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Thursday, April 24, 2014

The Bacterial Flagellum: More Sophisticated Than We Thought!

Posted by jlwile on November 18, 2013

This is a schematic of a bacterium's flagellum (image in the public domain).

The bacterial flagellum is a symbol of the Intelligent Design movement, and rightly so. After all, bacteria are commonly recognized as the “simplest” organisms on the planet. Nevertheless, their amazingly well-designed locomotive system has continued to amaze the scientists that study it. In 1996, Dr. Michael Behe highlighted the intricate design of the bacterial flagellum in his book, Darwin’s Black Box. While some have tried to explain it in terms of Neo-Darwian evolution, they have not come close to succeeding.
Not only is the bacterial flagellum amazingly well-designed, it is far more versatile than anyone imagined.

Some bacteria (like Escherichia coli) have multiple flagella, which makes it very easy for an individual to navigate in water. All the bacterium has to do is adjust which flagella are spinning and how they are spinning, and the single-celled creature can do acrobatics in the water. However, the vast majority of bacteria have only one flagellum. It was thought for a long time that because of this, it is difficult for them to make sharp turns in the water.

Two years ago, this thinking changed abruptly when a group of physicists from the University of Pittsburgh showed that the bacterium Vibrio alginolyticus, which has only one flagellum, can make sharp turns with ease. They showed that in order to execute such a turn, the bacterium backs up, lurches forwards, and swings its flagellum to one side.1 The entire maneuver takes less than a tenth of a second and results in a 90-degree turn. So not only is the bacterial flagellum an exquisite “outboard motor” that propels the bacterium through the water, it is also a rudder that allows the bacterium to make sharp turns at will!

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The Great Debate, Take 2

Posted by jlwile on September 26, 2013

The skulls of some primates. Based on genetics, most evolutionists believe the chimpanzee is our closest living relative, but physical characteristics indicate the orangutan is. (click for credit)

Last night I once again debated Dr. Robert A. Martin, a vertebrate paleontologist who is professor emeritus at Murray State University. The previous debate was on the broad subject of creation versus evolution. This time, the organizers of the event wanted us to narrow our discussion, so we chose to talk about dinosaurs and people. Before I discuss the debate, I want to thank Dr. Martin for participating in it. I personally think the best way to understand an issue is to hear from multiple sides, so I think debates can be extremely helpful to those interested in controversial topics. However, it is difficult to get evolutionists to participate in debates about the creation/evolution controversy. I thank Dr. Martin for being committed to education strongly enough to be an exception to that general rule!

Since Dr. Martin had the weaker position scientifically, I allowed him to choose whether to present his case first or second. He chose to go second, so I was up first. The initial activities (songs, introductions, and remarks from the organizers) made it clear that for some reason, the audience this year was overwhelmingly creationist. The previous year, creationists were in the majority, but there were many evolutionists present. That didn’t seem to be the case this year, so I started by thanking Dr. Martin for being willing to act as a lion in a den of Daniels.

In making my case, I concentrated on the evidence that indicates dinosaur fossils are not millions of years old. I stressed the soft tissue that is being found in fossils that are supposed to be millions of years old (see here, here, here, here, and here, for example). I also discussed the fact that several dinosaur bones from different locations around the world all have enough carbon-14 in them to indicate that their maximum age is less than 40,000 years old. I also discussed how living organisms like the coelacanth, Wollemi pine, and tuatara falsify the geological-column thinking that leads most scientists to conclude that humans and dinosaurs didn’t live at the same time.

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Richard Dawkins Produces Another Theist

Posted by jlwile on August 29, 2013

This is Dr. Laura Keynes, who returned to the faith of her childhood after reading the New Atheists and those who replied to them. (Click for credit.)

Dr. Laura Keynes grew up in Cambridge, arguably the intellectual center of the United Kingdom. She studied at the University College of Oxford on a full-ride scholarship and ended up earning a Doctor of Philosophy degree. Her doctoral thesis was on epistemology, the study of knowledge and justified belief. As her last name indicates, she is the great-grandniece of the famous economist John Maynard Keynes. She is also the great-great-great-granddaughter of Charles Darwin.

Why am I telling you about this young lady? Because she recently wrote an article entitled, “I’m a Direct Descendant of Darwin…and a Catholic.” Now the title didn’t surprise me at all. I know a lot of Catholics (and even more Protestants) who believe in evolution. Indeed, one of the leaders of the Intelligent Design movement, Dr. Michael Behe, says:1

You can be a good Catholic and believe in Darwinism. Biochemistry has made it increasingly difficult, however, to be a thoughtful scientist and believe in it.

However, as I read the article, I couldn’t help but smile. You see, Laura was raised Catholic but drifted away from the faith after her mother became a Buddhist and her brother rejected all organized religion. By the time she was studying for her Doctor of Philosophy degree, she was an agnostic. During that time, however, Richard Dawkins had opened up an international dialogue on the existence of God with his thoroughly awful book, The God Delusion. Well, Laura decided to read Dawkins and his fellow New Atheists, and she says:

I expected to be moved from agnosticism to atheism by their arguments, but after reading on both sides of the debate, I couldn’t dismiss a compelling intellectual case for faith. As for being good without God, I’d tried and didn’t get very far. At some point, life will bring you to your knees, and no act of will is enough in that situation. Surrendering and asking for grace is the logical human response.

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The Inquisition Strikes Again – Twice!

Posted by jlwile on August 8, 2013

This is 19th-century artist Cristiano Banti's interpretation of Galileo before the Inquisition in Rome. (public domain image)

In March of this year, I wrote a post about an article that would later appear in the peer-reviewed journal Acta Histochemica. It was an exciting report about soft tissue recovered from a fossilized Triceratops horridus horn. Unfortunately for the lead author, Mark Armitage, it was too exciting for the High Priests of Evolution. According to Creation Ministries International:

Until recently, Mark served as the Manager for the Electron and Confocal Microscopy Suite in the Biology Department at California State University Northridge. Mark was suddenly terminated by the Biology Department when his discovery of soft tissues in Triceratops horn was published in Acta Histochemica.

He is currently seeking relief in a legal action for wrongful termination and religious discrimination by the University.

Now, of course, the exact details of why Armitage was fired from California State University Northridge are not publicly known. However, the timing of the event speaks volumes. It’s not every day that a university employee gets fired right after publishing a paper in a peer-reviewed journal!

If the article was the motivation for Armitage’s termination, it wouldn’t surprise me. As more and more evidence against the ruling scientific dogma of the day continues to accumulate, the only thing the fervently faithful can do is call out the Inquisition in an attempt to squelch that evidence.

That’s what happened when Grand Inquisitor Jerry Coyne decided that Dr. Eric Hedin at Ball State University had to be silenced. He called in the attorneys and forced the university to cancel a course that introduced students to Intelligent Design, as well as the arguments against it. Obviously, the university had to give in to the attorneys, since there was no way it could afford to face an easily-avoided lawsuit. The only good news that comes from this Orwellian situation is that Dr. Hedin will not be fired.

Of course, squelching competing ideas is incredibly anti-science, and it never works. The evidence will win out, and science will eventually correct itself. Thus, the High Priests of Evolution are fighting a losing battle. The only thing their Inquisition can do is delay the inevitable.

Riddle of the Feathered Dragons

Posted by jlwile on July 31, 2013

Despite the fact that no evidence of feathers has ever been found associated with a Deinonychus fossil, this model of the dinosaur at Canada's Royal Ontario Museum is covered with feathers in an attempt to emphasize the supposed evolutionary relationship between dinosaurs and birds.
(Click for credit)

Dr. Alan Feduccia is a world-class evolutionary biologist whose research has focused on the natural history of birds. He is the S.K. Heninger Distinguished Professor Emeritus at The University of North Carolina, Chapel Hill, and even his abbreviated list of publications is the envy of most scientists. He has received numerous honors for his scientific accomplishments, including having an extinct species of bird named after him: Confuciusornis feducciai.

Despite his incredible scientific accomplishments, he is ridiculed by some in the scientific community because he doesn’t think that dinosaurs evolved into birds. There are those who call him a “BANDit” (BAND stands for “Birds Are Not Dinosaurs) and lump him in with the hated creationists and the global warming “deniers.” Why don’t these people listen to a man who has contributed so much to the biological sciences? Because they follow the consensus, and the consensus is that birds evolved from dinosaurs. Anyone who questions this consensus, regardless of the data they present, are simply ignored and ridiculed.

In his latest book, Riddle of the Feathered Dragons, Dr. Feduccia has something to say about this consensus:

The word “consensus” has no place in science and is never a validation of any hypothesis, yet one frequently sees trust in “consensus” for validation of important scientific concepts. (pp. 4-5)

I couldn’t agree more. When you hear the word “consensus” used to support a scientific argument, you know the speaker has stopped thinking. Rather than examining evidence for himself or herself, the speaker is simply allowing the majority to rule. Majority rule might be a good system in some social applications, but it is the worst possible method for doing science.

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Can Random Processes Produce Biological Information?

Posted by jlwile on July 15, 2013

A simplified model of a protein called phenylalanine racemase. The star points out the binding pocket. (click for credit)

In a previous post, a commenter asked an off-topic question. I try to focus the comments section on the topic at hand, but the question is an important one, so I decided to answer it as a separate article. The commenter is well aware that I think random processes cannot produce biological information. He included a link to an article by Dr. Fazale Rana in which Dr. Rana makes the claim that a recent study demonstrates that biological information can be produced by random processes. Obviously, the commenter wanted my take on the article.

Before I comment further, I want to make it clear that Dr. Rana has probably forgotten more biochemistry than I have ever learned. I have a lot of respect for him and am a big fan of his latest book. He and I disagree on some issues, but the issues on which we agree are far more numerous and far more important. This particular issue, however, represents one of the former. While I think the difference in our positions is largely semantic, it is important and worth defining.

In the article, Dr. Rana reports on a study1 that was published in the Proceedings of the National Academy of Sciences of the United States of America. In the study, the authors compared the binding pockets of all known proteins in nature to a database of randomly-generated peptides (molecules that are very much like proteins but not large enough to be considered proteins). In order to understand the results of the study, you need to know what a binding pocket is.

A protein is a large molecule, but the workhorse of the protein is typically called its active site. When a protein needs to modify a molecule in some way, it attaches itself to the molecule at its active site. This active site is held in a region of the protein called the binding pocket. So the binding pocket is the area on the protein that contains the active site. An example of a binding pocket is given above. The drawing gives you a simplified view of a protein called phenylalanine racemase, a good example of a protein that is used in a wide variety of living organisms. The star points out the binding pocket.

In the study, the authors found that there were remarkably few varieties of binding pockets found in all the known proteins, and that all those pockets were able to bind (at least in some way) to something in the randomly-generated set of peptides. The conclusion, then, is that random chance could, indeed, produce biologically-active proteins. After all, if randomly-generated molecules could bind to the binding pockets of the known proteins of life, then those known proteins of life could also be randomly generated.

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“Ancient” Bacteria Use Quantum Mechanics!

Posted by jlwile on July 11, 2013

The light-harvesting antenna complex of purple bacteria (Click for credit.)

The quantum world is a strange one. In a process called “quantum tunneling,” particles can pass through barriers as if they aren’t there at all. As a result of a process called “perturbation,” empty space can give rise to virtual particles that “blip” into and out of existence. Because of a phenomenon known as “quantum coherence,” a particle can be in several different places at once. These ideas defy common sense, but they have been experimentally verified in many different ways.

It turns out that photosynthesis (the process by which some organisms convert the energy in sunlight into energy that they can use) exploits quantum coherence in an incredible way. When light strikes a photosynthetic organism, its energy must be captured so that it can be used in an amazingly complex process that will convert it from radiant energy into chemical energy. It has long been known that photosynthesis is about 95% efficient when it comes to the first step of capturing light’s energy.1 Until now, however, scientists have not understood how photosynthesis could be that efficient.

After all, harvesting light in a biological environment is difficult. Even though photosynthetic organisms have a well-designed “antenna” system for capturing that light (an example is given above), a living organism is usually in motion. Its environment is also constantly stimulating it in different ways. As a result, even though the antenna system is well designed, it will be distorted and deformed as the organism moves and responds to its environment. This means there should be times when the antenna system is well-aligned, producing very efficient transfer of energy, but there should also be times where it is misaligned, reducing its efficiency. Nevertheless, photosynthesis stays very efficient, regardless of how the antenna complex is distorted.

How does the antenna complex stay efficient? The answer is incredible.

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Another Example of Three-Way Mutualism

Posted by jlwile on June 26, 2013

Mealybugs feeding on a hibiscus plant (Click for credit)

As anyone who has been reading this blog for a while knows, I am fascinated by the phenomenon of symbiosis: two or more species living together in a relationship. In my opinion, the most interesting form of symbiosis is mutualism: two or more species living together in such a way that each species benefits. I have written several different articles about it over the years (see here, here, here, here, and here, for example), and I personally think it is a picture of what creation was like before the Fall.

As scientists have studied mutualism over the years, they have found some really complex examples. In the past, I wrote about a three-way mutualistic relationship that exists between a grass, a fungus, and a virus. Later on, I wrote about a three-way mutualistic relationship that exists between seagrasses, clams, and bacteria. Well, I just learned about another example of a three-way mutualistic relationship. Scientists have known about it for more than 10 years, but it was the subject of a recent study that comes to some rather startling conclusions.

The biggest member of this relationship is the mealybug, which is shown above. It feeds on the sap of plants, but that presents a bit of a problem. In order to make all the proteins it needs to survive, the mealybug must have certain amino acids at its disposal. It can get some of them from its diet, but plants don’t make all the amino acids that the mealybug needs. As a result, it must manufacture some of them. By itself, however, it can’t get the job done. It can make some of the chemicals that are necessary to produce the amino acids, but it can’t make them all. If left on its own, then, the mealybug could not survive.

In 2001, Carol von Dohlen and her colleagues demonstrated that the mealybug has help in making those amino acids. A bacterium, Tremblaya princeps, lives in the mealybug, and it helps the mealybug make the amino acids it can’t get from its diet. However, the bacterium can’t do that job on its own. As a result, a smaller bacterium, Moranella endobia, lives inside it. Together, these two bacteria make the chemicals that the mealybug needs but cannot make itself. All three species are needed in order for the mealybug to survive.1

So here’s the arrangement: a bacterium inside a bacterium inside a bug. It reminds me of an exchange from one of my favorite Dr. Who episodes:

Lily:Where are we?

The Doctor:In a forest, in a box, in a sitting room. Pay attention!”

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Optics Is Starting to Catch Up to the Arthropods

Posted by jlwile on June 24, 2013

This is one of the digital cameras inspired by the design of arthropod eyes (Click for credit.)

There are two basic designs for animal eyes: “simple” eyes and compound eyes. Your eyes are called “simple” eyes, because each has only one lens. The lens focuses light that enters your eye onto a layer of tissue called the retina, which has light-sensitive cells. Those cells detect the light and send electrical impulses to your brain, which then produces an image of what the eye is seeing. In contrast, many arthropods (a broad class of animals including insects, crustaceans, spiders, etc.) have compound eyes. Each compound eye has many lenses, and each lens focuses light onto its own set of light-sensitive cells. The brain then collects the information from each of these optical units (called ommatidia) and produces a composite image.

Each eye design has its own strengths and its own weaknesses. A simple eye produces a very sharp image of whatever the lens is focused on. However, the farther anything is from the center of a simple eye’s vision, the more distorted it becomes. In addition, a simple eye has a narrow depth of field. When it focuses on an object, other things in the field of view are blurry if their distance from the eye is much different from the object being focused on. The compound eye, on the other hand, does not produce very sharp images. However, because its lenses are so small, there is very little distortion of objects that are away from the center of the eye’s view. In addition, the small lenses have a nearly infinite depth of field – objects stay in focus whether they are near or far from the eye.

The practical upshot is that compound eyes tend to be very valuable if you want a wide, panoramic view. In addition, they are very sensitive to motion. If you’ve ever tried to swat a fly, you understand that. The fly seems to see your hand no matter how slowly you move it or where you are relative to the fly. Simple eyes, on the other hand, are more valuable if you want very a very sharp, clear image of what you are focused on. So far, the cameras produced by human science and technology have been modeled after simple eyes. They give sharp, clear images of what the camera focuses on, but the view is not panoramic and the depth of field is narrow.

Now that has changed.

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Give Her What She Wants!

Posted by jlwile on May 9, 2013

Eurasian Jays like this one are monogamous, and the male gets his mate by offering her food (click for credit).

An old proverb says, “The way to a man’s heart is through his stomach.” Some birds, like Eurasian Jays (Garrulus glandarius), have their own take on that proverb. These birds are monogamous,1 and they have an elaborate courtship ritual. Part of that ritual involves the male offering food to the female. For these birds, then, the way to the female’s heart is through her stomach. Obviously, the male wants to offer the female something appealing, but how does he know what she wants?

It has been generally assumed that the male simply offers the female food that he likes. After all, the ability to consider another individual’s feelings is rather advanced. There is some evidence that great apes are able to consider the feelings of human beings,2 but in general, it has been thought that most animals don’t have the intellectual ability to realize that a different individual might have different feelings or preferences. A recent experiment involving Eurasian Jays indicates that might not be correct.

In the experiment, a male was separated from a female by a wire fence. The male could watch the female as she ate large meals of either moth larvae or mealworm larvae. The male was then given a single mealworm larva and a single moth larva. Consistently, the male would pick up the food that was not in the female’s meal and offer it to her through the wire fence. The researchers concluded that this was because the male realized the female would be tired of what she had eaten in her large meal, and therefore the other food would be more appealing to her. This, of course, would mean that the male realized the female might have a different preference than he did, and he took that into account when deciding what to offer her.3

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