DNA, Intelligent Design, and Theodicy, Part One

John C. Avise published a book last year entitled Inside the Human Genome: A Case for Non-Intelligent Design. I would like to share some ideas from this book for your consideration. Avise looks at the age-old question of theodicy (why a good God would permit suffering) in light of the our understanding of human genetics, especially the new revelations that have come from the Human Genome Project just in the last dozen years.

Avise's main point is that if the world were designed by a loving intelligence (which Intelligent Design proponents publicly hesitate to call God), the DNA system shared by all organisms from amoebas to humans would look a lot different from the way it is. And his first set of examples is the sheer number and horror of mutations that fill the human genome.

Many mutations are neutral, or can be easily overcome by technology. And some of them cause a great deal of psychological suffering, such as the mutation that causes trimethylaminuria, which is physically harmless but causes the victims to smell like rotten fish no matter how clean they are. But many other mutations are deadly or, worse yet, can cause a person to have a lifetime of suffering. Perhaps the most disturbing mutation is the one that causes Lesch-Nyhan syndrome. This one mutation, of a single amino acid in a protein, causes the victim to have an uncontrollable compulsion for self-mutilation: they chew their own lips and fingers, and find sharp objects to stab their faces and eyes. The victims are fully able to feel their pain and they know what they are doing, but cannot control it.

But there is more to the story. Most of these genetic syndromes have come into existence many times. Consider glycogen storage disease, in which a defective enzyme causes glycogen (animal starch) to build up in tissues throughout the body. A childhood friend of mine has this disease, which he inherited from his father; by middle age, he was almost constantly incapacitated by this disease. I do not know if he is still alive. Geneticists know of 86 different mutations that can disrupt the enzyme and cause this disease. That is, this genetic disease has mutated into existence 86 separate times. The author directs our attention to several databases, one of which is the Online Mendelian Inheritance in Man (OMIM), which lists over 18,000 genes, three-quarters of which have documented mutations. And these are just the single-gene defects!

The author's first point is that an intelligently-designed genome would not have such a stunning number of mutations. If God designed the DNA to make us adapted to the world we live in, could God not have done a better job? Evolution, in contrast, is dependent upon random mutations, upon which natural selection acts by eliminating the bad ones (that is, disfavoring and perhaps killing the individuals who express them) and favoring the good ones. The existence of a large pool of mutations, which natural selection has not completely gotten rid of, is consistent with evolution but not with Intelligent Design.

One answer that Intelligent Design proponents have to this problem is that the Designer created a mutation-free set of human DNA when our species came into existence, then abandoned the system to take care of itself. But if this is the case, the system was so poorly designed that it could not, in fact, take care of itself.

The connection to the problem of theodicy is obvious, and Avise makes it. Defenders of God (which is the meaning of theodicy) claim that God allows bad things to happen as an inevitable consequence of free will. Their platitude is that if fire did not burn, then it would not be fire. I can understand why God would not automatically give all of us a perfect set of genes; limitations, including genetic ones, are necessary for character development, to show God on judgment day what kind of people we are (from the traditional Christian viewpoint). But Lesch-Nyhan syndrome? Potentially deadly mutations in three-quarters of human genes? Isn't this a bit excessive?

I will summarize some of Avise's other points in the next entry. Please post your comments and/or send the link to this blog to others who might be interested.

Don't miss my new book, Life of Earth: Portrait of a Beautiful, Middle-Aged, Stressed-Out World, just published by Prometheus Books.

Science and Philosophy

(My struggle with computer and biological viruses continues, hence the delay.)

In an earlier entry, I wrote about why I do not read philosophy books. The main reason was that philosophers tend to think they can answer every question by just thinking about it hard enough with our modified ape-brains, a concept I found unacceptable.

But apparently there was a group of philosophers that I did not know about. It was with some excitement that I discovered, while reading a recent issue of Science, the existence of the field known as experimental philosophy. No, not the philosophy of doing experiments, a la Karl Popper; but using experiments to study philosophy. The author, Shaun Nichols, had my attention.

Nichols addressed one of the most difficult philosophical topics, the question of free will. If there is such a thing as free will, then humans have a soul, or at least a self, that can make decisions independently of the chemical reactions that occur inside the brain. If there is no free will (if determinism is correct), then everything we do can be traced by a network of cause and effect to our genes and our environments (prenatal, developmental, recent, and immediate). Now, in actual practice, it may be impossible to disentangle the causation; and so, just for the efficient operation of society, we have to assume free well (we cannot let murderers roam free just because they have a mutant version of a brain protein). But this does not answer the philosophical question.

Nichols admitted that the problem of free will was, from the viewpoint of philosophy, intractable. But he addressed the question of why people believe in free will vs. determinism. And this question can be addressed using psychological data. He pointed out that most people actually believe both viewpoints. When they are calm and discussing general principles, many people accept determinism; but when they are confronted with details of, for example, a gruesome crime, these same people will claim the perpetrator had free will and deserves punishment.

This is where the experiment comes in. The researchers studied the responses of experimental subjects (as usual, university undergraduates, the most thoroughly studied group of people in the world) to stories about realistic events: did the subjects blame the perpetrators of bad deeds (thus displaying a belief in free will), or did they not (determinism)? In one experiment, the students tended to blame the perpetrators for emotionally appalling deeds, but not for minor infractions. This demonstrated that their belief in free will was determined by the emotional impact of the deed. But prior to administering the questions, the researchers had presented them with one of two introductions. One introduction suggested that the universe is indeterminist (that people have free will); the other suggested a determinist universe. Students who had been experimentally preconditioned by the indeterminist introduction attributed moral responsibility to all of the infractions, whether minor or appalling. Students who had been experimentally preconditioned by the determinist introduction were less likely to lay blame for minor infractions—but they usually blamed the perpetrators of appalling deeds for what they did. This is an experimental affirmation of the hypothesis that people are more likely to believe in free will in circumstances in which an emotionally significant deed has been done.

If, in fact, our brains cannot know the truth, then philosophers seem destined to frustration—unless they take a new approach, such as experimental philosophy, which brings psychology, and thus science, into the realm of philosophical inquiry.

Reference: Nichols, Shaun. “Experimental philosophy and the problem of free will.” Science 331 (2011) (March 18): 1401-1403.

Welcome Aboard, Mrs. Ples—Your Cabin is Number 10,587,282A

There will be some continued delays in my posts because of viruses: they are filling me, and have filled all my computer connections. I am using a spare computer in a classroom right now.

After I returned from my fun creationist weekend (see previous seven entries), I began wondering about how Noah might have sorted out the biodiversity that he had to fit into the Ark, if you believe the Flood story of Genesis 6-9 literally. In particular, I wondered about what Noah might have thought about the apemen whose existence is now thoroughly proved from the fossil record.

First, consider human diversity. Creationists commonly claim that the genetic diversity of Homo sapiens was preserved on the Ark because, perhaps, the three wives of Noah’s three sons were black/Australoid, white, and oriental/Native American. There is no Biblical basis for this, but creationists have never had a problem with just making stuff up. Sounds like a good premise for a Britcom, actually, or an episode of News from Lake Wobegon. Mrs. Shem always fixed hummus, Mrs. Ham always fixed okra, and Mrs. Japheth always fixed lutefisk.

Then, consider what Noah might have done with Homo ergaster. This species of animal looked just like us except that the entire species had brains much smaller than ours. What would Noah have done if the Turkana Boy showed up? (Actually, an adult pair of his species; the Turkana Boy died in adolescence of a tooth infection.) The answer? This species did not yet exist at the time of the Flood, according to many creationists. Their remains are only in the most recent layers, such as in Africa’s Rift Valley, so they must have lived after the Flood. Which means that they must have been (presumably degenerate) descendants of Noah. Apparently the whole species developed small brains, which means either that God miraculously microcephalized them or else that natural selection favored microcephalic mutants. But I guess this would explain why they seemed to make nothing but Acheulean hand axes. What did they use for cutting meat? Hand axes. What did they use for trimming their toenails? Hand axes. What did they use for tightening stone screws in their Flinstone-mobiles? Hand axes. Makes sense.

Finally, consider what Noah might have done with the australopithecines. These animals walked like humans but might otherwise have been chimp-like. Among the famous australopithecines who did not make it to the Ark were Lucy (Australopithecus afarensis), Ardi (Ardipithecus ramidus), and Mrs. Ples (Australopithecus africanus). Presumably, Noah would have sent all of these apeman species to animal quarters. Noah, like modern creationists, would presumably have had no hesitation in classifying animals into human and nonhuman categories. (I understand that creationists consider the fossils of these species to also be post-Flood.)

But Noah’s confidence may have resulted from the fact that he lived in the Middle East, where there were no primates other than humans. The other mammal species were things like cows and sheep, all of which were clearly less intelligent than humans. This is perhaps the reason that the monotheistic religions, which posit an absolute distinction between humans and animals, evolved in the Middle East, according to Frans DeWaal. The religions that evolved in parts of the world where non-human primates are common did not, and perhaps could not, make such a clear distinction, because monkeys and apes resemble us quite strongly. Queen Victoria, when she saw Jenny the orangutan at the London Zoo in 1842, declared her to be “painfully and disagreeably human.”

Creationists have no more hesitation at drawing an absolute distinction between the saved and the damned than they do between humans and animals. Anyone who has, like me, been treated as damned by a creationist will know what I mean.

Don’t miss my new book, Life of Earth: Portrait of a Beautiful, Middle-Aged, Stressed-Out World, just published by Prometheus Books.

My Fun Creationist Weekend, Part Eight (final installment)

On the weekend of March 5, I visited two creationist museums (see previous seven entries). One was the museum in which Carl Baugh had displays which, he claimed, proved that humans and dinosaurs left footprints in the same layers of mud.

Before I went home, ending my fun creationist weekend, I visited Dinosaur Valley State Park to see some real dinosaur footprints, still in the river bed (see bottom photo). The water is high in spring, and only a few prints were visible: round holes that are the footprints of large herbivorous Paluxysaurus dinosaurs, and three-toed footprints of small carnivorous Acrocanthosaurus dinosaurs. Some of the prints are visible under water, especially when green algae grow inside of them (see top photo). This was the part of my Texas trip that was refreshing and realistic, and I recommend a visit to this park if you are in the area.

Before I left Glen Rose, I did one more thing that altered my mind. I stopped at a barbecue place. It is well known that you can throw a rock anywhere in Texas and it will hit a barbecue place better than almost any other in the world. I had the brisket. The waitress brought me a pile of meat. It was pretty good, but it usually takes me a week to eat this much meat. I quite literally left Glen Rose feeling like what I thought a Neanderthal would have felt like. Neanderthals, you may know, ate mostly meat, according to scientists who have studied their coprolites. But recently a scientist studied Neanderthal tooth deposits and found that they also ate grains. Well, I suppose they must have had a piece of Texas toast with their barbecue.

Don’t miss my new book, Life of Earth: Portrait of a Beautiful, Middle-Aged, Stressed-Out World, just published by Prometheus Books.

My Fun Creationist Weekend, Part Seven. The Ghost of Marlyn Clark

It is not with fondness that I remember Dr. M. E. (Marlyn) Clark, who was an engineering professor at the University of Illinois while I was a plant ecology graduate student there. Marlyn was, to put it mildly, grim. He scowled, and looked incapable of smiling. We were both members of Twin City Bible Church in Urbana, although in that large church our paths had not crossed. That is, until I was asked by the Board of Leadership to teach an adult education class about Christian views of creation and evolution in 1982. Having recently left creationism, I presented the theistic evolution side; I invited Clark to present the creationist side. This was a mistake. When he found out that there was another side other than creationism being taught at this church, he and his associates began a campaign of disinformation against me, about which I later heard from student members even of other churches in town. He demanded a sort of trial to be arranged against me at the church, at which I was not allowed to speak. I knew, of course, that Clark and the other creationists (who were militant members of Phyllis Schlafley’s Eagle Forum and strong supporters of bloody terrorist raids by Nicaraguan contras against the Sandinistas), but I expected at least a modicum of fairness from the church leadership. It turns out that, after this trial, the church leadership took no further actions and even insisted that the creationists not cause the class to be cancelled. However excruciating an experience this was for me, it was formative: it was the beginning of my transformation from comfortable Christian evolutionist to passionate Christian anti-creationist. Perhaps I have Marlyn Clark to thank for that. It is regrettable that Clark left this kind of negative memory. He did some fine engineering work with computer models of the human circulatory system; this part of his legacy remains a blessing to many patients with cardiovascular disease.


Then, 29 years later, I encounter him again, posthumously. On March 5, as I left Carl Baugh’s Creation Evidences Museum (see previous entries), I saw Marlyn Clark’s “Wall of Truth.” It was (see bottom photo) a model of geological strata from a creationist “Flood geology” viewpoint. That is, it was an attempt to fit the geological record into a creationist viewpoint. Creationists believe that all fossil deposits were produced during the Flood. Therefore, there could be human artifacts at all levels of the strata, from Paleozoic to Recent. And some creationists believe they have found evidence of this very thing. Clark donated money to build a wall, near the museum entrance, that summarized this evidence: a bowl that was found in a coal deposit, and which he assumed had to be the same age as the coal, as well as the hammer and footprints found elsewhere in Baugh’s museum. One thing you will notice right away about this wall: the putative human evidences are found at different levels. This means that humans had to emerge from their hiding places and run around on hundreds of feet of mud, without sinking in, several times during the Flood, leaving footprints at two different levels, and dropping a hammer at yet another. Whatever the putative evidence of the Wall shows, it does not demonstrate a Flood. The skulls and tusks at the top represent post-Flood australopithecines and mammoths. (The figure looking out over the Wall is a nine-foot-tall statue of Tom Landry. Baugh intends it as an example of what magnificent specimens of humanity the Homo bauanthropus men were, at least from the viewpoint of Texas creationists.)


When I left the deliberately-created psychological delusions of Baugh’s museum (described in earlier entries), and emerged into the fresh air, I thought I had left creationism in general and Marlyn Clark in particular behind. But I got into my car and looked up through my windshield. I saw what looked like a green merry-go-round (see top photo). It was not labeled but I recognized it instantly. It was Marlyn Clark’s Flood Tank. Over thirty years ago, Clark built a merry-go-round that was supposed to prove something or other about Noah’s Flood. It was no ordinary merry-go-round. First, it had the ability to lurch, not just spin. And around its perimeter is a water-tight ring into which water and sediments could be placed. Once the machine is running, you can watch the water slosh around and mix up the sediments. Clark’s hypothesis was that, if there was a worldwide flood, it would not have produced a uniform slurry of sediments (his null hypothesis), but would have made distinct layers (the creationist hypothesis). Of course, you don’t need a giant merry-go-round to prove this. If you mix soil into water, the sand will settle out first, then the silt, then last of all the fine clay. Soil scientists do this with their sedimentation columns all the time. Clark’s machine did in fact produce distinct sediment layers, and he proclaimed the triumph of his theories. Only in the most alternate of alternate realities might one consider an eight-foot-wide merry-go-round to be a realistic simulation of the Earth during a Flood. At the moment, the Noachian merry-go-round is non-functional. But maybe Baugh will set it up outside his museum. I doubt that he would let the kids ride it. But maybe a frog will get buried in the sediments and fossilized. Maybe a giant will leave a footprint.


Don’t miss my new book, Life of Earth: Portrait of a Beautiful, Middle-Aged, Stressed-Out World, just published by Prometheus Books.

My Fun Creationist Weekend, Part Six. Lies and Damned Lies at the Creationist Museum

On March 5 I visited Carl Baugh’s Creation Evidences Museum near Glen Rose, Texas. In the previous entry, I described some of the displays. But the most prominent display of all, nestled among scriptural scrolls, is the Darwin display. All it has in it is a few of Darwin’s book, one of which has one of his more lugubrious photos on the cover, and a collection of slave shackles and handcuffs (see photo).


The message is clear, just as it was in Bill Gordon’s museum in Oklahoma: belief in evolution causes human oppression and slavery. If you believe we evolved, then you think people can be treated like animals, but if you believe humans were created, then you will treat them like fellow children of God. The footprint displays were lies; but this one was a damned lie.


First, consider the clear message that it proclaimed: Darwinian evolutionary science causes such things as slavery. As anyone knows who has read the masterpiece 2009 book by Adrian Desmond and James Moore, Darwin’s Sacred Cause, both sides of Darwin’s family were abolitionists, and Darwin detested slavery. Moreover, Darwin transferred his early belief in the common origin of all human races from Adam and Eve into his later acceptance of the common evolutionary origin of all human races. Desmond and Moore’s book also documents the creationist beliefs of American slaveholders and their scientific sympathizers. Louis Agassiz was most notable among them, but there were many others. If we must draw a causal inference, it would be that because slavery was forced out of existence during the period of history in which scientists and some societies and churches accepted evolution, then evolution deserves the credit. No causal inference either way is, however, justified. Certainly Darwin did not cause black American slavery. This is something only hypnotized victims of Baugh’s sermon could believe as they glanced at the displays.


Second, consider what the display did not mention. The history of Christianity in the western world for the last two millennia has, until very recently, been the story of murder and oppression. Ask any Huguenot victim of the St. Bartholomew’s Day Massacre if Lamarck caused their plight. And nearly all of the five hundred sovereign Native American nations had been conquered, and many exterminated, by Darwin’s time. It was religious zeal (and greed and plunder) that caused the Spanish settlements started by Columbus to enslave, then torture and kill, the Caribbean natives, against which the lone Christian voice was Bartolomé de las Casas. The Pilgrims, so much revered by creationists and other Christian conservatives, surrounded Pequot villages, set them ablaze, and shot anyone attempting to escape. Here is what William Bradford wrote: “It was a fearful sight to see them thus frying in the fire and the streams of blood quenching the same, and horrible was the stink and scent thereof; but the victory seemed a sweet sacrifice, and they [the colonists] gave praise thereof to God, who had wrought so wonderfully.” While massacres based on the Christian religion are today rare, the uncomfortable fact remains that one of the conservatives’ favorite books of the Bible is Revelation, which depicts a violent Jesus making the Earth run red with blood.


Baugh’s display added stupidity to dishonesty. It was not until I got home and looked at the photograph (look at it again!) that I noticed that one of the slave shackles was from the “Georgetown County Plantation Police.” The printing seemed awfully crisp to be on a real, well-used slave shackle. So I googled the name. It turns out that fake Georgetown County Plantation Police paraphernalia are sold on the internet. Badges are more popular, but you can get the shackles on Amazon for $39.99. (“Customers who bought related items also bought Wild Planet Spy Gear Night Goggles!”) If Baugh just stopped at being a fraud, and satisfied himself with entertaining lies about giant humans and about how moonlight allowed pre-Flood humans to live almost a thousand years, it might be funny; but he has slipped into the world of attempting to stir up hatred of evolutionary scientists.


Don’t miss my new book, Life of Earth: Portrait of a Beautiful, Middle-Aged, Stressed-Out World, just published by Prometheus Books.

My Fun Creationist Weekend, Part Five. Mysteries of the Cretaceous World at the Baugh Museum

Before I begin this essay, I want to let you know that the National Center for Science Education has posted its Upchucky Award winners for 2011! And now, on with the essay.

I visited Carl Baugh’s Creation Evidences Museum on March 5. After Baugh had finished his presentation (see two previous entries), I looked at the displays I had driven down to Glen Rose, Texas, to see. The bed of the nearby Paluxy River is famous for the trackways of footprints that dinosaurs left in the mud 110 million years ago (according to scientists). But Baugh claims that it was only about 4000 years ago, and that humans had left their footprints in the mud also. In his museum you can see excavated pieces of Paluxy River limestone that have what are supposed to be human footprints in them. One of the stones has what is supposed to be a human footprint overlapping the print of a three-toed predatory dinosaur (see photos). Think about what it would mean if these displays are genuine. It would mean that the entire timeline of evolution, in which dinosaurs became extinct 65 million years ago but the human genus did not evolve until about two million years ago, is wrong. If you glance quickly at these displays, as most people visiting the museum were doing, it seems to be pretty clear that humans and dinosaurs lived at the same time on a young Earth. But if you look closely at the stones, as I did, you begin to notice a few things.

During the Depression, when the dinosaur footprints of the Paluxy River were already famous, some enterprising individuals carved human footprints in the stone and sold them. One might naturally assume that the footprints in Baugh’s museum were also carved. Baugh claims that, while some Paluxy human footprints were fakes, the ones in his museum are genuine. Unfortunately, the only way you can evaluate this claim is by looking at the footprints, as I did. They did not look like fakes to me, at first glance. But, I am not even a geologist, much less an ichnologist (expert in fossil burrows and tracks). How would I know? I was, however, suspicious. The footprints looked good—a little too good, as a matter of fact. Every toe was perfect. I could see no chisel marks, but I concluded that the human prints are fakes, even if Baugh did not carve them himself. For a summary of the human footprint story, click here. In other displays, you can see putative human sandal prints which are supposedly the same age as the dinosaur prints. And even what Baugh claims is a child’s handprint.

One of the footprints is quite large. Baugh has an explanation for this. The footprints were produced by a species of giant humans, which Baugh, no stranger to ego, decided to name after himself (Homo bauanthropus).

There are other items on display at the museum that, according to Baugh, prove that not just humans but technologically advanced humans lived at the same time as dinosaurs. One is the Cretaceous hammer (see photo). It is an iron hammer with a wooden handle that was found, according to the display, embedded in Cretaceous rock further south in Texas. How could a hammer get into a Cretaceous rock? There is actually an easy answer to this question. Somebody in the nineteenth century dropped a hammer into a crack in the Cretaceous deposits, and then erosion filled in the gaps. You can see eroded limestone filling cracks in today, down at the river.

The museum is designed for a quick glance at the displays, rather than careful thought. If you think carefully, however, you quickly realize that the creationist explanation makes no sense. Cretaceous deposits, in Texas and all over the world, are above the Paleozoic, Triassic, and Jurassic deposits, all of them full of fossils. And, in many parts of the world, there are Cenozoic deposits on top of the Cretaceous layers, and they, too, have fossils. That is, if all of the fossil-containing layers were formed during Noah’s Flood, then these Cretaceous layers had to be deposited in the middle of the Flood. Here’s what had to happen. The Flood had been going on long enough to deposit thick layers of sediments full of plants, animals, and technologically advanced people. Then the waters receded, and dinosaurs and humans who had been hiding somewhere came out and walked (not ran) over hundreds of feet of mud without sinking into it. One of the humans lost a hammer. Another lost a finger (see below). Then the Flood came back and buried all of them.

By the way, you don’t want to miss the Cretaceous finger. It looks like a finger from a statue, since there is no evidence of any internal structure such as bone. But Baugh claims it is a real finger, which apparently broke off of a giant who was fleeing the Flood.

The visit to the displays, just like the experience of Baugh’s lecture, creates an alternate psychological reality. Quickly glancing at the displays gives you the impression that humans and dinosaurs lived together on a young Earth. But one of the displays, as I describe in the next entry, proclaims that evolution is the major source of evil in the world in the past and today.

Don’t miss my new book, Life of Earth: Portrait of a Beautiful, Middle-Aged, Stressed-Out World, just published by Prometheus Books.