Blog Transfer

I began this blog in May 2015. I had just retired from the NIH, and I was fortunate enough to receive a grant from the John Templeton Foundation for two years that allowed me to do research on gene regulatory network theory and work on this blog and other things (see below). The blog posts here are therefore part of the work product or outputs of the Templeton grant.

As I hope most of my readers know, my book The Works of His Hands: A Scientist’s Journey from Atheism to Faith will be released on November 19 by Kregel Publications. This book was also a part of my promised outputs for the Templeton grant. I have created a new web page to help promote the book at

I have also decided, with the encouragement of my publisher, to combine my blogging activity with my book promotion in one website. My next blog post will be posted at the following link:

In order that readers still continue to get notifications of new posts, I will also post the title and the first few lines of each post here at The Book of Works, followed by a link to the full post on the new site. I strongly encourage all readers to follow me on The Works of His Hands.

The Book of Works will not go away, and I may eventually return to this site as my primary blog.

But for now, I will say, “See you soon, at the other place.”

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The Human Effect

In the 1960s, a climatologist named Edward Lorenz worked on developing a set of difference equations to study weather forecasting. This type of equation is used to model what happens to a system as a function of time: a variable is traced from the beginning (time = 0) in repeating steps (iterations) at each time (t = 1,2,3, etc.).

Lorenz found logical, expected results when a constant used in the equation was set at a particular level, but at higher values, the results showed a strange, oscillating pattern with time. The higher the value of the constant, the more irregular the cycles became, and at a certain point, they lost all semblance of regularity and fluctuated wildly in a chaotic fashion. Chaos theory was born.

Lorenz also found that when he rounded out the value used for the starting condition, using 5.21 instead of 5.21332, for example, the solutions over time showed a completely different pattern. This extreme dependence on initial conditions is sometimes called the “butterfly effect,” after the idea that a butterfly flapping its wings in China could create a storm in Texas a few days later. Chaotic dynamics occur in many, if not all, complex dynamic systems, like the stock market, national economies, heart physiology, and so on. And, of course, the most complex of all systems, human society, is totally ruled by chaos theory. I call this the “human effect,” and I believe it has some interesting philosophical implications.

Humans have been compared to a collection of gas molecules randomly colliding and going in unpredictable ways but en masse forming a highly deterministic and predictable system. But gas molecules make no choices; their individual behavior is truly random. Ours is not, which is what makes history so fascinating.

It’s entirely rational to propose that everything any of us do or say can have enormous effects on the state of the world. If I decide to stop during a walk and look into the window of a store, I will arrive at the bookstore five minutes later than I would have if I hadn’t stopped. That means I will enter the store just as another customer is leaving. I bump into him, we both apologize, he stops to pick up the books he dropped, I help him, we exchange a few words, and he goes on his way. That 45-second delay makes him too late to flag the taxi he would otherwise have gotten, and he needs to wait a good 15 minutes before he gives up on finding a taxi and calls Uber. The Uber driver picks him up. If the man had found the cab that I made him miss, the Uber driver would have picked up a woman a few blocks away. But since he didn’t, the woman gets into another Uber and finds that the driver looks familiar. It is in fact a man she knew in college, and after some conversation, they remember each other. They exchange numbers, meet a few days later, begin dating, fall in love, get married, and have children. Their children grow up, and the oldest becomes a scientist and discovers a cure for a disease. So the lives of thousands of people are saved by the child of the woman who took a different Uber because the man I bumped into was a few seconds later than he would have been if I hadn’t paused to look at the store window.

I just made that fantasy up, but such things happen all the time, and with some thought and research, examples are easy to find. The idea of the human effect is wonderfully illustrated in the film It’s a Wonderful Life. Aside from the film’s other great qualities, it is quite special in that it represents the first, and still one of the very few, example of a detailed and rigorous thought experiment on the basic principles of chaos and complexity theory. It has some pretty profound scientific and religious implications, which is why, of course, I like it.

As in all experiments, there is a model system—in this case, a typical small American town. The hypothesis to be tested is that the existence of a single individual (Jimmy Stewart’s character) has major, unpredictable, and irreversible effects on the behavior of the system. It provides an early glimpse of  the revolutionary idea (unknown at the time the film was made) that complex systems are highly dependent on initial conditions.

I know, this isn’t science—it’s melodrama. But my point is that this story should make us think about the reality that for good or ill, we are all critical to the reality of everyone else.

Humanity is a huge system. And everyone who is part of that system (which is everyone) has a role in what happens next. What this means is that nothing we do or say is ever lost, because the effects or ripples of our actions continuously rebound throughout history. I know that sounds silly. Imagine the millions and millions of people who have ever lived, and all the words and actions of all those people, all but the tiniest fraction of which are lost forever to our knowledge. But that is where my faith comes in. I don’t think they are lost.

All human lives are important, valuable, and (in my own religious view) holy. So choose what you do and say wisely, my friends. My life depends on it.


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God and the Rain

Why doesn’t God step in and stop bad things from happening?

On a cool cloudy day in Manhattan, a young mother walking with her three children (one in a stroller) was caught in a sudden downpour. She was pushing the stroller, holding the hand of her little girl, and juggling a bag of groceries on top of it. When the rain came down, she started to hurry, because she was afraid the baby, who had been sniffling, would get sick. The oldest was giving her trouble, and she yelled at him to be quiet while she hurried to cross a side street before the light turned. The rain was heavy, and visibility was bad. She didn’t see the car turning, and the driver, also in a hurry and not completely sober, didn’t see her. She and all three of her kids were killed.

Except that didn’t happen. Here’s the true version. I had gone to do some shopping, and having checked the weather forecast, I brought a small folding umbrella with me. When I got to the store, I was surprised to see my wife there, shopping. (This was before cell phones.) She was on the way home from work and also had an umbrella. We started walking home together just as the rain began pouring down in buckets. In the hope of staying dry, we each opened our own umbrellas. As we got to the first cross street, I saw the woman with the three kids bent against the rain and rushing to get out of it.

I was not a Christian at this time, but I had been going to church occasionally, and I was in the process of thinking about Jesus, the Gospels, and the possibility that God was real. Without more than an instant’s thought, I crossed the avenue, went up to the woman, and gave her my umbrella. She gave me a smile, said thank you in Spanish, and I could see the relief on her face. She held the umbrella over the stroller, and continued more calmly on her way, joking with her kids, and stopping at the corner for the light to turn back to green. My wife caught up to me and gave me a smile. We walked the rest of the way home under one umbrella, which was fine.

Did God prevent a tragedy there? We will never know. The first paragraph is clearly derived from my own imagination. Did the Holy Spirit come to me and whisper the suggestion of a charitable and selfless act? That is probably the case—first, because this was a time when the Holy Spirit seemed to be actively engaged with me; and second, because such charitable acts toward strangers were not among my habits. I had been born and raised in that city, where interactions with strangers are not part of the culture.

Perhaps this story is only one of millions of stories of God’s interventions to prevent tragedies that we can never know about, and the tragedies that do occur are those where the intended agent (in this case, me) chose not to follow the whisper of God’s urging. What I think is crucial is that if my fantasy is actually true and God used me to save four innocent lives, then we must all always be open to doing acts of kindness and mercy, because we, humans, acting here in the physical world, are one of the ways in which God intervenes for good. Theologian Thomas Jay Oord, in his new book God Can’t suggests that this is always the way that God works in love to bring about transformation in the world. I don’t know if that’s always true. But now, as a follower of Christ, I certainly do believe that at least once, many years ago on a rainy New York street, that is exactly what He did, and I was blessed beyond measure to be His instrument.

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Love and the Ocean

Last week I was standing at the ocean’s edge on a beach in eastern Long Island, and I remembered that at an earlier point in my life, while still an agnostic, I used to (in a way) worship the ocean. Whenever I would get to a seashore, on whatever continent, whether a sandy beach or a rocky coast, I would think “Here I am, sea, once again, back to be with you.” I would watch the waves and think in some way that they were expressions of friendship, much like the wagging of dog’s tail, or the wave of a human.

This kind of pantheistic nature worship is not at all uncommon among atheists or agnostics with some degree of spiritual connection. Even some theists, including Christians, will occasionally succumb to the marvelous beauty of God’s creation and lean toward worshiping the creation instead of the Creator. As Denis Alexander says in his book Is there Purpose in Biology?, quoting theologian Aubrey Moore:
“For the Christian theologian, the facts of nature are the acts of God.”

Alexander goes on to demolish the extreme forms of “natural theology” that hold nature to be an entity worthy of worship. He discusses the brilliant Christian pioneer of chemistry, Robert Boyle, who demythologized “the idea of nature as a quasi-independent entity.”

I had a rude awakening regarding the imagined friendship between myself and the sea. Those who read my post “How I spent my Summer Vacation” last year might recall my telling of an incident with a pair of dolphins off the coast of Maine that I interpreted as a positive spiritual experience with God’s creatures. But a few years before that event, I was in the same boat off the same coast and had an altogether more sobering and in fact life-threatening encounter with the reality of the ocean.

A rare hurricane was threatening the coast where we were spending our vacation, and I had to move the boat into a safe place. I decided to bring it back to the launch ramp where I could easily put it back on its trailer. This entailed going from where the boat was moored near our house to a small inlet a few miles along the coast. I started out with no problems, even though the outer bands of the hurricane were already hitting us. There was a heavy rain and the water near the mooring was choppier than usual. But we were on the leeward (protected) side of an island, and when I passed under the bridge that connected the island to the mainland, I immediately entered a different world, one that I was unfamiliar with.

The sea was rough, rougher than I had ever seen it, with swells 4 to 6 feet high and coming rapidly. After 10 minutes, I realized I could make no progress against the wind and current, and that I had to give up my plan and turn around. My 12-foot boat was barely under the control of the 20-hp outboard engine, and it was all I could do to keep the bow pointed into the wind and waves. I realized to my horror that turning around would be almost impossible, since as soon as the boat was broadside to the waves it would capsize.

At that point I called out in desperation, “Stop!” Of course, it didn’t, and I thought “the ocean doesn’t care about you at all.” I had no options— there were no other boats around, no people on the shore or the bridge. There was nothing I could do. Finally, I took a deep breath, gunned the engine to top speed, and turned the boat. Sure enough, one wave hit just as I was 90 degrees to the wind, and I almost went over, but the momentum of the turn brought me around. In another three minutes the waves propelled the boat back under the bridge, and I was safe. Exhausted, terrified, soaking wet, and a bit wiser, I dragged the boat up onto the dock of a neighbor.

So I no longer talk to the sea. I still love it, but I no longer think of it as anything other than what it is, a marvelous part of this splendid planet, in turn, created as a small part of this universe by God. The shock of understanding that nature doesn’t really care about us humans has long worn off. What counts is that God does care for us, and even more, that we care about each other, and that’s all we need.

Last week, as I watched the waves crash onto the shore and looked out at the vast ocean, I was not thinking about any relationship I once imagined I had with the world- wide seas, but instead I focused my attention on the distant figure of a swimmer as she (my beautiful wife)  moved in the water, and felt the real wonder of true love.

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Creation, Emergence, Magic and Twitter

I recently tweeted something that raised quite a few eyebrows among scientifically minded folks, both atheists and Christians.

The tweet implied that I believe that evolution cannot explain all human characteristics, and that a divine intervention in the form of a miracle must have been involved in the creation of a creature that can write symphonies and invent the internet. I gave the impression that I was relying on magic, and disputing mainstream scientific evidence.

What I believe is that evolution is one of the tools that God uses in creation. But it isn’t the only such tool. This is abundantly clear in the origin of life, where it is simply impossible to invoke our understanding of the evolutionary process to produce the first life forms. People who say that “life evolved” tend to think of evolution as equivalent to natural selection, but the fact is that biological (Darwinian) evolution requires some very special biochemical mechanisms (extremely accurate genotype replication and extremely accurate translation of genotype to phenotype) in order to function. These mechanisms could not have evolved by those same mechanisms.

Does this mean that I presuppose some magical, supernatural, or non-materialistic source for the emergent transitions that lead to origins, such as that of life or human consciousness? It might appear so from my tweet, which like too many of my tweets was not properly worded. Twitter is an entirely inappropriate format for the expression of deep philosophical ideas, as most (smarter) people have already discovered, and I am slowly beginning to learn.

First, let’s remember that some of what we now think of as purely scientific statements of natural reality would have previously been thought of as supernatural nonsense. This includes all of quantum theory and some aspects of relativity (time slowing down, space bending etc.). Second, while God is a supernatural entity, all of His creation (which includes all origins) is part of nature, and God is not a magician, but the creator of a lawful universe.

Most importantly, we must remember that while where we are today in terms of our understanding of reality is far beyond where we were yesterday, it’s also far behind where we’ll be tomorrow. That’s obvious from our technological progress and is also true (perhaps at a slightly slower pace) for our scientific understanding of nature.

So when I say that the natural processes that have been proposed cannot explain all the characteristics of humanity and there must be another source, what I really mean to say is that evolution as we know it is not sufficient to account for human exceptionalism. The other source is not God as opposed to naturalism, because I believe God is the single source for everything in nature. What I meant is that the other source is some as yet unknown, alternative tool that God uses to create.

What is that tool? We don’t know, but I believe it’s related to the phenomenon of emergence, where systems or collections of components suddenly become something entirely new, another (epistemic, though not ontological) level of reality. Does God wave a magical wand, or speak an incantation whenever one kind of reality undergoes this mysterious process and a new form of reality emerges? No, just as God does not need to magically create the mutations that are part of the evolutionary mechanism. But until we have the same depth of understanding of what emergence is and how it works that we have for evolution, we can only think of it as “another source.”

Does all of this mean that I am a Deist, or that I think that God never intervenes in the world of nature, but has front-loaded creation with all the tools needed to produce what we now see? No, because as a Christian, I know that God not only is present in our lives, but that He appeared in human form for the express purpose of intervention in the world of human beings. And the creation we know did not spring into existence all at once, but in temporal stages, as alluded to  in Genesis.

I might also be wrong about the emergence (as opposed to the evolution) of humanity. Perhaps, as some recent evidence indicates, the process was as slow and gradual as any other evolutionary change, with the appearance of new features like sophisticated language; artistic creativity; intellectual depth capable of inventing mathematics, logic, and technological solutions; awareness of ourselves and the world; romantic love; sophisticated sense of humor; complex music; compassion and altruism; and quite a few other considerably interesting new traits.

But so far, this evidence does not convince me, because neither I nor anyone else can even articulate what human consciousness really is, and so to explain it in terms of evolutionary mechanisms seems impossible.

The good news (which isn’t really news, since it’s been true forever and will be true far into the future) is that we still have a lot to learn, and I am of the firm belief that as we go forward to tackle these really difficult questions related to the nature of emergence, and as we try to gain a better insight of our own natures, we will find more tools of God’s creation and learn ever more about the nature of God, the creator of all.

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A Cosmic Rebuttal – and so much more.

Carl Sagan’s Cosmos came out while I was an atheist, and I thought it was a wonderful TV series. I loved the state-of-the-art graphics, and, of course, Sagan was a master documentarian. I know now that there was quite a bit of anti-religious propaganda in the script, but at the time it didn’t bother me, because, well, I was an atheist, so I didn’t notice it, and it wouldn’t have bothered me if I had noticed it. I believe it was quite mild compared to the in-your face anti-theism so prevalent today.

In fact, when Neil deGrasse Tyson announced he was doing a remake, I thought it was quite exciting. There was certainly plenty of new science in astronomy and cosmology to catch up on. This time, though, as a Christian I was keenly aware of the potshots and distortions of history and theology that were beamed out to the public in the name of science.

But my goal is not to review the Cosmos TV show. Instead, I want to discuss a new book recently published that is a marvelous antidote and a gentle rebuttal to the tone of Cosmos. The book is called The Story of the Cosmos, edited by Daniel Ray (an online friend) and Paul Gould. The chapters are all about cosmology, astronomy and related sciences, but there is not much about biochemistry, so I read it as an educated layman.

The Story of the Cosmos is a joy to read. The quality of the writing and the impeccable scientific content of the essays make this book a wonderful counter-argument to the Sagan/Tyson narrative of a meaningless, purposeless, Godless cosmos. The individual authors, all expert authorities in their fields, tackle subjects as diverse as black holes, fine-tuning, binary stars, meteorites, and the history and literature of the scientific study of the universe, all from a Christian theistic worldview. This book is all about declaring the glory of God by studying the heavens.

As would be expected, the different authors employ a variety of styles in their chapters, but all of them are eminently readable for the non-specialist (like me) and full of interest and insights. Educational and entertaining, this book would make a marvelous gift for a student of any age who is interested in learning about the science of cosmology without the tired anti-religious propaganda that pervades so much of popular scientific literature and media.

While I found every chapter to be intriguing and informative, I especially enjoyed Consolmagno’s humble and straightforward accounts of his laboratory work on meteors, Salviander’s story of black hole denialism, and Gonzalez’ treatment of a subject of great interest to me–exoplanets and astrobiology. William Lane Craig, the famous apologist, theologian, and philosopher, has an outstanding chapter that summarizes many of his familiar apologetic arguments and goes into new areas stimulated by newer findings.  The other chapters are equally beautifully written and interesting, and you might be hard pressed to choose your own favorites. Congratulations to editors Daniel Ray and Paul Gould for a magnificent job on this volume, which I believe will be essential reading for anyone interested in science and Christian faith.

I originally intended to post a review on the book’s Amazon page, but I was prevented from doing so. Apparently, something in my profile triggered a rejection of my review, because it reflected information in another reviewer’s profile. Huh? After a few attempts to correct this error, Amazon basically told me that the decision stands. The good news is that the book is selling well, despite the lack of a review from me. Here is the link to the Amazon page for ordering the book, or, of course, you could patronize your local bookstore. Either way, I strongly recommend obtaining a copy. It’s a great reference, and a pleasure to read. Order  it here.

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Militant Moderation

I recently had a “debate” with atheist activist Aron Ra. Aron is known for his sharp attacks on Christian apologists, as well as for being a staunch and highly educated defender of evolution. We first met two years ago, when he invited me for an interview on his YouTube channel, and we ended up having a pleasant and polite conversation (not, however, entirely lacking in disagreements).

The discussion we had a week ago was similar in tone. One reason Aron and I seem to get along, despite his fervent ant- theism, is mutual respect. He respects me for my scientific credentials and for my willingness to actively witness for the reality of evolution, including engaging in debates with well-known young-earth creationists. I respect him for his intelligence and the depth and breadth of his biological knowledge (especially in phylogenetics and cladistics).

At the very end of the discussion, just before the Q&A, Aron said (in response to my statement that I am not an apologist and not trying to convert atheists):

“One of the problems we have now in the US is we are so polarized. When you and I were young, the common man knew you have to be a fool to reject science. Science is real. But everybody also had this notion that they go somewhere when they die. And the atheists and the creationists were both on very far extremes. But now we have this polarized society where that middle-of-the-road guy, the person who holds both perspectives (science and faith) is almost absent. People are walking away from religion, and others are walking away from science. I would rather go back to that time than what we have now.”

I said I was in complete agreement, we thanked each other for the discussion, and we went to the questions.

I am very happy about that debate/discussion, not because I won or I convinced anyone that my position was correct, but because I feel that it could stand as a model for how to discuss things with someone you don’t agree with. And yes, as Aron and I proved, it’s possible to do so. One wouldn’t think it could be, listening to our President and his political opponents. (I don’t mean to imply that the two sides here equal).

Polarization is probably an understatement. In religion, in politics, in matters of sexuality and identity, people (especially people online) are ready to demolish, destroy, defame, denigrate, and otherwise attack those with whom they disagree.

I consider myself to be a militant moderate. This doesn’t mean that I tolerate actual fascists, racists, communists or radical crazies of any stripe. Buy unlike a good number of younger folk, I have had real life experiences with all of those, and I know how bad they are, and how dangerous they are for our society. But if we treat everyone who holds a different perspective than we do on the important issues of life and society as a pariah, we will continue to slide toward mutual hatred, and possibly violence.

We have already been there. In the late 1960s, the political divide over the war in Vietnam and Civil Rights was more contentious and violent that the current situation. It was exhausting and frightening. In one demonstration, a brick thrown by a construction worker narrowly missed me (it would have killed me). At Columbia University, I saw a cop beat a student bloody while smiling and cursing. And there were always those brave souls who threw bottles and stones at the cops from the safe back of the crowd. A lot of people were killed in the civil strife of those times.

What counts is our mutual humanity. All of us humans are one family, and it’s time to stop this incessant hatred. We can disagree, we can argue, we can vote for different people, we can worship different Gods or no god, but we cannot forget the universal truth taught by all religions – all people are our brethren. Learn to live with them, and perhaps even love them. It’s worth it.


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The Works of His Hands

I am happy to announce that my forthcoming book The Works of His Hands: A Scientist’s Journey from Atheism to Faith is now available for pre-order on Amazon. 

The book will be released by Kregel Publications on November 19, 2019. I will be announcing the release (and pre-order availability) on Twitter and Facebook in the early fall, but I wanted to give the readers of this blog an advanced notification.

All editorial work on the book is complete, and endorsements from advance readers are coming in. Alister McGrath, one of my favorite theologians (and people), has contributed a wonderful foreword, and the marketing team is preparing to spread the word.

My wife and I just got back from a week-long trip to Wheaton College (near Chicago) for the annual American Scientific Affiliation (ASA) conference, where I gave a talk related to my previous post on replication. I also chaired a session, presented a report on God and Nature to the ASA Executive Committee, met Ken Miller, Hugh Ross, and many old friends, took a tour of Fermilab, and had a great time.

I also had a chance to give out a few flyers produced by the Publisher to advertise the book.  The pre-order price of $16.99 is guaranteed until release.

TWHH Flyer

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Replication and Evolution

When most people, including scientists, even including evolutionary and molecular biologists, talk about evolution, they dwell on the critical aspects of variation and natural selection almost exclusively. These two processes are considered to be the heart and soul of the evolutionary process. But there is another process that must also exist for evolution to occur, and that is replication of the organism in the next generation. I am not talking about reproduction, which of course must occur. Replication is more than simply an organism reproducing itself. Replication is the means by which reproduction occurs with extreme accuracy, so that the characteristics of the original are inherited in the offspring. Replication is what makes inheritance possible. And the fact that replication is less than 100% accurate is what allows for the existence of variation, which is critical for evolution.

What we tend to overlook is that replication, while it cannot be perfect (so as to allow for variation), must be very, very good. If it weren’t, then whatever selective advantage an organism might have gained by a change in some allele would not be transmitted to the next generation, and no evolution would occur. If a bird had developed better vision than its siblings, that bird would have a great selective advantage during its own lifetime. But if that characteristic were not inherited by its offspring, evolution of better eyesight in that species would never happen.

Modern life replicates its phenotype with at least 99.99999% fidelity. This leaves enough room for naturally occurring errors (mutations) to produce the variation needed for Darwin’s theory to work. But what about the lower limit of replication fidelity? How good must replication be in order to avoid “error catastrophe”—which means, in this context, a level of error such that no selective advantage is possible?

The threshold for a mutation rate that would cause an error catastrophe has been determined theoretically and confirmed by experiment to be simply equal to the inverse of the size of the genome. Thus, if an organism has a genome of 10,000 bases, like some bacteria and viruses, a mutation rate greater than 0.0001 or 0.01% would lead to a loss of any selective advantage for the fittest organisms, and thus it would not allow for evolution to work. This seems like a very low mutation rate, and it is, but of course in large multicelled organisms with genomes in the billions of bases, the error rate is correspondingly lower. Since replication fidelity is equal to 1 minus the mutation rate, the minimal level of replication fidelity is 0.9999 for single-celled organisms, and 0.9999999 for animals and plants.

Are such high values for replication fidelity in early life reasonable to expect? Not when we consider that for even the most primitive modern organisms, replication, transcription and translation involves a host of error correction enzymatic processes, all of which had to evolve—but how could they if the prevailing error rate was too high to allow for evolution?

This seems to leave a large gaping hole in our attempt to understand the origin of life, particularly the origin of evolution. The best solution to this mystery is to posit some other type of evolutionary process whereby early primitive cells could replicate themselves (meaning their entire phenotype) with great accuracy that did not involve the extremely complex advanced mechanisms of DNA replication and DNA-directed protein synthesis. The RNA world (generally assumed to predate DNA world) doesn’t look much better. Even if we assume that the RNA-world genome is a set of RNA ribozymes, and that the smallest such self-replicating molecule might be as small as 50 bases, we still need to have a 98% accuracy in replication of RNA, which is far less than the 80% fidelity (at best)  observed in lab experiments. We have no idea what such an alternative evolutionary mechanism not working with replicating nucleic acid polymers might consist of.

But we can still address the fundamental question of replication fidelity evolution even if we have no idea how that evolution could have occurred. I recently completed a study of a simulation model for studying replication fidelity in early life that makes no assumptions about replication mechanisms.

The results (which I have recently submitted in a paper for publication) are interesting. To summarize, it seems very clear that regardless of what the unknown evolutionary mechanism might be, a smoothly continuous evolutionary path to high replication fidelity is impossible. At some point during the evolution of protolife to modern life, there had to be one or more major jumps (saltational events) in the degree of replication fidelity. We have a long way to go before we can get close to any idea of how life and evolution might have gotten started.


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Thoughts on Science, ID, Evolutionary Continuity, and Eugene Koonin

In 2007, the famous and highly respected evolutionary biologist, Eugene Koonin, published a paper in the peer-reviewed journal Biology Direct. The paper is titled “The Biological Big Bang model for the major transitions in evolution.” In the abstract, he summarizes the problem he aims to address as follows:

Major transitions in biological evolution show the same pattern of sudden emergence of diverse forms at a new level of complexity. The relationships between major groups within an emergent new class of biological entities are hard to decipher and do not seem to fit the tree pattern that, following Darwin’s original proposal, remains the dominant description of biological evolution.

In other words, he is stating the observed fact that there are frequent discontinuous jumps in complexity, with the emergence of entirely new classes of biological entities (including organisms and biochemical molecules).

His model evokes the cosmological concepts of rapid inflation and Big Bang singularity. In the biological case, the inflation is the result of “extremely rapid evolution,” and the biological “Big Bang” emergence of novel complexity “is envisaged as being qualitatively different from tree-pattern cladogenesis.” In other words, not at all Darwinian gradualism.

Koonin is an atheist who despises creationism and Intelligent Design (ID), and he is a fiercely independent and brilliant thinker. One might wonder how the tone and content of this paper was received by reviewers, except that we don’t need to wonder at all. Biology Direct is an open access journal that also uses open review, still fairly rare among scientific journals. The names of the reviewers are published, as are their comments and the author’s replies. I found this fascinating to read.

In one comment, the reviewer (William Martin) writes:

“In each major class of biological objects, the principal types emerge “ready-made”, and intermediate grades cannot be identified.” Ouch, that will be up on ID websites faster than one can bat an eye.

Koonin responds:

Here I do not really understand the concern… there is little I can do because this is an important sentence that accurately and clearly portrays a crucial and, to the very best of my understanding, real feature of evolutionary transitions…  if our goal as evolutionary biologists is to avoid providing any grist for the ID mill, we should simply claim that Darwin, “in principle”, solved all the problems of the origin of biological complexity in his eye story, and only minor details remain to be filled in… However, I believe that this is totally counter-productive and such a notion is outright false… I think we (students of evolution) should openly admit that emergence of new levels of complexity is a complex problem and should try to work out solutions some of which could be distinctly non-orthodox…

(Note: most of what I omitted in that quote are protestations against ID.)

Complaints by some academic scientists about language in scientific papers and presentations that sounds too much like ID or creationism are not uncommon these days. I fully agree with Koonin that such rigid adherence to the dogma of neo-Darwinism is counterproductive in the search for truth. It might, in fact, simply be true that some of the ideas of ID are more consonant with the reality of biological evolution than is generally acknowledged.

In fact, the prediction that ID folks might jump on this and similar ideas has come to pass to some extent. Randy Isaac recently drew my attention to a meeting in Austria where evolutionary biologists presented ideas contesting the standard model of Darwinian gradualism, and even discussed the forbidden word – teleology. Several members of the ID-based Discovery Institute also presented their work at this meeting.

An article about this meeting written by Discovery Institute’s newsletter “Evolution News” claims that some of the speakers from academia expressed fears of possible harassment or worse from their academic departments because of the kind of concern expressed in the reviewer’s quote above. It is certainly the case that hints of Intelligent Design sympathy are not well received in academic biology.

Eugene Koonin has no need to worry about reactions to his thoughts. His position (at the Library of Medicine in the NIH) and his reputation as a brilliant scientist are secure. Like Stephen Jay Gould and the more modern proponents of the extended evolutionary synthesis, Koonin is not afraid (thank God) to move the entire field of evolutionary biology forward with bold new ideas.

Science cannot be stopped by political, religious, or social viewpoints. At least not for long. It is my own belief that just as the original Big Bang theory put astrophysics and Christian cosmology in closer concordance, we will eventually see a similar trend in biology. God willing.


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