Darwin's Proof, part 2

This is the third in my posts dissecting Darwin's Proof by Cornelius G. Hunter. Chapter 3 is titled Swallowing a Camel: the fundamental argument against evolution, part 2. The title differs from chapter 2 in only one word, and the content is the same. I am not sure why this material was put in a separate, short chapter. The argument is the same and even the examples are basically the same. In chapter 2, Hunter described the complexity of cellular processes with an emphasis on how proteins are made--transcription, translation, and gene regulation. I guess here he shows how complicated those proteins are. He actually did that in chapter 2, since transcription, translation, and gene regulation depend on proteins.

First he discusses enzymes and how much faster they make reactions go and how specific they are. That is his argument. He points out that proteases differ in specificity, as if this is a mystery. Different proteases have differences in typically one or two amino acids at the active site to change their specificity, there is no problem for evolution there.

He says that enzymes are yet another mystery to solve when in fact this is one of the easiest of all to explain. We have evolved enzymes in vitro using nothing but mutation and selection. Some of the best examples are ribozymes that have been selected to catalyze various reactions. We can also make antibodies that act as enzymes by creating antibodies against transition states. Antibodies arise completely by chance. We have seen frameshift mutations give rise to new enzymes (nylonase) and random open reading frames in noncoding RNA give rise to functional proteins.

He then shifts the goal posts from how an enzyme could evolve to how it could fit into a pathway, implying that there is no way to add on to an existing pathway. We have numerous examples of adding reactions to existing pathways, such as the C4 photosynthetic pathway which utilizes already existing enzymes in a new path. He says an enzyme can only evolve if there is a need for it, which isn't quite right. A new enzyme can arise by chance, for example by gene duplication, and it just happens to be useful and evolves new functions. The origination is not based on need, and its success is better described as based on usefulness, not need.

He is aware of gene families but avoids that by asking how the first enzyme in the gene family arose. He seems to think the first member had to arise all at once. Hunter seems unable to think in terms of gradual improvements and changes in functions. Many gene families are part of even larger gene families. I already discussed how frameshifts and random ORFs can give rise to new proteins.

Hunter discusses other things, such as enzyme pathways, ion channels, and hemoglobin in the same way. He simply describes how specific or fast or complex they are, and feels he has made the fundamental argument against evolution. He discusses allosteric regulation of enzymes but seems incapable of thinking that the enzymes and pathways would still have functioned, though less efficiently, without the allosteric regulation. We have seen the evolution of regulation of enzyme activity in bacterial populations in the lab. He discusses the cooperative regulation of hemoglobin (indirectly) and fails to mention there are members of the hemoglobin family, such as myoglobin, that lack cooperativity.

When an explanation is available, he demands "detailed and specific accounts". It is clear that no matter how much detail is shown, it won't be detailed enough unless every single step is recreated. Since we have evolved enzymes in the lab, it seems even that has been supplied, but he still isn't convinced (or is unaware of these experiments).

He then says that aside from vague hypothesis that have more speculation than hard fact, evolutionists have no idea how such machines could come about by unguided forces of nature. In one sentence he dismisses tens of thousands of papers. The evolution of the hemoglobin family alone has thousands of papers. We have detailed accounts of the evolution of hormone receptors, of the Krebs cycle, of blood clotting cascades, etc. His dismissal is amazing.

At one point, he says that nothing, from clothing to cars, self assemble, even though in the previous chapter he had explain how protein, in fact, self assemble, as do many other cellular structures.

I should point out that all of his examples are at the biochemical level and had mostly evolved by 2.5 billion years ago. It is more difficult to determine the origin of these things. Most of the evidence for evolution doesn't work with biochemistry--we can't use biogeography, comparative anatomy, fossils, comparative development, etc. We basically just have comparative biochemistry and artificial selection experiments. Even with only these tools, we have a decent answer for how many enzymes arose, considering the evolution happened billions of years ago. In some ways, his argument is like the standard creationists confusion of the origin of life with evolution of life. In this case, it is the origin of the first cell with the evolution of life. Even if we granted him absolutely everything, the most he has is that a bacterial cell is hard to explain by evolution (and he fails at that). We still have the overwhelming evidence that the first cell gave rise to all of the other life on earth.

This chapter has almost no arguments, just a description of complexity and dismissal of the evidence. It is in the final page that Hunter gets rather bizarre again. He says that Darwin had no decent explanation for how evolution created complexity, so he shifted the burden of proof and simply argued that there is no evidence against evolution, therefore we must accept it. The irony is hard to take: he claims that evolution is based entirely on negative arguments and arguments from ignorance, even though his entire case is negative arguments and arguments from ignorance.

First, Darwin never really discussed "complexity" as such, but he did discuss complex structures, which I assume is what Hunter means. Has he ever read Origin of Species? Every page is loaded with observations that support evolution. Darwin never makes an argument from ignorance but instead supports his case with meticulous detail. The closest Hunter can come is when Darwin said that if a structure could be found that could not arise by small steps, his theory would break down. He uses one quote, in which Darwin showed how his theory could be falsified, to claim that all Darwin did is say, if you can't disprove it, it must be true. Darwin did much more than make that claim. He provided massive positive evidence that in fact organs had evolved.

Hunter then claims there is abundant negative evidence against evolution, although he has not shown us any. Instead he says that our fundamental understanding of the world inform us that spontaneous evolution is unlikely. Since when? That is what we are trying to determine. Hunter uses spontaneous and "on its own" repeatedly in these chapters to describe evolution, when in fact no one claims structures arise spontaneously or on its own.

Hunter repeatedly states there is no empirical evidence for evolution and says that evolution is accepted as a default explanation because it is naturalistic and cannot be disproven. The ease with which he dismisses hundreds of thousands of studies supporting evolution or the massive accumulation of evidence in the Origin of Species is amazing. This is especially so since he does not engage the scientific literature at all. He has absolutely no references or citations for these two chapters other than the few places he takes direct quotes, from textbooks. If Hunter is going to dismiss a hundred years of research, he should at least show he has read more than an introductory genetics textbook.

So the "fundamental argument against evolution" is that cells are complex. That is these two chapters in a nutshell. It is simply Micheal Behe's thesis in Darwin's Black Box. Since Cornelius G. Hunter cannot imagine how this complexity arose by evolution, it did not. All studies explaining evolution are dismissed as speculation. One suspect that anything short of evolving a cell in a test tube would be dismissed. Hunter seems unable to use inference from pieces of evidence to a larger picture.

Review of Darwin's Proof, part 1

I am reading Darwin’s Proof: the triumph of religion over science, by Cornelius G. Hunter, a book promoting intelligent design. It was recommended by a local pastor to discuss, and I thought it would be fun to dissect it. I will be posting a series of reviews here. They will be detailed chapter by chapter reviews, partly because I sometimes just like dissecting arguments in great detail, but also because I can then use these posts as working notes if I ever discuss the book with pastor Eckstein.

The first chapter is mostly just an overview of the book and a summary of what Hunter believes he proved in his previous book. Since I don’t have the other book (Darwin’s God), I cannot say anything about his claims. The one sentence I would take to task from this chapter is “evolution is considered to be a fact because Darwinists believe they have disproved the alternative: divine creation.” This is simply false. First, there are other alternative besides divine creations, such as Lamarckian evolution, orthogenesis, and mutationists theories. Second, evolution is supported by a wide variety of positive evidence in support, not just by negative evidence against creation. Since creationists argue almost entirely by negative attacks, this might be hard for them to understand. I would be willing to make a prediction already at this point: the book will be completely lacking in positive evidence for creation.

Chapter 2 is titled Swallowing a Camel, the fundamental argument against evolution, part 1. It was a disappointing fundamental argument—simply the standard creationists method of showing how complicated some biological process is, and thinking that is an argument against evolution. It’s the argument from personal incredulity. It doesn’t fail as standard creationist fair, complete with quote mining and arguments from chance.

It starts with the standard comparison of living things with a designed artifact, in this case a space ship. I discussed one aspect of that argument in the previous post. I should also point out that all such arguments boil down to: artifact X is complex and is designed, therefore all other complex things are designed. It doesn’t follow. Design is one way to get complexity, but not the only way.

The rest of the chapter is a Michael Behe style summary of basic molecular biology—DNA to store information, transcription, translation, gene regulation, and protein folding. Most of it is just a summary, with an emphasis on how complicated it is, with very little attempt to actually present an argument. It is assumed that showing it is complicated is sufficient. You might think that Hunter would first present the evolutionary explanation for the origin of this system, and then show what is wrong with it, but he does not present the case at all. And he most certainly does not offer an alternative explanation, other than the implied “God did it.”

I will address some of his specific arguments, misrepresentations, and rhetorical methods. Hunter repeatedly suggests that evolution claims complex structures arise spontaneously rather than by a slow process. I count four uses of “spontaneously” and another of “on their own”. He frequently uses anthropomorphic words to describe processes or molecules, including the following: search rapidly, patiently, stagehands, a reader “looking”. Does he think the molecules themselves have intelligence, or does he accept that they are acting by random collisions? He presumably is arguing that processes arose by intelligence, not that the molecules themselves are intelligent, and it is lazy to conflate the two.

At one point, he argues that “Living things don’t look like they evolved”. It is not at all clear what he thinks things would look like if they evolved, and he does not attempt to explain it. I hope he does not think that what something “looks like” is an argument. I would argue that they don’t look designed but cobbled together by evolution. He says the evolutionary explanation for the eye is “not very convincing”, apparently meaning not convincing to him.

He has a bizarre side track in the discussion of DNA, taking Francis Crick for task for saying “we have discovered the secret of life”. Hunter spends a page arguing that DNA isn’t really the secret of life, as if Crick’s phrase was anything more than a metaphor to emphasize the importance of DNA. This has nothing to do with evolution or design at all.

It is in his discussion of the regulation of DNA expression that Hunter finally attempts to do more than just say “this is complicated”. He claims that evolutionists have little more than speculation to explain how such a system arose, but fails to site any literature or summarize the explanations available. A quick search on “evolution of lac operon” on Google Scholar returned nearly 8,000 hits. Instead, Hunter quotes a genetics textbook that he feels fails to give a detailed description of the evidence or variations that would lead to the evolution of the lac operon. It is a genetics textbook with an aside about evolution and it is not the goal of the text to give a detailed account of the evolution of the process.

He fails to understand the processes by which molecules can evolve. He believes positive control of gene regulation is problematic (such as CAP activation of the lac operon), because instead of just knocking out a gene, we have to have an already existing dormant gene become activated. First, this is simply false. He assumes the system had to be assembled all at once. The genes of the lac operon would not have been dormant without CAP, rather they would have been constitutively on. CAP helps to insure that the genes are not on when glucose is available and is an additional but dispensable layer of regulation. Furthermore, most genes aren’t entirely on or off—they have degrees of activation. Turning a gene “on” now could have originally just been slightly increasing its activity, and over time it became more binary.

Hunter does not consider that genes have multiple or different functions during evolution and they need not always do what they are doing now. A great example of that is in the lac operon that he discusses. The beta galactosidase gene is cobbled together from other genes that originally functioned in glucose metabolism. He criticizes the genetics textbook for suggesting that such a shift in function might have occurred for a regulatory protein as rampant speculation. Even if we do not have direct evidence for it happening in this particular case, there are hundreds of documented examples of proteins changing functions, so it is not rampant speculation to suggest that it happened here.

This brings me to another problem. A critic can always find some system for which we currently do not have a detailed explanation of its evolution. The lack of current explanation does not mean it cannot be explained. Have we identified the pathways by which a similarly complex system arose? Yes, there are many such examples, including the ID poster child, the bacterial flagellum. There is no reason to think that any new molecular pathway is somehow different from these. The lac operon is less complicated than a flagellum. We should try to find a solution, but we do not claim to know the evolutionary origin of everything. Hunter also claims we should be able to construct the detailed step by step process by which a pathway arose, similar to Behe in the Dover trial. We can know that something has evolved because of an accumulation of evidence without knowing absolutely every step in the process.

A creationist book wouldn’t be complete without quoting out of context. Hunter quotes Alberts et al.: “The complexity of a process with so many interacting components has made many biologists despair of ever understanding the pathway by which protein synthesis evolved.” I knew from experience that the next sentence would contain a “however”. I looked it up, and it does. The next sentence is: “The discovery that RNA molecules can act as enzymes, however, has provided a new way of viewing the pathway.” They then summarize the evidence for an RNA world.

The most irrelevant discussion in the chapter is the discussion of protein folding. It doesn’t matter how complicated the process of protein folding is. The process of protein folding is a thermodynamic process, not an evolutionary process. It did not evolve. All that evolves is the primary sequence of proteins. If they happen to fold into a useful shape, they will be selected. The folding process itself does not evolve.

It is in this section that the inevitable misrepresentation of chance occurs: “You would need to search through many billions of sequences to find one that is functional. In other words, finding a sequence of amino acids that provide a useful function is like the proverbial needle in a haystack.” He goes on to show that if evolution started randomly searching when the universe began, it still wouldn’t have found a functional sequence. How many times do we have to do this, how many times will they use the same argument that has been shown to be a misrepresentation of evolution over and over? Evolution isn’t a random search.

The final section is rather bizarre. Hunter says that examples like insecticide or antibiotic resistance seem impressive, but they only occur because a “clever adaptive machine is at work”. In other words, when we do get evolution, it’s because we have an evolution machine! This machine must have been designed. He then strongly seems to endorse a Lamarckian or teleological view that organisms are striving to adapt and that mutations arise because this machine makes them arise. The evidence is overwhelming that mutations are random and not directed, but he implies otherwise. He explicitly and falsely states that mutations are concentrated in areas that produce helpful results, rather than randomly.

It is interesting how he misrepresents an example of evolution. He says that in one case of pesticide resistance of an insect, a gene that has been present all along was made more active. A special signal “was inserted into the gene” to lift production constraints. Notice the way he describes mutation. What really happened was that the DNA sequence was mutated to lift production constraints. His wording implies that something outside of the organism inserted a sequence. He also implies that such changes of gene regulation are contrary to what evolution predicts, rather than being long recognized as the most common way that evolution proceeds.

Getting screwed on the heath

If you were walking on a heath and found a watch, a snowflake, and a sharpened bone, what would you conclude?

The classic argument for design is the analogy between a watch and a living thing. But does it matter if we find a watch, a spaceship, or a bone on the heath? I don't think it does. I will explain, but first some background.

After my letter to the editor was published, Tom Eckstein contacted me by email, as he often does and we had an exchange of emails. Eventually, he suggested I read some intelligent design books he found convincing, as he often does. This time I decided to take him up on it, not because I think I will change his mind, but more for the sport. I thought it might be fun to dissect it in great detail on this blog.

The book I eventually settled on is "Darwin's Proof" by Cornelius G. Hunter. I have read the first few chapters and will give a detailed review of them soon, but before I do I wanted to make a more general observation. He starts chapter 2 with an analogy that would be familiar to anyone who has ever waded into this subject: he compares living things with a complex machine. In this case, he brings up the scenario of people stumbling on a complex alien spaceship, and the absurdity of someone suggesting that it wasn't designed but arose by natural means. This is of course just a variation of William Paley finding a watch on the heath 200 years ago.

My first thought was that we should just settle on one analogy. I have heard it as a watch on the heath, a computer, an alien spaceship, etc. Apparently people keep trying to come up with different analogies to prove their creativity, or that they find more convincing. But does it really matter? They all make the same point and are equally convincing. It's not as if you found a computer you would say it's obviously designed, but if you found a watch, you wouldn't quite be sure. Let's quit pretending they matter and just stick with the venerable watch.

My second thought was "what is a heath?" I've read that example a hundred times and I've never bothered to look up the word. Where we find the watch isn't important of course, but it's time to admit my ignorance. I looked up heath, and it is a wasteland or open barren area. A watch in a forest wouldn't be quite the same thing.

Finally to my main point, which is the failure of the analogy. I haven't seen this aspect addressed much, although the idea goes back to David Hume. I fully agree that any of those objects are obviously designed. The question is what aspect indicates their design? The assumption is that we know they are designed because they are complex, and therefore any other complex thing is designed. The conclusion fails even if the initial premise is true, and that has been discussed often, but I want to point out that the premise doesn't even hold. We do not think the watch is designed because it is complex.

Imagine you found a screw on the heath. This is not nearly as complex as a spaceship, computer, or watch. It's really quite simple, with no interlocking parts. Would you think it was designed or that it arose spontaneously? Obviously, it was designed. Someone who thought it arose naturally would be mocked as much as the person who thought the spaceship arose naturally. We infer design without the complexity. We don't need an imaginary scenario of finding things on heaths. We find old stone arrowheads all of the time. They are very simple, yet we know they are designed.

Or we could find a bone. Now if we just find a regular bone, maybe a vertebrae, we do not think this was obviously designed. This is true even though the bone itself is rather complex. But if we find a simple long bone sharpened into a point, we will conclude it is designed as a weapon.

An analogy is only useful if it accurately picks out points of similarity between two items. In the analogy of a watch with a living thing, it is thought that the element that suggests design in the watch is its complexity, and that is similar to the complexity of life. However, it is clear that the element that suggests design is not complexity. Very simple things like a sharpened bone are obviously designed, and more complex things, such as a snowflake, are not designed. We can infer design because we know something about the designer, humans, and the methods and purposes for which we design. So even before we look at whether the conclusion follows from the premise, we must reject the premise.

The bomardier beetle and me

My first recollection of an encounter with a specific creationist argument was the bombardier beetle, as a sophomore in college.  This beetle has a unique chamber that squirts gasses out at an enemy, and the claim was that this could not possibly arise by evolution.  I do not remember where I read it, but I was intrigued.  Now, I am very familiar with all creationists arguments and I would just roll my eyes at an old one like the bombardier beetle.  It is instructive to remember a time when that was not the case.

At the time, I didn't even recognize this as specifically creationists.  I did not have enough experience to know that all such arguments fail easily on inspection, so I thought there might be something to it.  I tried to do some research on it, in those pre-internet days, but I could find nothing.  I now know that is because it is a non issue in real science and the only place to find references to it would be obscure creationists publications.  The NCSE was just getting started and it would be 10 years before I discovered the Talk Origins archive.

I was unable to find anything about this beetle in my searches, and it remained a mystery for about 5 years, in graduate school.  Again, I am not sure where I stumbled on the answer.  I think it was in an essay by Stephen J Gould.  When I found the answer, I saw that what I thought was a fascinating mystery was in fact just a silly misrepresentation.  I have now come to expect that deflated feeling.  There is never even anything close to really interesting behind the creationist argument.  They are not even wrong in an interesting way.

It was in my first year as a professor that I debunked something on my own for the first time.  I was given a creationist article on the evolution of horses and asked to comment.  I knew that creationists often misquote, and there was a suspicious quote in there.  Fortunately, I found the book in our small library, read the original quote, and had a wonderful "ah-ha" moment when I saw what they had done and had the victory of figuring out an error myself.  I also found other mistakes in the article.

It was about a year later that I first discovered Talk Origins on this new thing called the world wide web.  There I immersed myself in creationists arguments and answers to them, and it was only then that I truly became able to recognize all creationists arguments or variations, so that I can now roll my eyes at once intrigued me.

I guess there are several points in this story.  First, it is good to remember that even educated people are usually not versed in creationism and evolution, and silly arguments can seem convincing.  Second is that it took a long time and practice to recognize the methods of creationists.  If you are only familiar with good scientific scholarship, you might not expect to have to look up every quote.  It takes a different, specific training to recognize the style of creationists arguments.  And third, the internet sure makes life easier.

Response to the letter to the editor

I posted my letter to the editor a week or so ago. Today I got a letter from a local Lutheran pastor (I am amazed at how many Lutheran churches there are in this town). I won't post his name or the letter here, since it was a private correspondence. He thanked me for my letter and wrote about how science shouldn't be a threat to religion.

It's gratifying to hear that, and it makes a few points. The first is that religion is not the enemy. This isn't the first time I've had a minister thank me for my support of science. People who deal with creationism spend so much time seeing the ugly anti science side of a few people that we can forget that most religions are supportive of science. They can help us to spread understanding of science, and we should not antagonize them. The view of science and religion expressed by this minister would be much more likely to make people appreciate science than pure logic.

The second point is that writing letters and doing small things can help. Even if you don't hear anything or think what you did didn't matter, there are at least a few people who appreciate it. At the very least, we can stop the erosion of support for science, and maybe even fight back a little bit. Too many scientists and science supporters are silent. Defend science, respectfully, or we will lose it.

Suprise: creationists trying to have it both ways

I am always amazed at the ability of creationists to hold two contradictory ideas simultaneously. A case in point is how they view the scientific community's attitude towards evolution. On the one hand, they are constantly telling us that more and more scientists are seeing problems with evolution, and make it sound like there is massive criticism of all of the holes in the crumbling edifice of evolutionary theory. On the other hand, they tell us that biology is a monolithic conspiracy that won't accept any dissent and the reason creationists can't publish is because scientists don't accept dissent. Which is it, are we rife with dissent or are we intolerant of dissent?

This came to mind because of a recent conference in Altenberg, Austria on the status of the Darwinian synthesis. This conference was called by a prominent evolutionary biologist, Massimo Pigliucci, and has many other prominent biologists at it. The one thing they all have in common is they think that the evolutionary synthesis needs some modifications or additional theories.

The Panda's Thumb has a summary and critique of a creationists' (Casey Luskin) response to this conference. Luskin claims that this is proof of how weak evolution is and how there are so many scientists critiquing it. As the link shows, Luskin is confusing disagreements about details with disagreements about the whole theory, as is typical of creationists. But what I would like to add is how this completely contradicts creationists' claims that scientists don't accept dissent.

If Luskin's characterization of this conference was correct, and it is a massive attack on evolution, then he can no longer make any claims that the rejection of intelligent design and their failure to publish is because science is close minded and doesn't accept dissent, or that critics risk losing their jobs. If on the other hand he wants to claim that there is a Darwinist conspiracy against ID, then he must admit that the Altenberg conference does not really question evolution, but only details. Choose one or the other, but quite trying to have it both ways.

Disproving the Flintstones

In my recent post on my letter to the editor, I mentioned that I could have discussed specific ways that the creation museum in Kentucky goes against science, and I mentioned that one simple thing to prove is that humans and dinosaurs coexisted. Since I brought up the point again in correspondence with Tom Eckstein, I thought I would expand on it here.

There are two possibilities, either dinosaurs coexisted with humans or they did not. We will test that, but also a slightly broader version as well. Either almost all organisms found in the fossil record coexisted, or organisms only coexisted with organisms found in the same strata.

There is an obvious way to test this. If humans and dinosaurs coexisted, then you might expect to find them buried together occasionally. Human bones and dinosaur bones could at least be in the same strata, even if they aren't actually in contact. We don't find that. But it doesn't have to just be bones. We could find dinosaur footprints near human bones or human footprints near dino bones or footprints. We could find human tools near dinosaurs--arrowheads and other tools are almost always found wherever humans have lived. We might find dinosaur remains in human cities. We might find dinosaur bones in human refuse or evidence that such bones have been scraped with tools or cooked in a fire. You might have pictures of dinosaurs on cave walls. You would expect at least a single instance like these if dinosaurs and humans coexisted.

You could argue that the absence of evidence doesn't mean evidence of absence. Maybe we coexisted, but just by chance there were no examples that fossilized. The likelihood of that depends on the abundance of the record. If we had only 10 dino skeletons it would be more likely than if we have thousands. If we rarely found human tools it would be more convincing than if human tools are very abundant. The fact is that there are tens of thousands of examples of dinosaur skeletons and footprints and the like and an even greater number of human artifacts, but there is not a single example in all of that to suggest we coexisted.

Still, maybe we don't have a large enough sample to rule it out. But we can expand our search. We can ask if dinosaurs coexisted with other hominids, like the Australiopithicenes. Or with other apes, or any other primates, or rodents, or deer, or carnivores, or whales, etc. We do know that humans coexisted with rodents and carnivores and deer. As predicted, we find their bones and footprints and tools together. So if we could show rodents coexisted with dinosaurs and also humans, then we could conclude that maybe humans and dinosaurs coexisted. But there is not a single footprint, bone, or other artifact of these groups of mammals that are found even in the same strata as dinosaurs, leave alone in contact.

And we can go farther. We can look at organisms that lived before dinosaurs, like pelycosaurs and other early reptiles. Not a single instance of them coexisting with dinosaurs is found either. We are now looking at a truly massive record of hundreds of thousands of bones and artifacts, and not a single one suggests coexistence.

Creationists claim that fossils separate based on things like hydrodynamic sorting, ecology, and the ability to escape the floodwaters. That fails miserably with almost any pair of organisms. But lets say it's possible: the reasons deer and dinosaurs are never found together is because for some reason the deer were better able to escape the floodwaters than all species of dinosaurs, or their bodies settled out differently. Then what about the contents of the stomach? We often find dinosaurs with their last meal still in their stomach. The contents are always other organisms that lived at the time, like other dinosaurs. Never a deer or other mammal. Certainly once a deer is in the stomach of a dinosaur, it will not sort differently. And this doesn't just apply to dinosaurs, it applies to mammals and all other organisms. With absolutely not a single exception, the contents in the stomachs of fossils are always species that are found in the same strata. The same is true for the contents of coprolites (fossilized poop). It is absurd to suggest that organisms only eat organisms with the same hydrodynamic sorting tendency.

There is actually even more evidence, like injuries caused by dinosaurs on other dinosaurs, but never by mammals, and adaptations, etc. But by now it is quite clear. If organisms coexisted, you would expect to see evidence for it. The complete absence of any examples of this rules out there coexistence. Notice that I am not being dogmatic. I am offering a falsifiable hypothesis. I am stating explicitly the kind of evidence that would make me throw out my hypothesis. If this is somehow not enough to convince the creationists that dinosaurs didn't coexist with humans, then they need to specify exactly what evidence would convince them.

Often creationists want "proof". They don't understand that's not how science works. Notice there is no piece of evidence that is proof that humans and dinosaurs didn't coexist. Rather there is an accumulation of data. There are thousands of little pieces of evidence, each one increasing the confidence in the hypothesis. And science can only compare two theories. There is not even a single piece of evidence to support their theory, just attempts to explain away the evidence. There is no single proof of the atomic theory either. It was the accumulation of data over many decades, and no single piece proved it. Even in 1905 it wasn't universally accepted, when Einstein explained Brownian motion using the atomic theory to give it what was probably the final piece. Any single piece of line of evidence can be explained away or interpreted in several ways. But when there are ten thousand arrows all pointing the same way, it is absurd to dispute it and the accumulated effect can be called proof.

Save gas by adding water?

There was an article in the July 16th Jamestown Sun about a couple of brothers in Duluth, MN who have come up with a device that is supposed to save gas in your car by adding water. The writer (Jana Peterson of the Duluth Budgeteer News) doesn't offer even a hint of skepticism or scientific knowledge.

Basically, what Jay and Rick Plante have done is come up with an electrolysis machine. It passes electricity through water, which breaks it down into hydrogen and oxygen. The hydrogen is then piped into the fuel/air mixture, where it is burned as regular fuel. The brothers have a kit available for a few hundred dollars to set up your car to run on hydrogen.

The device should work fine, with one major problem that anyone with a basic science background should know: you won't save gas. Yes, we can produce hydrogen by electrolysis. This hydrogen can burn in an engine (I have no idea how efficiently in engines not designed for hydrogen). The hydrogen only produces water as a product, no carbon dioxide or other pollution. Hydrogen has a reputation as a clean fuel, maybe the fuel of the future.

So what is the problem? The second law of thermodynamics tells us that we can't get energy from nothing. Useful energy is always lost. Are the brothers in fact getting energy from water? Water has almost no usable energy in it. The problem is in the source of the energy for electrolysis. What isn't made explicit in the article is that the electrolysis runs off of the car battery. Drawing a charge from the battery requires more energy to recharge the battery. Just as you get fewer miles per gallon when you run your air conditioner off of the battery, you will get fewer miles per gallon if you run your electrolysis machine off of the battery.

You get some of that energy back when you burn the hydrogen. But the second law tells us that some will always be lost. The energy you get back by burning the hydrogen is necessarily less than the energy used to make it in the first place. Ultimately, this device will not save gas, it will decrease your fuel efficiency and it will increase pollution. Amazingly, no place in the article is there any indication that the brothers have ever attempted to measure their fuel efficiency.

There are several other interesting points in the article. At one point, it refers to the water in the electrolysis machine as a brownish liquid. I suspect the reason that it is brown is because they are using steel wires, and these will oxidize during electrolysis. The wires are slowly rusting away, and would have to be replaced frequently. To prevent this, you would need to use a metal that won't oxidize, such as platinum, which would obviously be much more expensive.

Jay is quoted as saying "at $1.29 a gallon for distilled water, it's a lot cheaper than gas". He seems to believe that they are getting as much mileage for each gallon of water as for each gallon of gas. Even if the machine didn't lose energy, there would be no reason to assume this.

Jana Peterson made no attempt at all at skepticism. If science education were up to standards, anyone with a high school degree should realize there are problems here. At the very least, she could have asked an engineer whether this should work, or just asked the brothers what their mileage is before and after they added their device.

The brothers seem to really believe in their device. I don't think it is deliberate fraud. But it is fraud nonetheless, and this article will probably help them sell more of their devices, especially in the current energy climate.

At least I got one thing out of this article. I can now assign it to my students after our section on thermodynamics and see if they can spot the problems.

False Alarms

I recently wrote about the worst invention of all time, the automatic car alarm. I recently had another experience that places it even more firmly in that position. Under no circumstances should you reach through an open window to unlock your car. The system interprets that as a theft attempt and the car starts beeping. However, this is not like other times the system goes off and all you need to do is press the red button on your key. No, this time they are serious.

I pushed the button, locked and unlocked the doors, put the key in the ignition, started the car, pushed more buttons, and generally acted frantic. Eventually, I stopped it, but I am still not sure what sequence of events turned it off. It was beeping for probably 60-90 seconds, but it felt like 10 minutes. I had visions of the neighbors coming after me with pitch forks. Of course, I never had visions of the neighbors calling the police and trying to help me.

So not only do these alarms go off all of the time for no reason, under some circumstances, they are almost impossible to stop. For awhile I thought it would be beeping for hours, and failing to get a response other than anger the whole time.

What we need is a web site with a wide readership that can start a petition for auto makers to eliminate these worthless devices. We could get maybe several million signatures. This web site should also include a call for any documented examples in which a car alarm actually prevented a crime, in case it has ever happened. Somebody must know of one, but it is possible it has never happened. It should also have a poll with at least two simple questions: have you ever had a false alarm with a car alarm, and have you ever had a true alarm. I imagine thousands of people saying yes to the first and no to the second. My guess is several thousand to one. If possible, it could ask about how many false alarms have you had, although that might be difficult--I have no idea how many I have had. With this data, we could get an estimate of the ratio of true alarms to false alarms. As I said before, any device or test that had a false positive rate of several thousand to one should be immediately eliminated.

There, I got that off of my chest. I can at least dream of a mass movement against these satanic devices. Now I just have to remember to leave the windows rolled up.

Model Rockets

I've mostly written about science or pseudoscience, but I thought I would write about something else today. I can make this about my personal interests, and one of my interests is model rockets. I first built and flew rockets in junior high and then rediscovered the hobby over 20 years later. I now have a vast and impressive rocket collection of all kinds. I have two rockets in my office, and I have written before about how much I enjoy seeing any shots of the Saturn V.

I have been less active in the hobby lately, but I recently completed three new rockets and I thought I would display them here. It would be nice sometime to get my whole collection online, or maybe have a rocket page, but for now I will just show these.

The first is the Rose Roc, a helicopter recovery rocket. It is supposed to stay aloft a very long time, although I have yet to fly it. It was more difficult to build than I anticipated. It is shown here with the rotors extended, but during ascent they would be pressed against the body.
The next rocket is Borealis, a rocket with a very unique construction. It's the science fictiony kind of rocket I like:
The third rocket would be instantly recognizable to anyone who made rockets in the 70s. It is a remake of the Centuri Taurus, one of my favorite kits of old, with lots of transitions and side pods.
This is the first time I have uploaded images to this blog and I'm not sure I got it right. It might be possible to click on them and get larger versions. Sometimes that works for me, sometimes it doesn't.

Letter to the editor

It's well known in town that if evolution is misrepresented in our local newspaper, The Jamestown Sun, I will be writing a letter to the editor. I am in there again, after a few years of silence.

The Reverend Tom Eckstein is someone I am quite familiar with. We have exchanged numerous emails regarding evolution or creation and have met several times. I get along with him well, although we see things completely differently. He had a guest commentary in the paper on Saturday. It is too long to reproduce here, but you can see it here. I wasn't even sure if I should write a response to this. Most of it is Biblical exegesis and epistemology and he makes few specific scientific claims. There is no way to make a case about epistemology in a short letter. But ultimately I couldn't resist, and I did send a letter. I reproduce it below:

Readers of Tom Eckstein’s commentary on evolution might get the mistaken impression that there is scientific support for his views. Eckstein suggests that the creation museum in Kentucky does not reject science. It does reject very well established science. They are free to do so, I only object to the implication that any support for this view can be found from within science. It is dishonest to suggest that the consensus for evolution is somehow different from the consensus regarding whether the earth moves or matter is composed of atoms, or to suggest a parallel between the massive positive evidence for evolution with the absence of scientific evidence one way or the other for the virgin birth.

There have been no articles disputing macroevolution in the scientific literature in over 50 years but such an article would be necessary to support the claim that there is a scientific controversy. Eckstein is confusing minor disagreements about details, which occur in all healthy sciences, with disagreements about evolution itself, and he confuses the status and evidence for microevolution versus macroevolution (macroevolution is more strongly supported by the evidence). Eckstein is free to reject the scientific consensus, but it is not acceptable to confuse the public about the state of the science or to suggest support for his view from within science.

A non literal reading of Genesis goes back at least to Augustine in the 5th century who argued that Genesis has a logical rather than temporal framework and a spiritual rather than physical meaning, which is no less literal. This did not lead to erosion of belief in the Bible in the millennia that followed. Augustine also warned about the damage to faith in interpreting scriptures in a way contrary to scientific knowledge:

“Even a non-Christian knows something about the earth, the heavens, and the other elements of this world, ... Now, it is a … dangerous thing for an infidel to hear a Christian, presumably giving the meaning of Holy Scripture, talking nonsense on these topics; and we should take all means to prevent such a situation, in which people show up vast ignorance in a Christian and laugh it to scorn.”

There is plenty more I could have said, but there are a few points to keep in mind with letters to the editor. Most importantly they should be short and have only one or two points. It does no good to correct every mistake in a letter. Here, I just wanted to correct the impression that evolution is somehow more controversial than other sciences or that disagreements mean Answers in Genesis is correct. I also decided to give a brief reply to his Biblical exegesis, just so that people know there are other ways of seeing things.

But since I have a blog, I can add some of the other things I would like to say here. When I write a letter, I first write out every thought I have and then cut it way down, and make it sound more polite. So here are some things on the cutting room floor:

The creation museum, like the Flintstones, suggests that humans and dinosaurs lived at the same time. That is a testable hypothesis. If it were true, then we would expect to find dinosaur bones occasionally mixed with human bones, or dinosaur footprints found among human bones or villages or artifacts, or human arrowheads or charcoal found among dinosaurs. There are no such occurrences. Likewise the museum grossly mischaracterizes the geology of places such as the grand canyon.

By comparing the science for the virgin birth with evidence for evolution he implies they are similar questions with similar evidence. However, with the birth of Jesus there is an absence of scientific evidence one way or the other, while there is overwhelming positive evidence for evolution. It is true that scientists who believe in the virgin birth or any other miracle must believe that the laws of nature were suspended. They believe it when there is no scientific evidence to the contrary. A better example to creationism would be if someone today claimed to be the product of a virgin birth. If we had DNA evidence, hospital records, gynecological exams, and personal testimony all contradicting the claim, then it would be foolish to still support it. Likewise, it is foolish to support the claims in the creation museum. A scientist may choose to believe otherwise if the evidence were the other way.

I had a few other sentences here and there that I knew wouldn't be developed further so I left them alone, like macro evolution not just being an extrapolation of microevolution, or the various claims in the Bible that the earth is flat or the sun goes around the earth, etc., which no one takes literally.

Ultimately I sent the letter because I think we need to fight every little misrepresentation. If we don't, they will find seed and be considered true by some readers. There is a perception that evolutionary science is somehow different from other sciences. I hope I can make a few people at least understand the extent of scientific consensus.

Emu oil

After the parade there was a street fair and among the vendors I found an opportunity to learn about some questionable science.  There was a booth with a sign advertising healing and natural cures and chiropractic.  I went to investigate.

They were selling various products made from emu oil, something I had never heard of before.  This included emu oil based skin lotion, suntan lotion, and a pain lotion.  I sat in the "pain test" chair and was sprayed or rubbed with several of these lotions.  I was told the pain lotion "increased oxygen flow and thus stopped headaches".  I wasn't sure how a lotion would affect oxygen flow or how that would decrease pain (usually increased blood flow to a region is associated with pain and inflammation).

My notion before trying it is that these would be placebo like lotions and they would have no effect.  However, the anti pain lotion produced a very definite tingling sensation, much like that produce by Ben Gay.

I looked up their product on the web and found it contains several active ingredients, most notably methyl saliyclate and menthol.  Those are the same ingredients as in Ben Gay.  I suspect the sun tan lotion is also a legitimate sun tan lotion and contains sun blockers.

So the question is what does emu oil have to do with any of this?  Their literature didn't help much.  Almost all of the literature explained why their emu oil is better than other emu oils.  Theirs is more pure.  It warned us about the difference between distilled oil, refined oil, and various other distinctions.  There way was best, although no reason was given.  Also, they used hand fed Minnesota emus, and the Minnesota emus are better, don't you know.

A Google search for emu oil produces almost exclusively vendor hits for the first four pages.  I expect a lot of hits for vendors, but was surprised at how complete it was.  There were only three hits other than vendors in four Google pages.  One was a Wikipedia page.  Considering I had never heard of emu oil before, there seems to be a large market for it.

Emu oil is made from the fat of emus, which are raised as farm animals for their meat, leather, and other products as well.  In all of the pages, there was only one scientific reference (repeated ad naseum), to a study that indicated emu oil might have anti-inflammatory action (many other oils were tested and found to work as well).

The literature also emphasizes that emu oil contains several omega fatty acids.  However, those would only be beneficial if it was ingested, not for a topical ointment.  The literature also emphasized that Australian Aborigines used emu oil for a wide variety of ailments.  I was not able to verify that from a credible source.  However, the claim that natives used a particular preparation is a common theme in alternative medicine, and is not evidence one way or the other for efficacy.

It seems these products aren't completely bogus.  Any lotion needs a lipid base, and emu oil should work as well as palm oil or similar bases.  At least in some of their products, they add genuine active ingredients.  The question is whether being based on emu oil is any better than being based on any other oil.  Is there some reason to prefer emu oil over Ben Gay?  No evidence was given to support this.  The emphasis was on being "natural" and how the emus were raised how the oil was prepared (apparently, being distilled with care makes the oil better).

I always thought an emu was a cool animal.  They have a dopey face you just have to love.  There is nothing wrong with trying to use all of the animal for a product rather than wasting it, but you should not have to pay more for some imaginary special properties of the oil.  I've heard emu meat is tasty.  I suppose I wouldn't mind giving it a try some time, if I had the chance.  But only from a Minnesota emu.

I'm positive it was false

The worst invention of all time is the automobile theft alarm.  An incident yesterday shows why.

Jamestown is celebrating its 125th birthday this year.  There are a wide variety of activities.  They seem to be very well attended and its nice to see the strong sense of community this has highlighted.  Yesterday there was a parade, probably the biggest in Jamestown history.  It seemed like the whole city (of 15,000) showed up on a sunny morning of sitting with friends.

During the parade, a car alarm went off someplace nearby.  Not a single person of the thousands present even turned their head in response.  A short time later, a second alarm went off.  Again, not the slightest response.  Eventually, both alarms stopped, as they always do.  I assume it was a false alarm, although there is the remote possibility of a major crime spree.

Has anyone ever responded to a car alarm as if there was a theft?  Has any thief ever been deterred by such an alarm?  I wonder what the ratio is of false alarms to real alarms?  I'm sure is is in the range of thousands to one.

In medicine, if there was a test that gave 999 false positives for each true positive, no one would even think of using it.  Why do manufactures continue to torture us with these alarms, whose only function is to cause embarrassment for the owners?

On trees and imagination

I recently heard the question "What scientific fact is the hardest to believe?" I think I could come up with a different answer to that each time it's asked or each time I think of a different area of science. In this case, I was walking, saw a tree, and I thought about the amazing fact that it's one of my relatives.

We share an ancestor with a tree--or a mushroom or any other living thing on earth. My great great great........great grandpa was also the grandpa of that tree. That ancestor lived about 2 billion years ago, so we aren't exactly first cousins, but we share an ancestor nonetheless. Sometimes I have students who think that evolution only means we are related to monkeys, or other mammals, or other vertebrates. They find it very strange we are related to a mosquito, and harder yet that we are related to a tree.

Perhaps the most common argument against evolution is the argument from personal incredulity. A person sees some complex contrivance such as the eye, they can't imagine how it would arise in many small steps, and thus declare that it couldn't have. It never occurs to them that their ability to imagine something is not evidence. It is hard for people to imagine how an eye or a wing could possibly arise. And yet not only are our eyes related to those of other animals, molecules in them can be found in a tree or a bacterium.

Sometimes science is characterized as rigid, logical, or technical. Imagination is for the arts or humanities. But here we find that science tells us something is true that our imaginations cannot even grasp. Science and the world is stranger and bigger than our imaginations. Those who deny evolution are the ones limited to a rigid and unimaginative world.

Science doesn't just say something is true, it gives us the tools and evidence to see it, to imagine the unimaginable. When I teach cell biology, I spend most of the time talking about just a generic cell, not a human cell or a plant cell. A tree and a human might seem very different, but the molecular processes and cellular structures are the same in many ways. It is when you look at the cell that you see our relatives. William Paley argued that our eye is an amazing piece of engineering, more intricate than a watch. Yet the protein and pigments in our eye are also found in a bacterium, another of my relatives.

Science doesn't limit the imagination, it fires it. What could be more cool than going for a walk in the shade of your relatives, and being able to see the family resemblance.