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That’s Random! A Look at Viral Self-Assembly

Kathryn Applegate — Sat, 16 Mar 13 08:54:44 -0700

You hear it all the time: “That’s so random!” When used by people of my generation, the word “random” can simply mean “cool” or “surprising.” Or it can mean something like “disconnected,” as in the phrase, “I had a random thought” (which returns 189,000 hits on Google, by the way—random!).

Despite this usage, most of us know that randomness has something to do with probability, and that it often implies a lack of conscious intentionality. But what do mathematicians and scientists mean when they say something is random? Can a random process lead to an ordered, even predictable outcome? Is there evidence that God makes use of random processes to fulfill his creative purposes?

These are big questions, and we won’t address them all today. But I think randomness is an important topic to cover for two reasons: 1) it is integral to many processes in biology (and math, physics, chemistry, etc.), and 2) it is commonly misunderstood to be incompatible with Christianity.

As I said above, most of us know that randomness has something to do with probability. If you pick a card “at random” from a shuffled deck, you have a small probability of drawing an ace (4 out of 52, or a 7.7% chance). If you flip a coin, you have an equal probability of getting heads or tails.

Randomness also seems to imply a lack of intentionality or purposefulness. After all, you might hope for an ace when you draw a card, but you can’t choose one on purpose. You might call heads when you flip a coin, but you can’t know beforehand what the outcome will be. Thus the outcome is indeterminate, but is it purposeless? Not necessarily. Indeterminacy simply means the result cannot be predicted from the outset.

It should be noted that indeterminacy does not imply that God does not have foreknowledge of future events. Christians ought not to be uncomfortable with the idea of God interacting with his creation through chance. We often describe a seemingly-random (i.e. unplanned by us) sequence of events as being “providential,” or planned by God.

In biology, it is very hard or impossible to calculate precise probabilities for most processes, so when we say a process is random, we typically mean it is extremely unpredictable. Eventually we will discuss randomness within biological evolution, but first we must consider some simpler processes, like the self-assembly of a virus.

Viruses are remarkably efficient entities. Coiled tightly within a protein-based shell is a small amount of DNA needed for self-replication. The shell, called a capsid, is made of many repeating protein subunits and is therefore highly symmetrical (see figure). Important biomedical insights have certainly been gleaned from structural studies of viruses, but viruses also teach us about the emergence of order from non-order.

The virus life cycle has four main steps: 1) enter a host cell, 2) hijack the cell’s replication and translation machinery to make many copies of itself, 3) assemble into many virus particles, and 4) exit the cell to invade another host.

When I first learned about this process, I found it very hard to believe it just “happens.” The idea that a bunch of molecules bumping into each other inside a crowded cell could spontaneously assembly into a fully-functional virus seemed a bit far-fetched. Many viral capsids have over 100 protein subunits that must interact with each other in just the right way, or it won’t work. Surely there must be something driving this process, right?

There is! Random motion. I had to see it to believe it. I distinctly remember sitting in class during my first year of graduate school when the professor demonstrated self-assembly of a virus using a 3D model as shown in the following video. In less than 30 seconds, you can watch a jumbled heap of proteins become a beautifully ordered structure.

As the narrator explains, sub-assemblies form and break apart en route to the most stable structure, the full capsid. As the sub-assemblies begin to form, further associations with free subunits become more favorable and as a result occur rapidly, while the final steps may take considerably longer. While the subunits in the model are rigid, in reality the proteins take on multiple conformations, allowing the capsid to “breathe.”

Amazing as it is, the system we just considered—one virus capsid in a jar—is pretty simple. One wonders how self-assembly can happen in a crowded cell, where there are countless other molecules diffusing around, potentially getting in the way. We can’t directly see how it happens in a cell, but we can reconstitute the process in a test tube using different combinations of constituent molecules.

Consider two viruses, where each protein subunit in one virus is the mirror image of the corresponding subunit in the other. Putting the two viruses together by hand would be pretty tricky, because the constituent parts look so similar. But random motion can do the job in short order:

From this model, we can see clearly, in real-time, how distinct complex structures can arise from their parts randomly interacting with one another. Many large viruses also use special scaffolding proteins to assist in the assembly process, and some even use their own genomes as a scaffold. In addition, two closely-related viruses that happen to infect the same cell can exchange parts to create a new virus. This is one way viruses can evolve quickly to evade the host’s immune system.

Here we have seen how viruses demonstrate a principle inherent in God’s world—that order can emerge out of chaos from random processes. In my next post, we will look at some other biological processes that make use of—rather, depend on—randomness. This will set the stage for us to see that such processes can not only assemble a structure within seconds or minutes, but also generate complex, information-bearing molecules over billions of years. Even though the freedom inherent in nature sometimes produces unintelligently-designed structures (like viruses, which can kill us), we see that God has made, and continues to oversee by his providence, a good creation that, at least in part, is capable of creating itself.

Next weekend, we’ll continue this series about randomness and God’s divine will. Up next: how God created the body to heal itself, and how can random mutations can be both harmful and benign.

Growing in Faith

David Buller — Fri, 12 Oct 12 05:00:28 -0700

Growing up, David believed that Young Earth Creationism was the Christian position on origins and how God created. As he endeavored to learn more, he was intrigued by Francis Collins book The Language of God because Francis did not present evolution as a rival theory to Christian faith, but as something that described God's method of creation. David studied biblical interpretation and found John Walton's scholarship to be tremendously helpful in understanding the original purpose and intent of the Genesis narrative.

Reflecting on his personal journey, David thinks that it is important that we don't oversimplify questions related to science and faith, but that we explore them deeply in order to understand science in a robust, Christian way.

Series: Divine Action in the World

Alvin Plantinga — Tue, 04 Sep 12 04:00:33 -0700

My talk is entitled “Divine Action in the World.” I want to talk about a certain kind of objection to Christian belief that some people raise. They claim that central thoughts, central doctrines of Christianity, are contrary to science, and therefore, are suspicious or incredible or such that one can’t sensibly hold them—can’t be rational in accepting them.

There are several different kinds of arguments that people bring along these lines; I want to talk about just one. So first… the Heidelberg catechism, one of the forms of unity of the church I go to (the Christian Reformed Church), says

Providence is the almighty and ever-present power of God, by which he upholds as with his hand heaven and Earth and all creatures and so rules them, that leaf and blade, rain and drought, fruitful and lean years, food and drink, health and sickness, prosperity and poverty. All things, in fact, come to us not by chance, but from his fatherly hand.

And part of the way it comes to us—not by chance, but from his fatherly hand—part of the way God has designed our world, is that there is a great deal of regularity and dependability in our world. Of course, if it were not for this regularity and dependability, we couldn’t do the things that we actually do. I mean, for example, if I just wanted to walk off the stage—if, for example, all the sudden those stairs over there suddenly turned into a ladder going up—well, that would make it really difficult.

If you are trying to build a house, for example, you have this hammer, but all the sudden the hammer turns in to a goose or a pigeon. Again, that would make things really difficult…or if the nail turned into a worm…or if you get in the car and turn the key and the car turns into a camel, things would be really hard, much harder than they are. This regularity and dependability in our world is an essential condition of our being able to live in the world in which we actually do.

If the world were irregular enough, we would not even be able to live in it, but there are also, according to classical Christianity here (the Heidelberg catechism, for example) there are also special divine actions; sometimes God does things specially. There are miracles in Scripture: the parting of the Red Sea, for example, Jesus walking on water, Jesus changing water into wine. There are miraculous healings: Jesus rising from the dead, Jesus raising Lazarus from the dead, and so on. And according to classical Christians, many of them, perhaps most of them, are special divine actions. God, for example, responds to prayers. He works in the hearts and minds of his children to effect sanctification. There is, what Calvin called, the internal testimony or witness of the Holy Spirit, and there is what Thomas Aquinas called the internal instigation of the Holy Spirit. So, these things are all special actions on the part of God. God constantly causes events in the world. Ok, so far fair enough—what is the problem?

Many theologians seem to think there is a science-religion problem here. I don’t think any of the theologians of Biola think this, (I don’t know, but I doubt it) but many theologians do. For example, Rudolf Bultmann says, “The historical method,” which of course he thinks that is the method we should use, “includes the presupposition that history is a unity in the sense of a closed continuum of effects in which individual events are connected by the succession of cause and effect. This continuum, furthermore, cannot be rent by the interference of supernatural, transcendent powers.”

That’s what he says. Alright, there is this continuum that cannot be rent by the interference of supernatural (that would be God) or transcendent powers. So, it is a little bit like the laws of the Medes and Persians. You probably remember Daniel. Daniel was a favorite of King Darius, and well, the other courtiers became jealous of Daniel (they didn’t like it that the king liked him so well). So, they came to the king and said, “Oh king, live forever, we think it would be a great idea if you passed an edict to the effect that you alone can be worshipped. Everybody has to worship you and nothing else.” Well the king thought that over for a minute, and that sounded pretty good to him so he said, “I guess that it is a pretty good idea.” So he made this edict; he made this declaration: “Only King Darius is to be worshipped—no one else, nothing else.”

These courtiers knew that Daniel worshipped God, and they thought probably Daniel would keep right on worshipping God despite this edict. So they were watching Daniel, and he was, in fact, worshipping God. So they came to the king. Now the penalty for worshipping something else was to be thrown into the lion’s den and they said, “Well, king live forever, looks like Daniel has been violating this edict. You have got to throw him in the lion’s den.”

Well, the king didn’t want to do this because he really liked Daniel. He thought this was a miserable way to proceed, and he didn’t want to do it, but then they said to him, “O king live forever, and remember a law of the Medes and Persians cannot be abrogated, even by the king himself.” So once it’s put in place, not even the king himself can change it or abrogate it or go against it.

That is sort of the suggestion that you get here from Bultmann. Bultmann thinks, “Maybe God created the world and set it up in a certain way, but once he did that, not even he can interfere in it”—he uses that word interference—“not even he can do anything in it. He just has to keep hands off.” It is like the law of the Medes and the Persians.

Another theologian who agrees is John Macquarrie, who says,

The way of understanding miracle (and that would be one kind of special divine action) that appeals to breaks in the natural order and to supernatural intervention belongs to the mythological outlook, and cannot commend itself in a post-mythological climate of thought. The traditional conception of miracle is irreconcilable with our modern understanding of both science and history. Science proceeds on the assumption that whatever events occur in the world, can be accounted for in terms of other events that also belong within the world, and if on some occasion, we are unable to give a complete account of some happening, the scientific conviction is that further research will bring to light further factors in the situation that will turn out to be just as imminent and this worldly as the factors already known.

Ok again, no room there for special action. And the third thinker here, Langdon Gilkey (still another theologian), says something similar, but I will pass. I will not read that one in the interest of saving a little bit of time, but these three theologians, plus many others want to assert that there is something wrong with the idea of God acting in the world, acting in the world in a way that goes beyond creation and sustaining, or creation and holding things in existence. So they think, “Ok, God created the world; God sustains it in existence”…that is ok with them, but anything beyond that, God performing any miracles, raising Jesus from the dead, or for that matter working in somebody’s heart and mind in a special way, that, they say, is a real problem. The question is, what is the problem?

Well, the next little bit here…according to the Christian and theistic idea, God is a person; he has knowledge, loves, and hates. He has aims and ends. He acts on the basis of his knowledge to achieve his ends. He is all-powerful, all-knowing, and wholly good. Thirdly (noted above by the Heidelberg catechism), God has created the world. Fourth is God conserves and sustains and maintains in being this world he created, but fifth, at least sometimes, God acts in a way going beyond creation and conservation in miracles, but also in his providential guiding of history, his working in the hearts of people, his internal instigation of the Holy Spirit, and so on, and it is with that fifth category that these people have a problem. It is God’s special action in the world—action beyond conservation and creation—and miracles would be an example.

So we might think of these theologians as endorsing what we could call hands off theology. God has got to keep his hands off. God could create the world. God conserves the world, sustains it in being, but he can’t do anything else—that is as far as he could go. It is hands off theology, and Bultmann, even in this context, even talks about interfering. I mean if God did something in the world that would be interfering, which, when you think about it, is a sort of strange thing to say—I mean if God created the world, he is the omnipotent, omniscient, holy, good creator of the world—when you accuse someone of interfering, you are saying they are doing something they should not be doing, right?

So Bultmann thinks if God did something in the world that would be interfering, and he should be ashamed of himself. Ok, now why is this a problem? Their suggestion is that somehow it is contrary to science. It is contrary to science the suggestion that God acts specially in the world. I didn’t read that bit, but Gilkey says, "The causal nexus in space and time which the enlightenment science and philosophy introduced into the western mind is also assumed by modern theologians and scholars. Since they participate in the modern world of science, both intellectually and existentially, they can scarcely do anything else.”

From a presentation sponsored by Biola University’s Center for Christian Thought, and delivered February 12, 2012 at EV Free Church, Fullerton, CA. Used by permission.

Randomness and Evolution: Is There Room for God? (Videocast)

Joy Walters — Fri, 15 Jun 12 05:00:15 -0700

Today we present the fourth entry in our on-going BioLogos videocast series. So far we have looked at the fossil record and genetic evidence for evolution, as well as speciation and macroevolution. The latest entry addresses the idea of randomness as a part of natural selection, and whether it raises questions about the possibility of God using the evolutionary process as a means of creation. The script was written by biology student Joy Walters, with help from BioLogos president Darrel Falk.

For more, be sure to read Randall Pruim's recent series Randomness and God’s Governance, Kathryn Applegate's post That's Random: A Look at Viral Self-Assembly, and our FAQ How Do Randomness and Chance Align with Belief in God's Sovereignty and Purpose?.

Author's Note

I am so thankful that I grew up in a Christian environment, which both kindled and nurtured my relationship with Jesus Christ. The Biblical instruction I received from my parents, pastors, and teachers has been invaluable as I walk out my love for the Lord from day to day. However, there was one specific topic growing up which was not fully addressed, namely evolutionary theory.

Coming from a conservative Christian background, evolution was given little or no thought because of its seeming contradiction to the creation story in Genesis. To me, evolution meant a monkey became a human, and as far as I knew, I had never seen that happen! So, of course, it appeared too improbable to hold any truth. When it was discussed, an inadequate picture of its ideas was often painted, which caused immediate suspicion and rejection of the theory. I don’t think this was intentional, but most Christians have never learned an unbiased, in-depth theory of evolution that is completely detached from societal agendas and philosophical conclusions. Therefore, their explanations of the theory are often misinformed.

My senior year of high school, I took AP Biology, and finally learned the scientific reasoning supporting this theory. I was surprised by how logical and obvious the mechanisms of change (such as mutations, natural selection, genetic drift, and so on) were that gave rise to new species. My subsequent response was, “No wonder people believe evolution occurred.” At that point, I was convinced that microevolution (evolution within a species) existed, but I was still questioning macroevolution.

Now, being at Point Loma Nazarene University as an undergrad in the Biology-Chemistry major and a year-round, student intern at BioLogos, my understanding of evolution has expanded enormously. I have enjoyed critically thinking through the evidence for evolution and reading articles that tackle difficult issues at the interface of science and Christian faith. Ultimately, I know that God has created all things, but the processes he used surpass my small understanding.

My personal wrestling with evolution and quest for truth has led to times of prayer and studying God’s Word, which has deepened my love for him in ways I cannot express. The first chapters of Genesis, in particular, have come alive. My whole life, the creation story was a straightforward list of facts about the creation of the world; I never searched further. I didn’t even perceive the truths Genesis declared over my very identity and God’s character. The more I study his Word and handiwork, I glimpse the awesomeness and majesty of the Creator, who loves me much more than I know. There is still so much to learn, but I am confident that he will lead me into all truth as I seek him out.

I desire to give others the opportunity to see evolution accurately and to distinguish it from the traditional, philosophical, and personal conclusions that too often cloud the scientific theory. I believe these conclusions alienate Christians from evolution more than the scientific theory itself. Ultimately, I do not mean to convince someone about evolution, but simply to give them the freedom to understand it.

Therefore, my goal for this podcast is two-fold:

First, to offer a new perspective on randomness within natural processes that removes its negative connotations (especially as it relates to evolution).
Second, to expose why evolution is powerless to support conclusions beyond the physical realm.

This will hopefully encourage others to study evolutionary theory and draw their own conclusions about its meaning in the framework of their faith.

Scientists Tell Their Stories: David Wilkinson

David Wilkinson — Tue, 10 Apr 12 05:00:58 -0700

Transcript

My name is David Wilkinson, I teach at Durham University in the department of theology, I used to be a physicist and I still am fascinated by science and theology. I became a Christian at the age of seventeen, and at that point Christian faith was very new and exciting to me. I’d also decided to do a physics degree at university; now I’m not that type of person who built a telescope at the age of four or anything of that sort. I did physics at university, I have to admit, because I was quite good at mathematics and therefore I knew I wouldn’t have to work very hard doing physics. I could spend time doing real things at university, such as cricket and other things-- typically British of course.

However what happened for me as I began to study physics at Durham University was that my new-found faith and this new area of science began to enrich each other, and Kepler of course once said that science is thinking God’s thoughts after him. And I think what was happening in hindsight was that as I was encountering the God of creation in and through Jesus, so what God had created became more and more valuable, more and more interesting to me, just as when our children brought back drawings and paintings from their school class. They weren’t great pieces of art but they were put on our kitchen walls because we knew the person who had created them, and because I was being introduced to the God of creation, so the science itself began to live for me.

Another thing was that the science at university level, particularly as one starts to explore relativity and quantum theory, cosmology, is that as John Polkinghorne would say, “It breaks the tyranny of common sense.” This isn’t a mechanistic world of Isaac Newton and those theologians who think that every question is wrapped up. This is an exciting open world of exploration and questions, of freedom both for God to work and the universe to explore. And this became more and more fascinating to me as time went on. My faith enriched my science, and my science enriched my faith. Now that wasn’t always a process where there were easy questions to answer; there were often difficult questions. But I have to say that continually, the science and the faith have gone together and have enriched each other.

My own particular interest then over the years has been how one takes the issues of science and faith and communicates them to folk who aren’t Christians. As I go around the world these days, I find many people who are fascinated by some of the questions that modern science raises, questions such as the intelligibility of the universe. How can our minds understand the universe back to such an early stage? The fact that the universe is very carefully balanced, fine-tuned for the existence of life. The question of human significance in such a vast universe. The sense of awe and wonder as you look not just at the vastness of the sky but also the fact that underneath the complexity of the universe are rather simple, elegant, beautiful laws. And I find that many folk, whether they are people of religious faith or not, find themselves drawn in by these questions that say “Is there a deeper story to the universe? Are these pointers to something that goes beyond science?” I don’t believe that they can prove God in any way, but I do think that they are pointers towards a God who in Christ is the best explanation for all of these different areas.

Off camera: “Let me ask you one question here: you mentioned John Polkinghorne. You studied with him, I believe. Would you tell something about your relationship to John Polkinghorne, and you might begin by saying, ‘John Polkinghorne was my mentor or whatever’. Just a few things about your relationship with him.”

Wilkinson: One of the most important things for me in the science/faith relationship has been those mentors, those great men and women of faith and science who have helped me along the way. Those have been many for me. One of the key people for me in this area has been Sir John Polkinghorne. John was teaching theology in Cambridge, having retired as head of the Cavendish Laboratory in Cambridge, trained as an Anglican priest, and then started to teach theology just as I arrived in Cambridge also to study theology. And what I found in his thinking was a commitment to the rigor of science, and someone who not only philosophized about science but had a feel for science as a working scientist, but someone who’s prepared to take that science and contemporary science and use it in theology today.

If I have one criticism of my fellow theologians from time to time it’s that they’re often stuck in the physics of the 19th century rather than the 20th and 21st centuries. They’re still dominated by this clockwork universe, whereas Polkinghorne and others have taken seriously that the universe is very different. And Polkinghorne with many others have spent time with me answering my questions, being gracious to the type of questions I’ve wanted to push, but they’ve impressed me by showing integrity both towards Christian faith and to science by holding the two together and not compromising on either.

John Polkinghorne in a Nutshell

John Polkinghorne — Wed, 07 Dec 11 05:42:26 -0800

Today's video is courtesy of filmmaker Ryan Pettey, director/editor of Satellite Pictures and features physicist and theologian John Polkinghorne.

I grew up in a Christian home and I can't really remember a time when I wasn't, in some sense, part of the worshiping and believing community of the church. So Christianity has always been central to my life. Academically, I was good at mathematics and so I moved into theoretical physics and I spent about 25 years working in that and enjoyed it very much and regarded it as being a Christian vocation to use such talents as I had. But you don't get better as you get older in mathematical subjects and after 25 years I found I had done my bit for physics and I'd do something else. So the idea of seeking ordination and becoming a Christian minister of Word and sacrament seemed a worthwhile thing to do--also, to my wife fortunately. So she agreed with that and that's how I made this rather unusual change.

Physicists do, I think, have a sort of cosmic religiosity. They do find it necessary to take seriously the order of the world. They are wary of religion because they have a picture of religion that is based upon blind faith, submission to authority, and so they don't want to commit intellectual suicide. Neither of course do I. So I've also tried to show my friends that my religious belief, not only explains the order of the world, but has other motivations which are also important.

Science has [achieved] its great success by the limit of its ambition. It doesn't try to ask and answer every question, but essentially asks the question "how do things happen"? It's a very important question to ask and, of course, science has been stunningly successful in answering it. But it is not the only question to ask about the world. There are questions of meaning and purpose. Is there something going on in what is happening? Now science, by its very nature, when it's honest and true to itself, doesn't seek to answer those questions. But they are questions that we know are meaningful and necessary and I want to have as full of an understanding of the world as possible which means that I need the religious answers to, if you like, the "why" questions about the world, the meaning and purpose and value of the world, just as I need the scientific answers to the "how" questions about the process of the world.

I worked in quantum physics and of course quantum physics is totally different to the physics of the world of everyday. So in the quantum world things can sometimes be like waves--spread out and flappy. Sometimes they can be like particles, little bullets. Now nobody would think that that is a sensible thing. Only the nudge of nature itself, only the way the world actually is could drive us in that direction. And now, of course, we understand many things on that basis. And that is one of the things, incidentally, that persuades me that science is dealing with truth. Not the complete truth. There is always something more to find out, there is something around the next corner which we wouldn't have thought of before hand. But we have to keep on looking for the truth and when we find it we have to commit ourselves to it and trust it.

I think that discoveries of new truth in science and beyond science are always in some continuing relationship to the truth that has been there before. When Einstein came along and discovered general relativity he didn't throw Newton away. He showed the limitations of Newton's understanding and was able to extend them. Newtonian ideas are still good enough to send an explorer satellite to Mars so they are not exactly useless. In the same sort of way, I think there is a sort of development of doctrines as people sometimes say. The understandings of truth in the present build upon the understandings of the past. They may modify them in various ways, see them in a different perspective. But I don't think they just wipe them away and start with a clean slate.

I suppose everybody would like certainty, but it isn't available to us in that absolutely black and white way. We have reasons for our beliefs. I commit myself to my Christian belief for reasons that are sufficient enough for me to bet my life upon it. But we don't have absolute certainty in the 2+2=4 sense. And that is true of everybody. Everybody has to make a commitment beyond what they know for certain to be true. I would define faith as commitment to well motivated belief, accepting the consequences of that, not only for my intellectual attitude to the world, but also the way I live my life.

From Chaos to Order: The Random Process as the "Precision Tool"of God

Ryan Pettey — Tue, 13 Sep 11 22:00:20 -0700

For many, the importance of apparent randomness in evolution can be a major stumbling block when considering whether God could have created through an evolutionary process. After all, if God created for a purpose, how could there be room for “unguided and purposeless” processes? Aren’t randomness and design naturally opposed?

While these are indeed complex questions, some of the problems do stem from misunderstandings about what randomness means in a scientific sense and what role it plays in evolution. To help clarify some of these details, we offer these resources.

The “Randomness” installment of our Distinctions series (first posted earlier this year) looks at some of the basic misconceptions about the role of randomness in evolution. While it is understood by many simply to mean blind, undirected and purposeless, in truth, randomness is far more complex and awe-inspiring than this overly-simplified definition. Whether through genetic mutations or the combinations that occur between sperm and eggs, these processes can be seen as the continual unfolding of something that is decidedly not random--creation itself. Randomness, in essence, generates certainty. This is further illustrated in the second video.

In the clip “Randomness” from the upcoming film A Leap of Truth by Ryan Pettey, Richard Colling, Ard Louis, and John Polkinghorne offer several examples of random processes leading to order rather than disorder. As Dr. Louis points out, the scientific definition of “randomness” is quite different from our everyday understanding of the word. In fact, random generation is the most efficient way to generate complexity. Polkinghorne further notes that we live in a world where the balance of random mutations is almost perfectly tuned for fruitful life on Earth. This, we learn, is God's process: Randomness given time, can lead to that which is nearly certain.

This is beautifully illustrated in the following re-post from last year. Here, in a blog called "That's Random," Kathryn Applegate offers two examples of random motion leading to certainty in the process of assembling a virus. Because random processes can lead to that which is almost certain, it is not at all surprising that this has frequently been used by God over billions of years to create order out of chaos--God's creation, by God's way, in God's time.

That's Random

Here we have seen how viruses demonstrate a principle inherent in God’s world—that order can emerge out of chaos from random processes.

Miracles and Science: The Long Shadow of David Hume

Ard Louis — Mon, 02 May 11 18:43:36 -0700

In this paper, physicist Ard Louis, a "scientist who believes in the miracles of the Bible", looks at the implications science has on the acceptance of miracles.

Distinctions. Part 1: Randomness

Loretta Cooper — Thu, 21 Apr 11 12:58:07 -0700

Today we are happy to introduce the first in a new series of videos from The BioLogos Foundation called “Distinctions”. These short videos look to clarify some of the important scientific questions at the heart of the science and faith dialogue. In our first video -- featuring biologists Sean Carroll and Kerry Fulcher, Smithsonian Human Origins Program director Rick Potts, and Old Testament scholar John Walton -- we look at the concept of randomness. While it is understood by many simply to mean blind, undirected and purposeless, in truth, randomness is far more complex and awe-inspiring than this overly-simplified definition. Unlike our previous posts for the Conversations series, we won't be including a full summary, as we feel the videos speak for themselves.

There are certainly more resources addressing the topic of randomness, however. For further reading, be sure to check out our FAQ on chance and God's sovereignty, Ard Louis’ scholarly essay “How Does the BioLogos Model Need to Address Concerns Christians Have About the Implications of its Science?”, and the series of blogs by BioLogos program director and cell biologist Kathryn Applegate, beginning with her posts “That’s Random!” and "Understanding Randomness".

Credits: This video was directed by Loretta Cooper, President of Clarity Media Strategies and was scripted by Loretta Cooper and BioLogos Program Director, Kathryn Applegate.

An Afternoon with John Polkinghorne

Dean Nelson — Wed, 09 Feb 11 06:00:28 -0800

John Polkinghorne remembers the day when some of his colleagues thought he had lost his mind. He was already famous as a physicist for his work in helping explain the existence of quarks and gluons, the world’s smallest known particles. He was a member of England’s Royal Society, one of the highest honors bestowed on a scientist –Isaac Newton is also a member. His students at Cambridge University had likewise moved into leading roles in scientific research.

It was the end of the academic year, and he and some other professors had gathered in his office for a brief meeting. At the conclusion, they gathered their papers, ready to leave.

“Before you go,” Polkinghorne said, “I have something to tell you.”

The tiny audience settled back into their chairs.

“I am leaving the university to enter the priesthood. I will be enrolling in seminary next year.”

There was stunned silence in the room for several seconds, then murmuring, some of it kindly supportive. The lone Scotsman in the audience, an atheist, was both wistful and wary: “You don’t know what you’re doing,” he said. Others later wondered if John Polkinghorne was committing intellectual suicide.

His decision brought to light a much larger question that has been discussed for centuries, well before Darwin and Dawkins: “What Is the Relationship Between Faith and Science?” In the years following this decision to leave the physics world, where he specialized in one kind of unseen realities, and enter the spiritual world where he explored other unseen realities, Polkinghorne has become one of the most significant spokesmen for making the relationship between faith and science one of harmony, not conflict.

He has written more than 30 books on theology and science (and the relationship between the two), served on national boards to determine ethical standards for scientific research, and was knighted by the Queen for his contributions in ethics and science. He is the founding president of the International Society for Science and Religion. He was awarded the Templeton Prize – the highest honor given in regard to the relationship between science and religion. He has studied and lectured on most continents, at the most prestigious locations, including Yale, Princeton, and the Smithsonian Institution, and appears regularly on documentaries regarding the beginning of the universe, Albert Einstein, C.S. Lewis, and countless other topics. He was featured recently on The Science Channel in the U.S. for the program Through the Wormhole, narrated by actor Morgan Freeman.

While much is made in the popular media and some religious circles that one is either a person of science or a person of faith, he has never seen how the two could be in conflict. As both a physicist and a priest, he embraces and embodies both.

One thing that did not change when he moved from academia to ministry was that both involved a quest for truth. In both science and religion he moves from evidence to interpretation to motivated belief or conclusion – a process he calls “bottom-up thinking.”

After serving as a parish priest just up the hill from the Canterbury Cathedral, Polkinghorne returned to the world of academia in Cambridge – first as the dean of chapel, and ultimately as president of Queens’ College until he retired. He continues to study, write and administer the sacraments.

I met Rev. Polkinghorne at a theology conference in Boston in 2007, at the suggestion of an editor who had an idea for a book. The idea was to make the book biographical in form, so that the world could read about the life of this very fascinating man and important thinker. But the book would be bigger than that, too. It would use Rev. Polkinghorne as a launch-point to then discuss bigger questions about the relationship between science and faith. How can a scientist really believe in miracles? How, or why, does a scientist pray? And how could a physicist possibly believe in the Resurrection of Jesus? Behind these questions is, essentially, this one: Aren’t science and faith fundamentally at odds with one another? The answer is no, and the reason is that John Polkinghorne embodies the relationship between the two. I interviewed him at his home in Cambridge several times over the next few years, as well as in Venice, where he was lecturing at a God and Laws of Nature conference at the Venice Institute, and at Oxford, where the entire God and Physics conference was dedicated to Polkinghorne’s work and to commemorate his 80th birthday.

The resulting book, Quantum Leap: How John Polkinghorne Found God in Science and Religion, by Dean Nelson and Karl Giberson, will be released by Lion-Hudson Press of Oxford, in 2011.

The book captures Polkinghorne’s views on the big cosmic questions regarding Evil, the Trinity, Evolution, the Big-Bang Theory, Adam and Eve, Intelligent Design, Atheism, the Resurrection, Salvation, Eternity, and other issues that seem to pit science against faith.

Atheists, especially those in the present realm who sell millions of books, have a faith of their own, Polkinghorne says. It may be faith in selfish competition, in Marxism, or in freedom to live as one pleases without responsibility, but there are often elements of faith, nonetheless. Sometimes the faith is in those who proclaim to not have a faith.

A theme that emerges in both his writings and in personal conversation with Polkinghorne is the phrase “But that’s not the whole story.” Science, life, God, the universe, are always surprising us with something else, or Something Else, he says. So after all these years of research and reflection, Polkinghorne is comfortable with the posture that there is always more. To everything. Looking at the world both through the eye of faith and the eye of science improves the vision over what using just one eye or the other would provide, he says.

He appeared recently at Point Loma Nazarene University in San Diego, where I teach with Darrel Falk of BioLogos. He gave a 30-minute lecture on the relationship between faith and science and then let me interview him for 30 minutes. The interview has the feel of a couple of old friends talking.

“He doesn’t do all the work for you,” said one of his former parishioners. “He’ll discuss things with you and then say, ‘You can do some of this thinking yourself, you know.’”

That’s our hope as you watch this program – you’ll hear some things that will make you want to think more deeply. Because there’s always more to the story.

The Creator Speaks

Fri, 14 Jan 11 10:45:43 -0800

Today's video, courtesy of the Test of Faith project, presents a dramatic retelling of Job 38. Below is the original text from the New International Version.

Job 38

1 Then the LORD spoke to Job out of the storm. He said:

2 “Who is this that obscures my plans
with words without knowledge?
3 Brace yourself like a man;
I will question you,
and you shall answer me

4 “Where were you when I laid the earth’s foundation?
Tell me, if you understand.
5 Who marked off its dimensions? Surely you know!
Who stretched a measuring line across it?
6 On what were its footings set,
or who laid its cornerstone—
7 while the morning stars sang together
and all the angels shouted for joy?

8 “Who shut up the sea behind doors
when it burst forth from the womb,
9 when I made the clouds its garment
and wrapped it in thick darkness,
10 when I fixed limits for it
and set its doors and bars in place,
11 when I said, ‘This far you may come and no farther;
here is where your proud waves halt’?

12 “Have you ever given orders to the morning,
or shown the dawn its place,
13 that it might take the earth by the edges
and shake the wicked out of it?
14 The earth takes shape like clay under a seal;
its features stand out like those of a garment.
15 The wicked are denied their light,
and their upraised arm is broken.

16 “Have you journeyed to the springs of the sea
or walked in the recesses of the deep?
17 Have the gates of death been shown to you?
Have you seen the gates of the deepest darkness?
18 Have you comprehended the vast expanses of the earth?
Tell me, if you know all this.

19 “What is the way to the abode of light?
And where does darkness reside?
20 Can you take them to their places?
Do you know the paths to their dwellings?
21 Surely you know, for you were already born!
You have lived so many years!

22 “Have you entered the storehouses of the snow
or seen the storehouses of the hail,
23 which I reserve for times of trouble,
for days of war and battle?
24 What is the way to the place where the lightning is dispersed,
or the place where the east winds are scattered over the earth?
25 Who cuts a channel for the torrents of rain,
and a path for the thunderstorm,
26 to water a land where no one lives,
an uninhabited desert,
27 to satisfy a desolate wasteland
and make it sprout with grass?
28 Does the rain have a father?
Who fathers the drops of dew?
29 From whose womb comes the ice?
Who gives birth to the frost from the heavens
30 when the waters become hard as stone,
when the surface of the deep is frozen?

31 “Can you bind the chains of the Pleiades?
Can you loosen Orion’s belt?
32 Can you bring forth the constellations in their seasons
or lead out the Bear with its cubs?
33 Do you know the laws of the heavens?
Can you set up God’s dominion over the earth?

34 “Can you raise your voice to the clouds
and cover yourself with a flood of water?
35 Do you send the lightning bolts on their way?
Do they report to you, ‘Here we are’?
36 Who gives the ibis wisdom
or gives the rooster understanding?
37 Who has the wisdom to count the clouds?
Who can tip over the water jars of the heavens
38 when the dust becomes hard
and the clods of earth stick together?

39 “Do you hunt the prey for the lioness
and satisfy the hunger of the lions
40 when they crouch in their dens
or lie in wait in a thicket?
41 Who provides food for the raven
when its young cry out to God
and wander about for lack of food?

Uncertainty is Uncomfortable

Kathryn Applegate — Wed, 03 Nov 10 14:38:23 -0700

In this video “Conversation,” BioLogos Program Director Kathryn Applegate points to evolutionary science as a way to gain a richer understanding of the glory of God.

Scientists become fairly comfortable with a certain level of uncertainty within scientific data, notes Applegate, but that is not the case for most people. Uncertainty—especially where faith is concerned—can be scary for people who want a black and white answer. Yet science has all of the subtlety of a beautiful painting that is hard to encapsulate in a sound byte.

God speaks through the Bible and all sorts of other things that comport with the Bible, says Applegate. “Science is another way of studying what God does. How he created and how he continues to create. God is active and involved. We see that through the means of a continuous creation through evolution,” she says.

That is really exciting and allows us to better understand the character of God. God is infinitely creative and infinitely good. Looking to Genesis for scientific data is like looking at the notes on the page of a symphonic score without ever hearing the music—you miss all the richness. “Not that the notes aren’t important,” says Applegate, but they do not offer the complete picture and it isn’t the primary purpose of those texts.

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After You Believe

N.T. Wright — Wed, 29 Sep 10 16:35:43 -0700

In this video Conversation, BioLogos Senior Biblical Fellow Peter Enns speaks with the Rev. N.T. Wright about some of the concepts explored in his latest book After You Believe: Why Christian Character Matters (HarperOne, 2010).

Enns begins by asking Wright what prompted him to write the book.

Wright responds, “I wrote it because I became fascinated a few years ago with the way in which the vision of God’s purpose to put all things right in the end actually affects what we loosely refer to as the moral life.” Many Christians think in terms of how good and bad behavior dictates who will go to heaven or hell, while still others focus more on the saving grace of Christ—and from this, it is clear that there is a preoccupation with how one should live.

There is confusion in our culture about what is right, though, Wright notes. Does one try to live by rules? By making a moral calculation when faced with every dilemma? Or does one try to live “authentically” and hope it all turns out well?

None of these options are good, says Wright. For example, rules alone are bad because they can stultify and prevent one from growing up.

How then do we live? Wright suggests that we revive the ancient idea of character and virtue as seen in the New Testament.

When Paul talks about character in Romans 5, he writes, “hope does not disappoint us.” In fact, he offers the steps to a full human existence by highlighting the character traits that Christians are called to develop. Therefore, if we frame the question of morality in terms of a biblical eschatology (a vision of what the real end is) then all sorts of things can grow within us to make us into the people God wants us to be.

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My Faith Shouldn’t Be Alive (But It Is, and Here’s Why)

Rachel Held Evans — Wed, 23 Jun 10 13:51:29 -0700

There’s a great little show on the Discovery Channel that never fails to undo my best laid plans for Saturday afternoons. It’s called “I Shouldn’t Be Alive.” When the title alone isn’t enough to draw me in, it’s only a matter of time before the survivor of a plane crash (or rock slide or shark attack or hiking misadventure) begins recounting in excruciating detail his decision to cut off his own arm with a pocket knife (or eat his dog or drink his urine), rendering me completely useless on the living room couch until I’ve seen that the rescue helicopters have arrived.

We all love survival stories, which is perhaps why I like to compare my own faith journey to one--though with considerably less blood and suspense.

You see, my faith shouldn’t be alive. By all accounts, it should have perished the moment I started asking questions about faith and science. All my life I’d been taught that I had to choose—between believing the Bible and believing my science book, between honoring God and embracing evolution. To accept one was to effectively kill the other, I learned. They couldn’t both survive. They were incompatible.

And yet here I am—a girl who loves Jesus and accepts evolution, alive to tell the tale.

Survival stories usually begin in a dramatic setting, and mine is no different. For most of my life I’ve lived in Dayton, Tennessee, home of the famous Scopes Monkey Trial of 1925. Located in the buckle of the Bible Belt, Dayton is not the most convenient place to question a literal interpretation of Genesis. Most people here believe that evolution is part of an anti-Christian worldview, and the wounds from getting called “yokels” and “ignorants” by the press during the trial are still being nursed today.

I attended a small Christian college in town named after William Jennings Bryan, where one of the most popular professors at the time was a leading young earth creationist. This professor often told the story of how, as a sophomore in high school, he had dreams of becoming a scientist, but could not reconcile the theory of evolution with the creation account found in the Bible. So one night, he took a pair of scissors and a newly-purchased Bible and began cutting out every verse he believed would have to be removed to believe in evolution. By the time he was finished, he said he couldn’t even lift the Bible without it falling apart. That was when he decided, “Either Scripture was true and evolution was wrong or evolution was true and I must toss out the Bible.”

Having operated within this paradigm for so much of my life, I experienced a major crisis of faith when I encountered the overwhelming scientific evidence in support of evolutionary theory soon after graduating from college.

On the one hand, I felt betrayed. Pastors and teachers had assured me that science supported a 6,000-year-old earth and that only atheists with an agenda against Christianity believed it was older. And yet everything from the fossil record to biodiversity to starlight to DNA seemed to confirm evolutionary theory as sound, with the overwhelming majority scientists affirming it.

On the other hand, I was afraid to accept undeniable truth I’d encountered. I didn’t want to walk away from my faith. I didn’t want to throw out the Bible. I didn’t want to reject God. But everything I’d been told up to that point led me to believe I had to choose. Doubt is difficult to describe to those who have never experienced it. What’s most frightening about it is how one question leads to another, which leads to another, which leads to another, creating a sort of domino effect out of your skepticism and fear. I lay awake for hours at night, struggling with this conflict between my intellectual integrity and my faith. I begged God to “help me in my unbelief,” but His presence seemed to drift farther and farther away with every seemingly irreconcilable conflict between reason and faith.

I thought for sure my faith was a goner.

The first rescue helicopter came in the form of Francis Collins’ “The Language of God.” A friend recommended it, and it was the first time I’d ever read the work of a scientist so passionately committed to both his Christian faith and accepted science. The fact that it was even possible to be a Christian and believe in evolution gave me hope.

In the third chapter, Collins includes a quote from St. Augustine, who—centuries before Darwin made his landmark observations—warned Christians against interpreting the first two chapters of Genesis too strictly. Said Augustine, “In matters that are so obscure and far beyond our vision, we find in Holy Scripture passages which can be interpreted in very different ways without prejudice to the faith we have received. In such cases, we should not rush in headlong and so firmly take our stand on one side that, if further progress in search for truth justly undermines this position, we too fall with it.”¹

That was when I realized that my hyper-literalist interpretation of Genesis 1-2 was going down, and it was taking my faith with it.

I couldn’t let that happen.

So like a survivor cutting off his arm to escape from beneath a boulder, I severed my fundamentalist approach to Scripture. (Okay, so it wasn’t really that dramatic. Let’s just say I spent some time on the BioLogos site, ordered “The Lost World of Genesis One” by John Walton, and managed to survive the faith crisis with my love for God and for the Bible intact.)

So why tell my story?

Because I wasn’t alone out there in the wilderness of doubt, and not everyone’s faith survived. I have friends who walked away from their Christian faith right when their gifts and talents could have served it best. They walked away because they thought being a Christian demanded willful ignorance and fear of truth. They walked away because they felt betrayed by their pastors, parents, and professors. They walked away because they believed the lie that they had to choose.

And that makes me angry sometimes.

It seems like for every survival story, there is a story of loss…which is why I believe the BioLogos Foundation is so important. We’ve got to work together to reverse this trend. We’ve got to send out more rescue helicopters to young people around the country who are desperately holding on to what remains of their faith. These are unnecessary casualties of an unnecessary war, and the simple knowledge that faith and science can coexist can be enough to bring a lost soul back from the brink.

My faith shouldn’t be alive.

But it is, and not a day goes by that I am not grateful for the gift of a second chance.

Rachel's book Evolving in Monkey Town is available on Amazon. To hear about Rachel's journey, see our video conversation with her (below).

What Does it Mean to Believe in God the Creator?

Karl Giberson — Sat, 06 Mar 10 06:00:27 -0800

In this video conversation, Karl Giberson advocates for an understanding of the Creator that places more emphasis on his sustainment of creation and less on its origins. Giberson notes that one of the things that the New Atheists have succeeded in doing is setting the frame of the debate by suggesting that unless we can point to what God is “doing”, that is, what he is actively creating—then he can’t exist.

This is a very reductionist argument, says Giberson, which attempts to evaluate claims of God in the same way that one would evaluate something like the Second Law of Thermodynamics. This kind of rubric does not work because the Christian understanding of God has always been a much more “robust and philosophically deep concept” than that which the New Atheists will account or allow for.

“What does it mean to say that God brings a universe into being?” It doesn’t mean that God is “[always in there] tinkering like gravity”—but he is more significant than that because he is the grounding force of gravity. God works through secondary causes—thus we need a more sophisticated view of causality. Way before the Big Bang or any theory of evolution, Aquinas points out that origination is not the key part to creating, it’s sustaining.

We have to be careful about projecting our idea about human creation onto God because the notion of a human creator is an entirely different concept. For example, when humans create something, they finish, and then walk away. We don’t say that Da Vinci continues to sustain the Mona Lisa and that if he were to remove his “sustaining powers” that it would cease to exist.

That would make no sense at all.

“Yet, that’s what it means to say God created the world—because everything is grounded in his being.”