The Book of Works

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.

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.

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.

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.

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.

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.

My new book, The Works of His Hands: A Scientist’s Journey from Atheism to Faith is now in the final editorial stage, and the Publisher (Kregel Publications) has been working on starting the marketing and promotion process. The book is a first-person account of how I, formerly an atheist scientist, came to embrace Christianity while maintaining my scientific worldview. It includes several chapters on modern science and its compatibility with faith in a creator God.

You can find a link to a new website for the book by clicking on the “My Book” tab above. That site will contain updates as the book goes through the publishing process up to and beyond its release date of November 19, 2019.

I am honored and blessed to announce that famed theologian (and scientist) Alister McGrath from Oxford University has written a wonderful Foreword for the book, and a final cover design has been crafted and approved, as shown below.

When the book is available for pre-order, I will be sure to post that here, as well as on my Facebook and Twitter accounts.

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Speaking of books, I wanted to take the opportunity to highlight two other books that I have recently had the pleasure to read, written by fellow bloggers (and friends).

Jon Garvey’s God’s Good Earth: The Case for an Unfallen Creation (Cascade Books, 2019) is a beautifully written book that can be read for pure enjoyment and enlightenment, and/or used as a scholarly resource on the essential problem of evil in God’s creation.

Jon, a retired physician and the blogger behind “The Hump of the Camel” (and a frequent commenter on this blog) uses historical scholarship to argue that neither Scripture nor the early Church fathers maintain the view that the world was perfect before the sin of Adam and Eve. He presents a convincing case that the modern Christian concept of a curse on creation itself (not just the original sin of human beings) is not rooted in traditional orthodoxy nor in the Biblical text. The chapters on science are a powerful antidote to the prevailing popular view of evolution as a violent deadly struggle. In all of this, Garvey speaks to his readers in terms that all can understand.

The optimistic theme of the book, while controversial, is a rare commodity in the modern marketplace of ideas. This book is full of new ideas, fresh approaches, and profound insights. I strongly recommend it.

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Joel Edmund Anderson, whose blog is “Resurrecting Orthodoxy,” is a religious scholar and the author of the highly regarded book The Heresy of Ham about the extreme young-earth creationist views of Ken Ham. Joel has now published a new book, entitled Christianity and the (R)evolution in Worldviews in Western Culture: A brief review of Christianity and the development of western civilization…and why it is important to understand if one is to make sense of our world today (Archdeacon Books, 2019).

This is a delightfully written and comprehensive but also highly accessible treatise on philosophical ideas regarding Christianity and religious faith and the historical contexts in which they arose. Anderson covers pretty much all the main threads in Western philosophy and historical viewpoints, going back to ancient Greece. His chapters on the “so-called” Enlightenment and the 19^th century contain valuable insights into the origins of many of our modern ideas about the place of religion and Christianity in particular.

I found the descriptions of the major philosophical views and their authors to be refreshingly candid, highly readable, and engaging. If you (like me) tend to fall asleep at the mere mention of the name Kant or Hegel, this book is for you. Not only is the writing clear and jargon-free, but the essences of the ideas are presented in a way that allows for easy understanding of often difficult concepts.

The book also goes into scientific history and the relationship of science with the historical and philosophical trends in Europe.

This is a book for everyone, especially those who are looking for an accurate and insightful depiction of how our worldviews emerged from the thinking of the best and brightest philosophers throughout the ages.