The Book of Works

There are many essential equations that describe the physical reality of the universe. Einstein’s E = mc² is probably one of the most famous, and also the simplest. In the 1920s, physicist Erwin Schrödinger developed an equation that is of prime importance in quantum physics and chemistry. I first learned about (and worked with) this equation in an advanced physical chemistry course in college. The equation is critical in understanding the behavior of electrons, molecules and the wave functions of physics. Here it is:

It isn’t a simple equation at all – all of the terms have complicated meanings – but here I will only discuss one part of it.

Recently I saw an amusing post on Twitter by an atheist that was also in the form of an equation. It was this:

This was a somewhat clever attempt by the poster to say something about God. The square root of -1 (and indeed of all negative numbers) is called an imaginary number. So the atheist poster was trying to make the point that God is imaginary.

The reason such numbers are called imaginary is because the square root of a negative number doesn’t make sense. Such a thing violates basic rules of mathematics (actually the laws of arithmetic, see Sheila’s comment below) which say that the squares of all numbers, both positive and negative, are positive. Therefore, a negative number cannot have a square root.

But, unknowingly, the poster of this little doodle has made a profound theological point in direct contrast to the one he thought he was making. As it turns out, the square root of -1, while imaginary, is of critical importance in math and science. It is used often enough to have been given its own symbol: i. Now take another look at the Schrödinger equation above. Do you see the very first term? Yes, it’s an i.

So if God = i, then God is a crucial component in the basic laws of nature.

While this might seem a silly exercise in chastisement of an atheist with just enough scientific knowledge to get himself in trouble, there is also an important point here. And that has to do with what we mean by imaginary. God does exist in our imagination, and perhaps we cannot ever actually get a picture of the reality of God. Much like imaginary numbers. But this says nothing about the existence of God as a real and ultimate force in nature. The unintended metaphor of God being like the square root of -1 is actually quite powerful. Being imaginary does not equate to being false or nonexistent. Neither in modern science nor in theology (nor in many other areas). We already know that the basic principles of modern physics, from relativity to quantum mechanics, describe a world of reality that seems irrational to us. And here, again, we can use a metaphor from mathematics. There are also irrational numbers, the best known being pi, whose values can never be precisely known but only approximated.

So, if imaginary and irrational are critical adjectives needed to give an accurate scientific description of natural reality, how can the labeling of anything as imaginary or irrational (such as God) be an indication of non-existence? On the contrary, it would be quite strange if the creator and sustainer of all that exists were some analog of a 19^th century clockwork maker or engineer.

I would like to express my thanks to the atheist who came up with this brilliant meme, and I can only pray that he (and others) will see, as I do, the miraculous hand of God in his unintended profession of faith.

(I am hoping that one of my most faithful readers, Sheila Deeth, a mathematician, will see this post and comment, especially if revisions are called for).

First Happy New Year to all. Now, for the matter at hand.

Traditionally, the scientific field of origin-of-life research has been divided into two camps based on what theorists propose came first: replication or metabolism. The “replicators-first” group think that once molecules (like DNA or RNA) capable of self-replication appeared, metabolism was sure to follow. The other group counters that  replication is not possible without enzymes and metabolic processes in place first.

Both sides are probably right, since proteins require genes (DNA) in order to be made, and DNA requires protein enzymes to replicate itself. Without enzymes and metabolism, it’s hard to imagine efficient and accurate replication. But without replication, any advanced metabolism that arises in a particular proto-cell cannot survive into the next generation.

The most widely held scientific theory for any part of abiogenesis is that an “RNA world” of life arose first and then morphed into the modern DNA world. The idea came from the finding that some RNA molecules (like the ribosome) can act as pretty good catalysts called ribozymes. The implication was that RNA could be both a replicator and metabolic catalyst at the same time, thus solving the dilemma of which came first. And a lot of evidence was gathered to support the theory.

But the excitement about RNA as a major step in the origin of life faced several stubborn problems. Further research showed that the efficiency and accuracy of RNA replication in the absence of protein enzymes was really not good enough to allow for a stable informational state. One of the most serious issues was the tendency of long RNA strands to “self-anneal”: to fold up and stick to themselves or to other RNA strands. The annealing reaction is about a thousand times faster than spontaneous non-catalyzed replication, so left on its own, RNA will probably never replicate itself.

Enter Jack Szostack, the Harvard biochemist, Nobel Laureate, and a leading light in RNA World research. Szostack’s research group was actively trying to solve the annealing problem, and he had a brilliant idea. While there were no proteins around at this stage, there were amino acids, and it was likely that two or a few amino acids could be joined together in a small chain called an oligopeptide by an RNA molecule with catalytic activity like the modern ribosome. Szostak said in the introduction to his breakthrough 2016 paper:

In order for subsequent rounds of replication to be possible, reannealing of the separated single strands must occur on a time scale that is comparable to or slower than the rate of strand copying.

He reasoned that an oligopeptide might be able to interact with an RNA strand in a way that would prevent annealing or at least slow it down long enough to allow time for replication. If true, this could also be the origin of the evolution of longer peptides and eventually proteins. And, in a wonderful set of experiments, it worked! From the abstract of the paper:

…oligoarginine peptides slow the annealing of complementary oligoribonucleotides by up to several thousand-fold; This method for enabling further rounds of replication suggests one mechanism by which short, non-coded peptides could have enhanced early cellular fitness, potentially explaining how longer, coded peptides, i.e. proteins, came to prominence in modern biology.

The impact this paper had on the field of origin of life research is hard to exaggerate:. A major stumbling block to acceptance of RNA World as a viable hypothesis was overturned. Despite my long-held skepticism, I also began to accept the possibility that RNA World might have happened. It all made perfect sense. Better replication by longer and better peptides would give a selective advantage to a cell, allowing for evolution of more advantageous RNA sequences and the birth of long proteins.

But science is not an easy pursuit. (I can say that with authority after 35 years.) Things go wrong. A lot. And as shocking as it is, things can go wrong for Nobel Laureates also. As it turned out, Szostack’s great idea was wrong, and the Nature paper showing the evidence in favor of the idea was also wrong. In a retraction published on November 23, 2017, Szostack wrote:

…we have been unable to reproduce observations suggesting that arginine-rich peptides allow the non-enzymatic copying of an RNA template in the presence of its complementary strand… we now understand that the data reported in the published article are the result of false positives that arose from … random errors, including transfer and concentration errors, affected the ratio of the concentrations of the RNA template and its complementary strand…in reality these reactions did not contain enough complementary strands to completely inhibit the reaction.

What that paragraph means is that others in his lab were unable to reproduce the same results that are reported in the paper, and they found out why. Somebody made some mistakes, and the results were not due to what they thought, but were an example of that most terrible of all words for lab scientists – an artefact. In other words, the results were a mistake. But even worse news came next. When carefully doing the experiments again, and avoiding all errors, they found the opposite of what they first reported and had hoped to find:

Subsequent experiments suggested that arginine-rich peptides may not slow the reannealing of complementary strands, and that what we had previously interpreted as a decrease in annealing rate was actually an artefact…

In other words, it looks like peptides do NOT slow reannealing, and therefore there is still no known mechanism for RNA to self-replicate. It ain’t over yet. I am sure many labs with tweak the experimental conditions in all kinds of ways to see if something will work. And it might. But it doesn’t look likely, and if things stay as they are now, RNA world and origin-of-life research is back to square one.

What is the lesson here? Szostack admitted to Retraction Watch that “In retrospect, we were totally blinded by our belief [in our findings]…we were not as careful or rigorous as we should have been… in interpreting these experiments.” Yes, I have been there. It’s really hard for a scientist to remain objective and skeptical when everything seems to work just right, and your hypothesis is supported by the experimental data.

The other lesson is that the origin of life has no easy answers, and in fact I can’t think of another field in modern biology where the answers seem to be so hard. Maybe that itself is telling us something.

It’s that time of the year again. Everyone is running around, trees are being put up and decorated, presents being bought and wrapped, travel plans being made and tickets purchased. It’s all exhausting. Last year I posted a blog about my own childhood memories of Christmas – namely, none. We didn’t celebrate Christmas in any way.

I do remember hearing Christmas carols in stores. I remember hearing, and later singing in school, one carol in particular that I found very beautiful. Of course, I had to ignore the words, which were all about that silly and dangerous myth of Jesus Christ. But I loved the melody and the quiet peaceful sound of the opening lines: “Silent night, holy night.” Well, the silent part, more than the holy, I suppose. But then that wonderful line, “All is calm.” What a beautiful idea. All is calm. Have you experienced that? Ever? I guess I have a few times, but not very often. Calm is something that we rarely feel in this busy world, so it’s good to be reminded about it.

And this  wonderful song reminds us of more than that. It reminds us about where we should really be in our thoughts in this season. We should imagine ourselves, shepherds or peasants, hearing a nearby commotion, and seeing some kind of procession arrive at a barn near an inn. It’s chilly, with a bright moon and shining stars. As we walk up the hill to see what’s going on, we feel a need to be quiet. We see the strangers in their fine clothing, with their camels and servants. And then, as we come closer, we can see the mother and Child sitting on the straw of the barn, surrounded by amazing gifts. Except for the faint breeze, it is quiet. The strangers are kneeling with heads bowed. The father is standing over the child and His mother. We want to ask, we want to know, but we don’t speak, because we do know. This night, this silent night, is a holy night, and it’s because of the birth of this Child.

All is calm and all is bright. And the world has forever changed this night; something wonderful, something more precious than the gold on the straw has arrived. We cannot know what this baby has brought, or who He is. But we know that someday, we will know.

All those years ago, when I would stand still listening to Silent Night as it played from a speaker in a department store, or as I stood mouthing the words in my classroom (and leaving out the religious parts, as instructed by my mother), perhaps I also knew in my heart that someday I would come to learn what so many people in the world learned about the birth of that baby. And thank God, it came to pass. Now I know that on that silent and holy night, Christ the Savior is born. Sing hallelujah.

The following post is an excerpt from the Preface to my book manuscript, which is now in the final editing phase. The working title is The Book of Works (just like this blog). I am also about to start looking for agents/publishers, so any advice is welcome. 

There is a well known joke about a man caught in a flood who prays to God to be saved. He hears an answer to his prayer: “I will save you, my son.” So, with a glad heart, he waits for the miracle to happen. A boat comes by, and the people in it call for the stranded man to join them, but he says “No, thank you, God will save me.”  And he continues to wait for the miracle. Two more boats follow (as in any good folk tale), but his answer is the same.

The man drowns. When he gets to Heaven, he confronts God: “Why didn’t you save me, like you promised?” God says, “I sent you three boats. What more did you want?”

Here is another version of the story. Instead of a believer, our hero is an atheist. Caught in the flood, he thinks: it sure looks like only a miracle could save me, but I don’t believe in miracles, so I must save myself. He dives into the swirling waters and tries to swim to safety. He sees a boat, and hears people calling to him, but as a rational person, he knows the chances of there being a real boat there just when he needs one are so small as to make such an occurrence essentially impossible. So, he decides the boat must be an illusion conjured up by his mind, and he continues swimming.

After he drowns, he also goes to Heaven, where God asks him why he didn’t get into the boat to save himself. “Because it made no sense for there to be a boat there, and I used my reason to reject that possibility. Logic is stronger than belief in fairy tales.”

God says, “Yet here you are, in Heaven, in front of the real God who made you, as real as the boat that could have saved you.”

The meaning of both of these parables is, of course, that God works through the natural world, and the natural world is the miracle. The first man expected an angel to come down, swoop him up, and carry him to shore. He rejected the possibility that an ordinary boat with a mortal human could be God’s instrument of miraculous salvation. The second man assumed that his salvation was entirely in his own hands, and even rejected the evidence of his senses that a miracle could happen.  Some believers fail to see that the “mundane” world of nature with its scientific laws is itself divine, flowing from God’s will and character. They miss the miraculous nature of everything around them, looking instead only to what they consider to be the rigid and unbendable word of God. They share this blindness with many atheists who, like our second man, also find nature devoid of anything related to divinity, but think of all of reality as the rigid and unbendable consequence of arbitrary natural laws.

They are both wrong, of course, because God is not rigid or unbendable, and His laws of nature reflect this. The great gift of God to the universe is freedom. We see this when we examine the physical and the biological worlds in detail. God has created a universe in which the fundamental particles of matter have the freedom to exist in multiple states; it is only when they are observed that they make their “choice”. As for life, God has created it in a way to allow a breathtaking diversity. There is freedom in evolution – freedom to explore, to succeed or fail. And God has granted His special creation of mankind the most freedom of all. Freedom to choose moral options. To sin, or to love; to worship, or to scorn. To recognize that the boat is a miracle of salvation, or to reject it. My own salvation came through the understanding that the natural world, and its description by science, is a strong witness to God’s existence and majesty.

The nice thing about having a blog is that one can write and publish whatever one wants to, without having to go through peer reviewers, editors, or publishers. The bad part of that is that one can end up posting garbage. I don’t think I have posted too much garbage to date, and this is mostly because of the fact that I pass everything through one judge, my wife and chief editor, Aniko Albert. She has (always wisely) discouraged me from posting quite a few essays that were not really up to par. So this means if you don’t like something here, don’t blame me, blame Aniko.

I fully expected her to nix this post, since its pretty silly, and has some stuff toward the end that’s probably not only scientifically absurd, but pretty bad theology as well. But she just made a few comments, and let it go. She did point out that I should re-read NT Wright’s Simply Christian, which provides a convincing debunking of my entire premise. My response was, when it comes to theology, who are you going to believe, NT Wright or me? She laughed appropriately.  So, here it is, for better or for worse

I think this is not the only universe. So far I am merely in stride with modern scientific theories (the multiverse and all). Except I am not thinking so much of a multiverse as maybe a duoverse. Maybe there are more, but let’s stick with two for the moment.

Our universe is one of them of course, and the other….(well, goodbye science, here is where we part company) the other one is the Kingdom of God. Or Heaven.

Just as some folks think that the laws of physics might be different in other universes, the laws of physics are also different in the Kingdom. There are none. No laws of physics, no laws of anything except the law of God.

Genesis starts with “In the beginning, God created the heavens and the earth”. It has struck me that this a remarkable sentence. I have heard it said that God is timeless, but if that were true then the sentence would read “At some particular time, God created…’ By specifically identifying the time of creation as “in the beginning,” the author is assuming a beginning of time, before which there was… well, there was no before which. This is consistent with the scientific cosmological approach to time and the origin of the universe. God was not around either “before” the creation, since there was no before, so then the question (often asked by atheists) is where did God come from?

There is only one answer:  somewhere else, another universe that existed before the creation of this one. And despite the scientific fact that universes are wholly independent of each other (at least in theory), somehow God reached out from His universe, the Kingdom of Heaven, and created this one.

We know a lot about our own universe, even though the amount of stuff we still don’t know is vastly greater than what we do know. The main thing we know about our universe is that it is lawful. Nothing can happen in our universe that goes against the laws. Light cannot go faster (or slower) than its fixed speed, time cannot go backwards, and we cannot travel in time. (Sorry, Syfy fans.) Heat cannot flow from cold to warm, and you cannot make a perpetual motion machine. And so on.

I believe that this universe of natural and moral laws was created by God, and so did all the early scientists, most of whom believed that by probing into those laws, they were learning about God’s creation.

As far as the Kingdom of Heaven (KOH) universe, we cannot know anything, so whatever I say about it is pure speculation. And since my theory is that the KOH is devoid of natural laws, there is nothing at all scientific about these speculations. In the KOH, God rules by fiat. Whatever God chooses to happen happens. Water can flow uphill (no law of gravity), living beings in that universe can live forever (no second law of thermodynamics), and miracles are simply part of the natural order.

So aside from God, who else lives in the KOH? We do, of course, after we die. There is plenty of room, since there are billions of planets in the KOH, each just like Earth, or to be more precise each just like California (without the earthquakes and drought). Paradise, in other words. Perfect weather all the time. No disasters (no tectonic plates), no harmful germs, no poisonous snakes or spiders. Everything is perfect, because God continually makes it so.

If this seems like a foolish fantasy, of course it is. OTOH, consider some resorts here on Earth. With enough resources of energy, labor, money, etc. we mere humans can easily build centers of paradise, where all desires and needs are met, and where people can escape the dangers and hardships of the “real” world. With a magical universe like the KOH, with a loving all-powerful God in charge, such a paradise can be real and unending.

Mark Twain, as brilliant as he was skeptical, would have had (and did have) something to say about the KOH. In his story “Captain Stormfield goes to Heaven,” Twain mused about how people would pass the time in a paradise, where everything was perfect, forever. Twain had some humorous ideas about this “problem,” but never came up with a good solution.

I think that the actual reality of the KOH is beyond our grasp. My guess is that when we arrive there, we will find that our souls and minds and even our bodies were operating on a tiny fraction of what they can do. And whatever that might be, in the KOH we will finally be able to do, see, understand, appreciate, and enjoy all of the hidden splendors of our existence and of God’s amazing gifts.

Getting back to Professor Wright, I will admit that his ideas about Jesus Christ bringing the Kingdom of Heaven to be built by us right here on this planet in this universe are probably a lot better than my duoverse idea, which has a lot of holes. I guess we will need to wait (hopefully for quite some time) to find out which of us was wright…(I mean right). Until then, all I can say is the next post will be better (I hope).

The following is from the Biologos website. A reader posted  a poignant question about a month ago, which I (and others) answered. My answer seemed to be well liked by many of the Biologos Forum participants, and I thought I would repost it here. You can find the original (along with some other answers to the question posed) at the Biologos.org site.

The following is unedited from the original, except for correction of a few typos.

Are there any former militant atheists on this forum? If so, how and why did you convert to Christianity? I’m a reluctant agnostic. I long to believe in God and to follow Christ, but I’m plagued with relentless doubt. I’m always worried that materialism is right and that nothing beyond the norm exists. If that is correct then there is no point in anything at all and I find that thought bleak and depressing. The idea of the Christian God comforts me deeply and I really want to let go and believe but I dont know how to.

Wow, that sounds exactly like me about 20 years ago. I grew up as a militant atheist, and gradually decided that what I was learning in science (I am a biologist) wasn’t consistent with a purely philosophical naturalistic view point. I began to see that even science, (the observer effect in QM, and other facts of physics, as well as some of the immense complexities of biology) was suggesting something more than a perfectly rational, logical world. I was also curious about beauty, love, art, and all the human essentials, that seemed to be outside of pure naturalism.

And like you I longed for some kind of spirituality (which I had been deprived of growing up). I investigated some religions, including some new-agey stuff. Nothing satisfied me. I had had such negative training about Christianity that I never considered it.

But then a friend brought me to a Church. I was amazed at the love and kindness I found there. I felt myself moved, but still couldn’t bring myself to believe. I was “plagued with relentless doubt”.

How Christ finally found me is a long story, but it involved some personal experiences that convinced me that Jesus was real, and was trying to reach me. It was like a building pressure, which I finally surrendered to, and the dam burst. When that happened, when I could actually say to myself “I believe” my whole life changed.

I still have doubts. Sometimes when I first enter my Church, I think “What am I doing here?” But that goes away pretty quickly. Now my faith is a central part of my life, even though I still do science and will never lose my scientific worldview, which now includes the knowledge that everything I study is part of God’s creation.

I found this Biologos Web site when it first began, and it has been an enormous help to me over the years. I even wrote a blog post back in 2010 called Stochastic Grace that talked about my journey (I think you can find it if you search for it). My suggestions are to look around and read some of the blogs. Here you will find people who have no doubt that naturalism is the best way to understand the world as God created it, and who also deeply believe in God, and in Jesus as their personal savior.

I also suggest you not worry about finding God, because if you let him, he will find you. The key is to be open and to listen closely for his call. It could come in a dream, or in a coincidence, or in the touch of a loved one, a smile from a stranger. And when it does come, and you recognize it for what it is, allow yourself to accept it. You will know it when it happens, and you will pray your thanks for the gift of faith you have been given. Until then, love the world and the people in it, and know that even if you don’t know God yet, he knows and loves you. Peace.

When I decided to become an official, professing Christian, I was thrilled to see that I could honestly say that I believed in every word of the Apostle’s Creed.

I am very grateful that the creed I had to believe in was not the following:

I believe in one specific interpretation of the Bible, and reject all others.

I believe the Bible in its English translation of the Hebrew and the English translation of the Greek translation of the Aramaic is literally true in every word, and no interpretation is necessary. Ever. Except for the parables of Christ, of course. And, um, some other stuff (see below).

I believe that some things about the Bible that are not actually in the Bible are also infallibly true. For example, I believe that the calculation of the age of the Earth based on the Biblically stated generations and ages of the lineage of Adam is correct. In fact, I believe that the truth of that calculation, with all of its assumptions, extrapolations and sources of error is more infallible than any conclusion of modern geological, biological, paleontological, archeological or any other branch of modern science.

I believe that the story of the creation of Adam and Eve in Genesis 2 is an expanded and more detailed version of the sixth-day creation of humans in Genesis 1. It doesn’t actually say that in the Bible, but I believe it anyway, because, well, that’s what the interpretation I believe in says.

I believe that incest was not a sin for Adam and his children, because….well, that’s the only way Cain and the others could have found wives, and for my interpretation of Genesis to make sense.

I believe that when Genesis uses the phrase “And God saw that it was good,” the word good actually means “perfect”.

I believe that this way of reading the Bible is not only the only true way today, but has always been the only way real Christians have ever interpreted the Bible, going back to um, well over a hundred years. Maybe a bit more.

I believe in some very special scientific ideas. These include that after the flood, about 4000 years ago, there was a hyperfast period of evolution in which all the modern species of living things arose from their original Ark-bound kinds.

I believe that mutations cannot produce new information, because that’s what I have been told by a couple of  Bible-believing scientists. All the other so-called scientists, including so-called Christians, are wrong.

I believe that light traveled a lot faster in the old days, and radioactivity doesn’t really allow for age calculations, and….OK, enough.

If that had been the creed I was supposed to follow to be a Christian, I would still be searching for some religion to follow. Do we wonder why the children of fundamentalists are dropping out of the Church as soon as they begin to get an education and learn how to think? Are we surprised that the number of young people with no religious convictions or interest is continuing to climb? And that so many people lose their faith, simply because they cannot reconcile what their Church tells them they must believe with what they know to be true?

I am aware that some people have pointed out the danger of abandoning the central messages of the Christian faith. Accepting the idea of evolution and of a metaphorical interpretation of some biblical passages does not constitute an abandonment of the central messages of Christianity. If you are not convinced by my statement, watch the talk by Jim Stump at the recent Biologos Conference.

In fact, the false creed that I listed above is NOT the orthodox traditional Christian view at all. It is a modern kind of fundamentalism borrowed from 19^th century Seventh-Day Adventism, mixed with some pseudo-scientific “evidence” from a book written in the 1960s. Many mainstream Catholic and Protestant theologians – including two popes – and renowned Biblical scholars have spoken and written against the YEC interpretation  of the Bible, so the idea that this interpretation is in any way representative of Christian theology is simply untrue.

I have argued on this topic before, and I will simply close with one point that I think bears repeating often. Acceptance of evolution has nothing to do with rejection of God, Christ, the Old or New Testament, or any truly fundamental aspect of Christian faith. On the contrary, an understanding of the beauty and wonder of the lawful evolutionary process that produces all the magnificent forms of life we know about, leads to a deeper knowledge and worship of the majesty of the Creator.