How Evolution Works

I have been asked many times to explain how so called “macro-evolution” works. There are of course many excellent books and articles online and off that cover this, but I thought it might be a good idea to have a blog post that explains it quickly and simply that I can refer to when asked. The following is adapted from a book manuscript (which might get published some day).

To see how macroevolution (the origin of new species) works, we can use a hypothetical animal, maybe one in the cat family. Let’s call it a lipard. And let’s say that there is a population of these large cat-like carnivores living on a large plain with plenty of prey animals. The lipards have gotten better and better at hunting thanks to several improvements (microevolution) in  vision, muscle strength, digestion of meat, and other traits. And all of these positive changes eventually got shared by the whole population of lipards, due to breeding and natural selection (like all examples of microevolution).

But now the population of lipards becomes divided so that there are two groups of lipards that cannot interbreed. Perhaps one group crossed a river, a desert, or a mountain range and couldn’t get back, or they just wandered so far away that it wasn’t convenient to find mates in the other group.

Now both groups of lipards continue to accumulate new genetic variations through mutations, but because they are no longer interbreeding with each other, the new variantions in one group do not spread to  the other group. With time, each group begins to differ in their variations. Now, for each  group, natural selection could choose different genetic variants to be successful than in the other group.

Its also possible that some differences in the two groups could arise by chance, and not have any important effects on survival (like slight differences in skin color). But the key point is that none of the changes will spread to the other group, because the two populations cannot interbreed.

With the passage of time,  different traits will appear  in one of the groups that are not found in the other. In one group, the skin could become darker, and in the other, males could develop a large mane of hair around their heads.  Both groups continue to change independently of each other, and after a long enough time, neither group resembles the original lipards. One group has become lions, and the other has become leopards.

They still have a lot in common, but they are now two separate species. Please note that no lion turned into a leopard or vice versa. Both lions and leopards share a common ancestral species, the lipard, which now no longer exists. It didn’t go extinct – it evolved. Lipards themselves had evolved from an ancestor that they had in common with tigers and snow leopards, and even further back with cheetahs and domestic cats. And they all became separate species the same way: population isolation, separate genetic changes in the separate populations, and continued evolution by natural selection. This is what Darwin observed among species of finches in separate islands of the Galapagos chain.

We can keep looking backwards in biological history. All the cat-like animals are descended from a no-longer-living ancestor shared with bears, wolves, hyenas, badgers, and other carnivores. If we keep going we will find a common ancestor for all mammals, and then all vertebrates, and so on. For an excellent book that describes all of this in beautiful detail, there is nothing to match The Ancestor’s Tale by Richard Dawkins.

Is there any evidence for this scenario of how the diversity of life arose? Yes, tons. There is so much evidence, both in fossil records and from genetics, that there is no doubt at all that the theory of evolution for the origin of species is correct (though perhaps not complete – see “New Ideas in Evolutionary Biology”).

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God and Nature

For the past six years, I have been a member (and now a fellow) of the American Scientific Affiliation (ASA). From the ASA web site

The ASA was founded in 1941 as an international network of Christians in the sciences. As scientists, members of the ASA take part in humanity’s exploration of nature, its laws, and how it works. As Christians, ASAers want to know not just how the universe operates and came into being, but why it exists in the first place. 

We in the American Scientific Affiliation believe that God is both the creator of our vast universe and is the source of our ability to pursue knowledge — also, that honest and open studies of both scripture and nature are mutually beneficial in developing a full understanding of human identity and our environment

The ASA publishes a peer reviewed, scholarly journal, Perspectives in Science and Christian Faith, and a less formal online magazine, God and Nature . I have published papers, book reviews and articles in both.

The founding editor of God and Nature, Emily Ruppel Herrington, is stepping down to pursue other career interests. Emily is a good friend of mine, and she has done an outstanding job as Editor-in-Chief of the magazine.

I have been asked to step into the role of Editor-in-Chief of God and Nature, and I have accepted this honor with humility and gratitude for the chance to serve the Lord and the community of scientific believers who publish their ideas in that venue. I am fortunate that Ciara Reyes, a gifted editor, writer, and molecular biologist will continue to serve as Managing Editor.

I ask the readers of this blog to pray for the continued success of the magazine, and for me as I take on this new role. I am very likely to approach some of you to contribute essays, musings, memoirs, etc. to the magazine. Meanwhile I encourage everyone to consider joining the ASA, even if you are not an active scientist. Please check out the website for information on membership categories.

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Some Wisdom from the Past

Arthur Thomson, also known as Lord Kelvin, was an English physicist (and Christian) who wrote a book titled “Progress of Science in the Century” published in 1901. The century referred to was the 19th.. I have a copy of it among my collection of pre-20th century science books. It can also be found online. The book is a fascinating and eye-opening account of most scientific fields (especially physics and chemistry) and the enormous strides that had been made prior to the Einstein and Planck revolutions. Toward the end of the book, Kelvin discusses biology (which had barely begun to be a science) and some philosophy. The following is an excerpt from that section, that I believe contains some important wisdom for our own time.

The three main moods or attitudes of mind observable in human relations to nature — practical, emotional, and scientific. They find expression in doing, feeling, and knowing; in practice, in art, and in science; they may be symbolised by hand, heart, and head. And as one of the moods often has temporary dominance, we are all apt to err in over-doing, or over-feeling, or over-knowing. Our thesis then is that some measure of completeness of life — in ideal at least — is the condition of sanity in human development. A thoroughly sane life implies a recognition of the trinity of knowing, feeling, and doing. It spells health, wholeness, holiness,

Many other opinions of authoritative experts might be cited, varying greatly in their form, but with this common basis of agreement that the phenomena of life cannot be restated in the language of chemistry and physics. And yet, the reader may well ask, “Is this more than a pious opinion, an argumentum ad ignoratiam? Is not biological analysis still in its youth? Have not partial restatements been given of numerous functions? May one not look forward to the time when these may be completed?

This leads us, in concluding this discussion, to follow Prof. Karl Pearson in pointing out again the radical misunderstanding which exists in many minds in regard to scientific method. The material of science is “the routine of our perceptual experience”; we think over this, though we never understand it; we make sure by experiment that the sequence of sense-impressions which constitutes the routine is not illusory; we make sure that the routine is perceived by others also (for science is social), lest we should be the victims of an idiosyncrasy; and by and by, if we are clever enough, we give “a description in conceptual shorthand (never the explanation) of the routine of our perceptual experience.”

“The problem of whether life is or is not a mechanism is thus not a question of whether the same things, ‘matter’ and ‘force,’ are or are not at the back of organic and inorganic phenomena—of what is at the back of either class of sense-impressions we know absolutely nothing— but of whether the conceptual shorthand of the physicist, his ideal world of ether, atom, and molecule, will or will not also suffice to describe the biologists’ perceptions.”

That it does not at present seems the opinion of the more philosophical physiologists; if it ever should it would be “purely an economy of thought; it would provide the great advantages which flow from the use of one instead of two conceptual shorthands, but it would not ‘explain’ life any more than the law of gravitation explains the elliptic path of a planet.”

“Atom” and “molecule” and the rest are concepts, not phenomenal existences, therefore even if the physicists’ formulae should fit vital phenomena —which they do not seem to do—there would be no “explanation” forthcoming, for “mechanism does not explain anything.”

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Is God Imaginary?

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:

Schroedinger

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:

i2

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 19th 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).

 

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RNA and the Origin of Life

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.

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Merry Christmas

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.

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The Flood and the Boat

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.

 

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