DNA uses four nucleotide bases taken three at a time to code for an animo acid (click for credit).The genetic code is degenerate, but that doesn’t mean it is immoral or corrupt. In fact, in the case of the genetic code, degeneracy is a good thing! Let me explain. One of DNA’s jobs is to tell the cell what proteins to make and how to make them. As a result, it stores “recipes” for proteins, and we call those recipes genes. Well, a protein is produced when smaller chemicals, called amino acids, are linked together in long chains that then fold into intricate shapes. So in order to tell a cell how to make a protein, a gene needs to list a string of amino acids. If the cell puts those amino acids together in the order specified by the gene, the correct protein can then be produced.
How does a gene list the amino acids? As shown in the illustration above, it does so by using the four nucleotide bases known as cytosine (C), guanine (G), thymine (T), and adenine (A). A group of three nucleotide bases codes for a specific amino acid. For example, when a gene has three thymines in a row (TTT), this means “use the amino acid called lysine.” When it has three guanines in a row (GGG), it means “use the amino acid called proline.” So by grouping its four nucleotide bases three at a time, a gene specifies which amino acid should be used in building a protein.
Here’s the catch: There are only 20 amino acids in the standard proteins of life. As a result, there need to be only 20 codes to specify them. However, there are 64 possible ways you can group four nucleotide bases three at a time. Thus, there are 64 different possibilities for how a gene can specify an amino acid, but there are only 20 amino acids the gene needs to specify. As a result, most amino acids are specified by more than one set of three nucleotide bases. As I said above, a sequence of three thymines (TTT) means “use the amino acid called lysine.” However, two thymines followed by a cytosine (TTC) means the same thing. This is why we say the genetic code is degenerate. It has multiple ways it can specify most amino acids.
Clostridium difficile from a stool sample, magnified 3,006x (public domain image fron the CDC)
Clostridium difficile is a bacterium that produces toxins which can kill intestinal cells and cause severe inflammation of the intestinal walls. Mild infections from this bacterium can cause diarrhea, while severe infections can cause death. Over time, C. difficile infections have gotten worse. As one medical resource states:1
C. difficile infection has transformed from a nuisance into a potentially life-threatening illness with an attributable mortality rate of up to 16.7%.
The typical treatment for severe cases of C. difficile infection is a round of strong antibiotics, but that doesn’t always work. A significant number of patients end up experiencing one or more recurring infections within 60 days.2 As a result, medical researchers are trying to come up with new ways to treat this infection.
In a recent study published in the New England Journal of Medicine, researchers tested an…interesting…approach. They took 43 patients who had a C. difficile infection and split them into three groups. The first received the standard antibiotic treatment (in this case, 500 milligrams of vancomycin four times per day for 14 days). The second received the standard antibiotic treatment plus a bowl lavage 4 or 5 days into the treatment. In case you aren’t familiar with the term, a bowel lavage involves flushing out the intestines. It is usually done to prepare the intestine for medical imaging. The third group was given a shortened round of antibiotics (500 milligrams of vancomycin four times per day for 4 or 5 days), a bowel lavage, and then a poop transplant.
Yes, you read that right. After the bowel lavage, the patients were given a mixture of water, salt, and the feces from a healthy donor. Now don’t worry. They didn’t have to eat or even smell the stuff. It was sent into their intestine through a sterile tube that went up the nose, down the esophagus, through the stomach, and into the start of the small intestine. While the process sounds incredibly gross, the results were amazing!
The black circles in this figure represent the 73 quazars that make up the largest structure in the observed universe. The red crosses represent the 34 quazars that make up another massive structure. (Image is from reference 3.)
One of the more absurd assumptions that is routinely made in astronomy is called the cosmological principle. One way to phrase the principle is:
Viewed on a large enough scale, the properties of the universe are the same no matter where you are.
However, observations have never supported this assumption. Instead, the observable universe seems incredibly “lumpy,” with huge structures separated by vast areas devoid of structures. Nevertheless, cosmologists have doggedly taken the cosmological principle as their starting assumption when it comes to developing models of the universe, despite the fact that observations don’t support it.
Indeed, the cosmological principle is a necessary starting point for the Big Bang, which most, but certainly not all, astronomers think is a good description of the origin and development of the universe. As Paul Fleisher says in his book, The Big Bang:1
The cosmological principle is the central idea of the Big Bang theory. This rule says the universe is homogeneous and isotropic at very large scales.
Even if we go away from the Big Bang model, the vast majority of models that attempt to describe the universe start with the assumption that the cosmological principle is valid. There are some models that do not start with that assumption, but they are few and far between.2
I have always been skeptical of the cosmological principle, simply because it isn’t supported by observation. The universe doesn’t look homogeneous at all. Instead, it looks really “lumpy.” Nevertheless, when I read the scientific literature, the cosmological principle seems to be considered a fact in almost all of the astronomy-related papers.
Horizontal Gene Transfer (represented by the arrows and paths connecting the different lineages in the drawing) is a convenient way for evolutionists to explain around the fact that the data falsify their predictions. (Click for credit)
When I was a young, impressionable student at university, I was taught as fact that all organisms on this planet could be arranged in a hypothetical “tree of life” that showed how all of them evolved from a single, common ancestor. It didn’t matter that no such tree had actually been constructed. I was told that in time, we would be able to sequence DNA quickly and efficiently, and once that happened, the tree of life would emerge from the data in all its glory. However, once DNA analysis did become reasonably quick and efficient, the tree of life never emerged. Instead, the supposed evolutionary relationships that had been determined from the fossil record were contradicted by those that were determined from the genes. Worse yet, the genetic story of evolution changed depending on which specific genes were studied.
This was especially apparent in the analysis of single-celled organisms. As more and more genetic analyses were done on such organisms, it became increasingly obvious that there was simply no way to arrange their genetic information into any pattern that even remotely resembled a hypothetical tree of life. Some scientists understood what this meant: there is something seriously wrong with the evolutionary framework to which biologists have been clinging. As a result, they have started investigating other, more promising paradigms such as creationism or intelligent design. However, most biologists continue to cling to a view that has been falsified again and again by various data. As a result, they had to find a “way out.” They had to find some means by which they could explain around the fact that the genetic data falsified the tree of life.
Enter the concept of Horizontal Gene Transfer, also known as lateral gene transfer. In this process, a section of DNA is transferred from the genome of one organism to the genome of another, unrelated organism. In other words, rather than passing down a gene through the process of reproduction, horizontal gene transfer allows a gene to travel horizontally between unrelated organisms.
Now the phenomenon itself was known long before the problem with the tree of life had been documented. Way back in 1960, for example, Japanese scientists determined that an antibiotic-resistant bacterium could transfer its resistance to an unrelated bacterium that was not resistant to the antibiotic.1 In time, the mechanism was fully worked out, and it was demonstrated that bacteria could, indeed, swap genes back and forth. As it became increasingly clear that this was a common phenomenon among bacteria, it was recognized that horizontal gene transfer could “smear out” the tree of life for single-celled organisms.2
Since horizontal gene transfer was so successful at explaining away the failed evolutionary prediction of the tree of life when it came to single-celled organisms, it’s not surprising that this same “way out” is now being used to explain why certain genes in animals do not fit the pattern predicted by the evolutionary hypothesis.
Male DNA was found in 63% of the women studied.
(Public domain image)A gene called DYS14 is found only on the Y chromosome in human beings. Of course, only males have a Y chromosome, so it is reasonable to assume that the only place you will ever find this gene is in men, right? Wrong! William F. N. Chan and his colleagues examined the brains of 59 deceased women, and they found the gene residing in 37 of the brains studied! In other words, 63% of the deceased women studied had male DNA in their brains. Interestingly enough, in most of those brains, the DNA was found in several different places!1
How in the world did male DNA get into these women’s brains? The researchers aren’t sure, because they don’t have detailed medical histories for most of the women. However, the most likely explanation is that the DNA comes from the male children that these women carried. I have written about this phenomenon, called fetomaternal microchimerism, before. As I mentioned in that article, when I first heard about a baby leaving cellular remains inside his or her mother, I thought it couldn’t possibly be true. However, I was wrong. There is solid evidence to suggest that not only do babies leave a lasting, cellular imprint on their mothers, mothers do the same for their babies.
However, the possibility that children leave some of their DNA behind in their mother’s brain is very surprising. After all, the cells that make up the brain are incredibly sensitive. In fact, the contents of your own blood are toxic to your brain cells. As a result, you have an elaborately designed blood-brain barrier that shields your brain cells from your blood. This barrier is so vigilant that it allows only certain substances (such as the glucose and electrolytes that the brain cells need) to pass through it. As a result, your brain cells are protected from the majority of substances found in your bloodstream.2
These Bifidobacterium longum bacteria are often found in the intestines of infants. (Click for credit)The breast milk that a mother feeds her baby is laden with bacteria. Does that sound bad? It shouldn’t! While there are some pathogenic bacteria, most bacteria are incredibly beneficial to the life that exists on this planet. That’s especially true of bacteria that live in and on people. It turns out that most people live in a relationship with more than 150 different species of bacteria, and the individual bacteria that participate in this relationship far outnumber the human cells that make up a person’s body. In one sense, then, a person is not an individual. Instead, he or she is a walking ecosystem!
Scientists now call the collection of bacteria that lives in a person’s body the microbiome, and as the article linked above indicates, each person seems to have his or her own special mix of bacteria in that microbiome. Indeed, some researchers think that analyzing the DNA of the bacteria a criminal leaves behind can aid in identifying that criminal in cases where his or her own DNA is not available at the crime scene or too degraded to analyze properly.1
So where does an infant start collecting the bacteria that will make up his or her own microbiome? One of the sources is the breast milk that the infant drinks. It has been known for quite some time that breast milk contains bacteria, but the details have not been well studied. However, a group of Spanish researchers have begun to shed some light on those details. They studied the breast milk of 18 mothers who varied in weight, weight gain during pregnancy, and the mode in which the baby was delivered. They sampled the milk these mothers produced at three different times: the first secretions of milk produced after giving birth (called colostrum), the milk that was produced one month after giving birth, and the milk that was produced six months after giving birth. They sequenced the DNA of the bacteria found in these samples of milk, and they came up with some amazing results.2
A commenter tried to claim that the Ediacaran fossil assemblages offer an explanation around the Cambrian Explosion, but had he actually read the link that was provided, he would have known that they do not. Instead, the Ediacaran fossils cannot be connected in any reasonable way to the fossils found in the Cambrian. To emphasize this, I quoted from N.S. Sharma’s book, Continuity and Evolution of Animals:1
Although the stratigraphic distribution of Ediacaran fossils is clear enough, their biological interpretation remains controversial, providing what amounts to a Rorschach test. Several distinct body plans are represented. Most radially symmetric fossils plausibly represent polypoid organisms or the inflated holdfasts of colonial, dipoblastic animals–mostly unrepresented in the modern fauna. More complex fossils include a range of forms built of repeated, tube-like units. In a stimulating, if controversial proposal, Seilacher grouped such fossils into a clade that he christened the Vendobionta and viewed as an extinct experiment in multicellular organization. Others have questioned that interpretation, assigning various forms to colonial diploblasts or to stem members of several bilaterian clades. It is genuinely difficult to map characters of Ediacaran fossils into the body plans of living invertebrates. Long viewed as the principal problem of interpreting Ediacaran assemblages, this difficulty increasingly appears to be their central point. (emphasis mine)
A paper that was recently published online by the journal Nature demonstrates that Sharma’s characterization of these fossils is right on the money.
A picture of a mineral formation that was widely interpreted as an animal fossil (Click for credit)The Cambrian Explosion presents a serious headache for evolutionists. After all, the fossils found in Cambrian rock are supposed to be about 540 to 485 million years old. However, when you look at the complex animals preserved in such rock, you find every major body plan that exists in today’s animals. Worse yet, when you look in layers that are supposed to be older than Cambrian rock, you don’t find the supposed ancestors of these complex animals. Evolutionists have desperately tried to explain around the problem, but so far none of their explanations work.
In 2004, a ray of hope appeared. The journal Science published an article claiming to have found animal fossils that are 40-55 million years older than the Cambrian fossils. They also seemed simpler than the animal fossils found in Cambrian rock. These simple animals were called Vernanimalcula guizhouena, and the authors thought that they helped to mitigate the evolutionary headaches caused by the Cambrian Explosion. As the authors state in their paper:1
The morphology of Vernanimalcula demonstrates that the evolutionary appearance of developmental programs required to generate a multilayered bilaterian body plan preceded the entrainment of the growth programs required for macroscopic body size. Furthermore, the organization of these fossils, taken together with their provenance, indicates that the genetic tool kit and patter formation mechanisms required for bilaterian development had already evolved by Doushantuo times, long before the Cambrian. Therefore, the diversification of body plans in the Early Cambrian followed from the varied deployment of these mechanisms once conditions permitted, not from their sudden appearance at or just before the Cambrian boundary.
So these fossils showed that the Cambrian Explosion wasn’t an explosion at all. Instead, simpler versions of the complex animals that appear in Cambrian rock existed previously, and the Cambrian era simply represented a rapid diversification of a basic body plan that had already existed in a simpler form.
Of course, like many evolutionary propositions, once this claim was thoroughly analyzed, it was shown to be utterly false.
More than three years ago, I wrote about the young, faint sun paradox. The problem is fairly simple: Based on everything we know about the thermonuclear reactions that power the sun, it is getting more luminous over time. In other words, the sun is producing more light now (on average) than it did in the past. As a result, the farther you go back in time, the dimmer it should have been. This presents a problem, because the dimmer the sun is, the cooler all the planets (including the earth) are. According to what we know right now, the earth would have been too cold to support life 3.6 billion years ago. Modern paleontology assures us, however, that there was life on earth at roughly that same time.
How do those who believe both modern paleontology and our current understanding of the sun resolve this problem? Unfortunately, the all-too-often response is to deny that there is a problem at all. For example, one old-earth website claims that this used to be a problem, but it has since been solved. It cites a 2010 study1 that merely suggested a possible issue that might reduce the problem. Based on that single study, the website proclaims:
The solving of this paradox provides us with a clear answer that is easily understood, and should eliminate this paradox from being used as evidence of a young earth. Once again, science has prevailed over the claims of young earth creationism.
Of course, nothing could be further from the truth. Indeed, in just over one year, the very same journal published a paper that categorically showed that the solution proposed by the 2010 paper was insufficient. Even giving the proposed solution the widest possible latitude, it fell short of resolving the paradox by a factor of two!2
In fact, this problem is still so difficult to resolve in the old-earth view that the Space Telescope Science Institute hosted a two-day symposium in hopes of starting to find a solution to it.
The "brains" of this surgical device is an iPod (Click for credit.)
Last month, I wrote an article about an experiment involving spiders and an iPod touch. The results of the experiment were interesting, but I also thought it was really cool that an iPod was integral to the experiment’s design. Well, I just learned about something that I think is is even cooler. It turns out that an iPod touch is being used to assist in knee-replacement surgeries!
The system is called “Dash,” and it is made by a company called Brainlab. It consists of several accessories, such as probes, that attach to an iPod touch. Once everything is sterilized, the surgeon can use the probes to make measurements on the patient while the surgery is in progress. The iPod can then do some calculations on those measurements and show an image that will help the doctor install the artificial knee as accurately as possible. It can also use its WiFi capabilities to send those results to any other device, such as an iPad, if the surgeon wants a larger, more detailed image.
Why would a surgeon use a device like this? Well, in order for the replacement knee to function well, it must be aligned properly. In conventional knee replacement surgeries, the surgeon inserts a metal rod into the femur (the bone above the knee) to help with this alignment. Unfortunately, that process can increase the risk of certain side effects, such as fat embolisms. When using this iPod-based device, there is no need for an alignment rod. In addition, a surgeon who has been using it for more than a year says that the device provides better alignment than the conventional method. This leads to a larger range of motion for the artificial joint. Also, patients experience less pain and swelling after surgery.
