The Book of Works

Hello to my readers, and welcome back to the Book of Works. It has been a long, sometimes relaxing and sometime productive summer. In July, I went to the ASA annual meeting near Boston, where I gave a talk and moderated two sessions, but of course the best part (as it is with all conferences) was getting to spend some time with so many friends and colleagues in the science and Christian faith community. The highest point was hearing the talk by Francis Collins and then attending the informal sing-along he led. He is a remarkable man in so many ways.

The rest of the summer was busy with writing, teaching, and sending the last kid off to college. Finally, two weeks ago, my wife and I took off for our first-ever duo vacation. It was a somewhat unusual agenda I had planned. One of our goals was to carry clothes and other essentials to my stepson in Cambridge, so we drove. Along the way we stayed at places I had lived in or had once had family from. Nyack, NY and Winthrop, Mass were two of these places. Then from the Boston area we drove up to the mid-coast of Maine, where I used to spend the entire month of August during my first marriage in the 1980s.

I don’t usually post personal stuff on this blog, but I am going to make an exception and talk about a year that was pivotal in my life story. It was 1992, I was about to turn 45, and at a crossroads both in my marriage and in my professional scientific career. I considered myself an agnostic – I wasn’t sure about God, but I did think that there might be something beyond the materialistic view I used to have of the world. Something spiritual, something not quite explainable. But I wasn’t sure.

Near the end of our family sojourn in a cabin on the coast, I took my small (12 ft) outboard-powered boat out for a solo ride. For some reason, and for the first time, I ventured pretty far out from shore, past the islands that usually marked my limit of exploration and into a broad channel in the open Atlantic Ocean. All of a sudden I saw a dark and ominous shadow in the water right next to the boat. It was bigger than the boat and moving fast. I was terrified when, a few seconds later, I saw another one on the other side of the boat. Then one of the shadows rose and broke the surface. It was a dolphin. I slowed the boat down and began to relax. The pair of dolphins were not just playing – they were swimming next to me, then crossing in front of the boat, and soon I realized they were guiding me. They were aware I was too far out for such a small boat and were leading me back toward the shore. I followed them. Heading back in, with my wonderful escort, I began to feel not only calm but a sense of gratitude and love for these creatures of nature. After a short while, when I was back where I belonged, they disappeared, and I returned to shore in a state of wonder.

The spiritual sense that I felt from that experience on the sea stayed with me. My life changed, radically, in every way. I left my terrible marriage, moved to Italy, changed my research direction, started attending church, and so on.

A week ago, my wife and I were in Camden, Maine, not far from where I used to vacation two and a half decades ago. We signed on for a two-hour scenic cruise on a schooner. As we sailed out into the ocean, the day was gorgeous and the views spectacular. And then somebody pointed sternward. The captain turned and announced, “We are very lucky. folks. We have company.” I looked out just past the stern and there they were: two dolphins, breaking the water in plain view and putting on a small show for the passengers. But I know better. They were there for me. I had been gone for 26 years, and now I was back, a different man, and they were there once again, to give me a sign. I took it as a sign of encouragement and of affirmation.

I am still a spiritual person, but now I know that God is the source of that spiritual power. And I know that God has shown me signs of mercy and hope my whole life, even when I scorned His existence. I don’t know if I have made the right choices or lived according to His will, but I am hopeful that this sign of His favor might mean my path has not been in vain.

Thanks to all for your patience in reading this very personal account, and for your continued support of this blog. Praise God, from whom all blessings flow.

At this beginning of July, I want to take an opportunity to thank all those who read and comment on this blog. It has been a great three years, and I have learned a lot and enjoyed all the interactions resulting from the blog.

No, I am not ending the blog. But I am going to take a needed blog vacation for the summer. As my retirement (coincident with starting this blog) enters its 3^rd year,  I have grown progressively busier. Here is a sample of what I will be doing in July:

As Editor-in-Chief, I will be finalizing the Summer issue of God and Nature, with some great content, including nine essays on two focus topics (authors include Gareth Jones, Kevin Arnold, Jim Peterson), two poems, a great photoessay by Tom Oord, and an interview. The goal is to get everything done and published by the middle of the month.

Right after that, my wife and I have committed to doing a week of Vacation Bible School at our church with a class of science experiments for kids. We did it last year, and it was great, but it takes a lot of time and effort to make sure everything works.

And then at the end of the month I am off to Boston for the annual ASA meeting, where I am presenting a paper, moderating two sessions, reporting to the Executive Council, and of course meeting and greeting many friends and colleagues.

August is a bit less intense, and my wife and I will go on a real vacation to Maine and Long Island.

So I will be back here in September, hopefully rested, and with something to say. Meanwhile, may God bless all of you, and may the summer bring you joy and happiness along with whatever else it may bring.

The phrase “God of the gaps” was invented by the 19th century theologian Henry Drummond. He was speaking of the things that science could not explain yet, and which, he said, some Christians treated as “gaps which they will fill up with God”. Drummond, and many other Christian theologians and scientists after him, have urged Christians to avoid this temptation and instead to embrace all nature as God’s.

Recently the phrase has been used to counter various apologetic arguments for the existence of God. When a Christian says something like “the fine tuning of the cosmological and physical constants suggests a divine designer,” some atheists will counter that this “God of the gaps” argument ignores the possibility that science will eventually find a naturalistic mechanism that explains the values of those constants as a part of a physical law, as has happened in the past. Some Christian thinkers have agreed that using God to explain any natural phenomenon that has not been explained by a naturalistic mechanism runs the risk of making God “too small” or irrelevant, even leading to a loss in belief in the power or existence of God, who could then become superfluous to our understanding of reality.

If one believes, as I do, that God is the creator of all that is and sustains and maintains our physical world, how does one reconcile this belief with a scientific worldview and still avoid the use of God-of-the-gaps-style arguments?

It’s certainly true that ancient humans who had little to no knowledge of how the world worked inserted mythical gods and other unseen forces to explain things like thunder, illness, rain, etc. That was a true “gods of the gaps” approach to knowledge, but it has been discredited for centuries.

Does this mean science is replacing God, as so many journalists and online pundits loudly proclaim? If not, then what part of the physical universe, the province of scientific discovery, can be used in a theological analysis that points to God without invoking the God-of-the gaps fallacy?  The key is in using what we do know about the scientific explanations for mechanisms, rather than what we don’t know. This works because scientific explanations for mechanisms of natural phenomena are not the end of our understanding or curiosity about the world.

When physicists discovered that quantum theory explained the structure of atoms, the activity of electrons, and the existence of discrete lines in electromagnetic emission spectra from distant stars, a large gap in understanding the mechanisms by which light (and other EM radiation) behaves was solved.

But when Max Planck and Niels Bohr were asked about the philosophical meaning of the mysteries revealed by quantum mechanics, they answered that such issues were not of their concern – the science of quantum physics was correct, it worked, and it was up to others to work out the mysterious parts of the theory. And, in fact, further scientific advances, such as the testing of the Bell inequality and the universality of the uncertainty principle, have done nothing to “explain” the mystery, but have simply confirmed the scientific truth of a very strange physical reality.

When Darwin proposed the materialistic theory of evolution, and the Modern Synthesis decisively found the genetic mechanisms by which evolution works, that was considered to be the mechanistic gap-filling explanation for how life got to be the way it is. God was no longer needed to explain life, the argument from rational materialists went.

Evolution in biology provides a wonderful explanation of how life diverged from a primordial living cell, and the mechanism of evolution is extremely useful in understanding how biology works. But that same evolutionary mechanism points to several underlying philosophical mysteries about life. In fact, the mystery of the origin of life owes a good part of its intractability to the reality of evolutionary biochemical mechanisms.

What we have learned about the enormous complexity of life raises philosophical questions that go well beyond the straightforward and logical understanding of the mechanisms of natural selection and mutation of genotypes. Among those questions are those related to purpose. Why is there life, is there a purpose to life, and in particular to conscious, sentient life? What, in fact, is consciousness, who has it, and why? Answering such questions by reference to evolutionary mechanisms (as some try to do) is not good science, and it is also bad philosophy.

It serves no purpose to deny the reality of biological evolution in an attempt to find a role for God in the existence of life on earth. If a reasonable hypothesis for the chemical origin of life is found (which is likely), the gap of abiogenesis will be filled, but the deeper questions of the meaning of life will remain to be the subject of theological, not scientific, enquiry.

The question of the origin of the universe is another example of a gap filled by a scientific mechanism that leaves us with a profound mystery and a pointer to God. Assuming the Big Bang model continues to hold up (as it appears to), the very nature of time, space, matter, and energy has entered the realm of the unknowable at their origins before the Planck time.

So, yes, science can and will continue to fill gaps in knowledge with explanatory mechanisms, and I believe we have no need of what is meant by the worn-out phrase “God of the gaps” when doing Christian apologetics related to scientific knowledge. What we should be doing is using that scientific knowledge to find pointers to the “God of Wisdom”. That God is very real and belief in Him grows stronger with every new discovery. Mechanistic explanations for phenomena are not the end of our knowledge and understanding. There is no question that quantum physics is real and correct, and that it explains many things beyond emissions spectral patterns. But do we fully understand QM as a rational materialistic explanation? No, we do not. Entanglement, the observer effect, and tunneling are philosophically mysterious, and they have profound theological implications. This is not because of any scientific gap – the gaps have been filled. And it is the filling of those gaps that actually point to God, not the gaps themselves.

My favorite example of the God of Wisdom replacing the God of the gaps is Heisenberg’s uncertainty principle, which proves (a rare thing in science) that there are some things (in this case, the simultaneous momentum and position of an electron) we can never ever know. This well-established, fundamental cornerstone of modern physics by itself disproves scientism. I believe we will find more such unknowable principles, especially in biology.

My view is that for the past century and more, and as we progress in the future, scientific findings have and will continue to uncover new mechanisms to explain how the world works, and that those new mechanisms will continue (as they have always done) to point to God as the creator and sustainer of the universe. Because, as Lord Kelvin said 120 years ago, “mechanism explains nothing.” And “The fear of the Lord is the beginning of wisdom” (Proverbs 9:10).

The declaration in quotes is the title of an article in Tech Times reporting on a paper published in Human Evolution by Stoeckle and Thaler with the title Why should mitochondria define species? Not surprisingly, young earth creationists and others are linking this article all over the internet. I was first made aware of it by a friend, and then I read the original paper. The following is my analysis of that paper, originally posted in the Facebook group Celebrating Creation by Natural Selection (CCNS).

As expected, the Techtimes article completely misunderstood the original paper. It does not claim that 90% of all animal species began at the same time, 100,000 years ago, and it is in no way supportive of YEC. The paper, which I believe is poorly written and highly speculative, is an attempt to make sense of the fact that mitochondrial DNA bar coding is useful in identifying species. That fact is now consensus, and it derives from the fact that genomic differences between many species (like two worms or two similar insect species) can be quite small, but they are much greater in mt DNA (mt=mitochondria). The reason for this is that mtDNA has a far greater mutation rate than genomic DNA, since negative selection is not an issue (meaning a deleterious mutation in mt will not usually kill the cell in which it lives). So when two species are hard to differentiate by genomic sequence differences, they can be up to 2 or 3% different in their mtDNA. This also implies that there is very little variation of mtDNA within the individuals of any species. The purpose of the paper is to suggest hypotheses as to why the latter observation is true.

One possibility for explaining why mtDNA within a species shows less variation than between closely related species is that a particular species went through a population bottleneck followed by rapid expansion. A bottleneck can occur for several reasons, but generally involves a large decrease in the population, usually due to adverse environmental conditions. It can also result from migrations. Bottlenecks are very common during evolutionary history, as populations deal with all kinds of stressors. Bottlenecks are known to cause severe restrictions in DNA sequence diversity, both in genomes and mt. We know that humans went through a severe bottleneck between 70,000 and 150,000 ya. The authors propose that most other animal species also suffered some form of bottleneck within the past 100,000 or “several hundred thousand” years ago. That is one possible explanation for the relatively low intra-species mtDNA diversity seen in modern animals. Personally, I am not convinced by this explanation, since the genomic DNA diversity data does not seem to match, as far as I know. But even if this explanation is correct, it says nothing about all animals originating at the same time. What it might suggest is a large-scale environmental change (such as the start or end of an ice age) or several such changes affecting different species at different times, which we know happens continuously.

The authors of the original paper never discuss “origin” or beginning of species. They simply suggest that one or more bottlenecks have happened to a large majority of species within a relatively short time frame. While that explanation is far from consensus at the moment, even if it gains evidence, it does nothing to shake any part of evolutionary theory or our knowledge of how environmental change affects population genetics.

The dentist did his best with my root canal, and I went home, took some pain killers, and fell asleep. I woke up still feeling drowsy, so I went out into the backyard for some fresh air. Sitting at the table under the big umbrella on the deck was Darwin. He gestured for me to join him. I sat down and told him I was a big fan. “Yes, I know,” he said. “I read what you wrote about me being in Heaven, and you’re right. I also do appreciate your finding that letter I wrote to Wallace” (See The Story of my Greatest Discovery).

This made me very happy, although I was already starting to realize I was dreaming. Still, how often does one get to chat with Darwin? So I just went with it.

“Where are your horses?” he asked me. “We don’t use horses anymore. We have cars,” I told him, and I led him to my old Toyota for a ride. Darwin was impressed. He expressed amazement that at such enormous speeds none of the cars bumped into each other, but I told him it does happen. We drove into the town, and he asked where the factories were, why the air was so clean, why the streets were not filthy, and then he figured it out (“Ah, yes, of course, no horses”). The dream (which by now it clearly was, even to the dreamer) then took on one of those snapshot qualities, where we made brief appearances at various localities: a restaurant, a hospital, a school, a university, and a biochemistry research lab.

Back on the deck Darwin began a long lecture, only part of which remained with me when I woke up. He was ecstatic at the things he had seen. I started telling him about WWII, terrorism, and global warming, but he waved me quiet. “Of course, I know all about those things. We try to keep up to date with all the disasters down here, and we do get regular updates from freshly arrived victims, you know.” But he told me that things like computers, cars, and cures had gone unnoticed, at least by him.

“You know, despite everything, you people have made a great deal of progress in the past century and a half. And I daresay I expect this trend to continue. If I weren’t already in Heaven and in the know, I might venture to say that there is the appearance of a divine hand in all of this” – with a large gesture he indicated my humble house, the small garden, the driveway and the street beyond. Then he stared at me. “You are a Christian, are you not?”

“I am.”

“Good fellow. I can see now where I went wrong. I know that bad things still happen, but a lot less than they used to. So, if we extrapolate forward a bit, it appears that God is correct (as usual), and the Kingdom will indeed come to Earth. Now I understand why Jesus is always in such a good mood. Well, I must dash. Very good to have met you, and all the best.”

And then I was alone… well, not quite, my wife was sitting quietly next to me. I resisted the urge to tell her all about my visit from Charles Darwin. I thought I would wait a bit and tell her along with all of you readers.

Another rather interesting trait of slime molds and related organisms is that they are capable of rather impressive feats traditionally thought to be limited to “higher” animals. These include behaviors like problem-solving skills and the ability to learn. Amazingly, they also display the ability to anticipate environmental changes based on prior experience. Still, just like bacteria, the amoeba-like cells in slime molds do not possess an actual animal-like nervous system. If we think about it, from our admittedly biased perspective, the absence of a nervous system makes the behavioral repertoire of bacteria and slime molds even more astonishing.
Oné Pagán: The First Brain: The Neuroscience of Planarians (2014),

I looked up at the sky and all around and saw no sign of any birds. I was standing on a rocky beach in Maine. I had a bucket of lobster shells, which I threw onto the beach. A minute later two seagulls arrived from somewhere and began to feed. I knew this would happen (I had been disposing of lobster remains this way for many years), and I knew that the long-distance visual capability of seagulls was remarkable.

So is the vision of hawks, the strength of spider webs, the speed of deer, the cunning of squirrels, and so on. I know that all these features and every other characteristic of  living creatures are the product of evolution by natural selection. But I can understand why some people see the hand of an intelligent designer in the amazing structures and function of flowers, bees, and all of life.

And I now believe they are right. I think there is in fact an intelligent designer at work that explains all the magnificent beauty of biological life. But when I use the word intelligence, I mean something different than the kind of intelligence we are most familiar with.

We solve problems with our intelligent brains, as do many other animals. But is brain-centered intelligence the only form of intelligence that can exist? Apparently not, since we already know the brilliant things that computers and automated machines can do. We might be able to imagine other forms of intelligence that have nothing to do with the complex neural electrical circuits that are the components of smart brains.

Actually, all living creatures, including single-cell organisms like bacteria, possess a form of intelligence that is not remotely conscious or like anything based on brain function. The dictionary definition of intelligence is the capacity for learning, reasoning, and understanding. Clearly a single bacterium, or even a single ant, is unlikely to exhibit any degree of reasoning or understanding. But populations of bacteria and other “primitive” creatures do show the capacity to learn, and, depending on how one defines the words, to reason and understand. When observing these organisms, we are tempted to describe their behavior in anthropomorphic terms, because they seem to resemble familiar human characteristics.

For example, the quote by my friend, Dr. Pagán illustrates the remarkable way that slime molds can behave. Thousands of individual M. Xanthus bacterial cells can coordinate their behavior in order to more effectively attack and degrade other bacteria.  Many bacteria living in soil, with restricted mobility, solve the challenge of migration by growing in a pattern that results in net migration in a particular direction. Some single-cell amoebae are able to construct shells of glass from sand grains. The idea of a single cell building its own shell is remarkable.

The intelligence of “lower” creatures is not related to neural electrical impulses – it uses a completely different platform. What we see in all living creatures, no matter how simple and small, is biochemical intelligence. Bacteria, amoebae, ants, and plants communicate and perceive through chemical signals, not electromagnetic ones.

Bacteria use biochemical signals and receptors for those signals to communicate to those around them that they are there, and when a critical mass appears, the community of bacteria take the appropriate action (produce light, or virulence, etc.). Plants of all kinds also use biochemical signaling both for internal and external communications. No tree, flower, or grass possesses any neural systems.

Even in advanced, large creatures like us, most of the cells in the body act on signals from neighbors and hormones. The great majority of the activity of liver, skin, intestinal mucosa, and other somatic cells is invisible to the brain, and the very existence of a large intelligent brain is irrelevant to most somatic cells.

Biochemical communication between cells, the foundation of intrinsic biochemical intelligence, depends on the production of very specific proteins, which can act as signals and receptors, as well as on enzymes involved in the synthesis and degradation of these signals. Like all proteins, those involved with communication are produced in the ribosome according to the program of the DNA sequence and the genetic code. The genome determines not only what signals are produced and what the receptors do in response to binding to a signal, it also determines when this happens, thanks to intricately complex gene regulatory networks.

The actions of the signaling proteins and their receptors are automatic and preprogrammed. The organism has no choice in what happens when a signal is bound to a receptor and the bound receptor initiates some action by the cell. This might call into question whether we should really consider this to be intelligence, any more than we deem a computer intelligent.

But, in fact, there is more to IBI than chemically predetermined actions following the receipt of a chemical signal. When it comes to animal intelligence, we consider interaction with the outside world as an important part of intelligent decision-making and the exercise of will. Animals interact with the environment by means of their senses, and feedback from sensory stimuli is an essential part of neurological intelligence. Such feedback tends to be swift and in real time. A fox smells a rabbit, approaches slowly, sees the rabbit, and decides to give chase. The sensory input leads to the intelligent decision to pursue the prey.

Cells also have a way to get feedback from their environment that allows for intelligent choices and decision-making, but it is vastly different from animal sensory perceptions. The way bacteria and other simple organisms get the feedback they need is by dying.

Put another way, the feedback that tells cells whether their communication, defense, and other systems important to their lives are working well or need to be improved is natural selection. The best way to see this in action is the “viral” video from Harvard that shows bacteria evolving and expanding into zones of increasing concentrations of poison. As the bacteria spread, most of them die, and the survivors have undergone mutations allowing them to thrive in higher poison concentrations. It is this same process of evolution by natural selection (environmental feedback) that allows for the origin of the protein signals and receptors and is responsible for their continuous improvement and adaption to changing environments. The feedback here is extremely slow compared to sensory feedback, but it has the same effect. Remember, it isn’t the individual bacterium or social insect that counts, but the whole population.

This means that the intelligent designer is actually every biological population of organisms, and the method of design is populations using their intrinsic biochemical processes of communication and protein synthesis, coupled with input from the outside world by means of natural selection to give feedback regarding what works and what doesn’t. This is design by intrinsic biological intelligence.

When I first heard about epigenetics, I hated it. I still do, in fact, but I am slowly beginning to accept the fact that epigenetics is a fact. And it’s a terrible fact, like all facts that force one to radically change one’s long-held ideas.

In the 19^th century everyone knew about inheritance, but nobody knew about genes. Two similar theories of evolution were proposed, one in 1809 by Lamarck, and 50 years later a more complete one by Darwin. Both men proposed that species can change their characteristics over time and that such changes can even produce new species, and both saw the role of the environment as critical to this process. Lamarck’s theory was that when creatures experienced environmental changes to their characteristics, these changes could be inherited, resulting in evolution of the population.

Darwin’s theory saw evolution proceeding in two major steps. First there were heritable changes, and then environmental conditions selected which organisms would survive and reproduce based on the phenotypes produced by these inherited changes.

The 20^th century saw the flowering of Mendelian inheritance into a major science. The concept of the gene – the hypothetical inheritance particle – was substantiated by the discovery of the structure and function of DNA. Darwin’s theory was confirmed, Lamarckian ideas were utterly rejected – both on theoretical and observational grounds – and neo-Darwinism was born.

And that’s how things have stood for the past 60 years or so. The inheritance of acquired characteristics, as Lamarkian evolution has been summarized, was dismissed as nonsense, with no evidence and lots of counterevidence.

Until recently. Don’t you love science? It’s never boring. I first heard about epigenetics when I was researching the environmental causes of cancer. The idea was that in some circumstances, certain parts of the DNA molecule are modified with methyl groups that change the expression (usually by repression) of a gene. This modification of gene function can act like a mutation, since if a gene is not expressed, it’s just as if it had undergone a mutation. By itself, these findings were not terribly dramatic, because such methylation and its effects could not possibly be inherited, so I (and everyone else) thought of these epigenetic changes (called marks) as having no impact on basic Darwinian theory.

Oops. Over the past decade, it has become clear that sometimes these epigenetic changes, due to various exposures or environmental influences, can in fact be inherited, even after the exposure is over. At first it seemed that this only happened for a few generations. But no. That would be too easy. It now appears pretty likely that some epigenetic effects are long-lasting, perhaps permanent, just like a mutation in the DNA sequence. The crucial difference is that mutations are very rare, accumulate slowly, and are random, while epigenetic effects can be very rapid, much more frequent, and targeted to specific genes.

Welcome back, M. Lamarck. Having been educated for over four decades that Lamarckian evolution is a nonsensical, utterly wrong idea, I was not happy. But that’s science. Physicists have gone through this sort of thing routinely in the past century or so, and now it’s the turn of biologists.

The implications of long-term inheritance of epigenetic alteration of genomes are staggering. If epigenetics is a real mechanism of evolution, as real as the neo-Darwinian mechanism of mutation and natural selection, then everything in biology changes. The good news is that a lot of tough question might be answered, such as how phenotypic innovations can lead to major and rapid appearance of new biological features, without needing the very slow, laborious process of mutation accumulation (allelic variation) followed by selection. The bad news is that almost everything we thought we knew about evolution must now be re-thought.

As in all such paradigm shifts, traditional Darwinian genetic evolution is not disproven; it has been modified to include a host of new mechanisms (epigenetics being a major example, but not the only one). Lamarck is back, with his own molecular mechanism of epigenetics to be joined with Darwin’s genetic mechanism. The theoretical and predictive implications of this merger are both incredibly complex and very exciting. I propose that the new theory of evolution combining inherited germline mutations and inherited epigenetic marks be called Darmarckian evolution. And to all my colleagues who share my horror at such a heretical vision of how biology actually works, I can only say (as I have had to say to myself), “It’s science – deal with it”.