Once Again, It’s Just Not That Simple…

Two versions of the same species of coccolithophore - the heavily-calcified one is on the left
(image from the paper being discussed)

A few months ago, I discussed the acidification of the ocean. It is often called global warming’s “evil twin,” because it is caused by rising carbon dioxide levels in the atmosphere. Unlike global warming, however, the connection between carbon dioxide levels in the atmosphere and increasing ocean acidity is straightforward and has been confirmed by many observations. Thus, while it is not clear that increased levels of atmospheric carbon dioxide will lead to global warming, it is very clear that increased levels of atmospheric carbon dioxide lead to an increase in the acidity of the ocean.

The question is, “How will increased ocean acidity affect the organisms living there?” Many who call themselves environmentalists answer that question by saying increased ocean acidification will produce catastrophic results, threatening many species of ocean life. The reason? Many organisms that live in the ocean have shells made out of calcium carbonate. To make those shells, the organisms use carbonate ions that are dissolved in the seawater. However, as the acidity of ocean water increases, the concentration of carbonate ions in the water decreases. Thus, it is thought that increased ocean acidification will make it harder for these organisms to make their shells. Here’s how one publication from the National Academies puts it1

As ocean acidification decreases the availability of carbonate ions, these organisms must work harder to produce shells. As a result, they have less energy left to find food, to reproduce, or to defend against disease or predators. As the ocean becomes more acidic, populations of some species could decline, and others may even go extinct.

Now if that’s true, ocean acidification is a major problem. Indeed, if several shell-making organisms go extinct, we could be in real trouble.

However, this is a very simplistic way of looking at things. Yes, the availability of carbonate in the ocean will affect how easily shell-making organisms produce their shells. However, there are a host of other factors involved in the process. To single out one factor without considering the others is not very scientific. When all the factors are considered, the picture is not nearly as bad.

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Stone-Age Animation

When you flip this thaumatrope back and forth, it looks like the flowers are in the vase. (public domain image)
It’s sad to see how evolutionary thinking causes so many misconceptions in the realm of science. For example, evolutionary thinking has produced the idea that “stone age” people were primitive and barbaric. Of course, as is the case with most evolution-inspired ideas, this one doesn’t stand up in light of the evidence. The more research is done, the more we know that “stone age” people had an advanced culture all their own.1 A recent finding that I just read about in Science News adds more evidence to support the fact that there was nothing very “primitive” about ancient people.

The article starts out like this:2

By about 30,000 years ago, Europeans were using cartoonlike techniques to give the impression that lions and other wild beasts were charging across cave walls, two French investigators find. Artists created graphic stories in caves and illusions of moving animals on rotating bone disks…

While it’s very interesting that ancient artists were painting scenes that produced the impression of motion, the thing that really caught my eye was the part about the rotating bone disks. The article has three pictures that show how one of them worked (you can see them here), and when I saw those pictures, I immediately recognized it as a thaumatrope. However, according to everything I have read, the thaumatrope was invented in 1825. For example, here is how Ray Zone puts it in his book, Stereoscopic Cinema and the Origins of 3-D Film, 1838-1952:3

The fundamental principle behind the movies is persistence of vision, when a visual impression remains briefly in the brain after it has been withdrawn. This principle was demonstrated in 1825 with an optical toy called the “Thaumatrope,” invented by Dr. John Ayrton Paris.

Obviously, Mr. Ray is off by a few years!

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Animal Magnetism

Brown trout like this one return to the stream in which they hatched in order to spawn. (Click for credit)
Many species of fish, such as the brown trout pictured on the left, hatch in streams and then travel away from those streams in order to mature. However, when it is time to reproduce, they end up navigating back to the same stream in which they hatched so they can spawn there. How do they accomplish this? How do they know where they are and which way to swim in order to get back to that special stream? Based on behavioral studies, scientists have thought that these fish are able to sense the earth’s magnetic field and use it as an aid in their navigation. However, the specific source of this magnetic field sense has been elusive…until now.

A recent study has shed a lot of light on this magnetic sense, at least for trout (and presumably other similar fish, like salmon). The authors of the study set out to determine what gives the trout their magnetic sense, and they developed a rather ingenious method to aid them in their search. First, they took tissue samples from the trout’s nasal passages, because previous studies indicated that there was magnetite (a mineral that reacts strongly to magnetic fields) in those tissues.1 Then, they put cells from the tissues under a microscope and exposed the cells to a rotating magnetic field. In response, some of the cells rotated with the field.2 You can actually see a video of this happening here! Just click on the links for downloading the movies.

This is a very simple, very sensitive method for finding the cells responsible for the trout’s magnetic sense. As you can see from the video, the cells that are sensitive to the rotating magnetic field are smaller than the other cells in the tissue. Also, the authors found that only 1 in 10,000 cells in the nasal tissue have a magnetic sense. No wonder these cells haven’t been found until now! Of course, as the authors studied the cells more closely, they found evidence of thoughtful design.

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One Gene = One Protein? Not Even Close!

In a previous post, I discussed alternative splicing, an amazing aspect of our DNA that allows it to store information in a compact, elegant way. In brief, a gene is actually a recipe that the cell uses to make a particular protein. Since most of a cell’s DNA is in the nucleus, the “recipe” stored in that gene must leave the cell’s nucleus in order to be turned into a protein. To do that, the “recipe” is copied by a molecule called messenger RNA (mRNA). The mRNA then takes the copied “recipe” out of the nucleus to the ribosome, which is where proteins are made.

In eukaryotic cells (the kinds of cells found in plants and animals), however, something very interesting happens before the mRNA leaves the nucleus. Some parts of the mRNA are cut away, and the remaining parts are then stitched back together. The parts of the mRNA that are cut away never leave the nucleus, so they are called introns (they stay IN the nucleus). The remaining parts that are stitched together are called exons (they EXit the nucleus). For a while, geneticists didn’t know the purpose of introns, so in typical evolutionary fashion, many decided that they had no purpose, and introns were lumped into the category of “junk DNA.” Of course, as we have learned more about genetics, we have learned that the evolution-inspired idea of “junk DNA” is, itself, junk, although some evolutionists still cling to it.

Nowadays, of course, we know the reason that introns exist. It is part of the design of the Creator, allowing DNA to store information in an incredibly efficient way. Each exon represents a “module” of useful information. If the cell stitches the exons together in one way, it makes one protein. If it stitches the exons together in another way, it makes a different protein. As a result, a single gene can actually produce many different proteins. The introns not only serve as a means by which the cell can identify the exons, they also regulate the amount of the various proteins that are being made.

This process of alternative splicing is illustrated in the figure below:

Because of alternative splicing, a single gene can tell the cell to produce different proteins. (public domain image)

In the previous post about alternative splicing, I discussed how recent evidence suggests that up to 95% of the genes in the human genome participate in this process. However, I did not address how many different proteins a single gene can produce using alternative splicing. In some cases, the answer is truly astounding.

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Another Example of Three-Way Mutualism. Is This Just the Tip of the Iceberg?

A white-spotted pufferfish in a seagrass bed (click for credit)

Over two years ago, I wrote about an interesting three-way mutualistic relationship between a virus, a fungus, and a plant. Less than a year later, I wrote about how people are actually walking ecosystems, participating in a huge number of mutualistic relationships with many different species of bacteria. Last night, while reading the scientific literature, I ran across another example of a three-way mutualistic relationship, and it is equally as fascinating!

This three-way relationship starts with seagrasses. Coral reefs are the “stars” of the marine world, but seagrass communities can be considered its “workhorses.” While they make up only 0.2% of the ocean’s ecosystems, they produce more biomass than the entire Amazonian rainforest!1 Why are they so productive? Because they form a wide variety of marine ecosystems that serve as nurseries for many developing fishes and homes to a wide variety of sea creatures including turtles, manatees, shrimp, clams, sea stars, etc. Because of their amazing ability to support such ecosystems, seagrasses have been studied by marine biologists for some time. However, there has always been a nagging mystery associated with them.

The roots of seagrasses trap sediments which form a rich mud that is often several feet deep. The mud is rich because it contains all manner of decaying organic matter. However, the reason the organic matter decays is because bacteria decompose it. One of the byproducts of this bacterial decomposition is sulfide, and if that sulfide were allowed to build up to high concentrations, it would actually end up harming the seagrasses themselves. However, it never does. No one has proposed a satisfactory explanation as to why this doesn’t happen.

Certainly, the seagrasses transport oxygen to the mud through their roots, and that oxygen can turn the sulfide into sulfate, which is harmless to the seagrasses. However, detailed studies show that the sulfide produced by the resident bacteria accumulates far faster than it can be removed by the oxygen that is added to the mud through the seagrasses’ roots, especially during warm seasons.2 Thus, there must be some other way that sulfide is being removed from the mud.

Marine biologists had no idea what this other way was…until now.

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Human Body Hair is Useless, Right? WRONG!

Many evolutionists think that body hair in humans is useless. The data say otherwise. (Click for credit)
One of the many reasons scientists are rejecting the hypothesis of evolution (see here and here, for example) is that many of its predictions have been falsified (see here, here, here, and here for even more examples). The more we learn about the world around us, the more clear it is that the predictions of the evolutionary hypothesis just don’t work. This is probably most apparent when it comes to “vestigial organs,” biological structures that are supposed to serve no real purpose; they are simply leftover vestiges of the evolutionary process. As Darwin himself said, they are like the silent letters of a word. They don’t serve a purpose in the word, but they do tell us about the word’s origin.

I have written about vestigial structures many times before (here, here, here, here, here, here, and here) because they are so popular among evolutionists. However, as the data clearly show, the evolutionists are simply wrong about them, and the more research that is done, the more clear it becomes. The latest example is human body hair. This has always been a favorite among evolutionists. Here are two evolutionary descriptions of human body hair. The first comes from a book specifically designed to help the struggling evolutionist in his attempt to convince people that his hypothesis has scientific merit.1

Humans, like all other organisms, are living museums, full of useless parts that are remnants of and lessons about our evolutionary histories (Chapter 6). Humans have more than 100 non-molecular vestigial structures. For example, our body hair has no known function.

The second comes from a textbook2

Body hair is another functionless human trait. It seems to be an evolutionary relic of the fur that kept our distant ancestors warm (and that still warms our closest evolutionary relatives, the great apes).

As is the case with most evolutionary ideas, serious scientific research has shown that such statements are simply wrong.

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One Way To Think About the Complexity of the “Simplest” Life Form

A cluster of 14 computers. The simulation discussed in this article used a cluster of 128 computers. (Click for credit)
I have always been fascinated by the question, “How simple can life get?” After all, anything that is alive has to perform certain functions such as reacting to external stimuli, taking in energy and converting that energy to its own use, reproducing, etc. Exactly how simple can a living system be if it has to perform such tasks? Many biologists have investigated this question, but there isn’t a firm answer. Typically, biologists talk about how simple a genome can be. The simplest genome belongs to a bacterium known as Carsonella ruddii. It has 159,662 base pairs in its genome, which is thought to contain 182 genes.1 However, it is not considered a real living organism, as it cannot perform all the functions of life without the help of cells found in jumping plant lice.

The bacterium Pelagibacter ubique has the smallest genome of any truly free-living organism. It weighs in at 1,308,759 base pairs and 1,354 genes.2 However, there is something in between these two bacteria that might qualify as a real living organism. It is the bacterium Mycoplasma genitalium. It’s genome has 582,970 base pairs and 525 genes.3 While it is a parasite, it performs all the functions of life on its own. It just uses other organisms (people as well as primate animals) for food and housing. Thus, while it cannot exist without other organisms, it might be the best indicator of how “simple” life can get.

If you follow science news at all, you might recognize the name. Two years ago, Dr Craig Venter and his team constructed their own version of that bacterium with the help of living versions of the bacterium, yeast cells, and bacteria of another species from the same genus. Well, now a scientist from Venter’s lab teamed up with several scientists from Stanford University to produce a computer simulation of the bacterium!

Their work, which seems truly marvelous, gives us deep insight into how complex the “simplest” living organism really is.

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A Real-Life Example of “Convergent Evolution”

Several times in the past (here, here, here, here, and here), I have written about convergent evolution and the problems it poses for anyone who wants to believe that all the amazing organisms we see today are the result of a mindless evolutionary process. As a quick review, remember that in general, evolutionists claim that similarities are the result of common ancestry. All vertebrate limbs look very similar, for example, because all vertebrates evolved from a common ancestor. While evolution “tweaked” the design of each animal’s limb so that it could be properly adapted to its environment, the basic structure of the vertebrate limb is the same in all vertebrates because they all inherited that basic structure from a common ancestor.

Of course, as is usually the case for evolution, more and more data have been collected that are inconsistent with this idea. Dolphins and bats, for example, both use sonar to navigate and to seek out prey. However, there is no hypothetical sonar-using common ancestor that links them. Thus, while they are very similar in this regard, evolutionists have to say that this particular similarity is not due to common ancestry. Instead, it is the result of “convergent evolution.” Both animals evolved the ability to use sonar independently, along different evolutionary lines. In other words, evolution “converged” on the same system in two different, unrelated cases.

Now please understand that this similarity is very deep. Indeed, the genes that allow this process to happen are nearly identical in these two animals.1-2 So in order to understand the use of sonar in dolphins and bats, evolutionists have to believe that evolution just happened to come up with the same system (all the way down to the genes) for navigation and predation in two completely different lineages.

If this were the only case in which unrelated organisms have amazingly similar systems, it might be reasonable to chalk it up to evolution just being “lucky” enough to come up with the same system twice. However, as evolutionist Dr. Simon Conway Morris tells us, nature abounds with examples of this. Indeed, most evolutionists believe that eyes must have evolved independently in unrelated lineages as many as 60 times in order to be consistent with the data at hand!3

If all of that seems far fetched to you, don’t worry. You are not alone. Most reasonable people can see when an attempt to explain around inconvenient data becomes desperate.

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Another “Fact” I Was Taught Bites the Dust

One of the fascinating things about science is that its conclusions are constantly changing. Because of new experimental techniques and closer investigation, many “scientific facts” that I was taught at university are now known to be false. This makes science interesting, to say the least! As someone who has published original research that has drawn conclusions regarding the nature of the atomic nucleus, I often wonder how long it will take for some of those conclusions to be demonstrated false!

In a previous post, I discussed Bateman’s Principle, which some evolutionists considered to be a scientific law. However, we now know that not only is Bateman’s Principle not true in many, many species, it was also based on faulty experiments. In the course of the discussion that followed, a commenter mentioned another scientific “law” that is probably wrong – the idea that a woman is born with all the egg cells she will ever have. I decided to look into this topic, and I was amazed at what I had missed in the course of my normal scientific reading. Thank you, Shevrae, for alerting me to the new advances in this area.

In case you didn’t have a detailed course on human anatomy and physiology, you might not know that it has been considered a scientific fact since the 1950s that when a woman is born, she has all the egg cells she will ever have. This “fact” is based on some really good research. During the fourth month of development in the womb, it has been shown that female babies start producing oogonia, which are cells that start to develop into egg cells. However, they are stopped early in their development and are surrounded by a protective layer of cells. This structure (the cell that is “frozen” in development and its protective case) is called a primordial follicle.

When a woman is born, she has hundreds of thousands (sometimes millions) of primordial follicles in each ovary, but some degenerate during childhood. When she reaches puberty, she generally has about 400,000 primordial follicles in her ovaries. After puberty, hormone cycles regularly cause some of the primoridal follicles to continue development. The nature of the protective cell layer changes, and the cell inside the protective layer continues its development into an egg cell. Interestingly enough, however, the process will not fully complete unless the developing egg cell is fertilized by a sperm. If no fertilization takes place, the cell that has been developing dies without ever forming a true egg cell.

All of the above statements are (as far as we can tell) true. Based on these facts, it has been taught for more than 60 years that since a woman starts out with hundreds of thousands of primordial follicles when she is born, she never makes any new ones. Thus, a woman is born with all the potential egg cells she will ever have. New research indicates that this conclusion is false.

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Dinosaur Feathers? Probably Not.

A Sinosauropteryx fossil showing the 'fuzz' that has been interpreted as either proto-feathers or collagen, (Click for Credit)

In 1996, a farmer and part-time fossil hunter in the Liaoning Province of China found a fossil that he recognized was rather unique. It had all the hallmarks of a dinosaur, but it had some “fuzz” on the head, neck, back and tail that looked like hair or feathers. Over the years, two distinct interpretations of this “fuzz” have emerged. Some scientists, like world-renowned paleornithologist Dr. Alan Feduccia, considers it to be nothing more than collagen fibers that remain from skin structures such as frills. Others, like paleontologist Dr. Mike Benton, think it is the remains of “protofeathers,” an evolutionary precusor to bird feathers. Given the current “birds evolved from dinosaurs” craze, you can guess which view is held by the majority of those who have studied the fossil.

Of course, science is not done by majority vote. It is done by examining the data. So what do the data say about this “fuzz?” Well, in 2007, Feduccia and some colleagues published a study in the Proceedings of the Royal Society B. In that study, they examined the detailed structure of the “fuzz.” They showed that its structure is exactly what you would expect for protein fibers that would be used to stiffen a system of frills. In addition, they say:1

The fibres show a striking similarity to the structure and levels of organization of dermal collagen. The proposal that these fibres are protofeathers is dismissed.

Of course, that’s not the end of the story.

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