Creationism Archives : Page 14 of 30 : Proslogion

Horizontal Gene Transfer: Another “Way Out” for Evolutionists

hgt — 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.

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Bacteria in Breast Milk? Yes!

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

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Has NASA Finally Found Life on Mars?

A friend of mine told me about a news story he heard on NPR. He said that NASA had some “really exciting” results from the Mars rover named Curiosity, but they were not ready to release the results to the public yet because they wanted to confirm the data. My friend wondered if perhaps NASA had finally found the remains of life on Mars. I found the story on NPR’s website, and it sounds like my friend’s expectation could be right.

According to the story, the principle investigator, Dr. John Grotzinger, says:

This data is gonna be one for the history books. It’s looking really good.

Dr. Grotzinger is waiting to release the results, however, because NASA has been burned a couple of times before. Back in 1996, NASA scientists published a paper that claimed a meteorite from Mars (named ALH84001) held tell-tale signs of bacteria, indicating that there was once life on Mars. As more scientists studied the meteorite, however, several problems with that interpretation were found. As a result, even though some NASA scientists are still saying that the meteorite holds evidence of life on Mars, the data are inconclusive at best.

In addition, NASA scientists published a paper in 2010 claiming to have found a bacterium that could incorporate arsenic into its biochemistry. NASA said that this finding would change the way we think about bacteria and would help us better understand the possibilities for life on other worlds. However, in just a couple of years, two very detailed studies showed that the original NASA claim was incorrect. It’s understandable, then, that NASA scientists are being careful when it comes to the release of any surprising data from the Curiosity rover.

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A Large, Detailed Study Confirms Another Failed Evolutionary Prediction

lebrea — The La Brea Tar Pits as imagined by Charles R. Knight (public domain image)

Paleontologists have long recognized that the fossil record produces a serious problem for the hypothesis of evolution. Almost thirty years ago, Dr. David Wake and his colleagues stated:¹

With natural selection operating in a changing environment as an agent of adaptation, we expect to see changes at the organismal, ultimately physiological and morphological, level. How, though, can we explain the paradoxical situation in which environments change, even dramatically, but organisms do not?

In other words, evolution predicts that in a changing environment, organisms should change in order to adapt. However, when we look at the fossil record, we don’t see such change. Instead, while it is thought that earth’s climate changed dramatically in many different ways throughout the fossil record, the fossils themselves show that the organisms living on earth didn’t change much at all. This has been called the “paradox of stasis,” and while several attempts have been made to resolve the problem ², none of them have been found to be satisfactory.³

In an attempt to understand the paradox of stasis better, Dr. Donald Prothero undertook a series of amazingly detailed studies. With the help of a small army of students, Prothero studied the fossils of all the common birds and mammals that have been preserved in the La Brea tar pits of Los Angeles, California. According to the standard geological view, these tar pits preserved species that lived in the area over a period of time when the region experienced wild climate change. It is thought that 35,000 years ago, the Los Angeles, California area had a very similar climate to what it has today. During the height of the last ice age (20,000 years ago), however, it was significantly colder and significantly wetter. As the ice age waned, the climate returned to what it was 35,000 years ago.

From an evolutionary point of view, one would expect that over the course of this dramatic change in climate, the birds and mammals living in the area would have experienced some amount of evolutionary change in order to adapt to their surroundings. However, that’s not what this series of studies found.

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Desperately Seeking Innovation

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 based ¹, 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!

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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Bugs and Bacteria Working Together

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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The Great Debate

Last night, I debated Dr. Robert A. Martin on the question of creation versus evolution. I obviously took the creation side, and he took the evolution side. I debated him once before in 2009, and you can watch a video of that debate here. The format of this debate was a bit different from the one on the video. In this one, we each had 30 minutes to present our case, and then the audience asked us questions. The purpose of the questions was to focus the debate on what the audience found interesting in our presentations. Dr. Martin and I were each given a chance to address the question, and that usually led to more interaction between us. Everyone with whom I talked, including Dr. Martin, was very pleased with how it all turned out.

One thing I have to say up front is how appreciative I am of Dr. Martin. First, the fact that he was willing to do the debate at all is a testament to his commitment to real science education. I contacted several universities in Indiana, and none of them were interested in finding an evolutionist professor who was willing to debate. The common response by evolutionists is that they don’t debate creationists, because that would give the creationist view too much legitimacy. However, Dr. Martin realized that if no one came to give the evolutionary side, everyone at the conference would hear only one side of the story, and that’s not very good when it comes to science education. As a result, he was willing to drive from Kentucky to make sure that both sides were heard.

Second, Dr. Martin was incredibly gracious. He knew going in that this was a creationist event, so he knew that his view would be in the minority. In some ways, he was like a lion in a den of Daniels. However, he was very kind in how he treated everyone. Now don’t get me wrong – he took a strong stand for evolution. He often said things like the evidence for evolution is overwhelming, and that there is just no question about the age of the earth and the universe. But never once did he descend into the name-calling and other nonsense that is common among those who don’t care to discuss evidence. He limited his discussion to the science, and that was great.

Third, Dr. Martin was kind enough to stay longer than we had intended. Not surprisingly, there were a lot of questions, and at the scheduled end of the debate, the moderator stopped and said that we were officially out of time. However, Dr. Marin immediately said that he was willing to stay longer. As a result, everyone who stood up to ask a question was able to interact with us. Even after the debate was over, he stayed and talked with people one-on-one for quite some time. Clearly, Dr. Martin has a passion for science and science education. His demeanor and willingness to pleasantly engage people with whom he disagrees demonstrated that to me in no uncertain terms.

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The ENCODE Data and Pseudogenes

As I mentioned in two previous posts (here and here), the coordinated release of scientific papers from the ENCODE project has produced an enormous amount of amazing data when it comes to the human genome and how cells in the body use the information stored there. While the majority of commentary regarding these data has focused on the fact that human cells use more than 80% of the DNA found in them, I think some of the most interesting scientific results have gotten very little attention. They are contained in a paper that was published in a journal named Genome Biology, and they relate to the pseudogenes found in human DNA.

For those who are not aware, a pseudogene is a DNA sequence that looks a lot like a gene, but because of some details in the sequence, it cannot be used to make a protein. Remember, a gene’s job is to provide a “recipe” for the cell so that it can make a protein. Well, a pseudogene looks a lot like a recipe for a protein, but it cannot be used that way. Think of your favorite recipe in a cookbook. If you use it a lot, it probably has stains on it because it has been open while you are cooking. Imagine what would happen if the recipe got so stained that certain important instructions were rendered unreadable. For someone who has never looked at the recipe before, he might recognize that it is a recipe, but because certain important instructions are unreadable, he will never be able to use the recipe to make the dish. That’s what a pseudogene is like. It looks like a recipe for a protein, but certain important parts have been damaged so that they cannot be used properly anymore. As a result, the recipe cannot be used by the cell to make a protein.

Pseudogenes have been promoted by evolutionists as completely functionless and as evidence against the idea that the human genome is the result of design. Here is how Dr. Kenneth R. Miller put it back in 1994:¹

From a design point of view, pseudogenes are indeed mistakes. So why are they there? Intelligent design cannot explain the presence of a nonfunctional pseudogene, unless it is willing to allow that the designer made serious errors, wasting millions of bases of DNA on a blueprint full of junk and scribbles. Evolution, however, can explain them easily. Pseudogenes are nothing more than chance experiments in gene duplication that have failed, and they persist in the genome as evolutionary remnants…

Obviously, Dr. Miller didn’t understand intelligent design or creationism when he wrote that, as they can both explain nonfunctional pseudogenes. Before I discuss that, however, I need to point out that since 1994, functions have been found for certain pseudogenes. As far as I can tell, the first definitive evidence for function in a pseudogene came in 2003, when Shinji Hirotsune and colleagues found that a specific pseudogene was involved in regulating the functional gene that it resembles.² Since then, functions for several other pseudogenes have been found. In fact, a recent paper in RNA Biology suggests that the use of pseudogenes as regulatory agents is “widespread.”³

Even though functions have been found for many pseudogenes, the question remains: Are most pseudogenes functional, or are most of them non-functional? Well, based on the ENCODE results, we might have the answer. While the ENCODE results indicate that the vast majority of the genome is functional, they also indicate that the vast majority of pseudogenes are, in fact, non-functional.

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Defending the Indefensible, Part 2

A blogger by the name of Emil Karlsson recently wrote an error-laden piece defending Bill Nye’s rant against creationism. A commenter on this site posted the piece, and as a science educator, I had to point out many of its errors. Mr. Karlsson responded by posting a piece with even more errors. Once again, as a science educator, I had to correct those errors. Well, Mr. Karlsson has attempted to reply to that post, and not surprisingly, he has done so with even more errors. In an effort to educate those who are interested in understanding science and how it works, I will once again correct Mr. Karlsson’s errors.

Still Trying to Get Around What Mr. Nye Actually Said

Mr. Karlsson is still trying to make excuses for Nye’s obvious ignorance when it comes to evolution denial around the world. In an attempt to explain around Mr. Nye’s own words, Mr. Karlsson sets up a hypothetical interrogation in an attempt to claim that I am looking for “ammunition” to use against Nye. Here is his hypothetical interrogation:

Interrogator: Did you smash the windshield of Mr. X’s car?

Innocent suspect: No. I mean, I don’t like the guy and he annoys me to no end, but I would never go so far as to destroy his property just because we did not get along. Besides, I was having lunch at the cafeteria when it happened.

He then says there are two ways you can interpret this. First, he claims that my way is to ignore the suspect’s statement of innocence and his alibi and instead focus on the fact that the suspect admits he didn’t like the victim. He claims that his way is to look at the suspect’s entire statement and conclude that the suspect is not guilty.

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