Darwin's proof, chapter 10

I'm almost done reviewing Darwin's Proof. It's been slow going, because I have been doing it chapter by chapter and haven't had much time to post. The reading is easy. I should have time to get this done soon. This time, I will review the second to last chapter, chapter 10.

Things are getting repetitive by this point. Hunter relies heavily on having made the case that evolution is a religion, but I have thoroughly refuted that in previous posts. This chapter introduces the intelligent design theory. Kind of. If by introducing a theory you expect to find detailed analysis of data that are explained by it and mechanisms by which it works, you will be disappointed.

Hunter first tries to counter the criticism that ID is not a real theory. He avoids almost all direct criticism and fails to show simple ways that ID is like a theory, like showing its predictions or ways to falsify it. Instead, he brings up two philosophers of science. He mentions Popper's idea of falsifiability. Rather than showing how ID is falsifiable, he simply mentions that the criterion of falsifiability has problems, so we can ignore it. Yes, falsifiability is a slippery idea. It is naive to believe that one observation can falsify a theory, for example. That doesn't mean it is a useless idea. Scientific theories must be capable of refutation by some empirical means, and Hunter makes no attempt to show that ID fits the bill.

Next Hunter brings up Kuhn's concept of paradigm shifts, as a means of refuting the overwhelming consensus for evolution. He points out that consensus have been overturned in the past. While this is true, it is not an argument for ID. If it were, then every fringe idea would be given legitimacy. I agree that we must be careful when we use the scientific consensus as an argument for evolution. It is ultimately an argument from authority. But it is referring to the relevant authority in this matter, and it does mean the burden is on ID to show why this consensus is wrong or to give us reason to believe there might be a paradigm shift.

He counters the claim that ID is just religion by his claim that evolution is a religion as well, which I have already refuted. He also fails to note that ID starts with religious conclusions, and fits the evidence to the already determined conclusions. He uses his usual dismissive tone towards the evidence for evolution, for example claiming that we have little idea how complexity could arise, but we are sure it wasn't by design. There are textbooks written about how it could arise, and detailed studies of how particular structures have arisen. It is not taken on faith.

Next, Hunter veers off on a tangent about the privatization of God. He points out that in modern society, religious belief is considered a private matter, rather than public. He somehow blames this on evolution. He seems completely ignorant of the history of tolerance. The idea that religion should be private arose after hundreds of years of religious wars in Europe, and became popular in the 18th century, 100 years before Darwin. He thinks that in America, this separation of church and state is a new idea, resulting from the secularization of America, rather than one of the most important concepts for the founding fathers.

And again, he claims that we aren't really separating church and state, because evolution is in fact a religion. His entire thesis depends on this poorly supported conclusion.

Now it is time to tell us what ID really is and is not. He introduces the concept of irreducible complexity in a few sentences, without actually using the term, and without even trying to address the criticism of the concept. It is a given for Hunter. He tells us, again, that ID does not require absolutely perfect design (he is sure that evolution depends entirely on countering a perfect designer). Hunter tells us that evolution does account for some things, but we just need a designer for bigger things. In other words he uses the standard micro/macroevolution, god of the gaps argument. Evolution is fine except for the places where there is a bigger gap, then bring in the designer.

And he tells us that the criticism that ID makes no predictions is simply a mischaracterization of ID. Since that has been one of my main criticisms in these posts, I looked forward to being shown some predictions. However, I have just given his entire refutation of this claim. Rather than actually listing a few predictions, he simply says it is a mischaracterization. He also claims, again, that evolution predicts anything and everything, which I have refuted in many of the previous chapters.

Now we get into the ID research program. Hunter points out that design is used in areas such as archeology. However, whenever scientists use the concept of design, it is with knowledge of the designers, or inferences into the nature of the designer. Even when we study adaptations, it is with knowledge of the designer--in this case, evolution. We know that things are designed to maximize offspring. ID doesn't even tell us what things are desinged for. Hunter uses an example of the possible sequences for various hemoglobin molecules, but never bothers to show how it follows from a particular view of design.

Hunter mischaracterizes evolution, claiming that biologists believe that differences between proteins are the result of random changes or neutral evolution. In fact, we recognize many changes are the result of selection, and most importantly have ways to determine if change is neutral or adaptive. This is where Hunter gets dangerously close to making a prediction. Hunter is taking the position that all differences between proteins and all structures will have a function. This is a breakthrough, if they stick with it, and I have seen other ID proponents take this position as well. They claim that ID leads to the hypothesis that all DNA will be functional. The case that some DNA is in fact functionless, such as many pseudogenes, is very strong. It would seem ID has been falsified. You would at least think there would be legions of ID scientists trying to find the functional purpose of silent subsitutions, pseudogenes, and other oddities.

Hunter continues his confusion regarding convergent evolution. He thinks evolution fails to explain the similarities between marsupials and placentals, for example, and that ID explains them as a result of common design. I think Hunter is completely unaware of the vast structural differences between marsupials and placentals that hide beneath the superficially similarity. Evolution can explain why the marsupial mole is so different from the placental mole. If their similarities are the result of common design, then what is Hunter's explanation for their differences?

Hunter admits that evolution dominates the study of designed structures, but claims this is simply because it is the dominant paradigm. He then states: "Where evolution will accept and even look for nonfunction, ID will look for function. Where evolution will explain away the obvious designes in nature as chance products of natural selection, ID will simply model the design as design". There are so many problems in those sentences. First, evolution looks for function as well, as the default hypothesis for anatomical structures. Second, "chance products of natural selection" doesn't make sense, since natural selection is not chance. Third, I have no idea what "model the design as design" means. The simple answer to Hunter's claims is "show me the money." Show some examples of the use of ID as a driving force in research, and how it is more succesful than evolution. Then I will gladly accept your claim. Again, Hunter is claiming that everything has a fucntion. It seems this is the closest Hunter will come to making a prediction, so this would be the way to disprove ID.

Finally, Hunter goes through the different possible interpretations of ID, from creation ex nihilio to front loaded creation to design through natural laws. In other words, everything from young earth creationists to theistic evolution. He counts a theistic evolution that would not offend many active evolutionary biologists as ID. Clearly, if ID works entirely through natural laws, then we should study those laws, which is what biology does. He defines ID so widely that almost anything is ID. What he fails to do is to tell us how to distinguish between these. If ID were a real science, then the YECs, front loaders, theistic evolutionists, and progressive evolutionist would all be debating each other and coming up with observations to support one view over another. In fact, these groups do disagree with each other, but the debate is bassed entirely on scriptural exegesis, and not science. Hunter does tell us at that he supports creation ex nihilio (consistent with other YEC leanings in the book), but doesn't explain why.

Yet again, we get a chapter that promises to provide the substance but fails to deliver. Hunter has again failed to give a single prediction of ID, a single result arising from it, or a framework for a research program. He does occasionally claim that such things exist, but never gives an example. We have further comfirmation that ID is a vaccuous concept, based entirely on negative arguments.

SGU skepticism

I love The Skeptic's Guide to the Universe, the podcast by the New England Skeptical Society. I've listened to it every week for over 2 years. It is a great way to keep up on the latest science and pseudoscience, and it is entertaining as well.

I do have one problem with it however. This is just a friendly criticism. It in no way takes away from the enjoyment of the podcast. There will be things to disagree with in any program. It doesn't succeed if it doesn't make us think and occasionally challenge it. My particular criticism is also found in many other skeptical and pro science groups.

My most common problem with SGU is the unfounded technological optimism. In the SGU universe, science and technology can fix anything. The future is bright. All of our problems can be solved by science. I want to be fair. They do sometimes inject some caution. Steve Novella is more likely to hold back on the implications while his brother Bob is most likely to see nothing but potential.

One podcast in which this was seen was an interview with someone trying to create immortality. He believes that all of the things that kill us can be dealt with by medical science. There was very little skepticism of the claims, or acknowledgment of the limits we have seen.

I was a kid when Nixon announced the war on cancer. I read about how terrible cancer was and thought that at least it will be cured by the time I get old enough to get it. In fact, cancer is as much of a killer now as before. We often hear about the latest possible cure for cancer. Maybe something worked great in mice. The translation to human therapy is always messier. We get tiny increments. The same could be said about cures for malaria or the common cold.

The same could be said about gene therapy. Twenty years ago there was talk of curing numerous illnesses and making designer humans. Today there is still no unequivocal success with gene therapy. That doesn't mean we wont' succeed in some cases (and fail in others). But biological systems are complicated. Any manipulation alters the whole system, and simple extrapolations almost never work with living things.

The hope of medical immortality ignores all of this. Even something as long established as organ transplants have complications and limitations as serious today as decades ago.

We see this in the popular press as well. Stem cells have tremendous potential. But a reader of the popular press might believe that breakthroughs are only years away. The reality is probably more like decades, and it will work with some diseases and not others, and there will be complications and limits on its success.

Other places of misplaced optimism in the SGU are space travel and nanotechnology. The reality of space travel should give anyone with visions of a science fiction future pause. We haven't been back to the moon in 35 years. The energy and resources for any extended stay in space are tremendous. I do not know if we will ever be able to overcome them. Certainly, energy is a major limit. We have yet to find a good source of energy without major economic and ecological problems. Even wind energy affects birds and bats. Anyone with a skeptical background should know that hopes for limitless energy are almost always unfounded.

I believe science can solve many problems. But it also has limits. The 20th century should show us the limits of technology, and the unexpected side effects of it. We should pursue all of the leads we have, and find ways to make the world better. But I would encourage people not to exaggerate the benefits or ignore the limitations. We have to be skeptical of science as well as pseudoscience.

The SETI lottery

A question that occasionally comes up in skeptical circles is the scientific status of SETI (search for extraterrestrial intelligence). Some claim that it is a pseudoscience while others defend it as sound science. Although I do not believe it is pseudoscience, I think that it sometimes can be very weak science.

SETI does not have the approach to evidence that pseudoscience has. It does not reject criticism like pseudoscience. It does change it's approach in response to evidence or criticism. It is not based on theories that contradict known theories. Falsifiability is a little trickier. It is not clear how much negative evidence is required to reject the search. At best we can put a limit on the number of stars that might contain intelligence. Even that is weak, because intelligence may be communicating with us in ways that we are not searching. But SETI does not have the built in barriers to falsifiability of many pseudosciences. More importantly, SETI has been objective in it's criteria for acceptance.

I think the most important question for it's legitimacy is how it would react to a positive signal. If we got a putative signal, I believe the scientific and SETI community would rigorously dissect the evidence. Althernative explanations would be sought out, and if better explanations were found, then the case would be rejected. I say that based on how the community has behaved so far. If however, the SETI community grabbed on to some possible signal and clung to it with layers of excuses even as evidence against it mounts, the same way that PSI researchers cling to weak evidence for ESP, then it would be a pseudoscience.

Although SETI is not a pseudoscience, that doesn't mean it is necessarily good science. SETI is unusual as a science because it has no actual data. There is no theory. It is just a search. The biggest problem is that the search is based on nothing but speculations, largely based on our knowledge of one society, 20th century scientific humans.

There is no reason to believe that any other intelligence would care to communicate with other intelligences, just because we would. There is no reason to think they would put rescources into sending out a strong signal. We haven't, why should they? In the 20th century, we used radio communication a lot, so the search has focused on radio signals. However, it is likely that we will replace radio signals with fiber optic or other means of communicating before too long. Our period of radio communication may only exist for a century or two.

SETI searches particular frequencies of the spectrum because those frequencies would make the most sense for an intelligence to communicate with. Again, this assumes they want to communicate and that they think in a manner similar to us and that they have the rescources available to devote to sending out a beacon.

Some speculations are pure science fiction. There was a recent study that looked for so called "Dyson spheres". These are theoretical massive solar energy collecting panels encircling a sun. There is no reason other than imagination to think any civilization would ever make these. Even if they are made, the study relied on assumptions about the infrared signal they would produce. There are reasons to believe Dyson spheres would never be made. The massive amount of material needed to make a significant number of these is way beyond our technology. There have been proposals to collect solar energy just from earth orbit, and we haven't managed to do it. It wouldn't be economically feasible for a long time. Maybe in a century we could have a few orbitin the earth. And yet people envision millions of square miles of these orbiting a sun.

Often, as in the case above, we assume that an advanced civilization would have massive capabilities. We envision a future like the Jetsons. Do we forget that we were supposed to be living in the sky by now, if you asked people 60 years ago? Humans left near earth orbit between the years 1969-1972. We have not returned, and won't for at least a few more decades. Much as I wish it were otherwise, I doubt humans will ever leave our own near vicinity. There is a strain of technological utopianism in much of science and SETI. It ignores economics and social forces. It ignores the limits of technology, or the unpleasant side effects.

The usual argument given for SETI, in the face of the long odds and large amounts of speculation, is that the pay off would be so enormous that we should go for it, even with long odds. Kind of a Pascal's wager of science. I agree that a postive outcome would be one of the most thrilling results we could have. If it can be done with minimal investment of resources, and there are people willing to devote their lives to it, I have no objection. However, I would object to any significant investment of resources, and I myself could not spend my life on SETI. It seems very much like buying lottery tickets and hoping for a pay off.

Darwin's Proof, chapter 9

I am now on Chapter 9 of my review of Darwin's Proof. This will be a short review. The book stopped dealing with science about half way through. It is now purely a religious apologetic.

Hunter begins by explaining how when Jesus was crucified, people expected more from him, miracles or signs or to save himself. Likewise, we expect more from creation, some kind of perfection. Hunter tells us again, as in chapter 8, that creation is very imperfect, because of the fall. He openly rebukes 18th century philosophy, as well as the design arguments of William Paley. He calls this the "paradigm of perfection". He seems to recognize that creation isn't that perfect. He continues to insist that evolution depends on a view of perfect designing God. He continues with his idiosyncratic view that all evidence for evolution is really just an argument against the paradigm of perfection. Hunter never explains why evolution is very convincing to people from non Western religions, such as those in Asia, even though those religions generally do not view God as a perfect designer.

Of course, Hunter can't do away entirely with the idea that creation is somehow the expression of God's handiwork, so he explains that creation is a general revelation. God reveals himself in creation. Scripture is the more specific revelation. Many people would look at creation and think that this reveals a God of cruelty and poor design, but again, that is because of the fall. All of the good things in the world are the revelation of God, the bad things are the fall.

I found some of his views of general revelation to be amusing. Hunter explains how scriptures uses analogies to explain things. For example, the kingdom of heaven is like a little bit of yeast that works through a large amount of dough. False teachers are like a brood of vipers, etc. Hunter then asks if it was serendipity that creation just happened to be full of analogies to spiritual truths, or if God created the world to have these analogies. In other words, he is suggesting that vipers were created to give us an analogy for false teachers or yeast created to give us an analogy for small things producing a large effect. Does he really have that little confidence in the human imagination to suggest that analogies can't be found in almost anything? Does he really believe that everything around us, all of the creatures we see, are there just as Sunday school lessons for us?

Hunter suggests that a caterpillar in its cocoon is a symbol of the crucified Christ, to be resurrected soon. So metamorphosis, found in millions of arthropods, not just butterlies, a process with clear ecological benefits to the organism, a process on which other species and ecosystems depend, is nothing more than a Sunday school lesson. I could find such Sunday school lessons in anything I want, including fictional stories. I could use the butterfly as an analogy for a Hindu myth of death and rebirth. Even as theology, this is hopeless, leave alone as science.

Hunter says creation's purpose is to communicate truths and contribute to our salvation. He doesn't explain why an evolved world couldn't do the same thing. Hunter contradicts himself at the end of the chapter, stating the perfections in nature reveal the glory of God. Even he can't get away from the paradigm of perfection.

Hunter returns to his point that patterns in the world could be the product of an underlying purpose, rather than evolution. He points to the pentadactyl limb as such an exmaple. Perhaps it is part of God's design to have this pattern in separate creations. He ignores the most famous example of a deviation from that pattern--The panda's thumb. It has an extra digit that doesn't follow this underlying theme. Why would God make an exception to his pattern in just this one case? Hunter must be familiar with Gould's famous essay, and must know it was aimed at exactly the argument he made, that patterns reflect an underlying design element. Gould argued that both evolution and creation can explain well designed or universal patterns, but only evolution can explain the odd exceptions or poorly designed elements.

And Hunter yet again says that no matter what we we in nature, we would explain it by evolution. When I teach evolution, I challenge my students to think of things that could not be explained by evolution. I offer Pegasus, the flying horse, as such a creature. Evolution modifies pre-existing structures, it does not create things like wings from scratch. That's why all flying vertebrates have wings from modified limbs. If we regularly saw creatures such as Pegasus, we would disprove evolution. Hunter thinks we would explain it away. I am willing to openly say numerous observations that would falsify evolution, from Pegasus to a rabbit in the Cambrian. They would not be explained away. Evolution would be falsified. I'm willing to put the theory of evolution on the block like that. Is Hunter willing to do the same with his views?

What is meant by "explanation"

I have often stated that intelligent design fails to explain anything. It offers the explanation that things are the way they are because a designer made it that way, but that does not qualify as an explanation. Here I would like to produce a list of the different meanings we give to the word "explanation".

One meaning of explanation is to provide a causal explanation for something. We can explain malaria by saying that a parasite enters the body by a mosquito bite. The parasite then infects the blood cells and liver cells. The body's response to this infection, and the periodic release of parasites, explains the bouts of fever typical of malaria. This explanation tells us how A causes B (how Plasmodium causes malaria). It also explains things like why malaria is found in some parts of the world, and how to prevent it.

A related meaning of explanation is to break something down into its component parts. We can explain how a car engine works by explaining how the fuel injectors and pistons and transmission and cooling system and other components interact. This might also involve the causal relationships between the parts. Science often breaks larger things into their parts--organisms are described as groups of cells, and cells are broken down into organelles and molecules.

What both of these first two explanations have in common is that it helps us to understand one thing in terms of something else. Another kind of explanation is to explain why something is one way rather than another way. This is something that evolution excels at. Why do we have five fingers rather than four? Why do marsupials dominate in Australia rather than placentals? It is common in other fields as well. Why does the United States have a democracy rather than a monarchy? Why is hydrogen more abundant in the universe than helium?, etc.

At first I was thinking this was a complete list of the ways we use the word explanation. Of these meanings, intelligent design clearly fails to deserve the word explanation. If we want to know the mechanism by which organisms were created, we are out of luck. They just formed. Any attempt to make ID proponents explain how comes up empty. ID does not help us understand organisms in terms of other things as well. And ID most certainly fails to explain why it is this way rather than another. The answer is always the same--because the designer wanted it that way. The designer wanted to use a pentadactyl pattern for a limb, for his inscrutable reasons. The designer wanted to put marsupials in Australia.

But then I realized there is another level of explanation, for designed things. After all, someone might ask why the first iPods were all white, and an answer could be "Steve Jobs wanted it that way". Isn't that similar to the answers ID gives for why things are the way they are? Do we mean something else when we explain designed things?

But "Steve Jobs wanted that way" is not explanation, or at least it is an explanation only in the sense that we can understand his motivations. Is white Jobs favorite color? Did market surveys indicate white would be popular? Jobs is well known as a minimalist, and perhaps the white color and simple lines of the iPod are a result of this personality trait. Or perhaps it was pure whimsy or the flip of a coin. No matter what the reason, we still try to understand Jobs motivation in terms of personality or other motivations. We want to know why Jobs wanted it that way.

Intelligent design fails as an explanation in this way as well, although it need not, in theory. If we could claim to understand the motivation of the designer, then it could be used. Perhaps the designer's goals were maximal effeciency, or beauty, or minimalist lines. Of course, ID offers no such explanations, because there are too many exceptions to any such rules. Life can be inefficient and ugly and complicated. If we make any attempt to claim to know the motivations of the designer, we are accused of wandering into theology. ID proponents make it clear that the designer could want anything for any reason and these reasons are inscrutable to our human minds. ID really could be a science and could be considered an explanation if it offered some insights into the mind of the creator. I suspect it would fail when tested, but at least it could be tested, and at least it could be considered an explanation.

Some forms of creationism actually are explanations. Flood geology actually does attempt to explain the distribution of fossils in terms of causal mechanisms, involving the hydrodynamics of a great flood. It fails miserably at it, but at least it attempts an explanation. Intelligent design is reducing creationism down to the parts that aren't even an explanation. The reason to reject ID is simply because it fails to explain anything, by any definition of the word.

When children ask why the sky is blue, we sometimes say "because God wanted it that way". But that is a cop out. Why didn't God want it red? That is not an explanation. It simply says it's blue because it's blue. If we explain that blue is refracted less than other colors by the atmosphere, then we understand why the sky is blue in terms of other things. This also helps us understand why it is red at sunset, and why the sky of mars is not blue.

I realize this list of the use of the word explanation matches Aristotle's list of the kinds of causes--material, efficient, formal, and teleological. This match gives me confidence that I have a fairly complete list of the ways in which we use the word explanation. However, if there is a way that the word is used that I have not considered, I would appreciate pointing it out.

Darwin's Proof, chapter 8

I am up to chapter 8 in my continuing review of Cornelius Hunter's Darwin's Proof. By this point of the book, it has ceased any pretense of science and has become a religious apologetic. Here Hunter promises to discuss what God really is. There is still the promise that he might produce a positive argument about God or creation, rather than just attacks on the God presumed by Evolutionists. Such hopes would be misplaced.

Hunter again claims that evolution explains evil in the world, but it has failed to explain the wonders of the world. "We can barely believe that evolution's unguided forces somehow produce the most complex things we know of." Says who? This is simply an argument from incredulity at the core of so much evolution denial. His argument is simply that he can't imagine evolution produces complex things. It is not a demonstration why it cannot. A few paragraphs later he states "On the one hand, the brain obviously could not have evolved." He offers no argument for this. He simply expects his readers will see it as obviously true. He doesn't discuss the odd way our mammalian brain is built on top of a reptilian brain, or any other evidence.

He then moves to scripture, for most of the remainder of the chapter. He says that God did tell us how he created the ostrich, in the book of Job:

The wings of the ostrich flap joyfully,
but they cannot compare with the pinions and feathers of the stork.
She lays her eggs on the gournd
and lets them warm in the sand,
unmindful that a foot may crush them...

This is not a description of how the ostrich was created, or why it has these traits. It is simply a description of an ostrich. This is supposed to show us the intentions of the true God, as opposed to the evolutionists non scriptural God. But all this says is the ostrich is the way it is. Hunter repeatedly explains that scripture shows a God who creates "according to his good pleasure" (twice) or "as he wishes". In other words, anything goes.

Hunter then explains all of the evils and imperfections of the world, including death, as a result of the fall. Although it has been unclear until this point whether Hunter was ID, old earth creationist, or young earth creationists, this puts him in the young earth crowd. Hunter says that only after the fall would the ground produce thorns and thistles. Doesn't this mean that God continued to create after the fall? Species with thorns and thistles did not exist prior to the fall. Yet the Bible clearly says creation occurred prior to the fall. Which is it? Every species on earth has hundreds of traits to protect against the evils of the fallen world--protection against predators, disease, etc. Did God only create our immune systems after the fall? Did the gazelle only run fast after the fall? Did predators get sharp teeth after the fall? Every creature on earth was created after the fall, if Hunter is correct on this.

Hunter explains that creation is the Glory of God, so it is good and wonderful. But it is also fallen, so it is bad. There is no need to separate the two. Anything can now be explained.

Hunter poisons the well against reason and evidence. He says that in a fallen world, humanity will produce deceptive philosophies and we won't think clearly. Deceptions will sound like fine-sounding arguments. In other words, he his saying don't trust your reason, and although evolution makes perfect sense, it is the work of the devil and the fall.

As usual, Hunter then does a good job of making points for science. He has two pages of quotes from biologists pointing out that creation cannot be tested. Anything is possible with creation. For example, he quotes John Rennie of Scientific American "when and how did a designer intervene in life's history? By creating the first DNA? The first cell? The first human? Was every species designed, or just a few early ones?" Perfect question, in my opinion. How does Hunter respond?

Hunter complains that since we cannot answer these questions, scientists insists we not consider God from science. Instead of complaingin, how about trying to answer them? Make a real theory. It is possible to imagine a creationism that does tell us whether God created once or a few times, whether he created the first cell or the first human, and test it. We aren't saying God must be excluded, just that all non specific vague statements and untestable hypothesis are excluded, whether they involve God or not.

Likewise Hunter quotes Paul Moody: "it is really not an explanation at all; it amounts to saying 'things are this way because they are this way'. Furthermore, it removes the subject from scientific inquiry. One can do no more than speculate as to why the creator chose to follow one pattern in creationing animals rather than to use differing patterns." Again I say right on. What is your answer? But there is no answer. He has two pages of such spot on critiques of creationism but there is no reply at all. I reread the pages several time to see if I am missing anything. As far as I can tell, he just expects his readers to be indignant at these people excluding God, without bothering to explain why we should be.

The closest he comes it to object that this amounts to defining God out of the picture. But he makes no attempt to show how we could do science with the supernatural. He certainly does not understand that excluding God from science does not mean excluding him from reality. It is simply recognizing a limit of science: science can only study the natural. Hunter complains because scientists willingly admit science cannot answer every question. He says that in the guise of neutrality, science rejects God outright. Science no more rejects God than it rejects Picasso because we do not invoke Picasso for explanations.

Then there is one paragraph in which Hunter is right. He says that

Science says that we need not invoke God. Science can make good progreess and describe the world accurately without reference to God. If God created the world, he could have done so only via natural laws. There must be no direct divine intervention.

He is right. Science asks how much of the world can be explained with natural laws, and so far it has found no place where natural laws are inadequate. It still might in the future, but there is no need now. If science is a problem for religion, it is not because science actively contradicts God, but simply that God doesn't seem to be necessary. However, Hunter has no problem with the fact that we can explain the weather without reference to God, or chemical reactions without reference to God, or explain the motions of the planets without reference to God. I have never understood why this indignation arises only against evolution, instead of all of science.

The last two pages of the chapter tells that we are all sinners and God saves us. I have no idea what any of this has to do with the topic of the book or the chapter. It is simply a pure Sunday sermon, with no relevance to creation. Perhaps it means something to people who are sure that evolution leads to damnation, and that is why it is here. Certainly these pages make it clear that this book does not even pretend to be a scientific treatise and it not intended for anything other than the true believer in creationism.

When logic and truth are not the same thing

I recently gave an assignment to students in which they must come up with any explanations they can think of for various biogeographic patterns. I tell them to consider evolutionary and non evolutionary explanations. Inevitably, the only explanations people can come up with involve evolution in one form or another, or just that God wanted it that way for obscure reasons (occasionally other explanations are offered but can be eliminated by closer examination of the patterns).

Recently a student offered a variety of evolutionary explanations, but then added a paragraph at the end, making it clear she did not accept evolutionary explanations. First, she concedes that perhaps small changes occur by evolution, allowed by or supervised by a creator (in other words, microevolution is OK). Then she adds the following sentences:

A creator would be infinitely more wise than any human, and it may be that we cannot always come up with human explanations for everything. Evolution might appear to be the logical explanation for many occurrences, but logic and truth might not always be the same thing.

I was struck by such an open argument from ignorance. The student admits that logic and evidence favors evolution. She has no alternative explanations for it, nor do others. But nonetheless, evolution should not be accepted, because you never know what we don't know. There is not even a reason given to suspect it is not true, although presumably it is faith.

This shows the problem we have in teaching evolution. It is possible to give an airtight case of convincing evidence for evolution, but that is not enough to persuade. No counter argument is even needed, other than "logic and truth are not the same thing", whatever that means. I suppose it means that something completely illogical can be true.

This is an argument used for many other fringe beliefs, even those that do not depend on God. One of the most overused quotes is from Hamlet, "There is more on heaven and earth, Horatio, than are dreamt of in your philosophy." People feel they have Shakespeare's approval to dismiss an overwhelming consensus, because there is much that we don't know. We can show that UFO's could not possibly change direction that rapidly, could not travel those distances, could not pass without leaving a trace, etc. However, the aliens know much more than is dreamt of in our philosophy, and they can do anything. We don't need to actually explain how. The known physical laws of the universe just show the limits of our knowledge.

Perhaps a point worth making to someone who admits the evidence supports a view yet still thinks it is not true, is to point out that even if they are right, the view is still useful. Whether evolution is true or not, there is no doubt it is very good at making predictions about everything from the fossil record to similarities of genomes. If in fact it was a creator that made these patterns in the rocks and DNA for his mysterious purposes, evolution manages to be a good predictor of the creator's intentions, for whatever reason. So studying and teaching evolution and the patterns it describes is still useful and necessary for understanding life, at least until we get a better predictor of the creator's mind. Perhaps the ultimate reality really is forever beyond human comprehension. But that doesn't mean we should give up entirely and reject whatever tools help us to make at least a little sense of reality.

Darwin's proof, chapter 7

It's been a long time since I've posted. I've been busy with work and other things. I hope to be able to post more often in a few weeks. For now, I will continue my review of Darwin's Proof, by Cornelius Hunter. Most of the posts before this deal with Hunter's book, if you would like to review them.

The review of Chapter 7 will be much shorter than the previous. Usually I have copious notes over each page, but I have almost none in this chapter. This chapter is theology. In Chapter 6, Hunter objected to the religious assumptions of evolutionary biologists. Although he criticized the view of God behind biologists view of design, he never replaced it with an alternative view. Even with theology, creationists seem to rely on negative argumentation rather than a positive case. However, I thought that in this chapter, he would finally present a view of God that can explain all of the observed facts. He seems to think biologists create a straw man God, so I was interested in the proper view of God. He did not supply it in this chapter.

The chapter is simply a review of how God has been viewed over the centuries. As far as I know, it is accurate, although I am not an expert on the history of theological views. He points out that by the 19th century, God had become a more rational God, and less based on faith or revelation. He seems to find this objectionable. He objects to applying reason to God. It is this rational God that Darwin and the evidence for evolution argued against.

He gives reasons for the change in theological views. For example, people tried to use reason to explain evil. It all makes sense to me and seems like an improved God, but it is clear I am supposed to object to it. As usual, Hunter does a good job of convincing me of the evidence against his views. He presents Hume's argument against design and anthropomorphizing God very well. He never explains any errors in Hume, other than it is too rational. By the 19th century, God became more distant and science and religion became separate. This seems to have been for good philosophical reasons, but again, Hunter objects.

In the whole chapter, he never presents his alternative God. I keep waiting for it, but it never arrives. I have only to presume he is doing the usual smoke and mirrors of creationists. When the evidence doesn't fit with a rational God, retreat to a mysterious God. I assume Hunter's God is a God whose purpose is beyond our comprehension, who is so inscrutable that we cannot possibly make sense of his creation. In other words, he is an untestable, any thing goes God. Although Hunter never explicitly states this, I will work under that assumption.

Hunter doesn't seem to realize that the rational God to which he objects follows directly from intelligent design. The whole basis of ID is that God is a rational designer: That we can use reason to see the works of God; That we can infer God from his handiwork. The ID God is the god of Paley and the 19th century. Hunter objects to the view of God that follows directly from his views on evolution. If we retreat to Hunter's God of mystery, there is no positive case left for ID. None of the arguments about designers or irreducible complexity or information hold up. So in Hunter's hand, ID consists of negative arguments against evolution and negative arguments against a rational God, but has absolutely no positive content, scientific or theological.

Hunter again objects to Darwin when Darwin, discussing the nested hierarchies of classification, said "if species had been independently created, no explanation would have been possible of this kind of classification." Hunter objects to Darwin claiming to know the inscrutable ways of the creator and telling him how he should have created. But even if we move to Hunter's God, Darwin is correct. Hunter's God does not explain this classification. All Hunter can say is that God did it that way for his mysterious reasons. That is not an explanation. An explanation has to consist of more than "it is that way because it is that way." Hunter, and ID in general, fails to even deserve being called an explanation. In two chapters on the theology of evolution, Hunter has yet to have a single sentence that actually explains why any of the patterns we see exist, or why things are this way rather than another way.

Ultimately, what Hunter objects to is that evolutionary biologists give ID the benefit of the doubt. They assume it makes testable explanations that follow from a designer, and then point out the tests fail. Hunter loudly objects to such crude theology. A proper understanding of God does not lead to any conclusions or any testable claims. It is especially ironic that his greatest objection to evolution is that it explains too much.

Darwin's proof, chapter 6, part II

I am critiquing CG Hunter's Darwin's Proof. In the last post I discussed the overall argument of chapter 6. Here, I will discuss particular details or errors made by Hunter.

Hunter often makes the distinction between micro and macroevolution, but not explicitely. In discussing Darwin’s finches, he agrees they show species aren’t fixed, although he qualifies it with “true, the amount of evolution was tiny." Here he subtly hints at a micro/macro evolution distinction, which he continues to do throughout the book. He never suggests a possible limit to change, just that observed change isn't much. Basically, he admits there is evidence against the fixity of species, but that doesn’t mean there isn’t fixity of “kinds”. We just don’t know what a kind is, or what evidence would show they aren’t fixed. He claims there is no evidence that small scale change is capable of of large scale evolution, but he also never gives any reason to think it isn't capable of it, other than the limits of his imagination. He ignores the evidence for large scale evolution or the fact that many patters, from DNA to biogeography, appear at larger scales exactly as they appear at smaller scales.

At one point he states “evolution is anything except divine creation. This is the reason evolution is such a flexible theory.” No, evolution is not anything except divine creation, except in his mind. He says this only because any and all possible materialistic explanations for life would be equally offensive to him, so he lumps them together. And after defining evolution this way, he complains because evolutionists bring up God when they discuss alternatives. Of course, they don’t bring up God when they bring up materialistic alternatives, but they necessarily bring up God when the alternative is God.

Hunter repeatedly adds little asides about our ignorance of every detailed step in the evolution of some particular structure or organism: “God, according to Darwin, would not have made the brain or the bat that we find nature, though he had little idea about how they actually worked.” “Darwin pointed out there are patterns between species that do not reflect good design. Darwin could not explain how such creatures evolved with any level of details, but his could be explained later.” Etc. Hunter seems to be of the common opinion that if we can’t explain every last step and intermediate in the evolution of organism, then we can’t say anything. But science doesn’t work that way. Instead, we ask what patterns would we expect to see in the world of evolution is true, and see if those patterns are observed. We see if alternative theories could also explain those observations, or predict patterns. Design fails to predict any pattern.

Hunter's attempt to deal with pseudogenes is the most problematic section of the chapter. He actually makes a case for evolution. First, he says that evolution doesn’t predict pseudogenes. It's true that if we only had evolution, we wouldn't automatically know pseudogenes must exist. It’s not that based on first principles we predict the existence of pseudogenes, but rather that evolution has a testable explanation for them and predicts the patterns we see in pseudogenes.

Hunter says that pseudogenes do not always align as they should and they may be scattered about, or that some pseudogenes actually have a function. He does not give any reference for this, so I cannot determine exactly what he is talking about. However, he does admit evolutionary biologists have an explanation for these, but then falls back on his usual argument—because we have explanations for exceptions, evolution can explain any pattern. But the explanations for exceptions to the expected pattern must be independently testable. We do not just explain away data, but come up with theories to explain when we will see one pattern and when another.

Then Hunter has his most revealing paragraph, which is worth quoting in full:

Finally, the idea that pseudogenes arose and were passed on does not require evolution. Yes, the pseudogenes of species have been inherited from their ancestors, but this does not mean that we must resort to the unlikely story of evolution to explain them.

I cannot make sense of this. The middle sentence is an open admission that pseudogenes have been inherited from their ancestors, but the sentences before and after this say that this does not require evolution. Isn’t that what evolution is? If two organisms both inherited a gene from an ancestor, doesn’t mean that common descent is true? The only sense I can make of this paragraph, is that he argues this isn’t evidence for natural selection as the cause. No one claims this is evidence for selection. There are two questions: are organisms related by common descent, and was selection the mechanism that caused changes? Much of the evidence for evolution is evidence for the former, including the common position of pseudogenes. Also, notice how he adds the word “unlikely” to describe evolution, as if its unlikelihood has already been established.

He then describes the gene to make vitamin C, and how it is inactivated in exactly the same way in all primates, implying inactivation in a common ancestor. Why would a gene that doesn’t work be designed into similar species in the same way, evolutionists say. How does Hunter respond? “the similarity of the pseudogene among primates proves little. There are multitudes of similarities between the primates that evolutionists could use as evidence.” How is that even an answer? In the previous paragraph, he admitted that pseudogenes have been inherited from common ancestors, and here he admits the same psuedogene is found in many primates for no functional reason. This proves little? He admits this shows common ancestry, and it proves a lot to anyone not blinded by ideology. He is correct that there are many similarities between primates that we could point to as evidence, and most of them are evidence. Especially striking are similarities in detail that have no functional reason to be similar, and that follow a nested pattern of similarity. What more could Hunter possibly want? In this section, Hunter has made as strong of a case for common descent as I could have. Furthermore, it is clearly evidence for common descent, not just evidence against design, although he claims that is the case.

Hunter discusses the universal genetic code as evidence for evolution, and he does what is by now a predictable moving of the goal posts. Whenever possible, he changes the discussion to the origin of life. He discusses the complexity of the genetic code and how it could have arisen, rather than whether it is evidence for common ancestry.

Hunter’s attempt to deal with the nested hierarchical patterns produced by evolution also fails. First, he claims it is not evidence for evolution because evolution could produce other patterns as well. This is outright false. Evolution will always produce a nested pattern. We see this in other things that share ancestry by common descent, like languages or chain letters. He then again quotes scientists such as Darwin saying that if things were independently created, there would be no explanation for these patterns. Hunter finds this offensive, because it is possible that God could have done it that way. The problem is with his understanding of the word “explanation”. For most people, explaining something means understanding one thing in reference to something else, understanding a cause, understanding why it is this way rather than another way. In that sense, creationists have no explanation. However, for creationists such as Hunter “it’s that way just because it is” is an explanation. Godditit is an explanation.

Discussing the fossil evidence, first Hunter makes the absurd claim that fossils are not evidence for evolution, but just evidence against creation. Evolution clearly predicts intermediates, regardless of whether creation is offered as an alternative explanation. He then tries to cast doubt on the fossil record by saying:

When similar forms are arranged, there are always ambiguities. In some cases, there are too many species, leaving evoluionists with a multitude of possible lineages and the need for explanatory devidecs such as convergent evolution. Some species may overlap in time and show no sign of merging one into the other. Or there may be unique and advance forms appearing too early

This is so confused I don’t know where to begin. I don’t know what “too many species” means. He seems to be complaining that in some cases the fossil record is so complete that we are not certain of all of the branching relationships. How does that call into question the evidence? He dismisses convergent evolution as an “explanatory device” which is what he does with every kind of evidence. He still sees any explanation we have for deviations from a single pattern as an ad hoc excuse, made to rescue the theory. Convergent evolution is an objective, testable explanation for patterns. If Hunter had ever studied cladistic analysis he would know this. Similar species overlap in time all the time, including today. That is not a problem, and why he thinks they should be merging I have no idea. “Advanced” forms can appear before some more primitive forms that are on another branch. Evolution is a bush, not a ladder. There are no examples of advanced forms appearing before the necessary precursor forms, such as a rabbit in the Cambrian period. That would disprove evolution.

What is most striking in reading Hunter's discussion of the evidence for evolution is how he often nicely represents the evidence for evolution. Even with his misrepresentations, he makes a decent case. His attempts to dismiss it are less convincing. He is just uncomfortable with the complexity of a theory. His main complaint is that evolution doesn't produce one and only one result. Evolution has an annoying habit of explaining both the main patterns we see in life, as well as all of the nasty exceptions. The fact that his theory does the same, or any possible successful theory must do the same, is lost on him.

Darwin's proof, Chapter 6, part 1

After a long delay, I am ready to review chapter 6 of Darwin's Proof, by Cornelius G Hunter. You will find the reviews of earlier chapters in other recent posts. I think chapter 6 is getting into the meat of the book. Previous chapters have been routine criticisms of evolution. In this chapter, Hunter gets into his main philosophical argument. I believe this is the argument for which he is best known--I understand it was the main focus of his earlier book. Again this argument is not unique, but he makes it in perhaps a slightly different way than other creationists.

What is Hunter's key argument? He argues that evolution is a religion, just like creationism. More specifically, he claims that the evidence for evolution depends on theological assumptions and would not be valid without these. Unfortunately for Hunter, when you look at the implications of his argument, it only shows why intelligent design fails as science.

To understand Hunter's argument, we need to take one of the categories of evidence for evolution. Let's take the existence of vestigial organs. He does the exact same analysis with every kind of evidence for evolution, so we can use this as an example. First, he claims that it is not really evidence for evolution itself. Evolution would not necessarily predict this. Usually he is wrong about this, as I will show. He argues that it is only evidence if it contrasted with some version of creationism. So he says that the only way vestigial organs are evidence for evolution is if you argue that God would not produce useless structures. It's not that vestigial organs are direct evidence for evolution, rather vestigial organs are evidence against creation. At this point, he usually quotes a few biologists saying that this item (vestigial organs, etc.) could not possibly have been created by God. His final point is that this argument depends on theological assumptions about God. It assumes one particular kind of God. Who is to say that God wouldn't produce useless structures? Evolutionary biologists are assuming a particular kind of God, such as a God like a human designer, and vestigial organs are only evidence for evolution if you assume the existence of that particular God. Thus, vestigial organs are only evidence for evolution within some theological frameworks and depends on religious assumptions.

Unfortunately, his argument fails at every level. All of the kinds of evidence he discusses are in fact predicted or explained by evolution, and would be evidence for evolution even without consideration of creationism as an alternative. Common arrangement of pseudogenes are clear evidence for common descent, by themselves. The biogeographic patterns of organims make most sence and are explained by common places of origins of groups of species. The nested pattern of similarities of organisms are exactly what is expected from evolution, and Darwin was the first person to explain why this pattern would exist. The same is true of all of the other kinds of evidence. For all of these, Hunter claims that they are not directly predicted by evolution, but only work as evidence against creationism.

The easiest way to see that this is not so is to consider what we would think if no one had ever thought of creationism as an explanation for species. If Hunter is correct, the evidence for evolution is only evidence against creationism, not evidence for evolution. In that case, if there was a world where no one had ever considered the possibility that God created species, none of this evidence would be convincing. There isn't a single category of evidence that wouldn't be convincing in such a world. Both Humans and Chimpanzees lack the gene to make vitamin C, and is inactivated with exactly the same mutation in both species. This can be explained by a single mutation being inherited by both species, without any reference to God.

In fact, there is such an example of common descent without comparison to theological arguments. The languages of the world are related by common descent. How do we know this? Languages form nested patterns of similarity. Languages have vestigial spellings and odd meanings and words. Languages show geographic patterns similar to organisms. Languages have old manuscripts that show a pattern of progressive change. All of these are evidence that languages evolved from a common ancestor, without having to bring in any theological assumptions. These are the same kinds of evidence used to show evolution of life.

Of course, Hunter can find many quotes of scientists saying that God would not have made vestigial structures or nested patterns, etc. That's because they are arguing against creationism. Like it or not, creationism is a commonly held belief out there, so it is common to show how evolution explains things better than creationism. Hunter objects to the fact that these scientists bring up God when they do this. How exactly can you argue against a religious claim without bringing up religion?

That is the essence of Hunters argument. When scientists argue against religious arguments, they use religious assumptions, therefore evolution is religion. He never explains how we could possibly argue against ID or creationism without ever actually mentioning the designer or God at the heart of the theory.

However, Hunter is correct in one key point: whenver anyone argues against creationism, you have to make some theological assumptions. If I argue that there is no logical reason for God to put the exact same mutation in both Humans and Chimps, I am making assumptions about what God would and would not do. If I say that the vertebrate eye seems to be poorly designed and God would not make such an eye, I am assuming that God would want to make well designed things. Hunter repeatedly points out that this might not be the case. God could have made things this way for his own inscrutible reasons. He never actually offers a single explanation for why God would have done it this way. Over and over he says that God could have had reasons to do it some other way or that God need not be like we think he is. Every time he says this, I expect to be given some alternative explanation for God's motives, but it never arrives. All we get is the point that we are making at least some assumptions about God. And Hunter is completely correct about this.

Somehow, Hunter seems to think this is a victory for ID. However, it actually shows the complete vacuity of ID. He is right. God could do anything he wanted for any reason he wanted. God need not be logical. God need not actually want a well-designed world. God could have reasons completely beyond our understanding. So God could do anything. In making this argument, Hunter is showing that ID is completely untestable and makes absolutely no predictions. There is no observation that could not be explained by ID.

ID need not be this way. If it had the guts to say something specific about the designer, it would be testable. If we could say that God designs things to be optimal in function, we could test it. We could see if in fact structures are optimal or suboptimal, and thus possible disprove ID. If we could say that the designer would not only make things that have a function, we could see if there are in fact non functional structures. Scientists, generously trying to treat ID like an actual theory, do just this. They say, "if God designed like X, then we should see Y. We don't see Y, so God did not design like X." An ID proponent such as Hunter considers this to be silly. Any statement more specific than "God designs" is unacceptable. Thus, ID is not science.

However, proponents of ID aren't consistent in letting God get away with anything. They are constantly pointing out that some structure--a flagellum, an eye, etc.--is very well designed, by human standards. They are then making assumptions about God. They are treating God like a human designer. They say "the eye is well designed, according to human criteria, so there must have been a desinger". They make theological assumptions about what God would and would not design in this case. Yet if a scientist then tries to use those same assumptions, we are making unjustified intrustions into theology. You can't have it both ways. If we accept Hunter's unwillingness to make any theological assumptions about design at all, then we can not make any positive case for design either.

That is the core argument of this chapter of the book: Scientists treat ID like a falsifiable theory, but doing so reuqires some theological assumptions, so evolution is a religion. That is circular and points out the deepest flaw in ID. The argument also depends on the claim that all evidence for evolution is actually just arguments against design. The irony of the latter argument should not be missed: ID consists almost entirely of negative arguments against evolution, with no positive case at all. Yet Hunter is claiming that evolution consists only of negative arguments against ID. Perhaps he sees it that way because that is the mind set ID proponents always take. His case in this regard is especially weak and consists of a lot of handwaving.

I considered Hunter's main argument in this post. In my next post, I will dissect some specific claims in this chapter.

Darwin's proof, chapter 5, part II

I am continuing my review of chapter 5 of CG Hunter's Darwin's Proof. The mistakes are very dense in this part, so discussing only six pages of his book will require a lot of ink.

Hunter next deals with the evidence from genomic comparisons. He first tries his hand at the fact that humans and chimpanzees have 98.7% of our DNA in common. First, he says that this difference is too small to account for the difference between humans and chimps. Of course it can account for it. That has nothing to do with evolution. However humans and chimps differ, it is encoded in our DNA. However much our DNA differs, whether it is 99% or 50%, that accounts for how we differ, for creationists as well as evolutionists. Hunter seems to be denying that DNA actually determines the characteristics of humans and chimps. What does he suggest does account for our differences, if not our DNA? He points out that humans and mice have almost nearly 98% of our genes in common, just like humans and chimps, but here he is subtly switching comparisons. With the human mouse comparison he is simply comparing how many of our genes have an ortholog in mice. He is not comparing how similar those genes are, which is what is being compared in humans and chimps. When we do that comparison, mice and humans are 91.3% similar.

He then points out that evolution doesn't predict 98.7% similarity. Of course it doesn't. He is right that it could be 99% or it could be 80%. No one claimed evolution predicted that number a priori. The number isn't evidence for evolution. The significance of the number is that a relatively small difference in DNA can account for dramatic differences in the organisms; it was never given as evidence for evolution directly. The evidence is found in the pattern of similarities when we compare the DNA of many organisms, and their correlation with other characteristics. The high number just reminds us that we are not as unique as we think--in fact it is similar to the difference between a horse and a donkey (99%).

Next Hunter tackles what I think is wonderful evidence for evolution, the fact that coding regions are more similar between species than noncoding regions. This happens because the noncoding regions are unconstrained and selection will not remove mutations, but most mutations in coding regions are removed by selection. How does he address this? He points out that it can be explained by evolution only if the noncoding regions are nonfunctional, so that is an assumption we are making. No, it isn't. It has been tested. Certainly the fact that the third base of a codon is usually redundant is testable. The fact that pseudogenes aren't transcribed is testable. The fact that introns are degraded after excision and dramatic changes in their sequence has no effect is testable.

Then Hunter tries his usual gambit--he says evolution would have no problem if we didn't see that pattern, or any possible pattern. If we saw something different, we would just assume that the region that didn't change must have a function. No we wouldn't. We would assume that, based on evolutionary theory, but would have to find the function. If a conserved region was observed and we could not find a function, it would be unexplained by evolution. As it is, the opposite is true. Every time we find a conserved region, we soon find a function. It is a great way to identify importan cis regulatory elements, for example.

The next topic Hunter addresses are examples of small scale evolution, like the beaks of the finch or the peppered moth. He admits we have seen these, but says that these changes appears to have limits. He says this several times in various ways, but never cites any evidence at all that there are such limits. I would love to find them. In fact, I give students in any of my classes an outomatic A if they can find any evidence for such a limit. Hunter ignores the vast literature comparing the changes in the fossil record with observed changes. This literature has shown that the kinds and rates of changes that we see today are consistent with the changes in the fossil record. Hunter claims that small scale changes do not appear to be able to extrapolate to large changes when in fact the literature shows just the opposite.

Hunter quotes mines Ernst Mayr saying we don't know how genotype changes bring about the changes in phenotype. Mayr was pointing out that we didn't know exactly how genetic changes bring obout phenotypic changes. That is being very well addressed today by the field of evo devo, which is in fact filling in this last gap in our knowledge and showing how specific DNA changes lead to specific phenotypes. But even without these advances, this is at best an argument from ignorance.

Then Hunter moves the goal posts and points out that small scale evolution requires a reproductive apparatus in the first place, so how did that come about, huh?

Hunter's last section is on the origin of life. Yes, he has a section on the origin of life in the chapter on evidence for evolution. When has the origin of life ever been presented as evidence for evolution, rather than a question for evolution? Every biologists knows there is a lot we don't know about the origin of life. It is an unanswered question. No one has ever brought it up as positive evidence for evolution. Hunter already had two chapters on problems with evolution, and it would make more sense to put the origin of life there. In fact, he did. He just felt like bringing it up again here because he really likes the areas where we are less certain and he really likes to get back to ultimate origins as often as he can.

Hunter doesn't even try in these chapters to address several other kinds of evidence, such as development or biogeography. In fact, I have never seen anyone deal with biogeography. Overall, his attack on the positive evidence is very feeble. He mostly grants the evidence, but then declares it unconvincing or ambiguous. Never does he hint at the true depths of evidnece or go into any detail.

Darwin's proof, chapter 5

I am continuing to review Darwin's Proof, by C. G. Hunter. Here, I will review chapter 5, which, like chapter 4, tries to debunk the evidence for evolution. I cannot find a distinction between the material in chapters 4 and 5. It appears the material was separated into two chapters just to keep the chapter size smaller.

To understand Hunter's approach to evidence for evolution perhaps I can use a comparison. The same approach could be used to call into question any science. Let's look at Mendelian genetics. Geneticists claim that their theory predicts certain ratios in the offspring of crosses, such at a 3:1 ratio. However, there are many crosses in which we don't see that. Some crosses produce 2:1 ratios or 9:4 ratios. Sometimes the traits aren't even inherited from the father at all but only the mother. Geneticists will give various explanations for these anomalies, but they have so many excuses and explanations that any ratio at all is consistent with genetics.

That is what Hunter does. He gives a simplistic idea of what evolution should predict, then points out that there are many examples that do not fit this prediction. He admits that biologists have explanations for the exceptions, although he never bothers to tell his readers what they are so they can judge for themselves. He dismisses the explanations as ad hoc excuses and claims that because there are so many exceptions, any possible data will fit with evolution. Not once does he suggest that these explanations are actually tested. He implies that the explanations are accepted by biologists out of desparation, rather than being hotly debated.

I discussed the irony of this before--being able to fit any data describes intelligent design, for which all possible worlds really are consistent with it. Of course, any correct theory will explain what we actually see, but Hunter is wrong that all possible patterns can be explained by evolution, as I will discuss.

The first kind of evidence Hunter discusses in this chapter is the molecular clock. His first error is in thinking that the ticking of a constant clock is evidence for evolution, rather than a tool to determine relationships. The molecular clock was not even observed until a century after Darwin, and many evolutionary biologists have and continue to dispute it's reliability. Of course, Hunter quote mines these disputes to suggest the evidence for evolution is in question. The evidence for evolution is the nested pattern of similarities of DNA, not the fact that the changes occur at a constant rate. All biologists know that the clock isn't constant. He says that the fact that different parts of the genome tick at different rates is a problem for the theory, when it is not. This is one of those areas where we have well tested explanations for differences from his simplistic prediction. He says that a problem with the molecular clock as evidence for evolution is that we must first calibrate the clock with the fossil record. He again is unable to distinguish between molecular evidence for evolution and a clock as a tool to infer the time of speciation.

Hunter relies heavily on some papers criticizing molecular evolution by Christian Schwabe. It wasn't easy to find these papers, since they were published in the 1980s. Such outdated references should immediately cause suspicion. I eventually discovered that Schwabe is a chemist with some very radical views on evolution. He did publish some criticisms of molecular evolution 25 years ago, but all of his criticisms have since been addressed. Quite simply, Schwabe was wrong. Hunter never bothered to find more recent evidence or responses to Schwabe's criticism. Schwabe especially found problems with the evolution of the hormone relaxin, but a recent analysis has resolved the problems (Wilkison, TN, TP Speed, GW Tregear, and RA Bathgate. 2005. Evolution of the relaxin-like peptide family. BMC evol biol 12:5-14).

Hunter acknowledges that we have explanations for the descrepancies from perfect ticking of the clock (although he does not tell his readers what they are), but suggests that these are ad hoc rescues that could be used to explain any patterns, as I discussed above. These explanations are testable and are not accepted until they have been tested. We have evidence for lateral gene transfer, positive selection, etc. He implies that any pattern of molecular similarity would be consistent with evolution, but the truth is that we would have rejected common descent if genes of similar species weren't similar or if most genes did not fit in nested heirarchies.

Nezt, Hunter addresses the nested heirarchical pattern of evolution. This is good, because most creationists fail to even acknowledge this evidence. He says, correctly, that evolutionists say if we didn't find this pattern in nature, evolution would be falsified. He tries to avoid this by claiming that evolution in fact would explain any pattern, not just heirarchical ones. He says this would be true if evolution were very fast or non gradualistic. He pretends that disputes about gradualism within evolution include radical nongradualistic change that could produce non heirarchical patterns. I suppose if evolution were so fast that all evidence of ancestry were obscured, we would not see a heirarchy, or almost any other evidence for evolution. Such a radical theory would not be the theory we have. If organisms evolved that the current theory would be falsified, even if we replaced with a different theory of rapid evolution. Hunter thinks that if we replace one theory with another naturalistic theory, it is cheating. He would only be happy if evidence against evolution causes us to reject all possible naturalistic theories.

The fact is we have seen a heirarchical pattern with non living things that evolve by common descent, even with fairly rapid change. This includes the evolution of languages, chain letters, and Biblical manuscripts. The only way that Hunter can pretend evolution will predict a non heirarchical pattern is by basically inventing a new theory. Perhaps he can at least admit that even a moderately gradual theory of evolution will predict only a heirarchical pattern.

Hunter thinks that highly conserved proteins, which evolve very slowly, are a problem for evolution, because they could not have arisen in the first place (since they evolve slowly). It never occurs to him that proteins can evolve rapidly at first, but once they get a critical function they evolve much more slowly. In fact, we know of such proteins.

He also tries to attack the strong correlation between mophological phylogenies and molecular phylogenies--the fact that we get the same tree using both methods. He acknowledges this would be good evidence if it can be shown that there is no functional reason for them to be similar--if for example the hemoglobin of a frog can substitute for the hemoglobin of a mammal. He then makes an argument from ignorance, saying we do not know if this is the case or not. In fact, there is a vast amount of evidence showing that many molecular changes are neutral and proteins are interchangeable. This is even true of the coding part of proteins, but it is more obviously true in the various kinds of silent DNA--introns, psuedogenes, etc. There is no functional reason the difference between these should correlate with the difference between anatomical traits.

Nelson next mines the literature for a few instances when DNA trees don't correlate with morphological trees. Yes, we know that both kinds of trees have uncertainty and they won't have a perfect match. Very often when they don't match, we understand why--some of his exmaples involve lateral gene transfer or phylogenies that separated nearly a billion years ago and will have long branch attraction. He must at least admit that these problematic trees are exceptions for a rule of strong correlation. Again, he admits that there are explanations for the mismatches, and then implies that these are ad hoc excuses.

There is more in this chapter, but I have gone on long enough. I will finish in another post.

Power question 4: where did the dinosaurs come from?

Wow, question four was anticlimactic (these are AIGs "4 power questions for an evolutionist" I have been reviewing them in the previous few posts). Riddle tells us that he sees a lot about dinosaurs and what they were, but nothing about where they came from. Did he bother to do the most basic research, or just see if it was presented to him when he watched a documentary? The origins of the dinosaurs is no mystery. We know the earliest dinosaurs were creatures like Compsagnathus. These evolved from a group of primitive archasaurs, which evolved from early diapsids. Question answered. There are many books out there that can list specific species and show cladograms of the appearance of dinosaurian traits.

Basically, this question is exactly the same as his previous question, where is the fossil evidence? He says we should have thousands of millions of transitions, which is the same thing he said before, exagerating the completeness of the fossil record. This really isn't a new question at all, just more specific and easier to answer.

Riddle again does a typical quote mine. He quotes several biologists as saying things like the origin of dinosaurs has been debated for decades, etc. Without even looking up the quotes, I can tell that these quotes are just introductory remarks to a detailed discussion of the evidence. The fact that there is some disagreement about exactly which species might be ancestral does not mean there is no evidence for the origin of dinoaurs.

Of course, another answer to this is, so what? If not the dinosaurs, he could find some other group that we are rather uncertain of their ancestry (the turtles come to mind). We will probabliy never have a complete ancestry of every group that has lived. Science doesn't have every answer, which is the basic idea Riddle doesn't seem to get. This question isn't even addressing the evidence for evolution, except indirectly on the issue of fossil intermediates. He again makes no attempt to engage in a discussion of the intermediates in dinosaur evolution or any other group.

Riddle's basic approach throughout his presentation is to point out places where there might be some uncertainty in science and say since they don't have every t crossed, evolution is false. He then says that creationists do have the answers, we know how and when and where things were created--basically God did it. He really does consider that an answer. When it comes to the question of how, he says the Bible tells us--God said it, and it was. That is how. He considers that a complete answer, but is bothered by the incompleteness of the scientific answer. The answer to all four of his questions is the same three words, God did it. Somehow, he doesn't see that this isn't an explanation at all and is simply an argument from ignorance. No attempt is made at all to actually engage or explain the patterns we see. God could have created any pattern for life. The fact that we see these patterns is just because.

Riddle does finish with the inevitable story of his being born again. It seems that every creationist was once an evolutionists before they saw the light. After carefully looking at the evidence, they were convinced by creation (it was an objective look, uncolored by their religious beliefs). And he sees the Bible as all or nothing: if you can't trust the first chapter of the Bible you can't trust any of it (and by trust he means read it litteraly).

I was disappointed by this video. It's not like I expected something new, but I thought if you were to condense it down to the four best questions, there should be something better than a few arguments from ignorance and outright denial of the fossil record.

Power question 3: the fossil record

I have come to Mark Riddle's third "power question" for evolutionists (for the first two see here and here). The third question is the fossil record. Unfortunately, this one is not stated as an actual direct question, other than something like "Where is the fossil evidence?". Answering that question isn't a problem at all, of course, but the question is so vague and the whole presentation so lacking in content that it is not at all clear what evidence is sought.

Riddle's approach here is the standard creationists arguments and uncreative. Mostly he says we should find millions of transitional fossils but we find none. To do this he has to first misrepresent what we should see, and then misrepresent what we do see.

He uses the standard argument that we should see every single transition, completely ignoring all studies on the completeness of the fossil record (the incompleteleness is not an assumption, by the way, but a conclusion from observation). No place is this better seen than when he says that we should see everything from a 1 celled creature to two celled to three celled and 10 cell and a hundred cell, etc. Anyone with basic knowledge of fossilization knows that individual cells rarely fossilize. Furthermore, there is no reason to think that multicellular life arose by adding one cell at a time. Single celled creatures have evolved into clumps of a dozen or so cells by simply growing them in culture for a few months. Why do we even need fossils when we can show it can happen in real time?

Riddle claims that the fossil record does not show a pattern of increased complexity, by showing that the Cambrian has a high level of complexity. He completely ignores the pattern of increasing complexity shown in precambrian times, from prokaryotes through simple algae through the Ediacara fauna , the small shelly fauna, trace fossils of increasingly complex burrows, and only then the blossoming of life in the mid Cambrian.

Riddle repeatedly declares there are no transitions but doesn't address a single claimed transition. The one and only time he deals with specifics is the following: "What about a whale with hind legs? These are four inch growths on a 70 foot whale. That's not a leg, that's a pimple." He believes that is an argument. No Mark, it is a leg, with a femur and radius and ulna. And there are transitions with longer legs that have the ankle characteristic of ungulates, and with intermediate blowholes and almost every stage. There are dozens of transitions just in the whale lineage alone.

Basically Riddle claims there should be millions of transitions by expecting a perfect fossil record. In fact, we have tens of thousands at least. He simply ignores them. There is absolutely no content to his presentation, no attempt to explain the transitions we have. He doesn't even do the usual creationist misrepresentation of what a transition should look like. He just says there are none. This is one of those common creationists refrains that is simply repeated over and over, hoping that repition will make it true. Donald Prothero's new book, Evolution, what the fossils say and why it matters, is a beautiful refutation of this claim.

Eventually he says that evolutionists claim maybe a half a dozen transitions (even these he doesn't explain). He says not to let them go off on Archeopterix, but stick to the foundation. The foundation apparently is the lack of transitions. So what he is saying is don't let them distract you with discussions of specific transitional fossils, ask where are the transitional fossils.

Needless to say, Riddle offers no positive explanation for the fossil record and patterns within it at all.

This section is by far the worst in the video so far. The other two questions at least identified topics of relative scientific ignorance. This question is amazingly lacking in content. It is argument by bald assertion. If a creationists were to approach an evolutionist with this question, he or she would be buried if the evolutionist has even a basic knowledge of the fossil record.

Power question 2: where did life come from

In a recent post, I addressed a video from AIG on "the four power questions to ask an evolutionist". I discussed the first one, "where did the matter of the big bang come from?", in that post. Today I will address the second power question: Where did life come from?

The basic answer I gave to the previous question applies here as well. I think the best answer is: we are not sure. I have seen some people object to this because it implies a greater level of ignorance than we have. It is true, we know a lot more about the origin of life now than 50 years ago. Maybe some people would think I am saying we don't have any idea. But it is also true that there is no consensus theory for the origin of life.

I like to imagine a student coming up, all ready to be combative and asking "where did the matter for the big bang come from?", the professor says "we aren't sure", and the student realizes that his question doesn't matter. The advantage of saying we don't know the answer to questions like this is that it makes clear that the student is making an argument from ignorance, and it also makes clear that they are simply replacing the phrase "we don't know" with God. It is important that people realize science doesn't explain everything. There are things we don't know. A theory isn't rejected because it can't explain every last point. Evolution explain what happened to life once it formed, not how it formed. Even if we were 100% ignorant of the origin of life (which we aren't), that is not an argument against the stuff we do know. Even if we don't know where the matter came from, it doesn't mean the big bang didn't happen. It is a thought that probably hasn't occured to many creationists.

Even though that is the easiest answer, I will discuss other points brought up in the video. Several times the speaker (Mike Riddle) makes the inevitable confusion about chance. He says that the scientific theory for the origin of life is: time + chance = life, which is of course completely absurd. He brings out the usual calculations of the chances of getting a protein by chance and shows it is impossible and includes a quote mine from a scientist saying "the simplest cell couldn't have arisen by chance". The fact that we don't think it happened by chance, and that is the scientists point, is ignored. After he says that time + chance = life, he asks sarcastically "doesn't that make you feel good? Doesn't it make you feel special?" He is using how special a theory makes you feel as a criterion to evaluate it.

Riddle makes a basic mistake in chemistry. He says that matter is made up of atoms, atoms combine to make molecules, molecules combine to make amino acids, and amino acids combine to make proteins. Funny, I thought an amino acid is a molecule. What molecules combine to make an amino acid?

He then discusses the Urey-Miller experiment, as creationists always do, with the usual problems. First, he suggests that Miller left oxygen out of his mixture because he knew oxygen harms life. Miller left oxygen out because the best evidence at the time suggested it wasn't present, not to get a predetermined result. Riddle points out that there is now evidence there might have been more oxygen, and says that the evidence is ignored by scientists. Anyone who would make that claim simply doesn't know how science or scientists works. Riddle acts as if Miller's was the only experiment or only atmosphere that was tried, when in fact many other atmospheres have been shown to work.

There is no indication that there are other possible ways for the building blocks to arise, including in space. There is no indication that even if the atmosphere was oxidizing, there could be microenvironments that were reducing, such as deep sea vents. In the video, Riddle is trying to argue that there is no possible natural explanation for the origin of life. Even if he completely disproved everything about the Miller experiment, he would not have shown that all explanations fail.

He then lies. That's the only way to describe this misrepresentation. He says that oxygen is harmful for the origin of life. But oxygen is needed to make ozone, and without ozone we would be "fried", so not having oxygen is bad for life too. Since both having and not having oxygen is bad for life, it must have been created. I wonder if he has any idea what the real effect of not having ozone is. Life wouldnt' be "fried". Rather, we would have more UV radiation and more mutations for organisms exposed to the UV. What he seems to fail to understand is that water also filters out UV radiation. Ozone protects organisms on land from UV light. For organisms in the ocean, it is irrelevant.

Finally he points out that all life has left handed amino acids, but the Miller experiment produces a mixture of right and left handed amino acids. He considers this an insurmountable problem. It's simple. Living things used one kind of amino acid from the primordial soup but not the other (we don't know why). The right handed amino acids formed, but just weren't used by the first cells. Is it necessary that every organic molecule in the primitive ocean be utilized by life? Cyanide was made in the Miller experiment, but it isn't used by living things. Does that disprove the validity of the experiment.

The strangest part of this discussion was when Riddle pointed out that when we die, our amino acids revert to a mixture of right handed and left handed amino acids. He seemed to find this very significant, but I am not sure why. To me, what that means is that even now we are surrounded by right and left handed amino acids in the environment, just as the first cells were. If we can have right handed amino acids in our environment now but maintain all left handed in cells, why couldn't they? I got the impression that he thinks it requires an act of God or miracle to maintain living amino acids in the left handed form even today, not just at some creation point in the past. In other words, he is invoking God not just for creation, but for the every day miracle of having left handed amino acids. Maybe he had another point to make, but I cannot see it.

The first two power questions are simply arguments from ignorance. The boil down to: evolution, or the big bang, can't explain absolutely everything, therefore it's wrong. If we don't know, then God must have done it. Since God started those things, he did everything else too.

When we argue with creationists, we should agree beforehand to just discuss the evolution of vertebrates, or some other narrow, well documented topic. In the end, that's all they care about. In fact, we could just look at human evolution. If I were to say the universe was created by God, life was created by God, God did the Cambrian explosion, but evolution produced humans, they would object. So why are we arguing over these other things? I suggested this to Pastor Eckstein. We will restrict our discussion to the evolution of vertebrates. If one of us can convince the other about that topic, then we can worry about the Cambrian explosion or the origin of life. This prevents the constant moving of the goalposts and arguments from ignorance that creationists love.

Attack of the killer storks

I think I just read the coolest science news of the year. In random samples in this week's Science they describe the discovery of killer storks on the island of Flores in Indonesia. Flores is the island on which the "hobbit" was found--three foot tall dwarf hominids, possibly related to Homo erectus, that went extinct just 13,000 years ago. Now they have discovered 6 foot tall carnivorous storks on the same island. We don't know if the storks ate the humans.

What could be more cool than giant flesh eating storks? Once you have that discovery on your resume, how can you top it? The only thing I can think of comparable is a town being terrorized by giant killer bunny rabbits in the 1972 movie Night of the Lepus. (I remember seeing that movie on the CBS late movie as a kid. The CBS late movie was great--every night, in what is now the David Letterman time slot, they would show low budget movies, typical drive-in fair. I saw more great cheesy movies that way than any time since).

Which scares a creationist more, evolution or theism?

I have been looking over the material an angry parent sent me from AIG, and I have realized something that I haven't always emphasized or seen before. I realized that AIG and YECs in general are much more interested in attacking theistic evolution than attacking evolution. I always knew they didn't like theistic evolution, but I failed to see how that is more important than evolution itself.

One of the pamphlets I have is titled "6 days or millions of years?". Being a scientist, I assumed it would contain the various creationists attacks on the evidence for an old earth. At no place in the 48 page booklet does it address any evidence for an old earth at all. In fact, the only place where evidence is even brought up is the following sentence on page 16: "The age of the earths, as determined by man's fallible methods, is based on unproven assumptions so it is not proven that the earth is billions of years old." That is the only place science is even mentioned in an indirect way.

So what is the rest of the pamphlet? It is a diatribite against a non literal reading of the Bible. It discusses whether the days are literal days or metaphorical days, whethere there are two creation stories or one, whether an old earth and the fall of man can be reconciled, etc. The enemy is clearly not the evidence for an old earth, it is those Christians that read the Bible differently than them.

I think they know that is the real danger to their viewpoint. Most creationists aren't going to be easily swayed to evolution if they must reject God first. But many will happily embrace evolution if they dont' think their immortal souls are on the line. One of the main purposes of an organization like AIG is to convince Christians that any interpretation that includes evolution will damn them to hell. Theycan ignore actual evidence, because if the can convince people that the Bible can't be read any other way, most of their followers will not even look at the evidence.

The other pamphlets are similarly lacking in science, heavy on damning liberal Christians. Pastor Eckstein's recent article in the Jamestown Sun, which I discussed this past summer, was two thirds Biblical exegesis and why other interpretations of the Bible are wrong. I found that part insulting, because he was basically using a newspaper editorial to argue a theological point and condemn many religions. That clearly is the most important point for him and most creationists. The evidence is simply the result of "fallible man" and is mostly irrelevant.