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Thursday, April 24, 2014

Really Generous Bacteria!

Posted by jlwile on April 8, 2014

This is an electron microscope image of a bacterium from genus Prochlorococcus.  The colors were added artificially. (click for credit)

This is an electron microscope image of a bacterium from genus Prochlorococcus.
The colors were added artificially. (click for credit)

The image you see above is of a tiny bacterium from genus Prochlorococcus. It is part of a phylum of bacteria called Cyanobacteria, and the members of this phylum are an incredibly important part of the world’s ecosystems. They live in water, converting sunlight and carbon dioxide into sugar and oxygen via photosynthesis. Estimates indicate that cyanobacteria are responsible for producing about 20 to 30 percent of the earth’s oxygen supply.

Prochlorococcus are particularly important cyanobacteria. They are thought to be the most abundant photosynthetic organism on earth, with an estimated worldwide population of an octillion (1,000,000,000,000,000,000,000,000,000).1 More importantly, they tend to live in parts of the ocean that are nutrient-poor. Their photosynthesis helps to alleviate this problem, of course, making them a food source for other organisms that might try to live there.

Dr. Sallie Chisholm at the Massachusetts Institute of Technology (MIT) first described the organisms in 1988 and has continued to study them over the years. She and her colleagues were recently looking at them under an electron microscope and noticed what she described as, “these pimples – we call them ‘blebs’ – on the surface.”2 Dr. Steven J. Biller, a microbiologist who is also at MIT, recognized the blebs as vesicles, which are tiny “sacs” made by nearly every cell in nature. Since the vesicles were found on the surface of the cell, the scientists decided the bacteria were using them to get rid of whatever was inside the vesicles.

They studied the water from their laboratory samples and found that it was, indeed, rich with vesicles that had been released by the Prochlorococcus, and they were surprised by what they found inside.

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More Amazing News About Breast Milk

Posted by jlwile on January 27, 2014

This is an oligosaccharide - a molecule made up of a few simple sugars linked together. (click for credit)

This is an oligosaccharide – a molecule made up of a few simple sugars linked together.
(click for credit)

Approximately a year ago, I wrote about the bacteria in human breast milk. While that may sound like a bad thing, it is actually a very good thing. Over the years, scientists have begun to realize just how important the bacteria that live in and on our bodies are (see here, here, here, here, and here), and the bacteria in breast milk allow an infant to be populated with these beneficial microbes as early as possible. Not surprisingly, as scientists have continued to study breast milk, they have been amazed at just how much of it is devoted to establishing a good relationship between these bacteria and the infant who is consuming the milk.

For example, research over the years has shown that human breast milk contains chemicals called oligosaccharides. These molecules, such as the one pictured above, contain a small number (usually 3-9) simple sugars strung together. Because oligosaccharides are composed of sugars, you might think they are there to feed the baby who is consuming the milk, but that’s not correct. The baby doesn’t have the enzymes necessary to digest them. So what are they there for? According to a review article in Science News:1

These oligosaccharides serve as sustenance for an elite class of microbes known to promote a healthy gut, while less desirable bacteria lack the machinery needed to digest them.

In the end, then, breast milk doesn’t just give a baby the bacteria he or she needs. It also includes nutrition that can be used only by those bacteria, so as to encourage them to stay with the baby! Indeed, this was recently demonstrated in a study in which the authors spiked either infant formula or bottled breast milk with two strains of beneficial bacteria. After observing the premature babies who received the concoctions for several weeks, they found that the ones who had been feed bacteria-spiked formula did not have nearly as many of the beneficial microbes in their intestines as those who had been feed bacteria-spiked breast milk.2

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Cellular Communication – Another “Truth” Destroyed

Posted by jlwile on January 20, 2014

The insulin-producing cells in the islets of the pancreas use a communication strategy that is probably not the most common form in nature (click for credit).

The insulin-producing cells in the islets of the pancreas use a communication strategy that is probably not the most common form in nature (click for credit).

Naturalistic evolutionists are forced to look at the world very simply. After all, they think there is no plan or design in nature. Instead, they believe that random events filtered by natural selection are responsible for all the marvels we see today. Because of this unscientific way of thinking, they tend to look for simple processes to explain amazingly complex interactions in nature. Cellular communication is a perfect example of how this simplistic way of looking at things can produce serious errors.

In order for the different cells of an organism to be able to work together, they must communicate with one another. One of the most well-studied versions of cellular communication is called endocrine communication, and the insulin-producing cells in the islets of the pancreas (illustrated above) provide an example of how it works. These cells produce insulin, which is then released into the bloodstream. When cells in the liver, skeletal muscles, and fat tissues are exposed to this chemical, they absorb glucose (a simple sugar) from the blood. By controlling the release of insulin from the pancreatic islets, then, the body can control how much glucose is in the blood.

Now, of course, this is a great design for cellular communication that needs to affect a wide array of cells in many different places. It makes the release of the chemicals easy to control but their effect long-ranging. As a result, when the body needs widespread communication in different cells, endocrine communication is used. However, there are often times when cells need to communicate with other cells that are nearby. This is called paracrine communication, and biologists have taught (as fact) for many, many years that paracrine communication happens in essentially the same way as endocrine communication. For example, one of the volumes of the Handbook of Cell Signaling says:1

Paracrine interactions induce signaling activities that occur from cell to cell within a given tissue or organ, rather than through the general circulation. This takes place as locally produced hormones or other small signaling molecules exit their cell of origin, and then, by diffusion or local circulation, act only regionally on other cells of a different type within that tissue. (emphasis mine)

In other words, a cell releases some signaling chemicals, and those chemicals simply have to find their way to their targets via diffusion or some other local means of movement. Of course, such a signalling scheme is rather inefficient for communication with nearby cells, and new research indicates that it’s not the way paracrine communication is done.

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DNA Is Even More Sophisticated Than We Thought!

Posted by jlwile on December 17, 2013

The information in DNA is stored in sequences of four different nucleotide bases (A, T, C, and G). In a gene, three nucleotide bases code for a specific amino acid, and that three-nucleotide-base sequence is called a 'codon.' (click for credit)

Over the years, scientists have learned a lot about DNA. Nevertheless, the molecule continues to surprise us with its exquisite design. Not long ago, scientists demonstrated that a single gram of DNA can store about 500,000 CDs worth of information. It has also been shown that the code used by DNA to store this information has been specifically designed to allow living organisms to respond to their environment in many different ways. In addition, we know that DNA stores its information in “modules” that can be rearranged in many different ways. This allows a single stretch of DNA to contain many different meanings, depending on how the modules are put together.

In the December 13 issues of Science, researchers have demonstrated yet another incredible design feature of DNA, and according to the University of Washington, the scientists who made the discovery were “stunned.” To understand what was done and what the discovery means, however, you need a little bit of background information on DNA and how it is used by the cell.

DNA stores its information in sequences of nucleotide bases called adenine (A), thymine (T), guanine (G), and cytosine (C). As shown in the illustration above, those nucleotide bases link together to hold DNA in its familiar double helix shape. The meaning of each sequence depends on where it is in the molecule. In many organisms, a small fraction of the DNA is made up of genes, and in most of the organisms with which you and I are familiar, the genes consist of two regions: exons and introns. The exons of a gene contain the recipe that tells the cell exactly how to make a protein. This recipe is given in groups of three nucleotide bases, which are called codons. Each codon specifies a certain chemical called an amino acid. When the cell stitches amino acids together in the sequence given by the codons, it makes a useful protein.

Introns are “spacers” that exist between the codons in a gene. Once derided by evolutionists as “junk DNA,” we now know that introns are a powerful means by which the exons are split up into functional information modules. The cell can stitch the modules together in different ways, so that a single gene can instruct the cell on how to make many different proteins. This is called alternative splicing, and it is a incredibly powerful design feature that allows DNA to store its information with amazing efficiency. Indeed, thanks to alternative splicing, there is a single gene in fruit flies that can tell the cells to make 38,016 different proteins!1

Now don’t get lost in all the terminology. Think of it this way: genes tell the cell how to make proteins. However, to increase the information storage capability of DNA, these genes are split into two regions: exons and introns. The introns separate the exons into modules of useful information, and the cell stitches those modules together in different ways so that a single gene can tell the cell how to make lots and lots of different proteins.

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Insults Do Not an Argument Make

Posted by jlwile on December 4, 2013

This book by Dr. Stephen Meyer has elicited a lot of insults from its critics, but not much reasoned response.

Nearly two years ago, I wrote a review of double-doctor Alister McGrath’s book Why God Won’t Go Away. It ends with an amusing anecdote about a young man who meets Dr. McGrath and asks him to sign one of his theology books. The young man tells Dr. McGrath that he has Richard Dawkins to thank for his conversion to Christianity. He had read Dawkins’s The God Delusion and thought it was so unfair and one-sided that he had to look at the other side. When he did, he become convinced of the reality of Christianity.

While one might pass this off as an isolated incident, it’s not clear that’s the case. Not long ago, I blogged about another person who was raised Catholic but became an agnostic in her teens. She read The God Delusion and similar works, thinking it would drive her to atheism. Once she read Dawkins and his fellow New Atheists, however, she read authors on the other side of the debate. In comparison, she found the arguments of Dawkins and his ilk intellectually deficient, so she returned to her Catholic faith.

Note what happened in both of these cases. Each person decided to look at both sides of the issue. They looked at the arguments of those who claimed there is no God, and they looked at the arguments of those who claimed there is a God. Both decided that those who argued against the existence of God had a significantly weaker position. As a result, they ended up believing in God.

But what makes the arguments of the New Atheists so weak? It’s not just that they have little evidence to back up their claims. It’s more than that. I think one of the reasons their arguments are so weak is that they try to make up for their lack of evidence with insults and bluster. Somehow, they think they are making their case stronger, but to most reasonable people, it has the opposite effect. A few days ago, I ran across a story that makes this very point.

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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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Sofishsticated Swimming

Posted by jlwile on November 13, 2013

This is a glass knifefish like the one used in the study (click for credit)

Many aspects of nature are a mystery to science, and at least part of the reason is that nature has been designed so incredibly well. There are systems running in nature that are simply too complex for us to understand and, as a result, their functions remain a mystery. Not all that long ago, for example, many biologists were silly enough to actually think the human genome was mostly junk, simply because they couldn’t understand what the vast majority of the human genome does. Of course, as we have learned more about DNA, we have learned that what was once considered “junk” is vitally important (see here, here, and here, for example). Since the Encode project published its first major results, most reasonable biologists have slowly started to realize what creationists have said all along – there really isn’t much (if any) junk DNA.

Even on a larger scale, there are many aspects of nature that are very hard to understand. A recent article in the Proceedings of the National Academy of Sciences of the United States of America provides an example:1

Animals often produce substantial forces in directions that do not directly contribute to movement. For example, running and flying insects produce side-to-side forces as they travel forward. These forces generally “cancel out,” and so their role remains a mystery.

Why would a moving animal expend energy to produce forces that are perpendicular to its motion? Those forces don’t contribute to the animal’s forward motion, and they tend to cancel each other out. As a result, they are often called “antagonistic forces.” Such forces seem like an utter waste of energy. Nevertheless, lots of animals do this. In addition, some animals exert antagonistic forces even when they are not moving in a given direction. Hummingbirds, for example, produce antagonistic forces when they are hovering over a flower.

To understand the purpose of antagonistic forces, the authors of the study examined the glass knifefish (Eigenmannia virescens). When this fish is “hovering” in the water, it uses its fins to produce antagonistic forces. It has been thought that these forces might improve the fish’s ability to control its position and orientation in the water, but no one understood how.2

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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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People Weren’t The First to Develop an Internet!

Posted by jlwile on August 26, 2013

This microscope image shows an arbuscular mycorrhizal fungus in a clover plant's roots.
(Click for credit.)

The microscope picture above shows you a clover root (the mostly transparent material in the picture) whose cells have been “infected” with a fungus (the thick, dark material in the picture). At first glance, you might think the fungus is a parasite that takes nutrients from the plant, but that’s not really true. While the fungus does take nutrients from the clover, it also supplies the plant with critical nitrogen- and phosphorus-based chemicals that the plant has a hard time extracting from the soil. This is a mutually-beneficial relationship, which is often called a mutualistic relationship.

As anyone who has read this blog for a while knows, I am fascinated by such relationships. I have blogged about them many, many times before (see here, here, here, here, here, and here, for example). In fact, I have blogged about this specific kind of mutualistic relastionship before. It is called a mycorrhiza, and it is very, very common in nature.

About 95% of all vascular plants develop mycorrhizae,1 and these relationships come in many different forms. For example, in the relationship shown above, the fungus forms a highly-branched structure called an arbuscule, which comes from the Latin word arbusculum, which means for “little tree.” This arbuscule is formed inside the walls of the root’s cells, and the fungus is called an arbuscular mycorrhizal (AM) fungus. Such fungi cannot exist by themselves. They can only exist as a part of a mycorrhizal relationship. There are other forms of mycorrhizae as well, but the study I want to discuss is specifically about AM fungi.

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The Blue Planet

Posted by jlwile on August 21, 2013

The blue dot pointed out in this picture is the earth as seen from Saturn.
(Credit: NASA/JPL-Caltech/Space Science Institute) Click for a full-sized version.

Astronomers call earth “the blue planet,” because when you look at it from space, it often appears blue. That’s because most of the earth is covered with water, which reflects blue light better than the other colors of light. So when white light from the sun hits the earth, more blue light is reflected than any other color (as long as there isn’t an enormous amount of cloud cover).

The Cassini space probe that is currently in orbit around Saturn recently had a chance to photograph the earth. It appears as the tiny blue dot pointed out in the photo above. Please click on the photo to get the full-sized version. It really is magnificent. At the time the photo was taken, the earth was 898 million miles away from the Cassini space probe. Nevertheless, it appears as a vivid blue dot on a mostly dark background. In addition, if you “zoom” in close enough, you can actually see the moon orbiting the earth:

The earth (left) and moon as seen from 898 million miles away.
(Credit: NASA/JPL-Caltech/Space Science Institute) Click for a full-sized version.

Notice the differences between the earth and the moon. The moon is smaller, but more strikingly, it appears a stark white next to earth’s blue.

The earth has been intricately designed as a haven for life. Its blue color is a beacon proclaiming that, and the beacon can be seen from nearly 900 million miles away!