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Tuesday, September 2, 2014

Same Chemical, Different Chemical Formula?

Posted by jlwile on October 31, 2012

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:

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?

Posted by jlwile on October 29, 2012

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 (Click for credit)

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

Posted by jlwile on October 26, 2012

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 based1, 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!

Posted by jlwile on October 24, 2012

New evidence indicates that proteins and DNA still exist in preserved Tyrannosaurus rex bone cells (Click for credit)

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

Posted by jlwile on October 22, 2012

Plato from Raphael's "The School of Athens"

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?

Posted by jlwile on October 18, 2012

Satellite image taken on March 16, 2011, showing reactors at the Fukushima Daiichi Nuclear Power Plant leaking radioactive gas into the air.

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

Posted by jlwile on October 16, 2012

A beanbug, Riptortus pedestris (click for credit)

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

Posted by jlwile on October 12, 2012

The cover of Fodor and Piattelli-Palmarini's book

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.

Direct Evidence that a Father’s Age Affects Autism Risk

Posted by jlwile on October 10, 2012

A magnified image of stained human sperm (click for credit)

While there is some disagreement on the subject, most medical scientists would agree that Autism rates are on the rise in the U.S. and in many other parts of the world. What’s the reason for this increase? Like most medical issues, there are probably a variety of reasons. Some have suggested that the increase in autism can be linked to childhood vaccination, but the data argue strongly against it. Most likely, there are a series of genetic and environmental factors that play a role in the increase.

For quite some time now, there has been strong evidence that the age of the father has a significant effect on the chance of his child having autism.1 There has been evidence that the mother’s age also plays a role, but its effect is much smaller.2 However, these studies simply demonstrate a correlation between parental age and autism. They do not show that increased parental age plays a direct role in the cause of autism. However, a recent study published in the journal Nature has changed that. It seems to provide a direct link between the age of the father and autism in the child.

The authors of the study examined the entire genomes of 78 parent-offspring trios (mother, father, and child) to directly determine what mutations the child received from the father’s sperm cell and what mutations the child received from the mother’s egg cell. Because they were specifically interested in the cause of neurological disorders, they used a large number of trios that contained a child with either autism or schizophrenia. In the end, 44 of the children had autism spectrum disorder, and 21 were schizophrenic. In addition, the genomes of 1,859 other people were sequenced to serve as a population comparison.

The authors focused on the de novo mutations in the children. These are mutations that do not exist in either parent but do exist in the child. Thus, they must arise from a mutation that occurred when the father made his sperm or the mother made her egg. Such mutations happen in every production of egg and sperm cells, and the authors wanted to know which parent (if either) was more responsible for them. The results were surprising, to say the least!

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Homeschool Graduates and Community College

Posted by jlwile on October 8, 2012

Monroe Community College in Rochester, NY (click for credit)

I try to keep up on all the latest research related to homeschooled students. Unfortunately, I seem to have missed a small study that was published in the summer 2008 edition of the Journal of College Admission. The study wasn’t done on homeschooled students; instead, it was done on community college admissions officers. The authors sent surveys to them, asking about their perceptions of homeschool graduates. I found several of the paper’s points rather interesting and worthy of some discussion.1

First, the paper reports on the results of another study I somehow missed. The study is a bit old (1998), but the results are worth noting. It examined the community college transcripts of 101 homeschool graduates and compared them to those of students who graduated from a traditional high school. The study found that both full-time and part-time homeschool graduates had significantly higher grade point averages (GPAs) than their peers. In addition, the study examined the results of the Texas Academic Skills Program, a test that all students who attend state-funded, post-secondary educational institutions in Texas are required to take. The test covers reading, writing, and mathematics. Once again, the homeschool graduates achieved significantly higher scores than their traditionally-schooled peers.2

Second, the paper discusses the admissions process for homeschool graduates at community colleges. It notes that only 50% of those that responded to the survey have an official policy regarding the admissions process for homeschool graduates. That surprised me. After all, you would think that community colleges would cater to nontraditional students, and homeschooled students are clearly nontraditional. Also, many homeschooling families are looking for ways to make college more affordable, since they generally have a number of children. As a result, you would think that community colleges would be a natural choice for many homeschool graduates. It seems to me, then, that it would be natural for the vast majority of community colleges to have an official policy regarding how homeschool graduates should be admitted.

Now while only 50% of the responding colleges had an official policy for the admission of homeschool graduates, 80% said that they had procedures in place that would allow for the admission of such students. Thus, even without an official policy, some community colleges still make it possible for homeschool graduates to be admitted. That’s good news, of course, but it makes me wonder why a school that allows for the admission of homeschool graduates doesn’t have an official policy regarding how that should be done!

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