The Book of Works

Neil deGrasse Tyson’s recent debate at the American Museum of Natural History on the question of whether we live in a real or a simulated universe was fascinating. The first interesting thing is that such a hypothesis is considered worthy of scientific discussion. After all, what this hypothesis proposes is that we might be living in a much more advanced analogy of a computer game, something akin to the false world of the film The Matrix. The argument is that if we (assumed to be of not very high intelligence) can simulate reality, then it is extremely likely that some of all those putative intelligent creatures who exist somewhere must have already become incredibly good at simulations, and we could very well be living in one.

Apparently this hypothesis is being taken seriously by some scientists. All of them atheists. My question is, if you are going to talk about simulators (those who made the simulations), how exactly is that different from talking about a creator? Or to be clear, God. In fact, this subject came up in the discussion, and the fact that the panel was edging quite close to forbidden territory was pointed out more than once.

The consensus, if there was any, seemed to be that if we are a simulation, in other words, created, then there should be clues to that in the rules by which we are playing the game, better known as the laws of physics. In fact one of the panelists, Dr. James Gates, said that he has found evidence of error-correcting codes in some of the equations of symmetry related to string theory. And that this appears to be evidence that the universe was computed, and not a random event of accidental causes.

It certainly does seem that we are living in a mathematical universe, according to Max Tegmark, another physicist, who wrote a book on the subject. Many theists have been pointing out for a long time that the fact that the physical laws that govern everything are generally simple and elegant mathematical formulas is just what one would expect in a universe created by a Being. And this doesn’t even touch on the setting of the physical constants, which is also consistent with some super-intelligent game designer far, far away.

So back to my question. Why is it that the idea of a simulated universe is acceptable for scientific discussion, but the idea of a universe created and maintained by God is not?

Gates says that for non-scientists, acceptance of the simulation hypothesis as an accurate view of our universe is equivalent to belief in a deity. He goes on to say that if there is a programmer who is philosophically equivalent to a creator but who cannot be observed, then the whole thing is outside the realm of science, a statement agreed to by the whole panel.

At that point, Chalmers (a strong atheist) admits that a simulated universe could be theological, but could also be purely naturalistic, say if the actual simulator of all of our reality in this universe was the work of some teenage hacker in the next universe up.

He also admits that this sounds very much like a God hypothesis, with the important caveat that he would never worship such a simulator/creator largely because he sees no evidence of any sort of goodness in the creation, and thus no sign that the simulator/creator is essentially good.

And people are still surprised when I state that science is the best road to faith.

I believe that God is the creator of all that exists.

We don’t know how God created our universe, or even if there is only one universe or there are many independent ones. We don’t know if life arose from natural processes on Earth, arrived here on a meteor from some extraterrestrial source, or was a direct creation by God. We don’t know where our souls come from – if they’re a natural product of evolution (like our bodies) or breathed into the first human by God. There are so many things we don’t know.

But there are also many things we do know. We do know that life began as single cells, and that evolution by natural selection led to all the species that have ever existed. We know a lot about how life works, about the intricate, amazing details of biological function that are the natural results of adaptive evolution, and we can worship the creator of such majesty.

There is a big question we are faced with, though. Where is the God who answers prayers, who interacts with us on a personal level, in this majestic creation? Did God create the universe and withdraw? Does God play a role in the history of life and our planet, in order to further His purposes? Did God intervene in the world?

We cannot find the answers to these questions using the human tools of knowledge – scientific investigation and analysis. We might get some clues this way, we might see some pointers, but not enough to be sure. No, the path to truth does not lead through our human knowledge, but through God.

So let us see what God has said and done. We know that God came to walk among us in the form of a man. Christ spent over 30 years amongst us, the last two or three in active ministry. What did Christ, God incarnate, do during that time? Did He create any new species of animal or plant? No, He did not. He spoke of plants, flowers, birds and animals, but He created no new ones. Did Christ reshape any geological features of our landscape? Did He water the desert, lower any mountains, widen the Jordan River? No, He did not. Did He change the course of history? Not during His lifetime. He created no new laws of nature.

What sort of miracles did the Lord do in his time on Earth? He healed the sick, turned water into wine, calmed the seas, raised the dead, cast out demons, made the blind see.  When challenged by Satan to turn stones into bread for His own sustenance, he refused. Christ performed His miracles, showed His Godhead, only for the benefit of people in need, not for glory, not to demonstrate His powers, not to win converts. And what did God tell us when he preached His sermon, and spoke to us in parables, and stories? He told us to believe, to help each other, to love each other and to love Him. To have mercy, to be forgiving, to find the Kingdom of Heaven in ourselves, in each other, and in Him.

All that He did and said, all of these miracles, and all of His teaching, all of His ministry to the poor and the outcasts, all of His parables and mercy were directed to one object – His love for His people, us. Jesus Christ, the living God, came to us for our sake. He came to Earth to speak directly to us; he bent His laws of nature for us: to heal us, to help us, to redeem us, to show His love for us.

I can believe that Christ hears my prayers, answers me in dreams, in visions and in miraculous events, even if He does not intervene in His own Creation for any other purpose. This is neither an absent God, nor a God who is constantly involved in managing His creation. God intervenes for us. For me and for you and for all.

On Feb 10, I posted a link to our review of Michael Denton’s book Evolution: Still a Theory in Crisis that was published on the Biologos Blog. That review did spark some interest on the Biologos site, but the discussion quickly went off topic and deteriorated. I have decided to repost the entire review here, and would welcome any reblogging or referrals, since I believe that the book (despite its unfortunate title) is an important one in the dialog between Evolutionary Creationists and proponents of Intelligent Design.

The authors of the Review are myself and my wife, Aniko Albert. The original publication of the review on Biologos was also accompanied by an Introduction by Jim Stump, and a brief commentary by the Biologos Editorial team. The review follows:

This book is a update to Denton’s 1985 book of the same title (minus the word “still”), but it is an important departure from the earlier work.

We are well aware that book reviewers bring their own biases and beliefs with them as they read. So, because we are convinced this is an important book that needs to be discussed fairly, we will start by owning up to our own worldviews related to the issues covered. We are adherents of Darwinian evolution, and we think that Charles Darwin’s insights underlie all of biological science. By this we mean acceptance of the principle of descent with modification of all life from a common ancestor, through the mechanisms of genetic variation and natural selection. We are also evolutionary creationists, and believe as a matter of faith that life ultimately derives from the divine Creator. We are unconvinced by arguments against Darwinian evolution, including those from young earth creationists and intelligent design advocates. Our worldview did not initially dispose us favorably to a book with this title written by a well-known proponent of ID and published by the Discovery Institute.

Denton describes his own worldview throughout the book as “structuralism”, which is all about the form that matter (including biological matter) takes. This contrasts with “functionalism” (the basis of Darwinism), which is about how things work, including  adaptation. His hero is Richard Owen, a pre-Darwin naturalist who wrote extensively on the concept of natural law as the basis for biological forms. Denton takes the pre-Darwinian 19th-century concept of Types—clades, such as vertebrates and mammals—as his central theme. According to Denton (and Owen), Types are the manifestation of built-in biological laws; and what distinguishes them are structural homologs that cannot be explained by either slow, progressive steps (the gradualism of classical Darwinism) or purely adaptationist natural selection. This philosophical view fits well with the standard anti-evolution paradigm of Intelligent Design.

On almost every page, Denton claims that Darwinism is refuted, contradicted, or “stands on sand.” According to Denton, the key hallmarks of Darwinism are a strict adherence to adaptationist functionalism and an insistence on gradualism. Gradualism has long been a focal point of attacks on Darwinism by ID advocates, and is the basis for the irreducible complexity argument.

But at this point, things get interesting, because Denton does not go there. He never mentions irreducible complexity in the entire book. His attack on what he calls Darwinism is presented almost entirely in the words and research of current evolutionary biologists. He devotes a whole chapter to Evo-Devo, and quotes Sean B. Carroll extensively. When he argues (using examples like vertebrate limbs, feathers, flowers, insect legs, or human language) that there is no evidence for stepwise selective mechanisms for major innovative changes that define clades, he quotes Gould, Koonin, A. and G. Wagner, and Pigliucci—not Johnson, Behe, or Dembski.

Denton agrees (as does everyone else) that natural selection is the best explanation for microevolution. Denton expands microevolution to a process that occurs in clades (such as mammals or even vertebrates). But, like the creationists, he argues that macroevolution is a different story and requires an entirely different mechanism to explain the jumps from fins to limbs, or scales to feathers.

And here is where we fully expected to see the phrase “evidence for design” fill in the blank of how such innovations come about, if not by Darwinian natural selection. But that is not what Denton says in this book. Not at all. In fact, the word “design” rarely occurs in the book, and never in the context of any kind of explanation for the origin of a biological form or mechanism. What Denton does say is this:

“There is a tree of life. There is no doubt that all extant life forms are related, and descended from a primeval ancestral form at the base of the tree.” (p. 112)

And this:

“Descent with modification implies a pattern of descent through time, where extant forms have descended with modification from common ancestral forms, right back to the last common ancestor of all extant life. But the fact of descent with modification cannot be taken as…. support for any sort of gradualism. [emph. added] (p. 195)

And:

“However, my claim that life is an integral part of nature is not an argument for design or a defense of Plato’s cosmology, but an ontological verdict on the fabric of reality…” [emph. added] (p 281)

So is Michael Denton saying that evolution (which he calls descent with modification) has occurred from the start of life until the present, and that the complex and innovative structures that mark the major phylogenic branches of the tree of life took place by natural means rather than by special creation or intelligent design? Yes, that is what he is saying. So, you might be asking (as we were), why exactly is evolution “still a theory in crisis”? The answer is that the crisis is all about what so many evolutionary biologists have been saying: neo-Darwinism is not correct. Slow accumulation of random mutations in structural genes just doesn’t cut it when we are talking about innovative variations that give rise to new clades.

Gould said this with punctuated equilibrium. Kimura toppled the adaptationist exclusivity with the neutral theory. James Shapiro (who is strangely absent from the book) has been talking about the very same thing for years, as has Pigliucci, Wagner, Muller, Jablonka, Laland, Newman, and all the others of the Third Way and the Altenburg 16. Simon Conway Morris (another strange omission in Denton’s list of scientific allies) has turned evolutionary biology around with his demonstration of convergence and constraints on evolutionary possibilities.

So what Denton is proposing here is closer to the Extended Evolutionary Synthesis, which is struggling with neo-Darwinism to be the standard model for evolutionary biology, than to the vaguely crafted, creationist-flavored non-hypothesis of the original ID movement. Denton presents epigenetics, transposition, the emergence of new properties from complex precursors, and (we were happy to see) includes a strong emphasis on the role of gene regulatory networks in the production of innovative structural phenotypes. So, importantly, Denton is not appealing to a creative intelligence in lieu of biological mechanisms, but weighing—as many evolutionary biologists are also doing—the relative importance of natural selection as a driver of evolutionary change.

In this book we find what has been lacking in many ID arguments: the threads of a coherent scientific hypothesis to explain the great question of emergent novelties during evolutionary history. There is no mention of the impossibility of explaining complex and novel biological structures and systems by natural causes or the red herring of statistical improbability. In contrast, Denton constantly stresses that biology is based as much on natural law as is physics. His arguments against gradualism and panadaptationism are biological rather than metaphysical, and are very much in line with those of the Extended Synthesis.

While this is very welcome and we think a great step forward, we admit that the continuous trumpet call of “anti-Darwinism” in the book is grating and gratuitous, and  (like the title) could limit the book’s contribution to conversations among Christians on the reality of evolution.  Some of the rhetoric comes across as protesting too much. Origin of Species should not be treated as an inerrant text. Of course Darwin made errors, as did Newton, Einstein, and all real scientists in the past and present.

While Darwin did stress the importance of incremental gradual changes, and he did hold that natural selection should be invoked as an adaptationist explanation for all new features, these ideas are not so much errors as overstatements. If we define extreme-Darwinism as the dogma of Darwinian inerrancy, then we can substitute “extreme-Darwinism” for “Darwinism” in almost every instance of its use in Denton’s book. By that small “insertion mutation”, we almost render the entire book fully in line with one mainstream current of evolutionary biology.

Denton’s Evolution (the sequel) is an important book, because it might represent an intriguing and fascinating opportunity for real progress in the sometimes bitter debate about evolution among Christians. That might be an optimistic view, but we are not alone in this idea. Darrel Falk, past president of BioLogos, has written a review of the book for Amazon that reflects our own thoughts quite closely.

In his review, Darrel says:

“…Denton’s work is highly embedded in the well-established fact of common descent of all living organisms… Hence if this work does become central to the future of the Intelligent Design Movement it would be great if they would focus in on a coherent theory like that which Denton espouses…”

We can only agree that it would be great indeed. We think that Darrel’s enthusiasm stems from the same source as our own optimism that this book represents a potential for a real breakthrough in discussions between evolutionary creationists (EC) and the ID movement. There is nothing that forces EC to adhere to an extreme Darwinian or neo- Darwinian stance, and one of us (SG) has written about the new Extended Synthesis as being the best framework for EC to follow (Perspectives in Science and Christian Faith, in Press; God and Nature, In Press).

Denton’s new book may very well be a catalyst in the eventual reconciliation of two Christian scientific philosophies of the nature of life. If that does happen, we believe it will be a joyful day in Heaven, and we can only say: The Lord be praised!

In 1991, on a trip to London, I had some free time and went to the British Library. I saw a lot of manuscripts on display, but nothing on science. I asked a guard for directions to the scientific manuscripts, meaning some room where they might be on display. He seemed puzzled, but was very helpful. “What do you mean, sir?”

“Like Newton,” I said, feeling hopelessly American in a civilized country. “Isaac Newton,” I added for clarity.

“Ah,” he said. “Are you a scholar, sir?”

Tough question. I decided to throw modesty to the wind.  “Yes, I’m a professor in New York.”

He smiled and asked me to follow him, which seemed strange.  I thought, “Jeez, all I want to know is how to find the science section!”

We passed through a door, and entered a guarded corridor. The second guard, even more friendly than the first, was told that the American scholar was interested in seeing some manuscripts of Isaac Newton. I was brought into the manuscript reading room and given a bound book containing a large variety of letters, manuscripts, etc. from the 16^th century. Several pages were original manuscripts of Isaac Newton (in Latin) on ancient solar and lunar calendars, including a table of calculations. I actually had the original Isaac Newton manuscripts in my hand. When I was able to come to my senses, I realized what an incredible opportunity I had.

I looked up Darwin in the catalog, and found that there was a file of over 300 pages of correspondence between Darwin and Alfred Russel Wallace, famed naturalist and co-discoverer of evolution by natural selection. I was given the collection and began to go through it with all the reverence a priest would feel looking at an original manuscript written by the Apostle Paul.

Darwin’s letters were all handwritten on small quartered sheets (both sides of the paper) and many were not dated. Wallace’s letters were typed blue carbon copies. This told me that the collection had come from Wallace.

I leafed through these letters with a great deal of pleasure. Some of Darwin’s notes were barely legible, which didn’t surprise me, since I knew that during his fits of illness writing became difficult for him. I was skimming through some of the later letters when one caught my attention. It was written on a folded sheet of note paper with a black border.

The letter is short and it contains part of an ongoing discussion with Wallace about heredity. At that time no one knew anything about heredity or genes except Mendel, and Mendel’s work had been all but lost. Everything I had ever read about Darwin maintained that he believed, like everyone else, that inheritance of characteristics was like blending of paint colors, meaning that the characteristics of both parents are blended together in the children. Yet in this letter (dated 1867), Darwin writes (the following is the complete text of the letter as hand-written by Darwin):

My dear Wallace

After I had dispatched my last note, the simple explanation which you give had occurred to me, & seems satisfactory.

I do not think you understand what I mean by the non-blending of certain varieties. It does not refer to fertility; an instance will explain; I crossed the Painted Lady & Purple sweet-peas, which are very differently coloured vars, & got, even out of the same pod, both varieties perfect but none intermediate. Something of this kind I sho[uld] think must occur at first with your butterflies & the three forms of Lythrum; tho these cases are in appearance so wonderful, I do not know that they are really more so than every female in this world producing distinct male & female offspring. I am heartily glad that you mean to go on preparing your journal. Believe me – yours very sincerely Ch. Darwin

In other words, Darwin tells Wallace that he crossed two different color pea plants and got only one or the other color, but no blended, or in-between varieties. Darwin is describing quantum inheritance, or genes, and was in fact using the same methodology as Mendel. I read the letter over and over again. Darwin knew about genes. This was the first indication I or anyone else had seen that Darwin had some inkling about the real mechanism of genetic inheritance, and I thought that was pretty important.

I sent a copy of the letter to Richard Dawkins (whom I admired as a leading proponent of Darwinian evolution and a brilliant Darwin scholar), and he later discussed this letter (and kindly gave me credit for its discovery) in an essay to be found in The Devil’s Chaplain.

 The best part of the story is my imagining Charles Darwin sitting in Heaven and paying close attention to the literature of the past century. I am sure he has followed the development of the field of genetics with great satisfaction, since the research confirms and provides a firm framework for the reality of his theory of evolution by natural selection. But I also can imagine him being a bit frustrated by the fact that he was so close to seeing the whole truth himself. And the evidence of how close he came had been locked away in a single letter in the British Library for over a hundred years. As the person who had the honor and privilege of bringing this letter to light, I feel that Darwin’s spirit is smiling down on me. Nothing could top that.

This past Good Friday, I posted the following two paragraphs (shown in italics) in the facebook group, Celebrating Creation by Natural Selection. One of the comments was a question shown below in bold. What follows that is my answer.

I don’t know a lot. I don’t know how life began, or whether the universe will end. I don’t know what most of the Biblical passages I read really mean. I don’t know if the work I am doing on gene networks has any relevance to anything important. I don’t know how to take good photographs or figure out how my printer works. I don’t know why I am loved by my beloved. I don’t know what the purpose of human existence might be.

But I do know a few things. I know that I am loved. I also know that God came to walk among us, and that Jesus Christ died on this day for my sake. I know that I do not deserve such love, but that I have it anyway. And I know that the day after tomorrow, I will rejoice in the glory of the risen Christ, and that death is defeated and my sins are forgiven.

What I know isn’t much. But it’s all I need.

How did you come to know these things, i.e. by what method did you come to know these things? Is it at all important to you whether you came to know these things by a method that has reliably provided more and more accurate understanding of the universe around us, as opposed to methods of knowing things that are notoriously unreliable in leading to accurate conclusions?

Yes, it is very important to me to use reliable ways of knowing when I say that I know something. That is one reason that in none of my 200 scientific publications, nor in any of my 4 books have I ever said that I know something definitively. Nor to my knowledge have any of my colleagues. The process of knowledge accumulation in science is very slow and always subject to change. This doesnt mean that the scientific method does not lead to knowledge, it does. But not in the way many logical positivists think (and while many atheists deny that they are logical positivists, that denial is not very reliable).

The path to knowledge through the scientific method (at least in modern times, when all the good questions are hard) is very tortuous. It is still a worthwhile path to follow, and one that (usually as a side benefit) can provide humanity with valuable technological tools. On another level, the path to scientific knowledge of the truth of how the universe works gives us a sense of satisfaction for some unknown reason. If this knowledge does not or even cannot lead to any material improvement for the benefit of humanity, then what purpose is served by understanding the origin of the universe, the origin of life and diversity of species, and the reality of the Higgs field? If you answer that it is a benefit because of the satisfaction of gaining true knowledge, I would agree with you, but also point out that that is a very metaphysical statement that cannot be verified by the methods you believe are most reliable.

What I believe, as did Newton, Boyle, Faraday, Polkinghorne, Collins, and so many others, is in a different metaphysical claim (also by its nature, not verifiable by scientific methodology), namely that the purpose of acquiring such knowledge, is not only for personal satisfaction, but the joy of understanding God’s creation.

The question remains, what method did I use to come to the knowledge I referenced in th OP? The answer is two fold. I began as a strict and militant atheist. As a scientist, I began to see that what I was learning about reality seemed to fit a far more complex and ephemeral model of the nature of existence than the materialistic model I had previously held true. This did not make me a theist, but it opened the door to a different way of knowing. And, by the grace of the Holy Spirit, Christ walked through that door into my heart and soul and taught me an entirely new method of knowledge, one that I have tested repeatedly and found as reliable as any method I have ever used.

I still do science, and always will. And I use the scientific method to do so. And if I ever find out anything true and interesting (it has happened a couple of times, and if Im lucky it might happen again), I will thank God for the priviledge of being allowed to contribute to the knowledge of his Creation works. But the knowledge of Christ’s love for me, does not depend on that. It is a gift, and its wonder is beyond knowing.

Today is simply Saturday,  the day between. We know very little about what happened on this day, but we can imagine.  We can imagine a man, much like us. A man defeated, alone, miserable and afraid. This man, who was once called a rock, today thinks of himself as simply – Simon. Imagine him sitting in a strange house in a city not his own, staring out the window, seeing nothing but his own failure, and the loss of all of his hopes and dreams. I have felt this way at times, and perhaps you have also.

He thinks of the glorious promise that he has witnessed the past months, the miraculous and wonderful things he has seen and heard. He thinks of the Man who showed so much faith in him, the Man who has now gone, died, left them all alone, without hope or will. But most of all he thinks of his own terrible failure and betrayal. A failure that his leader had predicted, and which he himself would never have imagined possible.

Yesterday, that black day, had proven to the man once called the rock, that he was made of no more than weak, mortal, human clay. Three times he had confirmed his human cowardice, his unworthiness to lead, or even to live. On this Saturday, the man who now once again thinks of himself simply as Simon, is filled with an unimaginable despair at the loss of everything he once valued, most especially his own dignity.

Have you  been there? Have you had to face the fact that you are unworthy because of your actions? No excuses, you simply failed. The time for heroism, for standing tall, for being more than you thought you could be, the time to prove yourself truly a rock of faith, of hope, of goodness, the time had come, and you…you had failed to heed the call. In your weakness or fear, you had simply turned away, waving your hand in dismissal. “No” you said “I don’t know anything about that, Leave me alone”. And not just once, but often. And then it was over, the terrible moment passed, and you were left with only the taste of the ashes of your own personal failure, as the whole glorious edifice you believed in and had worked so hard for, came crashing down in chaos and defeat.

I have been there. That is why I have long been so fascinated by this day without a name, that lies between the day of anguish and the day of triumph. On this day, Simon sits in agony and stares, not yet knowing that tomorrow everything will change again. Today, he is still unaware of tomorrow’s miracle that will change everything in the world forever. Today is the lowest point in his life, but tomorrow he, along with his dispersed friends, will be witness to a breathtaking renewal of hope. The resurrection of tomorrow means not only the resurrection of the living God, not only the rising of the Son of Man, but also the rising of man himself. A man like Simon, weak, afraid, defeated, failed, a man whose despicable actions on the Friday have left him hopeless and full of self-loathing, also rises on Easter Sunday, and once more becomes Peter the Rock.

Like us he is all too human, and yet like us, he is capable of all that he later accomplished. I do not believe he ever forgot his acts of betrayal. But through grace and faith, and his human moral strength, he rose above them, and he fulfilled his destiny as a great fisher of men. So of all the miracles of tomorrow and the days and years that follow, for me the greatest is the miracle of the redemption of the man – the mortal, ordinary fisherman named simply, Simon.  Peace be with you on this day.

One of the first skills I ever mastered, when I was about 10 or 11, was how to flip baseball cards. One kid would flip a card spinning into the air and let it come down, heads or tails. The second player would then flip one of his cards, and If he matched the result of the first card flip he got to keep both cards. If he got the opposite result, he lost his card.

You would think that card flipping would be a random game of chance, like tossing a coin or rolling dice. It wasn’t. After a great deal of practice (about ten times the amount of time I spent doing homework) I was able to flip cards in a way that gave whichever result I wanted. I was able to flip up to 50 heads in a row, and other kids could do it also.

I didn’t realize at the time, but what I had done was a very successful experiment to demonstrate the difference between deterministic chance and true stochastic randomness. Card flipping is like coin tossing, or the weather or the stock market. It is deterministic, but usually cannot be predicted or controlled, unless you know all the myriad hidden inputs that give the result. Unlike card flipping, nobody can control the result of a coin toss, not to mention the weather or the market.

We know about stochastic events in physics, the spin of electrons, the decay of radioactive atoms. But in biology what we have are a lot of deterministic but highly complex events. To some degree, all cellular processes are ruled by the chemical law of mass action, which is based on the probability that enzymes “accidently” bump into their substrates. Life found a way to work around this by having important reactions take place not in solution, but on solid surfaces, like ribosomes, or membranes, or other cellular structures.

There are plenty of chance events in biology. Mutations are the most well known, but  mutations are deterministic and not truly stochastic. They are caused by replication errors, by faulty DNA repair, and by chemical and radiation damage from the outside. It has long been known that there are hot spots for mutation, depending on type of base, and on the surrounding sequence characteristics. We don’t know enough to be able to predict mutational outcome, but that is more analogous to the butterfly effect in weather prediction, than to quantum uncertainty (which has been postulated to be a driver for mutation).

I am in the middle of a project to investigate the theory of gene regulatory networks (GRNs) courtesy of a grant from the John Templeton Foundation. Andreas Wagner, one of the leading pioneers in this field, is exploring how models of these networks, (which are groups of genes that regulate each others’ expression) function. He has found that the final phenotype of a gene regulatory network is not predictable from its original state.  In my work, I find the same thing, but surprisingly this is true even in very simple network models.

These regulatory networks are crucial to cell functioning, and probably to evolution, according to the new Extended Synthesis model. And yet, we see with GRNs  (as we do with mutations) evidence for deterministic chance.  I know that my GRN models are deterministic, because I made them. And very simple model networks do follow expected mathematical laws (on average, at least), but as network complexity increases, such laws quickly become impossible to formulate. Eventually, one sees evidence of true chaotic behavior.

In so much of biology, what we see as highly complex and random chance events, appear that way to us, because we cannot know all the contributing factors, even using simple constructed models. But, if we were God-like, things would be quite different. God is not limited by mathematics, nor by any form of ignorance of causal factors. What we see as chance, God decrees as natural law.

This is not a new idea, but it is exciting that the work many scientists are now doing on the deeper principles of biological control and evolutionary mechanisms are reinforcing that idea. I am certain that we will continue to make progress in our understanding of how God’s most marvelous creation (life) works  Perhaps we will eventually learn (again, for me) the secrets of how to flip baseball cards.

This famous quote from the film “Jurassic Park” is actually not as vacuous as you might expect from a Hollywood blockbuster. In fact it is pretty well true. Life does tend to find ways to spread, adapt, survive, and prosper, even in the most unlikely environments and situations. And how life finds its way tells us a lot about how evolution works.

Recently on the Biologos website, a young-earth creationist expressed doubt that evolutionary processes could work, since the probability of just the right mutation coming along to produce the right change in phenotype is so low. He linked an article on creation.com* on the topic. These are some of the things the author says:

Why would anyone expect a deactivated gene to stick around for a million years or more while an unlikely new function develops?

…gene duplication is usually, though not always, bad.

New functions arising through duplication are not impossible, but they are vanishingly unlikely,..

I answered these points with the following comment:

“Richard Dawkins wrote a book called Climbing Mount Improbable, which deals with this issue very well. The title alone gives the answer. What biology can do that nothing else can is overcome statistical improbability to an amazing degree.

If we start with a population of a million cells growing on a dish and add a poison, they will all die. But if first add a mutagenic chemical, we find that many of the cells (say 10%) will develop mutations. The majority of those mutations will be harmful, and 90% of those mutated cells will die. That leaves 10,000 cells in the dish with nonlethal mutations.

Now we add the poison. All of the cells with no mutations die. What about the 10,000 mutated cells? Almost all of them die also, because their mutations do nothing useful about the poison. But 2 of those 10,000 (0.02%) cells have a mutation that changes the way the cell transports or metabolizes or excretes the poison, and those 2 cells survive. And they reproduce. And after a few days, we don’t see an empty dish. We see a dish with two visible colonies of healthy, growing cells. With a week or so, the dish is full of cells that have resisted the poison. I have personally done such experiments.

Yes, this is microevolution. The cells are still the same species, but a mutation has overcome enormous odds, in this case 2 in a million – and it doesn’t matter how rare, unusual, or unlikely such an event is, because biology doesn’t care about statistics: all it needs is one success. One in a thousand or (if the population is large enough) one in a billion. Statistical arguments just don’t work until we get to values on the order of 10^-20.  Above that, saying that something is unlikely in has no import in biology.

As I have said many times, analogies to software, human information systems, systems engineering,  civil engineering like building bridges, and other non-biological systems are simply not useful when trying to understand the biological world. While those are wonderful systems that humans can be proud of, they pale to insignificance when we contemplate the wonders of God’s amazing creation – life.

Life is remarkable, because it can indeed find a way. Not always, of course, and there are real constraints on what life can do. We are learning more and more about those constraints, and finding some of the basic laws that life must follow. But within that very broad framework, there is so much possibility, so many avenues of progress, that we can only stand in awe at the magnificent, divine handiwork of evolutionary action in the making of life’s diversity.

*http://creation.com/mutations-new-information

Being pure is supposed to be a good thing, and I guess sometimes it is. But sometimes it isn’t Having pure air to breathe or pure ingredients to work with are universally seen as good. But in other, more abstract contexts,  the idea of purity cab be a dangerous myth. A good example is the idea of a pure race. There is, in fact, no such thing anywhere on Earth. Genetic studies have shown that isolated populations once thought to be unmixed with other human groups, such as Icelanders or Japanese, are nothing of the kind. They all show the normal degree of genetic interbreeding with other population groups found in all Asians, Europeans and Africans.

In politics the concept of purity has been deadly and a force mostly for evil. In the early part of the last century, ideological purity led communists to massacre socialists and anarchists because of their failure to adhere to the pure doctrines of Stalinism. The same kind of purging of anyone who deviated at all from the true pure path was done by the fascists and Nazis during their rise to power and their march to destruction.

In fact, if we think of purity as the opposite of diversity (as it is), it isn’t hard to see that there isn’t much good about purity when it comes to human politics or sociology. Purity of thought is a particularly dangerous notion in our modern political arena. On both the left and the right, there is a possibility that committed ideologues will pursue their heartfelt certainty of being absolutely right, to the extent of limiting diverse opinions that might clash with fundamental tenets of their worldview. This is not a good characteristic to have in a leader of an extremely diverse nation.

What about in science? Certainly in science there are pure truths, and all scientists agree on what is true and what isn’t? The answer is no, scientists rarely agree on what is true and what isn’t, because the idea of pure scientific truth is as mythological as that of pure races. This isn’t to say that there are no well-established facts. The validity of the law of gravity or the reality of evolution, for example, have both been demonstrated thoroughly. But that’s only the first step in science. Knowing how evolution works, or how gravity fits in with other aspects of the physical world, like quantum mechanics, are questions with quite of bit of diversity of views.

Diversity of opinion is not only welcome in science, it is the vital engine for scientific progress. Purity is the enemy of science, as it is the enemy of religion. Yes, purity is the enemy of faith, because our understanding of God and His purposes and works requires just as much diversity and creative ideas as does progress in science. If you object that religion is dogmatic and doctrinal by nature, you haven’t been paying attention. Remember that a favorite atheist argument against religion is that since there are so many of them, how can we tell which one is right? The reason there are so many varieties of Christian faith, for example, is that people’s  religious ideas and practices are naturally diverse, and many great minds  have rebelled against stifling and rigid purity of thought.

So I am not a fan of purity at all. I like the impurities of diversity much more. Whether it is the shapes and colors of people, the way we think, the kinds of plants and animals that inhabit our world with us, the way we do things, or the way we worship, I am not interested in purity. Let’s have pure water, pure soap, and pure hearts, and leave it at that.

A strange situation has arisen regarding a paper in the well-respected, free online journal, PLOS One. The paper, called “Biomechanical Characteristics of Hand Coordination in Grasping Activities of Daily Living”, was published by four Chinese scientists in January. The paper appears to be in all respects a good piece of research into the complex biomechanical interactions among fingers and joints in the human hand. But there is something very odd about this paper. Towards the end of the Discussion, the text reads:

In conclusion, our study can improve the understanding of the human hand and confirm that the mechanical architecture is the proper design by the Creator for dexterous performance of numerous functions following the evolutionary remodeling of the ancestral hand for millions of years. 

Not only that, but the abstract of the paper also includes reference to a Creator:

 the biomechanical characteristic of tendinous connective architecture between muscles and articulations is the proper design by the Creator to perform a multitude of daily tasks in a comfortable way. 

To be clear, there are no other indications in any other part of the paper that the authors have any interest in defending Intelligent Design, creationism, or any aspect of religious thought. It almost appears as if these two sentences were inserted as a mistake or a joke. It is very strange indeed.

As might be expected, there has been an outcry from biomedical scientists.  James McInerney, Chair of Evolutionary Biology at the University of Manchester and Editor of the journal Molecular Biology and Evolution, tweeted:

Other scientists have expressed their concern and dismay over the use of the word Creator on Twitter, in comments to the journal and elsewhere. Some commenters have defended the journal and suggested that McInerny’s tweet was unfair. The journal itself put out a statement promising to look into the matter to see how such language got past peer review and editors. In my view, PLOS One is a good journal, and in these times of print journals’ outrageous pricing behavior, its existence as a free access source is very much needed.

That aside, however, the question still remains: why did a reference to a Creator appear in a purely scientific paper (coming from China, not known to be a hotbed of creationism), and how did it get through to publication?

As a Christian who believes in a Creator of the universe, I share my scientific colleagues’ consternation at this insertion of a faith statement in a scientific paper, where it absolutely does not belong. I also hope that this incident does not spark a hunt to ferret out anything in the scientific literature that might be interpreted by some as having religious connotations or relevance. We have enough of that going on in academic science already. I also agree with those who think that McInerny’s reaction against the journal, was not called for.