Even Eyes Contain Bacteria!

Mouse eyes were studied in the article being discussed, but the results are probably applicable to many mammal eyes.

Writing about coral in the Journal Science, paleontologist Dr. George D. Stanley noted:

Symbiosis is the most relevant and enduring biological theme in the history of our planet.

If you aren’t familiar with the term, “symbiosis” refers to organisms of different species living together. There are three general forms:

(1) Parasitic symbiosis, in which one organism benefits and the other is harmed

(2) Commensal symbiosis, in which one organism might benefit but neither is harmed

(3) Mutualistic symbiosis, in which all organisms in the relationship benefit

I have written extensively on mutualistic symbiosis (see here, here, here, here, here, here, here, here, here, and here, for example). Not only does it fascinate me, but it was also the major scientific issue that led me away from atheism. When one sees the amazing mutualistic relationships that exist all over nature, it becomes clear that these organisms were designed to work together.

Bacteria tend to develop a lot of mutualistic relationships. Indeed, you would not be nearly as healthy as you are if it weren’t for the many mutualistic bacteria that live in and on your body. And while it is widely-known that you can find mutualistic bacteria in many parts of a mammal’s body, it was thought that you would never find them living in the eye for any extended period of time. That’s because mammal eyes contain an enzyme called lysosyme, which kills bacteria. However, new research indicates that at least one species of bacterium, Corynebacterium mastitidis, makes its home in at least some mammal eyes.

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A Frustrating Book, But A Good First Step

A new, honest book about the creation/evolution controversy with the church.
When the creation/evolution controversy comes up in Christian circles, it is often accompanied by a lot of strife. Some Christians think that evolution comes straight from the Devil, while others think that when Christians refuse to accept the fact of evolution, they are harming the cause of Christ. Unfortunately, most of the major Christian organizations that focus on the subject fuel this acrimony. As a result, when I heard that the Colossian Forum had convinced Dr. Todd Wood (a young-earth creationist) and Dr. Darrel R. Falk (a theistic evolutionist) to write a book about the subject, I was intrigued. I actually pre-ordered a copy of the Kindle version, but later was happy to find that the publisher had sent me a free paperback copy to review.

The book, entitled The Fool and the Heretic, is made up of chapters written by Dr. Wood (the “fool”), chapters written by Dr. Falk (the “heretic”), and short interludes written by Rob Barrett of the Colossian Forum. There are also discussion questions at the end of each chapter. Drs. Wood and Falk are diametrically opposed when it comes to the question of origins, and that becomes clear right up front. Indeed, the first chapter (written by Wood) is entitled “Why Darrel is Wrong and Why It Matters,” and the next chapter (written by Falk) is “Why Todd is Wrong and Why It Matters.” Because of those titles, I almost named this review, “Why Todd, Darrel, and Rob are all wrong and why it matters,” because that’s the main conclusion I was left with when I finished the book.

Both initial chapters present the standard view from each camp. Dr. Wood says that Dr. Falk is wrong because when you try to interpret the first eleven chapters of Genesis to be anything other than historical narrative, you end up doing great theological damage to the rest of the Bible. Dr. Falk says that Dr. Wood is wrong because the evidence for evolution is overwhelming, and when Christians reject that evidence in order to hang on to an outdated view of Scripture, it ends up causing great damage, especially to those who are interested in pursuing the truth. They will eventually encounter this overwhelming evidence, and it will produce a crisis of faith, which sometimes results in leaving the faith. Of course, neither of those assertions is new, and in my view, neither of them is correct.

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Big News in Epigenetics!

The Grand Prismatic Spring in Yellowstone National Park holds bacteria like the ones in the study being discussed.
(click for credit)

The more we learn about creation, the more it surprises us. While it is true in all areas of science, it seems particularly true in genetics. When I was at university, I was taught as definitive fact that each gene in my DNA determined the makeup of one protein in my body. We now know that is false. I was also taught as definitive fact that the only way a parent can transmit a trait to its offspring is through the sequence of nucleotide bases in DNA. As a result, if a new trait appears in a population, it must be due to a change in the species’ DNA sequence. We now know that is false. For example, I was taught as definitive fact in university that cave fish are blind because of mutations to their DNA. We now know that is false, at least for one species of blind cave fish.

So we now know that there are ways to inherit traits that go beyond the DNA sequence that you inherit from both parents. For example, we know that if you train mice to fear a certain smell, the next generation can inherit that fear. It’s not that the parents train the fear into their offspring (the offspring were raised separate from their trained parent). They actually inherited the fear. How in the world can a parent pass on a fear of something to its offspring? That’s what the field of epigenetics (which literally means “on top of genetics”) wants to find out.

We know that it has something to do with how an organism regulates the activity of its genes. An organism can alter chemical aspects of the DNA that are not related to its actual sequence, and that alteration can decrease the use of a gene, increase the use of a gene, turn a gene off so that it is not used at all, or turn a gene on so that it will start being used. For example, most people are not born lactose intolerant. After all, they drink their mother’s milk or a milk-based formula. Milk digestion requires the enzyme called “lactase,” which is coded for by a gene. While everyone has that gene turned on at birth, in some people, it gets turned off later on, causing lactose intolerance. Nothing has changed in the person’s DNA sequence – the gene is still there and has not been broken. However, that gene has been turned off by epigenetic mechanisms. It is thought that this process is responsible for epigenetic inheritance. To some extent, we must be able to inherit the “off” and “on” status of our parents’ genes.

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What a Way to Bring in the New Year!

An aerial view of the Large Hadron Collider’s layout. The particle accelerator is used for high-energy physics experiments. (click for credit)

I wasn’t planning on writing a post today, but as I was going through my email, I saw a wonderful message from a homeschool graduated who used my curriculum, and I just had to post about it. I am keeping the person’s name and some of the professional details confidential (using square brackets to paraphrase and ellipses to cut), because I don’t want the person’s presence on a creationist blog to be harmful to his or her career. It’s sad that I have to do that, but many of the high priests of science are the most anti-science people on the planet, excommunicating those who do not accept their dogma.

Here is the wonderful message I received:

I am writing to thank you for your excellent high school science courses. As a homeschooler, I really appreciated the readability of the texts. The challenging material helped me to develop effective study habits, while your clear enthusiasm for each subject led me to develop a lasting interest in the sciences, especially physics. In fact, after working through Module 8 (“Gravity and Relativity”) of your Advanced Physics Course, I decided to pursue a career in physics. Though I didn’t really have any idea of what that would entail, I figured that your science courses would be an ideal preparation, and indeed they were! Largely due to to the strong foundation that your courses (Physical Science, Biology, The Human Body, Chemistry, Advanced Chemistry, Physics, and Advanced Physics) had provided me throughout middle school and high school, I was able to complete my BS in physics a year early. This helped me to be successful in the treacherous grad school application process, and I am now a [graduate student at a well-known university] pursuing a PhD in experimental particle physics; I’m [doing original research at facilities like the one pictured above]; these are goals that I have looked forward to for a long time. Your courses have been key in successfully beginning to achieve these goals…so thank you for helping to make all of this possible!

As one further note, I’d also like to add that I really appreciate how your texts touched on more advanced topics, even if only to ultimately concede that they were “beyond the scope of this course.” Though I found it a bit frustrating at the time, it really motivated me to keep pushing deeper into the subject, making it all the more satisfying to finally encounter the topic in a later class. For example, your brief description of solving the Schrodinger equation for hydrogen (page 50 of your Advanced Chemistry text) had me on the edge of my seat until finally reaching this problem in undergrad Quantum II. Currently, my Quantum Field Theory textbook tends to make the same sort of statements…and it reminds me of your superlative texts (though when I come across statements like these in QFT, it tends to make me relieved rather than frustrated – I’m happy to leave that particular calculation to the theorists!).

Anyway, I’m sure you get many messages like this, but I just really wanted to let you know how much I enjoyed your texts and how much they have aided me in the career path that they inspired me to pursue…

Merry Christmas and Happy New Year!

There are so many wonderful things to say about this student’s message to me, but I will limit myself to two:

1) I love the fact that this person was “on the edge of” his or her seat because of a solution to the Schrodinger equation!

2) This once again demonstrates that Bill Nye has no idea what he is talking about when he claims that creationist materials are a detriment to science. This student learned junior-high and high-school science from creationist materials, and those materials inspired him or her to be doing the kind of original scientific research that Nye can only dream about doing.

Mistake in Satellite Placement Used To Further Confirm Relativity

The incorrect placement of ESA satellites in orbit has been used to confirm general relativity to the highest precision yet. (click for credit)

One of the things I continually stress with my students is that science doesn’t have to make sense. In fact, most of the theories in my scientific field make no sense at all. Why do I believe them? Because they make predictions which are later verified by the data. That’s the acid test of a scientific theory. If it can make predictions about something that is not known and those predictions can then be tested by experiment or observation, the theory is scientific. If observations or experiments actually confirm the predictions, then it is a reliable scientific theory. For example, young-earth creationism is a reliable scientific theory, because it makes predictions which are later confirmed by the data.

The same can be said of Einstein’s theory of general relativity. Make no mistake: It’s a very strange theory. It says that what we see as the force of gravity is not really a force at all. It is a consequence of how mass warps space and time. Now that’s just crazy. We know that we stay on the surface of the earth because the force of gravity continues to pull us to the center of the earth. An apple falls from a tree because the force of gravity pulls it to the earth. The earth stays in orbit around the sun because the force of gravity keeps it there. Sir Isaac Newton himself gave us an equation for gravity, and that equation has been tested over and over again and found to be reliable. It begins “F =”. The “F,” of course, stands for force. Why,then, would you believe something as silly as what Einstein said? Because his theory made several testable predictions, and when those predictions were tested, they were confirmed.

One of the stranger predictions of general relativity is that mass warps space and time enough that it actually affects the passage of time. When you are near a large mass, time passes more slowly than when you are far from that same mass. According to Einstein, then, time is not constant in the universe. It ticks at different rates, depending on the mass in the area. Once again, to you and me, that’s just crazy. However, it has been confirmed in many different experiments. Indeed, the Global Positioning System would not work if we didn’t take into account that time is ticking differently on the GPS satellites than it is on the surface of the earth. Of course, one hallmark of good science is to continually test your theories, even when they have been confirmed. My publisher told me about a recent example of this being done, and it is worth discussing.

Back in 2014, the European Space Agency launched several satellites into orbit around the earth. Satellites are generally put in a circular orbit, so their distance from the earth never changes. However, a malfunction in the rocket used to place two of the satellites caused them to be put into an elliptical orbit. As a result, their distance from the earth regularly varied. The ESA corrected the orbits as much as they could, but they remain elliptical to this day. The difference between their closest and farthest distances from the earth is about 8,500 kilometers.

While this was a disappointing mistake, two physics research teams realized that they could use it to further test Einstein’s prediction of time being affected by how close you are to a massive object. After all, at regular intervals, these satellites moved closer to and farther from earth. Their position could be accurately measured in real time, using the International Laser Ranging Service, which shoots lasers at the satellites and measures the time it takes for the light to reflect off them and return.

The teams independently examined the time measured by the clocks aboard the satellites, and they each produced a graph similar to the one at the top of this post. Both of them showed that the time measured by the clocks aboard the satellites varied just as Einstein had predicted: As the satellites drifted away from the earth, time started passing more quickly for them. As the satellites drifted towards the earth, time passed more slowly for them. What makes their results noteworthy is that this test is more precise than any other that has ever been done. Their results tell us that the maximum error in Einstein’s prediction is about 0.003%.

Like it or not, the general theory of relativity is the best description scientists have for gravity, as these misplaced satellites have further confirmed.

Directed Evolution Wins Nobel Prize

From left to right: Dr. Frances Arnold, Sir Gregory Winter, Dr. George Smith
(Credits:Beavercheme2, Aga Machaj, Univ. Missouri-Columbia)

Yesterday, the Royal Swedish Academy of Sciences announced that the Nobel Prize in chemistry will be shared among three scientists who all used directed evolution to engineer proteins that solve problems. A reader who saw a news story about the announcement asked me to explain what “directed evolution” means, and I am happy to oblige. In directed evolution, scientists use the concepts of variation and selection to take a molecule that already exists in nature and adapt it to do something that they want it to do. Using a concrete example that comes from the research of Dr. Frances Arnold (one of the recipients) is probably the best way to explain the process.

Dr. Arnold’s lab started with a naturally-occurring enzyme charmingly named P450 BM3. Enzymes speed up specific chemical reactions, and P450 BM3 speeds up the reaction in which an oxygen atom is inserted between a carbon atom and a hydrogen atom in a fatty acid molecule. This is an important step in the process by which a living organism breaks down fatty acid molecules. Dr. Arnold’s lab was interested in doing the same kind of reaction, but on a different type of organic molecule: a small alkane. The enzyme P450 BM3 couldn’t initially do that. However, it could weakly speed up that reaction on large alkanes.

Since the enzyme could at least do that, Dr. Arnold thought that she could “tweak” it until it did exactly what she wanted it to do. However, enzymes are absurdly complicated molecules, and human science isn’t very good at making or understanding them. So she decided to let better organic chemists (bacteria) do the heavy lifting. Her lab took the gene that tells bacteria how to make P450 BM3 and subjected it to mutations. They then saw whether or not the resulting enzyme made by bacteria was any closer to being able to do what they wanted it to do. Maybe it did a better job speeding up the reaction on a large alkane, or maybe it was able to speed up the reaction on a shorter alkane. If that was the case, they saved that gene and allowed it to mutate more, seeing if any more progress could be made. If not, they threw it away and tried again.

This is why the process is called “directed evolution.” Dr. Arnold’s lab induced mutations (which are a source of genetic change in organisms) and then selected any enzyme that ended up being better at what they wanted it to do. With enough of those steps, they were able to get what they wanted: an enzyme that inserted an oxygen atom between a carbon atom and a hydrogen atom in a small alkane. In the end, the process had changed just over 2% of the molecule, but that was enough to change it from an enzyme that acted on fatty acids to one that acted on small alkanes.

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A Failed Test of Fossil Record Interpretation

When you read about earth history in most textbooks, lots of definitive statements are made concerning events that occurred in the distant past. For example, in Biology: How Life Works, Volume 1 (Morris et. al., Macmillan 2014, 2016), students are told:

A giant meteor struck Earth 66 million years ago, causing the extinction of dinosaurs and many other species…Researchers have documented other mass extinctions, but the event that eliminated the dinosaurs appears to be the only one associated with a meteorite impact. (p. 7)

Any unsuspecting student reading those words would think that we know that a mass extinction of dinosaurs occurred 66 million years ago, that it was definitely cause by a meteor impact, and that there have been other mass extinction events as well.

The problem, of course, is that definitive statements like the ones above come from interpretations of the fossil record. The fossil record itself is spotty at best, and the interpretations are based on all sorts of unverifiable assumptions. So the obvious question becomes, “How accurate are those interpretations?” That’s awfully hard to test, since we can’t go back in time and confirm them. However, the great thing about science is that original thinkers can come along and figure out ingenious ways to test what you might think is untestable.

A team of researchers from the Florida Museum of Natural History, the University of Bologna, the University of the Bahamas, and the State University of New York at Geneseo decided to test how well we know things like the mass extinction events discussed in the textbook I just quoted. They took a series of geological samples from the Po Plain in Italy that are supposed to represent what went on over the past 126,000 years. They specifically examined the mollusks in those samples, which leave behind hard shells.

Their test was both simple and brilliant: Imagine that a mass extinction event occurred right after the samples were taken, and all 119 identified species of mollusks that are currently living there had been wiped out. Would this hypothetical mass extinction be properly interpreted from the fossil remains in the geological samples that had been taken? Not surprisingly, the answer was a solid, “No!”

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Are All Animals Really Omnivores?

An alligator eats a pond apple (courtesy of the Everglades NPS)

I was teaching one of my online biology courses yesterday and discussed something virtually every biology student learns: classifying organisms as producers (who make their own food), consumers (who eat other organisms for food), or decomposers (who decompose dead organisms for food). I then mentioned that consumers can be further classified as herbivores (eating only plants), carnivores (eating only animals), or omnivores (eating both plants and animals). I then asked the students how they would classify an alligator. Of course, they classified alligators as carnivores. I then showed them the picture above. That alligator is eating a fruit (a pond apple) on purpose.

It has long been known that alligators and crocodiles ingest plant material, but it was originally thought to be accidental. Perhaps the alligator was biting for a fish, missed, and took in some plant material that was floating in the water. However, recent research shows that in most species, the ingestion is probably not by accident. It is a part of the dietary strategy.

After class, I was looking at the scientific literature and ran across an incredible report about a similar phenomenon in bonnethead sharks. Once again, it has been well known that these sharks ingest seagrass, but it was thought to be accidental. Furthermore, since a carnivore’s digestive system is tuned towards breaking down meat, it was thought that the sharks gained no nutrition from the accidentally-ingested grass. We now know that this is definitely not the case.

The authors of the study fed bonnethead sharks a diet that was mostly seagrass with just a bit of squid. The seagrass had been labeled with a specific isotope of carbon (carbon-13), which makes up only about 1% of naturally-occurring carbon. This allowed the them to identify the chemicals from the seagrass and figure out what happened to them after the seagrass had passed through the sharks. They found that the sharks were actually digesting the seagrass and using it for nutrition. In fact, even though their diet was 90% seagrass, the sharks gained weight! Finally, the authors found that the sharks’ digestive tracts showed the activity of enzymes which are designed to break down plant matter. They write:

We show that a coastal shark is digesting seagrass with at least moderate efficiency, which has ecological implications due to the stabilizing role of omnivory and nutrient transport within fragile seagrass ecosystems.

If sharks and alligators can eat and digest plant matter, probably all animals we think of as carnivores are at least capable of eating and digesting plant material. Combine that with the fact that animals thought to be strict herbivores have been found deliberately eating other animals, and we come to the strong possibility that all animals are really omnivores.

Of course, one “take home” message from all this is that creation is marvelously complex, and our attempts to categorize it are incomplete, at best. However, it also has implications when it comes to the issue of origins. Most young-earth creationists (including myself) think that before the Fall, all animals were herbivores. We also believe in a global Flood, where Noah and his family had to care for different kinds of animals on the ark for a bit more than a year. Some of those animals were carnivores, but they could not have been fed other animals (except perhaps some sea creatures from time to time). Creationists critics often say both situations are impossible, because some carnivores must eat meat, or they will die.

If a species of shark can gain weight on a diet of mostly plants, it is at least conceivable that prior to the Fall and for a year on the ark, the animals that gave rise to the “carnivores” we see today could have lived on a diet of only plants.

“Nylon”-Digesting Bacteria are Almost Certainly Not a Modern Strain

This marine bacterium has the ability to digest nylon waste products, despite the fact that it doesn’t live in an environment that contains nylon waste products. (click for credit)

Evolutionists are fond of stating “facts” that aren’t anywhere near factual. For example, when I was at university, I was taught, as fact, that bacteria evolved the genes needed to resist antibiotics after modern antibiotics were made. As with most evolutionary “facts,” this turned out to be nothing more than wishful thinking on the part of evolutionists. We now know that the genes needed for antibiotic resistance existed in the Middle Ages and back when mammoths roamed the earth. They have even been found in bacteria that have never been exposed to animals, much less any human-made materials.

Of course, being shown to be dead wrong doesn’t produce any caution among evolutionists when it comes to proclaiming the “evidence” for evolution. When Dr. Richard Lenski’s Long Term Evolution Experiment (LTEE) produced bacteria that could digest a chemical called “citrate” in the presence of oxygen, it was hailed as definitive “proof” (a word no scientist should ever use) that unique genes can evolve as a result of random mutation and selection. Once again, that “fact” was demonstrated to be wrong in a series of experiments done by intelligent design advocates. They showed that this was actually the result of an adaptive mutation, which is probably a part of the bacterial genome’s design.

Recently, I learned about an impressive genetic study by young-earth creationists Sal Cordova and Dr. John Sanford. It lays waste to another evolutionary “fact” I was taught at university: the recent evolution of nylon-digesting bacteria. The story goes something like this: In 1975, Japanese researchers found some bacteria, which are now charmingly named Arthrobacteria KI72, living in a pond where the waste from a nylon-producing factory was dumped. The researchers found that this strain of bacteria could digest nylon. Well, nylon wasn’t invented until 1935, and there would be no reason whatsoever for a bacterium to be able to digest nylon before it was invented. Thus, in a mere 40 years, a new gene had evolved, allowing the bacteria to digest something they otherwise could not digest.

Of course, we now know that this story isn’t anywhere close to being true.

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Study Demonstrates that Most Animal Species Came Into Existence at the Same Time?

Most of an animal’s DNA is in the nucleus of the cell, but there is DNA in the powerhouse of the cell, which is called the mitochondrion.
In a comment on a previous article, a reader informed me of a study that I had not seen. It was published in the journal Human Evolution and its results are consistent with the idea that 90% of all animal species came into being at roughly the same time. This is certainly not what the hypothesis of evolution would predict, so some creationists as well as some intelligent design advocates have presented the study as evidence against evolution. In my reply to the comment, I expressed skepticism, even though I would love for the conclusions of the study to be correct. Now that I have read the study itself, I am even more skeptical.

The authors of the study analyzed the DNA of many different species of animals. However, they did not look at the DNA found in the nucleus of the cell. That DNA, called nuclear DNA, is responsible for most of an organism’s genetically-defined traits. They looked at mitochondrial DNA, which is the small amount of DNA that is found in the mitochondrion, the structure that produces most of the energy that the cell ends up using. To give you an idea of how different mitochondrial DNA is from nuclear DNA, the nuclear DNA of a human being is over 3 billion base pairs long, while human mitochondrial DNA is just over 16,000 base pairs long. You don’t need to know what “base pairs” are to see that there is only a tiny, tiny amount of mitochondrial DNA in a human cell compared to nuclear DNA.

Now even though there isn’t a lot of mitochondrial DNA, some sections of it seem to be very characteristic of the species of animal from which the cell comes. For example, a 2016 study analyzed a section of mitochondrial DNA (called the COX1 gene) among different species of birds. It showed that the COX1 gene alone was enough to separate 94% of the birds into species. Similar studies indicate that the COX1 gene can separate other species of animals, so the sequence of the COX1 gene is often referred to as the DNA barcode of the animal. This is what the authors of the study I am discussing focused on.

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