Proslogion : Page 70 of 113 : Thoughts from a scientist who is a Christian (not a Christian Scientist)

A Large, Detailed Study Confirms Another Failed Evolutionary Prediction

lebrea — The La Brea Tar Pits as imagined by Charles R. Knight (public domain image)

Paleontologists have long recognized that the fossil record produces a serious problem for the hypothesis of evolution. Almost thirty years ago, Dr. David Wake and his colleagues stated:¹

With natural selection operating in a changing environment as an agent of adaptation, we expect to see changes at the organismal, ultimately physiological and morphological, level. How, though, can we explain the paradoxical situation in which environments change, even dramatically, but organisms do not?

In other words, evolution predicts that in a changing environment, organisms should change in order to adapt. However, when we look at the fossil record, we don’t see such change. Instead, while it is thought that earth’s climate changed dramatically in many different ways throughout the fossil record, the fossils themselves show that the organisms living on earth didn’t change much at all. This has been called the “paradox of stasis,” and while several attempts have been made to resolve the problem ², none of them have been found to be satisfactory.³

In an attempt to understand the paradox of stasis better, Dr. Donald Prothero undertook a series of amazingly detailed studies. With the help of a small army of students, Prothero studied the fossils of all the common birds and mammals that have been preserved in the La Brea tar pits of Los Angeles, California. According to the standard geological view, these tar pits preserved species that lived in the area over a period of time when the region experienced wild climate change. It is thought that 35,000 years ago, the Los Angeles, California area had a very similar climate to what it has today. During the height of the last ice age (20,000 years ago), however, it was significantly colder and significantly wetter. As the ice age waned, the climate returned to what it was 35,000 years ago.

From an evolutionary point of view, one would expect that over the course of this dramatic change in climate, the birds and mammals living in the area would have experienced some amount of evolutionary change in order to adapt to their surroundings. However, that’s not what this series of studies found.

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What Do Spiders Do With All Those Eyes?

spider_eyes — This photo shows four of the eight eyes on a jumping spider. The middle two are the principal eyes, and the other two are the anterior lateral eyes (ALEs). (click for credit)

Most spiders have eight eyes, and their arrangement varies depending on the type of spider. In fact, when studying a spider, scientists often use the number and arrangement of the eyes to help them classify the specimen.¹ What does a spider do with all those eyes? Well, in the case of a jumping spider, we know that the two large eyes near the center of the head are the spider’s principal eyes. They can see sharp images, are sensitive to color, and can move to track a target.

The eyes that are right next to the principal eyes are called the anterior lateral eyes (ALEs). They cannot move, do not seem sensitive to color, and as far as we can tell, don’t really allow for the spider to see images. Instead, it has always been thought that these eyes help the spider detect motion.² But what about the principal eyes? Do they detect motion as well? Three researchers decided to determine the answer to that question by conducting a interesting experiment with some spiders and an iPod touch.

They ended up using removable paint to “blind” specific eyes of jumping spiders from the species Phidippus audax. For 16 of the spiders, they used the paint to “blind” only the principal eyes. They then used the paint to “blind” only the ALEs of 14 other spiders. Finally, they used 16 spiders with none of their eyes “blinded” as a control group. One at a time, they put the spiders in an “arena” that had four walls. Three were foam-core walls, and the fourth wall was the screen of the iPod touch. They allowed each spider to acclimate to the arena and waited for its head to face the screen. When that happened, they remotely started an animation of a black circle either looming towards the spider or retreating from the spider. The results they got were quite interesting.

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Same Chemical, Different Chemical Formula?

In my previous article, I discussed a chemical found in both the great orange tip butterfly and the marble cone snail. I made the statement that the researchers were surprised to find that the chemical was identical in both species. A commenter asked a good question: When would the same chemical be different (across species or not)? I thought the best way to answer that question was with a new post.

When most of us think about chemicals, we think about simple molecules like water: H₂O. The chemical formula of water tells us that there are two hydrogen atoms linked to one oxygen atom. In a glass of water, there are all sorts of molecules like this, and they are all identical. If we do something to change the chemical formula of the molecule, we come up with a completely different chemical. For example, if I were to add one more oxygen to the molecule, I would get H₂O₂, which is hydrogen peroxide. It is utterly different from water, so in molecules like these, even a change of one atom makes a world of difference.

However, the biological world isn’t quite the same. The molecules are incredibly complex, often composed of thousands of atoms. Consider, for example, proteins. These are large molecules made by linking smaller molecules, called amino acids, together. When amino acids link up together in a specific way, they tend to make a specific protein. An example would be the protein known as cytochrome c. It is a relatively simple protein found in almost all living organisms. It is simple because, as proteins go, it is rather small. In most living organisms, cytochrome c is composed of “only” about a hundred amino acids.¹ That might sound like a lot, but there are proteins in living organisms that are composed of more than 25,000 amino acids!² So as proteins go, cytochrome c is rather “simple.”

There are many ways to picture a protein, but one way is called a “ribbon diagram.” In this way of picturing a protein, you get a three-dimensional view of the overall backbone of the protein. Here is the ribbon diagram for cytochrome c:

cytochromec — The ribbon diagram of cytochrome c, with the active site pointed out (Click for credit)

The green ribbons represent the structure of the backbone of the protein, and they are composed of many amino acids linked together. The gray bars represent the active site, which is where the protein does most of its work.

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Did Butterflies Evolve from Sea Snails?

orange_tip_butterfly — The great orange tip butterfly has a toxin in its wings that is identical to the toxin used by the marble cone snail. (Click for credit)

A former student of mine recently alerted me to a study that was published in the Proceedings of the National Academy of Sciences. The authors were studying the proteins found in the wings of a great orange tip butterfly, Hebomoia glaucippe. As they sorted through what they found, they were surprised to find a toxin known as glacontryphan-M.¹ The fact that it is a toxin wasn’t surprising to them. After all, Monarch butterflies have cardiac glycosides in their bodies, which are toxic to many birds.² It is thought that this is a defense mechanism, because birds that eat a monarch butterfly and get sick are unlikely to eat more monarch butterflies.

Here’s what’s surprising: the toxin is also found in a sea snail known as the marble cone snail, Conus marmoreus.³ You can see how it gets its name:

The marble cone snail uses the toxin for hunting. It injects the toxin into its prey, paralyzing it. That makes the prey very easy to eat. Obviously, the researchers were surprised to find the same toxin in two separate species that are supposed to be distantly related in terms of evolution. More importantly, they were surprised at the fact that the two toxins are chemically identical.

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Desperately Seeking Innovation

One of the biggest problems facing evolutionists is the explanation of how brand new information can be added to a genome. After all, if flagellates eventually evolved into philosophers, an enormous amount of truly original information had to be added to flagellates’ (and their descendents’) genomes. However, genomes are so well-designed and highly-structured, it is difficult to imagine a naturalistic process that could add information to them. Nevertheless, evolutionists have tried their best. One of the more popular notions is gene duplication followed by mutation. We know that genes can be duplicated. It happens quite frequently. The thought is that when a gene is duplicated, one of the copies can continue to produce the protein it is supposed to produce, while the other copy is free to mutate and find some completely new function.

While the thinking behind this idea is logical, experimental evidence to support it has been hard to find. As a result, evolutionists tend to jump on any experimental finding that might suggest the idea is accurate. This is well illustrated by an article that was linked by a commenter on a previous thread. The article claims that researchers have finally shown how a gene can pick up a brand new function, which can then be amplified and modified over time.

Unfortunately, the article’s claim is not accurate. I had already read the scientific paper on which the article was based ¹, so when I read the article, I understood how incorrect its claims are. However, I am sure the commenter and many other readers of Science Daily do not. As a result, I want to discuss the study’s actual findings. They are very interesting, and they tell us a lot about the genetics of bacterial adaptation. However, they don’t tell us anything about how genes acquire brand new functions or about how information can be added to a genome.

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Remains of Cells: In DINOSAUR Bones!

In 2005, Dr. Mary Schweitzer stunned the scientific community by publishing data that indicated she had found soft tissue in a Tyrannosaurus rex fossil that is supposed to be more than 65 million years old.¹ While many in the scientific community were unconvinced at the time, several lines of evidence now indicate that she was correct. Since that time, other examples of soft tissue in fossils that are supposed to be millions of years old have been found: muscle tissue in a salamander fossil that is supposed to be 18 million years old, retinal tissue in a mosasaur fossil that is supposed to be 70 million years old, and what appear to be bone cells from the same mosasaur fossil. Now, Dr. Schweitzer has come back into the picture with some strong evidence that she has also found bone cells in her Tyrannosaurus rex fossil, as well as one other dinosaur fossil.²

There are three different kinds of bone cells in vertebrates: osteoblasts, osteoclasts, and osteocytes. If you use a microscope, you can tell them apart just by looking at them. Osteoblasts are the cells that build bone, while osteoclasts are the cells that break down bone. Both are important, because your bones adjust to the needs of your body, so there are times that you will need to build more bone, and there are other times you will need to break down some bone. The third group of bone cells, osteocytes, are the most common. They maintain the bone.

The study that found bone cells in a mosasaur fossil found osteocytes, and that’s what Dr. Schweitzer’s team found as well. Now, of course, just because they found microscopic structures that looked like osteocytes isn’t necessarily surprising. After all, the fossilization process could be detailed enough to preserve the shapes of individual cells. If these structures really are just the fossilized shapes of the osteocytes, it is exciting, but not incredibly surprising. However, Schweitzer’s team has done some detailed experiments to show that these aren’t just shapes. Indeed, these osteocyte structures still contain proteins and probably even DNA!

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People Prefer Purpose

Back in the fourth century BC, Plato argued that any true explanation for a physical process must be teleological. In other words, Plato thought that the processes occurring in nature are driven by design and purpose, and any proper explanation for such processes must include that design and purpose. While most scientists reject such explanations these days, there has been a bit of a resurgence of this school of thought in recent years. Intelligent design advocates as well as creationists, for example, argue that design-based explanations lead to a better understanding of nature.

While most people think that any teleological approach to nature must assume some sort of Creator or Designer, that’s not necessarily the case. Not long ago, I reviewed a book by Dr. Thomas Nagel. Even though he is an atheist, he argues that any explanation of origins must be teleological in nature. He doesn’t know exactly what such an explanation is, but he argues forcefully that any non-teleological approach will never explain everything we currently understand about science.

Interestingly enough, I ran across a psychological study that seems to indicate that teleological explanations appeal to the “gut instincts” of people. Now I am not a huge fan of psychological studies. There are an enormous number of variables involved in studying how and why people think the way that they do. As a result, I am instinctively skeptical of such studies. However, I thought the results of this one were interesting enough to discuss.

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Remember That Nuclear Disaster in Japan?

On March 11 of 2011, the most powerful earthquake known to have hit Japan struck near the east coast of Honshu. The earthquake generated a tsunami that reached a height of more than 130 feet. Just last month, the Japanese National Police agency reported that there were at least 15,870 people who died, an additional 6,114 who were injured, and 2,814 who are still missing as a result.¹ Obviously, it was a disaster of truly stunning proportions.

One of the many things that happened as a consequence of the disaster is that some of the reactors at the Fukushima Daiichi Nuclear Power Plant went into meltdown, and radioactive substances were leaked into the ocean and released into the air. People in a 12-mile radius around the power plant were evacuated so that they would not be exposed to too much radiation. As a result of the meltdown, there is increasing political pressure for Japan to end its reliance on nuclear power. According to the Christian Science Monitor, Prime Minister Yoshihiko’s party has recommended that Japan phase out all nuclear power by the year 2030.

Back when the nuclear disaster was in the news, I commented on it (here and here). Since then, I have been following the scientific literature to see what those who have been monitoring the situation are saying regarding its long-term effects. Recently, a study and some commentary on the study were published in the journal Energy & Environmental Science, and they are surprising, to say the least.

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Bugs and Bacteria Working Together

Mutualistic symbiosis, the process by which organisms of different species interact so that all of them benefit, is a very common phenomenon in creation (see here, here, here, here, and here for a few examples). A recent study in the Proceedings of the National Academy of Sciences, USA highlights a very interesting case of mutualistic symbiosis that not only has some important implications for farmers, but also relates to the creation/evolution controversy.

The study examined insecticide resistance in bean bugs (Riptortus pedestris) and similar insects. The authors considered one of the most popular insecticides used by farmers across the world, fenitrothion. It has been known for some time that certain insects, such as the bean bugs in the study, can develop resistance to that insecticide. This is a problem, since bean bugs not only damage bean crops, but also some fruit crops.¹ The authors were interested in what causes this insecticide resistance. As they state in the introduction to their paper:

Mechanisms underlying the insecticide resistance may involve alteration of drug target sites, up-regulation of degrading enzymes, and enhancement of drug excretion, which are generally attributable to mutational changes in the pest insect genomes.

In other words, when an insect develops resistance to an insecticide, it is generally assumed that there was a change in the DNA of the insect. A mutation might have damaged the site where the insecticide is supposed to bind; the activity of a gene involved in the destruction of unwanted chemicals might have been enhanced so that the insect destroys the insecticide; or perhaps the activity of a gene involved in getting rid of waste is enhanced so that the insect just excretes the insecticide.

The authors show that for the specific case of fenitrothion resistance in bean bugs and similar insects, none of these mechanisms play a role.

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An Excellent Quote

Not long ago, Dr. Jerry Alan Fodor (a professor of Philosophy) and Dr. Massimo Piattelli-Palmarini (a professor of cognitive science) wrote a book entitled What Darwin Got Wrong. I haven’t read the book, but what I have read about it indicates that the authors strongly believe Darwin was right when it comes to the idea that all species descended from a common ancestor. However, they strongly disagree with the mechanism that Darwin proposed (and most Neo-Darwinists accept) for the process by which that happened. While most modern evolutionists contend that mutation acted on by natural selection is the main process by which species adapt and change, the authors argue that it is only one of many considerations. In fact, they go a step further and claim that there is no scientific reason to elevate natural selection above these other processes which it comes to their relative importance.

Since I have not read the book, I cannot comment on the validity of their arguments. However, I ran across a quote from the introduction that makes me want to read the entire book. They call their introduction “Terms of Engagement.” After laying out the terms and outlining the contents of the book, the authors write:

So much for a prospectus. We close these prefatory comments with a brief homily: we’ve been told by more than one of our colleagues that, even if Darwin was substantially wrong to claim that natural selection is the mechanism of evolution, nonetheless we shouldn’t say so. Not, anyhow, in public. To do that is, however inadvertently, to align oneself with the Forces of Darkness, whose goal it is to bring Science into disrepute. Well, we don’t agree. We think the way to discomfort the Forces of Darkness is to follow the arguments wherever they may lead, spreading such light as one can in the course of doing so. What makes the Forces of Darkness dark is that they aren’t willing to do that. What makes science scientific is that it is.

[Jerry Fodor and Massimo Piattelli-Palmarini, What Darwin Got Wrong, Farrar, Straus, and Giroux, First American Edition 2010, p. xx]

I couldn’t agree more. When those who call themselves scientists want to shut off debate on an issue, they are exposing themselves for what they are: rabidly anti-science. Science is all about following the evidence, regardless of where that evidence might lead. It is unfortunate that some (if not many) in the scientific community attempt to silence those who are simply trying to follow the evidence.