Coral Bleaching: A Death Sentence or An Adaptive Mechanism?

A coral reef in the Phoenix Islands Protected Area, near Coral Castles (click for credit)

A coral reef in the Phoenix Islands Protected Area, near Coral Castles (click for credit)

I do a lot of scuba diving, and I love coral reefs. They are probably the most beautiful things you can see under water, and they are usually teeming with fish and other wildlife. While there are other wonderful things to see in the ocean, I can’t think of anything better than nearly depleting a tank of air while slowly swimming over and around a coral reef.

However, there are times when coral reefs aren’t so beautiful. Compare the picture above, for example, to the following picture:

Bleached coral (click for credit)

Bleached coral (click for credit)

What’s the difference? The coral pictured above has bleached.

Corals have an amazing mutualistic relationship with microscopic algae called zooxanthellae. The corals provide protection and certain necessary chemicals to the zooxanthellae. In exchange, the zooxanthellae make oxygen, sugar, and other chemicals for the corals, and they also help the corals remove waste. It is a relationship that works wonderfully for both of them. However, there are times when corals expel their zooxanthellae. This causes them to turn white (as shown in the picture above), which is why it is called “bleaching.”

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Dr. James Tour Tells Us How Little We Know About the Origin of Life

James Tour is a giant in the field of organic chemistry.

James Tour is a giant in the field of organic chemistry.

A few days ago, a reader asked me to review an article by Dr. James Tour, as well as a video of a talk that he gave. I was initially hesitant to do so, because Dr. Tour is a giant in the field of organic chemistry. For example, he is the T. T. and W. F. Chao Professor of Chemistry at Rice University. For those who aren’t familiar with the academic structure of universities, only the most elite professors are appointed to a position that is named in honor of someone else. This is called an “endowed professorship,” and anyone who holds such a position is in the upper echelon of academia. He has won several awards for his outstanding research accomplishments, including being named by Thomson Reuters as one of the top ten chemists in the world in 2009. Not only is his research outstanding, but he is also an excellent teacher, having earned the George R. Brown Award for Superior Teaching at Rice University in both 2007 and 2012. What could I possibly add to the words of someone so knowledgeable and distinguished?

After reading the article, however, I do think I have something to offer. Because of the nature of what he is trying to discuss, his article is very, very technical. There were times, quite frankly, when my eyes glazed over a bit. I didn’t listen to a lot of the video (it seems to cover the same ground as the article), but it is also quite technical. For those who do not have the fortitude to make it through such a technical article or talk, I thought I could summarize it.

The “take home” message is straightforward: We have no idea how some of the most basic molecules necessary for life could have been produced by unguided processes. Why does Dr. Tour feel compelled to write a detailed article making a statement that, in my mind, is quite obvious? He explains:

Those who think scientists understand the issues of prebiotic chemistry are wholly misinformed. Nobody understands them. Maybe one day we will. But that day is far from today. It would be far more helpful (and hopeful) to expose students to the massive gaps in our understanding. They may find a firmer — and possibly a radically different — scientific theory. [Note that “prebiotic chemistry” refers to the chemistry that occurred on earth before life existed.]

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Watch Your Assumptions: They Can Lead To False Conclusions!

Poor assumptions can lead to myths instead of facts (image from shutterstock.com by Thinglass)

Poor assumptions can lead to myths instead of facts (image from shutterstock.com by Thinglass)

I am always on the lookout for experiences that can be turned into a “teachable moment.” Over the past two weeks, I have had two such experiences, so I thought I would write about them. The first one was a result of my article entitled Reflections on the Ark Encounter, which is a positive review of the latest attraction produced by Answers in Genesis. The day after it was published, I got a Facebook message from someone who had shared my post with a friend of hers. In reply, this friend asked if I was a “real” scientist. She assured him that I was and shared my Facebook page with him. She was rather taken aback when her friend sent her the following reply:

A mimeographed “PhD” from whatever fundamentalist “college” he sent his box tops to is not qualification to shine a real scientist’s shoes, let alone make claims about the natural world. Further, any parents who buy into this complete fiction, and indoctrinate their kids in this manner, are guilty of emotional and mental child abuse, and in my opinion should be prosecuted. I cant think of a better way to sabotage a child’s future in a modern, scientific and technological society.

This didn’t surprise me, of course. I am used to having my credentials questioned and being insulted because I don’t slavishly “toe the line” when it comes to today’s scientific consensus. That comes with the territory. Indeed, Dr. Dan Shechtman was asked to leave his research group because he dared to question the scientific consensus. Of course, the data eventually proved him to be correct and the scientific consensus to be wrong. However, that was until after being ridiculed as a “quasi-scientist” by one of the greatest chemists who has ever lived!

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A Really Undeniable Book, Written By a Real Scientist

A book that discusses some undeniable truths.

A book that discusses some undeniable truths.

Dr. Douglas Axe is a very interesting scientist. He did his undergraduate work at the University of California, Berkeley and got his Ph.D. in chemical engineering from Caltech. His thesis was focused on molecular biology, which is why you find his scientific papers published in The Journal of Molecular Biology, PloS One, and Biochemistry. He is also a co-author on a paper that appeared in the Proceedings of the National Academy of Sciences of the United States of America. Currently, he is the director of the Biologic Institute, which is a research organization that encourages its scientists to do their research from an Intelligent Design point of view. He is also one of the authors of Science and Human Origins, a book that surveys the evidence for human evolution and concludes that humans cannot be the result of an unguided, neo-Darwinian process. I recently had the pleasure of reading his latest book, Undeniable: How Biology Confirms Our Intuition That Life Is Designed.

The first thing you might notice about the book is its main title, which is the same as the main title of an error-riddled book written by Bill Nye. While Nye likes to call himself “The Science Guy,” some of his behavior is decidedly anti-science (see here and here, for example), and his book makes it clear that he doesn’t try to understand some of the issues that he discusses publicly. Unlike Nye’s book, this book is written by a real scientist who actually does educate himself on the issue about which he is writing. Indeed, most of what he writes in this book is directly related to the scientific work he has published over the years.

Before getting into the meat of the book, I think that a personal story he shares is worth noting. While he was a graduate student at Caltech, one of his final exams asked which biological molecule was likely the first “living” molecule. In other words, the person writing the exam wanted the student to relate what was currently the most fashionable conjecture regarding the origin of life. Here is how he describes his answer and its result:

I decided to give the expected answer in full and then – for extra credit – to state why I found that answer unconvincing. I explained why, contrary to the consensus view, I didn’t think any molecule has what would be needed to start life. As shrewd at that seemed at the time, I learned when my exam was returned (with points deducted) that we students were expected to not only know current thinking in biology but also accept it without resistance. We were there as much to be acculturated as educated. (kindle version, Chapter 1, emphasis his)

That is so true. If you ever wonder why so many scientists resist new thinking in the origins debate, it’s because they have been taught to resist it! Fortunately, some scientists (like Dr. Axe) don’t don’t take that lesson to heart. Instead, they do what scientists should do: question the existing paradigm when the data speak against it.

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Reflections on the Ark Encounter

A view of the Ark Encounter (click for a larger image)

A view of the Ark Encounter (click for a larger image)

Yesterday, I toured the Answers in Genesis Ark Encounter with my wife and a friend. I wanted to visit the encounter as soon as it opened, but because of trips to Italy and China, yesterday was the first opportunity we had. I didn’t know what to expect, so I went in with an open mind.

I originally thought the Ark Encounter would be like the Creation Museum, with a parking lot close to the entryway. I was wrong. When we parked and got out of the car, we could see the ark, but it was a long way off. A building in the parking lot served as a “bus terminal,” where we were picked up and taken to the Ark itself.

When we got off the bus, my first thought was, “Wow. That’s big.” I have seen many models of the Ark over the years, and they all attempt to give you an idea of how big it was, usually by having scale models of trucks or elephants beside it. However, there is simply no substitute for seeing the massive structure built to its actual dimensions! Answers in Genesis bills the Ark as the largest timber-framed structure in the world, and I can believe that. *

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A Real-Life Example of The Prodigal Son

"The Return of the Prodigal Son" by Italian artist Pompeo Girolamo Batoni

“The Return of the Prodigal Son” by Italian artist Pompeo Girolamo Batoni

Over the many years since I became a Christian, I have heard hundreds of sermons. Some were given by impeccably-credentialed theologians, others by intellectual philosophers, others by experienced scientists, and others by regular people who were honestly sharing what God had laid on their hearts. Most of them, of course, were given by pastors who have dedicated themselves to studying and explaining the Word of God. While I have learned from many of those sermons, only a precious few made such a lasting impact that I can remember them to this day. The sermon I heard yesterday, however, is one I will never forget. It was given by a student from Anderson University who has been leading the children’s ministry at our church. This young lady, who is still in the midst of finishing her undergraduate degree, shared a powerful message that brought me (and many others in the congregation) to tears.

The main text of her message was the parable of The Prodigal Son, which is given in Luke 15:11-32. I have heard many, many, many sermons that used this parable as its main text. This one, however, was different. It gave a personal, real-life example of a father, his prodigal son, and the rest of his family. More importantly, this young lady was the prodigal son’s sister, and her father’s actions taught her (and the congregation at our church) what it really means to show the love of Jesus.

When this young lady was 13, her brother had a sexual relationship with a foster daughter who was living with her family. The foster daughter became pregnant, but no one knew. Her brother and the foster daughter conspired to accuse her father of molesting the foster daughter. It was all done so convincingly that this young lady believed her brother’s accusation, despite her father’s protestations of innocence. She was taken away from her family because of the allegations, and a restraining order was put in place so that her father could not see her.

Because of many things that happened over the next few months, it became clear to her that her father was, in fact, innocent, and that her brother had done the unthinkable: he had betrayed their entire family for his own selfish reasons. She eventually got to live with her mother again, and her father fought to get the restraining order lifted. That was eventually successful, so she at least got to see her father, but in the end, her father went to jail (where he is to this day) for a crime that he did not commit.

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A Desperate Attempt to Solve an Intractable Problem

Artist's conception of a large asteroid hitting the earth (click for credit)

Artist’s conception of a large asteroid hitting the earth (click for credit)

One of the many problems associated with an ancient earth is the young, faint sun. In a nutshell, we think we understand the way a star produces energy, and based on this understanding, a star starts off dim and grows brighter over time. Based on what we know, then, the sun should have been about 25% dimmer 3.8 billion years ago, when most evolutionists think life first emerged on earth. However, if the sun really were 25% dimmer back then, the earth would be far too frigid to support life.

This problem has been recognized for more than 40 years now, and evolutionists have worked hard on it (see here and here), but a solution has remained elusive. However, a recent paper has proposed a possible solution, and I found it interesting, because it illustrates exactly how desperate evolutionists are to get rid of this intractable problem.

In essence, the paper says that the way to fix the problem is to have earth pummeled by very large (greater than 100 kilometers in diameter) asteroids. They are so large that the authors call them “planetesimals”:

Planetesimals exceeding 100 km in diameter pummeled the early Earth for hundreds of Myr, resulting in large volumes of melt produced both by immediate depressurization and by subsequent mantle convection driven by the impact.

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CRISPR – A Gene-Editing Technology with Promise and Peril

CRISPR, teamed up with Cas9, is a powerful gene-editing tool. (click for credit)

CRISPR, teamed up with Cas9, is a powerful gene-editing tool. (click for credit)

Not too long ago, a reader sent me an email that said:

I just found out about CRISPR and Cas9. From what I have learned about them they are very powerful and will lead to great things (good and terrible alike).

I was wondering if you could write a blog article on them when you get a chance. I would love to hear your perspective.

The reader is exactly right. CRISPR and Cas9 team up to make a powerful gene-editing tool that has incredible potential. While much of that potential is positive, some of it is quite negative.

To best understand the good and the bad of CRISPR and Cas9, you need to know what they are and what they can do together. CRISPR stands for “clustered regular interspaced short palindromic repeats.” Originally discovered in bacteria, it is a strand of RNA that is hooked to a CRISPR-associated protein, called a “Cas.” Cas9 is just one possible protein that can be associated with CRISPR, but it is the one that is most commonly used.

If your eyes are already glazing over, stick with me, because it’s important to understand how this works. RNA is a molecule that links to DNA. A specific RNA molecule targets a specific sequence of DNA. So, if you construct an RNA molecule correctly, it can search an entire DNA molecule, looking for a specific DNA sequence. It can then attach itself to that sequence. That’s what the RNA strand on CRISPR does. It is sometimes called “guide RNA,” because it guides the Cas9 protein to a specific part of an organism’s DNA. Consider the following illustration:

Illustration of CRISPR-Cas9 finding a DNA sequence (taken from the video posted at the end of this article)

Illustration of CRISPR-Cas9 finding a DNA sequence
(taken from the video posted at the end of this article)

In the illustration, the guide RNA has found the DNA sequence that it was made to target. Since Cas9 is attached to the guide RNA, it is now positioned at a specific place in the DNA molecule.

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Gospel of Jesus’ Wife Is a Fake

The papyrus fragment that is now known as 'The Gospel of Jesus' Wife.' (click for credit)

The papyrus fragment that is now known as ‘The Gospel of Jesus’ Wife.’ (click for credit)

I am in China right now, and I have been here for almost two weeks. However, internet access is sporadic (at best), which is why I haven’t added any articles recently. Things are a bit better today, though, so I thought I would share my thoughts on a story I recently ran across.

On September 18th, 2012 at the International Congress of Coptic Studies in Rome, Dr. Karen L. King announced the existence of an astounding 4-cm by 8-cm papyrus fragment. It contained what she thought was a 4th-century Coptic translation of a gospel that she suggested had probably been written in the late second century AD. While the discovery of any ancient papyrus that has writing on it is interesting, this particular fragment was especially interesting because it contained the following phrase:

Jesus said to them, ‘My wife…”

As a result, this papyrus fragment came to be known as “The Gospel of Jesus’ Wife.”

In a peer-reviewed paper that was later published in the Harvard Theological Review, Dr. King presented the results of several tests that had been done on the papyrus fragment. Those tests led her to conclude that it was from the 8th century AD and was not a forgery. In the same issue of the journal, however, another scholar wrote an article concluding that the papyrus was a forgery. The Vatican weighed in as well, dismissing the fragment as a “clumsy forgery.”

Since then, there has been a lot of discussion about the papyrus fragment, and a website was set up to provide all of the latest information about it. Based on subsequent tests done on the fragment and its ink, Dr. King became so convinced that the fragment is authentic that she told Time:

I’m basically hoping that we can move past the issue of forgery to questions about the significance of this fragment for the history of Christianity, for thinking about questions like, ‘Why does Jesus being married, or not, even matter? Why is it that people had such an incredible reaction to this?’

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Galileo and his Thermometer

Galileo's thermometer (left) and a closeup of the tube (right).

Galileo’s thermometer (left) and a closeup of the tube (right).

If you read my two previous posts (here and here), you know that my wife and I were recently in Italy, and I was really inspired by some of the things I saw. The art and history are amazing, but for me, one of the major highlights of this visit to Italy was seeing the Galileo Museum. It is filled with scientific instruments and lecture demonstration equipment from the past, and seeing those things helped me to understand the sheer genius of the natural philosophers (scientists) who learned an enormous amount about Creation without the help of fancy, technological gadgets. Instead, they relied on their creativity and their physical insight.

Consider, for example, the glass piece pictured on the far left. It consists of a small vessel, a long, narrow tube rising up from the vessel, and a small bulb at the top of the tube. Believe it or not, that’s a thermometer. Actually, it is more properly called a “thermoscope,” and the first one was designed by Galileo (with the help of some other natural philosophers) in 1593.* Until that time, it was difficult to make any systematic measurement of temperature. People could tell whether it was hot, warm, cool, or cold, of course, but they couldn’t make precise measurements of how hot, warm, cool, or cold it was.

In the late 1500s, Galileo came up with an ingenious solution. He understood that air expanded when it was warmed and contracted when it was cooled. He decided to use that fact to get an accurate measurement of the change in temperature. He designed a device similar to the one above, in which water filled the bottom vessel and ran partway up the thin tube. When the surroundings warmed up, the air above the water (in the tube and in the bulb at the top) expanded, and that pushed the water down the tube. When the surroundings cooled, the air above the water contracted, and that pulled water up the tube.

In other words, the higher the water climbed in the tube, the lower the temperature. By making tiny marks on the side of the tube (shown in the right-hand portion of the picture at the top of this post), he could assign a number to the water’s height. This allowed him to accurately measure changes in temperature. In my elementary science book, Science in the Scientific Revolution, I have students make a very simple version of Galileo’s thermometer with water, a glass, and a plastic bottle.

A clever variation on Galileo's thermometer.

A clever variation on Galileo’s thermometer.

A major drawback of Galileo’s thermometer is that it must be very tall to measure large changes in temperature. While at the Galileo museum, however, I saw a very clever way of getting around that problem, which is shown in the picture on the left. Instead of a tall, straight tube, this thermometer’s tube is a spiral. That way, the water still can travel a long distance through the tube, but the device isn’t absurdly tall. As soon as I saw this device, I thought, “Of course. What an ingenious way of getting around the height problem.”

Despite the fact that I understood exactly how this variation on Galileo’s thermometer would work and why it was superior to the original design, I doubt that I would have ever come up with it on my own. I’m simply not that clever. However, Galileo and the natural philosophers of his day were. The more I learn about people like Galileo, the more I appreciate how intelligent the great thinkers of the past were. Contrary to popular belief, I think it’s possible that they were actually smarter than we are today.

NOTE:

*Please note that a device like this one is often called a “Galileo thermometer,” but Galileo had nothing to do with its design.
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