Friday, June 30, 2017

Friday Science: Adam and the Genome 4

Here's chapter 2 of a new book by Dennis Venema and Scot McKnight called, Adam and the Genome: Reading Scripture after Genetic Science. Both are men of faith. Chapter 2 is titled, "Genomes as Language, Genomes as Books."

Previous posts
Personal Preface
Forward and Introduction
Evolution as a Scientific Theory

1. 1. In chapter 2, Dennis Venema gives a basic explanation of how genes replicate themselves and activate proteins. It is actually a quite impressive simplification of genetic science. In the process, he gives us a small taste of the genomic evidence for evolution. At the end of the chapter, he says, “It is no exaggeration to say that (the very, very few) trained biologists who reject common ancestry do so because of prior religious commitments, not for scientific reasons” (40).

He actually quotes from a blog post of one of the them. Todd Wood is a young earth creationist by faith. He is quite clear, however, about how the evidence looks. “Evolution is not a theory in crisis… There is no conspiracy to hide the truth about the failure of evolution… I say these things not because… I’ve ‘converted’ to evolution… Creation students, listen to me very carefully… evolution is an extremely successful scientific theory. That doesn’t make it ultimately true… It is my own faith choice to reject evolution” (41).

I am just a beginner when it comes to such things, but my guess is that the situation is this. We could suppose, by faith, that God created in an instant the genomic map of all organisms to look as if they could have gradually evolved following processes we now can observe on a small scale. But the most natural explanation, if we had no prior commitments to go either way, would be to conclude that there has been a gradual development from simpler to more complex organisms over millions of years.

2. Some of the chapter consists of some basic genetics. Most of us have heard of DNA. DNA exists in a double spiral. Sections of DNA are called “genes,” and sections of genes are called “chromosomes.” Humans have 46 chromosomes, 23 from our father and 23 from our mother. Women have two “X” chromosomes. Men have an X and a Y chromosome. In children, women always contribute an X chromosome, while men contribute either an X (making it a girl) or a Y (making it a boy). So Henry VIII should have had himself executed for not having a boy.

There are only four basic building blocks in DNA, chemicals called cytosine, guanine, adenine, and thymine. Cytosine only bonds with guanine, and adenine only bond with thymine. So you can replicate a strand by breaking it in half and then making all these “nucleotides” available. The right ones will find the right plug-ins and bond. In fact, this is how our cells reproduce.

It is also how our DNA puts into motion our physical characteristics. Something called “messenger RNA” duplicates one of the DNA strands, takes that information off and uses it to produce a variety of proteins, which in turn activate things like our eye color or hair color or nose length, etc.

There is apparently a lot of dead space in our genes, stuff that doesn’t do much of anything. In fact, only about 5 to 6 percent of our genome are the actual genes. Three genes make a codon, which collectively code for the production of a particular protein.

3. Errors and mutations do happen. Perhaps a nucleotide doesn’t bond to the right corresponding nucleotide. Perhaps a “stop” mutation cuts off the gene so that it doesn’t finish giving complete information. Perhaps there is a deletion mutation, which throws off the three codon pattern.

For a parent-child generation, of the some 3 billion pairs of nucleotides in our DNA, there might be about 100 mutations, most if not all of which will go completely unnoticed.

4. None of the above is particularly controversial. What is controversial is how to interpret what we observe when we set the genome of humans alongside chimpanzees, gorillas, orangutans, even chicken, dogs, and whales. Venema gives the example of insulin in dogs and humans. The gene sequence has a great deal in common.

In fact, it has enough in common that dog insulin would work in a human. Apparently, there is a lot of wasted space in DNA so that there can be quite a bit of variety and it all still work. This is not how a German would design it—too much unneeded and irrelevant space. But you can imagine that if a process was wandering somewhat randomly, it would be convenient if you only had to randomly come close for something to work.

Then he puts the sequence of chimpanzees, gorillas, and orangutans alongside as well. Even closer agreement to the human sequence. Chimpanzees and gorillas are slightly closer to humans in sequence than orangutans.

Later in the chapter, he looks that the olfactory sequence for primates. It turns out that there are the remnants of genes that do not function that are present in, say, wolves. Humans, chimpanzees, gorillas, and orangutans all have a certain stopped gene that is complete in wolves. This is a shortened gene that doesn’t do anything. Humans, chimpanzees, and gorillas all have a certain gene deleted that wolves have and orangutans still have. Humans and chimpanzees have a deletion that the gorillas and orangutans still have. Meanwhile, each of these primates have a mutation in this sequence that none of the others have.

So this could all be God having fun, knowing that in the early 2000s humans would be able to unlock these codes. Wait for it, Gabriel, Francis Collins is almost ready for that joke we planned 6000 years ago. But if we were just going on the evidence alone, we might hypothesize that orangutan split off from a common ancestor first, then gorillas, then lastly chimpanzees and humans. This explains why some still have functioning genes that wolves and others still have working and why others have the same traces of earlier mutations.

Similarly, the stretch of human genes that corresponds to the part of the chicken gene that codes for an egg shell has a large number of nucleotides in the same sequence. It’s just that the key genes to make a shell are missing in humans. But there is a lot of junk in that stretch of human DNA that corresponds to a stretch of chicken DNA that works.

5. I found his opening to the chapter brilliant, since I love languages. First, he compared genomes to languages. He has a background in West Frisian in the Netherlands and put two sentences up next to each other, Apparently they sound much the same:

English: “Butter, bread, and green cheese is good English and good Frise.

West Frisian: “Bûter, brea, en griene tsiis is goed Ingelsk en goed Frysk.

By implication, the young earth creationist would have to say that God created these two languages to look and sound very similar, but he created them this way from the very beginning. He created them to be very, very similar but there would be no historical relationship between them.

If we had no prior assumptions, however, we would more naturally conclude that at some point, perhaps in the 600s AD, a common group of Anglo-Saxons split, some going to the island of England and others staying nearby on the continent. Over time, little variations arose in the way they wrote and pronounced certain words. Today, you can see a common ancestry, but the isolation of the two has resulted in some interesting “mutations.”

He shows the same in English translations of John 14:6 from the 1300s to today. Wycliffe spelled truth, “treuthe.” Tyndale in the 1500s spelled it “truthe.” The original 1611 KJV said “trueth.” And the 1769 edition of the KJV says “truth.” Same word, variations over time.

4 comments:

Martin LaBar said...

Thanks for this good post.

Edward T. Babinski said...

WHAT ABOUT THE BOOK'S TREATMENT OF "ORIGINAL SIN?" Reconciling Christian theology of the Adam and Eve tale (different from the Jewish theological explanation!) seems a bit of a task. For instance...

Hadn't animals been acting both aggressively and cooperatively toward one another for ages before upright primates ever existed? So why would God expect the first upright primate couple to act with far less aggression than all the rest of the animals on earth--and then damn all the children of the first couple to hell when they did? Death, fear, anxiety, quick hormonal fight or flight reactions, including aggressive impulses (as well as cooperative impulses) were all part of the early upright primate genome inherited from its primate cousins. So why damn the first couple to eternal hell? The very evolutionary process that God employed to create the genomes of upright primates ensured a host of problematic behavioral imperfections right from the start.

Put another way, men and women are 'sinful' because of what? Evidence suggests it is because of the very process God employed to bring about the human species. You wonʼt find many shrinking violets in your ancestry. We are here because we had ancestors who did what it took to reproduce and survive in a world that was filled with competing groups of primates, pain, fear, anxiety, starvation, sickness, death and extinction events, long before the "image of God" arrived. What we inherited from our biological ancestors seems to have been the very traits that allowed them to produce more of their kind, traits often involving selfishness, aggression, unbridled curiosity (as well as traits involving cooperation and forgiveness). Consider the “anger reaction," aggressive outbursts that we all lapse into from time to time. Those are to be expected evolutionarily speaking, because our threat system has evolved so that it is activated rapidly, because defenses that come on too slowly may be too late. We have been prey more than predators, even for most of human evolutionary prehistory, and there isnʼt much time to react when the tiger is about to pounce, or a fellow primate is coming at us to keep us away from his food, or his mate, or even his harem in case of Pan chimpanzees (though Bonobos are certainly different in not having harems, and having sex freely with other chimps). Is having a rapid-response amygdala for threat response our “sinful” fault; or is it part of the way our brains evolved to function?

Christian apologists object that such a biological interpretation tends to reduce sin or evil merely to our acting on long evolved biological impulses, ignoring forms of evil made possible by our transcendence—evils such as idolatry of self, viewing other people as mere objects, and the like. But such traits could just as well be explained as being rooted in our survival instincts. As the anatomist and Christian Daryl Domning admits, our “sinful” human behaviors do appear to exist because they promote the survival and reproduction of those individuals that perform(ed) them. He adds that “there is virtually no known human behavior that we call ‘sin’ that is not also found among nonhuman animals. Even pride, proverbially the deadliest sin of all, is not absent.” Domningʼs “conclusion” is that animals are “doing things that would be sinful if done by morally reflective human beings.” Moreover… “Logical parsimony and the formal methods of inference used in modern studies of biological diversity affirm that these patterns of behavior are displayed in common by humans and other animals because they have been inherited from a common ancestor which also possessed them. In biologistsʼ jargon, these behaviors are homologous. Needless to say, this common ancestor long predated the first humans and cannot be identified with the biblical Adam.”

Edward T. Babinski said...

CONTINUED, PART 2

Or to quote Ed Friedlander, “We do not like to be reminded of the ways in which we resemble animals. We sinners like to think our motives are more holy than those of animals. And since we generally assume animals cannot have eternal life with God, thinking about animal deaths and about our own place in nature frightens us.”

Or to quote Sally Carrighar, “A preacher thundering from his pulpit about the uniqueness of human beings with their God-given souls would not like to realize that his very gestures, the hairs that rose on his neck, the deepened tones of his outraged voice, and the perspiration that probably ran down his skin under clerical vestments are all manifestations of anger in mammals. If he was sneering at Darwin a bit (one does not need a mirror to know that one sneers), did he remember uncomfortably that a sneer is derived from an animalʼs lifting its lip to remind an enemy of its fangs? Even while he was denying the principle of evolution, how could a vehement man doubt such intimate evidence?”

Many Protestant and Catholic theistic evolutionists believe that at some point a soul appeared in two (or more) of our animal ancestors. One of these, or perhaps their representative, was assigned the name “Adam.” These ensouled humans were spiritual orphans, apparently. Their parents would have looked and acted much like them, with only a handful of DNA mutations distinguishing them, biologically, but these first ensouled humans would have suckled at the breasts of a soulless mother, and picked up their first lessons on how to behave by observing and interacting with soulless parents and friends. Does such a view make much sense?

Having acquired a “soul” that, according to Christian theology, now needed to be “saved,” what kind of salvation was available to our ancient ancestors who first chipped stones, carved spears, built fires, and later drew pictures of animals on the walls of caves in France? They seemed pretty involved in simply staying alive and noticing animal life, perhaps practicing some sort of religion involving the recognition of animal spirits. Which reminds me that besides the cave paintings from long ago, the oldest known human-made religious structure was built about 12,000 years ago, and is decorated with graven images of animals which would be prohibited by Exodus 20:4 thousands of years later. Early human artists also left behind carved images of large breasted women. No doubt the folks who pursued the healthiest women that could also keep their man warm at night, not necessarily the most “sinless” women, gave birth to the most offspring, leading to our species with its genes and behaviors.

Another question, how might a scientifically savvy Christian bridge the chasm between natural and supernatural conception in the case of Jesus? Did the Holy Spirit employ a set of freshly constructed chromosomes that fused with Maryʼs? In that case, some divinely produced DNA would need to be produced that appeared to have come from a human father with a long evolutionary past of his own. Thatʼs because the divinely implanted paternal chromosomes have to line up right beside the naturally evolved maternal chromosomes in Maryʼs zygote. So letʼs say the Holy Spirit injected a ready-made Y chromosome into Mary (along with 22 others from falsified meiosis in a non-existent human father), complete with endogenous retroviruses, fossil genes, and other hallmarks of evolution that would be capable of lining up beside Maryʼs chromosomes to form a fully complementary set. So the Holy Spirit would have had to add a Y chromosome that was faked to look like it had been passed down, with occasional mutations, from an endless line of evolutionary descendants. And we know what “those” guys were like. Weʼve already gone over that.

Edward T. Babinski said...

THREE ADDITIONAL QUESTIONS OR POINTS CONCERNING CHRISTIANITY AND EVOLUTION

"It is a difficult task fitting evolutionary ideas into the Christian framework, beginning with Paul’s exposition in Romans 5:12 that ‘Therefore, just as sin came into the world through one man, and death came through sin, and so death spread to all because all have sinned’... And what about Paul’s thoughts on the direct connection of sin with one man and redemption with another in Romans 5:18, ‘Therefore just as one man’s trespass led to condemnation for all, so one man’s act of righteousness leads to justification and life for all.’ Was the trespass that Paul mentions perpetrated by some particularly evil Homo habilus or an especially cunning Homo erectus? The common modern explanation is that Genesis 1-3 is to be interpreted metaphorically. If that is so, why does God require a bloody, horrific, non-metaphorical sacrifice of his Son? This is the difficult task of reconciling evolutionary thought and Christianity... One also has to wonder what it means to live in a ‘fallen’ world where no such fall has occurred [where death, predation, aggression, have always been, long before any species vaguely resembling an ‘Adam’ ever evolved]. So without an historically 'good' creation 'in the beginning,' and without an historical Adam and Eve or historical fall, the problem of natural evil becomes one of even more stark contrast. The answer to suffering parishoners that we ‘live in a fallen world’ makes less sense if every living thing was cursed with death–and over 90% of every ancient species was cursed with extinction–long before human beings even showed up in this less than Edenic cosmos."
-- Terry W. Ward in a letter published in Christian Century, April 22, 2008 [with edits]


"Did a separate group of hominids reach a certain point at which their brains could handle a 'soul?' And where was the cutoff point? Can you imagine the heartbreak of knowing your mom and dad aren’t endowed with the image of God? Try this on for size: 'Grandma and grandpa aren’t going to heaven — not because they sinned, but because they were animals.'”
-- Tim Widowfield, Strange Bedfellows — Evolution and Christianity http://vridar.org/2013/02/15/strange-bedfellows-evolution-and-christianity/


"So long as people believed, as St. Paul himself did, in one week of creation and a past of 4,000 years - so long as people thought the stars were satellites of the earth and that animals were there to serve man - there was no difficulty in believing that a single man could have ruined everything, and that another man had saved everything."
-- Pierre Teilhard de Chardin, Christianity and Evolution