sizes of the various ancestral groups, and extends back to the (orangutan/gorilla/chimpanzee/human) common ancestor population with greater precision. As before, these results continue to strongly support the hypothesis that the human lineage has never been as low as two individuals at any point in our evolutionary history. Indeed, these new results confirm that the human : chimp common ancestor population was large (about 50,000 members). As Darrel Falk and I have discussed here on BioLogos in the past, all methods used to date (numerous approaches, all using independent assumptions) would have to be wildly wrong (by several orders of magnitude) if indeed our species arose from just two individuals.