Modern Science Archives : Page 20 of 53 : Proslogion

CRISPR – A Gene-Editing Technology with Promise and Peril

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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Flowers Use Electricity to Communicate With Bees!

A bumblebee on a flower (click for credit)

Most people know about the incredible relationship that exists between bees and flowers. Flowers produce pollen and nectar, which the bees love. So the bees come to the flower to collect them. Because a single bee visits several different flowers, it ends up passing pollen from one flower to another, which is the way flowering plants reproduce. In this way, flowering plants feed bees, while bees aid in the plants’ reproduction.

There are several means by which flowers attract bees, such as shape, scent, color, and even ultraviolet-reflective patterns. Over the past few years, researchers have found an additional one: electricity. Back in 2013, researchers determined that while bumblebees develop a positive charge, flowers tend to develop a negative charge. In addition, different species of flowers produce different patterns of negative charges. Using some pretty clever experimental techniques, the researchers showed that bumblebees use those patterns of negative charges to help them identify the best sources of nectar and pollen.¹

Most of those same researchers now report that they have identified how the bumblebees detect the electrical charges displayed by flowers. They use the hairs (called filiform hairs) that cover their bodies. While these hairs detect motion and sound, the authors showed that they also respond to electric fields. The way they respond allows the bees to “read” the electric field on a flower.²

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Another Creationist Prediction Confirmed

A cluster of the bacteria discussed in the article

Dr. Richard Lenski, an evolutionary biologist at Michigan State University, has been running a long-term experiment on evolution. Indeed, it has been named the LTEE (Long-Term Evolution Experiment). It started back in 1988 and is still running today. It has followed 12 populations of the bacterium Escherichia coli through more than 50,000 generations, examining how environmental stress changes the bacteria’s genetic and physiological characteristics. More than 6 years ago, I discussed how the project was confirming the creationist view of the genome, and it continues to do just that. In addition, it has inspired another experiment that specifically confirmed a creationist prediction while, at the same time, falsifying an evolutionary one.

To understand what has happened, we need to go back to 2008. In that year, the LTEE showed that even though Escherichia coli normally can’t make use of a chemical called citrate when oxygen is present, one of the their populations developed that ability after 31,500 generations of existence.¹ As a result, it was dubbed the “citrate plus” population. How did that happen? At the time, no one knew. However, evolutionists thought it was the result of some rare event or combination of events, exactly the kind upon which evolution depends. New Scientist put it this way:

By this time, Lenski calculated, enough bacterial cells had lived and died that all simple mutations must already have occurred several times over.

That meant the “citrate-plus” trait must have been something special – either it was a single mutation of an unusually improbable sort, a rare chromosome inversion, say, or else gaining the ability to use citrate required the accumulation of several mutations in sequence.

Lenski himself was bold enough to write:

So the bacteria in this simple flask-world have split into two lineages that coexist by exploiting their common environment in different ways. And one of the lineages makes its living by doing something brand-new, something that its ancestor could not do.

That sounds a lot like the origin of species to me. What do you think?

Not surprisingly, a recent experiment has shown that the evolutionary predictions of Lenski and New Scientist are wrong. At the same time, it demonstrated that the predictions of both intelligent design advocates and creationists were correct.

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People Can Compensate for Bad Genes!

In DNA, a gene is made up of exons and introns. The exons determine the protein that is made.

DNA is incredibly complex, so it’s really not surprising that the more we examine it, the more it challenges our notions of how it works. Consider, for example, genes. They make up less than 2% of human DNA, but they are important, because they tell the body what proteins to make and how to make them. At one time, evolutionary scientists actually thought that the vast majority of the rest of human DNA was useless junk. However, like most evolutionary ideas, that notion has been falsified by the data.

Despite the fact that they represent less than 2% of human DNA, genes are obviously important, because most of the chemical reactions that occur in our bodies are controlled by and depend on the proteins that genes specify. Because of the amazing design behind DNA, however, a single gene can actually produce many, many different proteins. This is because, as shown in the drawing above, a gene is actually constructed of introns and exons. The exons represent functional modules in the gene, and the introns separate those modules. When a gene is read, the exons can be grouped in many different ways, producing many different proteins. Because only the exons are used in the production of proteins, geneticists often study an organism’s exome, which is the collection of all the exons in a organism’s DNA.

When it comes to animals, studying how the exome affects overall health is difficult, but straightforward. Scientists can damage the gene of an animal and see what health consequences arise. This is referred to as a gene knockout, and it is an invaluable tool for learning what a gene does. For example, when the gene lovingly referred to as PRDM9 is knocked out of mice, they become sterile.¹ Thus, we know that the PRDM9 gene is essential for reproduction in mice.

When it comes to humans, it’s not ethical to do gene knockouts. However, you can study a population and find examples of people who have a natural mutation that has disabled a gene. By comparing that person’s health to similar people who have a working version of that gene, you can learn something about how the gene affects health. A recent study published in the journal Science did just that, and the reported results were surprising, to say the least!

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How Christianity and Science Can Interact

James Joule, one of the 19th century's most important physicists. — James Joule, one of the 19th century’s most important physicists.

Over the past few years, I have been writing a series of elementary science courses for home educated students. Since the courses discuss scientific concepts in chronological order, I have spent a lot of time learning the history of science. In the process, I have found that a lot of what I was taught in school (including university) about how science developed is simply false. I have also become acquainted with the views of many great scientists from the past, which has allowed me to learn from them. I want to discuss one of those great scientists in order to share something I have learned.

James Joule was born in 1818. Because his father was a successful brewer, chemistry was in his blood. He was taught at home for many years, and then his father sent him to study under John Dalton, the founder of modern atomic theory. Dalton suffered a stroke two years later, but his influence on Joule continued long after he stopped teaching. Even though Joule ended up taking over the family brewery, he spent a lot of time doing experiments, mostly focused on trying to explain electricity and magnetism in terms of Dalton’s new atomic theory.

However, the more experiments he performed, the more interested he became in the heat that was generated in electrical systems. As he studied heat, he eventually demonstrated that he could convert mechanical energy into heat. This allowed him to argue that heat is just another form of energy, which went against the scientific consensus of his day. Of course, today we know he was correct, and because of that, the standard unit for measuring energy is named after him (the Joule).

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Trees Exchange Nutrients Through an Underground Network!

This forest contains Norway spruce and larch, two of the trees studied in the experiment that is being described. (click for credit)

Ever since I learned about it, the phenomenon of mutualism has fascinated me (see here, here, here, here, here, here, here, here, and here). If you aren’t familiar with the term, it refers to a situation in which two or more organisms of different species work together so that each receives a benefit. One of the most common examples of this kind of relationship is found among fungi and plants (see here and here). The fungi (called mycorrhiza) extract nutrients from the plants, but in exchange, they provide the plants with critical nitrogen- and phosphorus-based chemicals that the plants have a hard time extracting from the soil. As a result of this relationship, both the plants and the fungi thrive. It is not surprising, then, that the vast majority of plants in nature form relationships with mycorrhiza.

Swiss researchers were recently studying trees in a forest, and they learned something rather surprising about these mycorrhiza. They facilitate the exchange of nutrients between different trees in a forest, even trees of different species!¹ Why is this so surprising? Well, it is thought that trees in a forest are in constant competition with one another. They compete to expose their leaves to the sunlight so they can produce more food via photosynthesis. They compete for the nitrogen- and phosphorus-based chemicals that they must absorb from the surrounding soil. They even compete for the water in the soil. Despite this perceived competition, however, there seems to be at least some cooperation as well.

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Bill Nye Couldn’t Be More Wrong!

Me with a family whose eldest is about to finish an MD/PhD program.

I have probably harped on Bill Nye’s errors far too much (see here, here, here, here, here, here, and here). Partly, this is because he continues to make them, when even a small amount of self-education would fix that problem. Partly, it is because some of his errors are so incredibly egregious. This post is a result of the latter situation.

In his error-riddled book, Undeniable, Nye makes the following statement:¹

Inherent in this rejection of evolution is the idea that your curiosity about the world is misplaced and your common sense is wrong. This attack on reason is an attack on all of us. Children who accept this ludicrous perspective will find themselves opposed to progress. They will become society’s burdens rather than its producers, a prospect that I find very troubling. Not only that, these kids will never feel the joy of discovery that science brings. They will have to suppress the basic human curiosity that leads to asking questions, exploring the world around them, and making discoveries. They will miss out on countless exciting adventures. We’re robbing them of basic knowledge about their world and the joy that comes with it. It breaks my heart. (emphasis mine)

This is one of the most egregiously false things that Mr. Nye has claimed, and that’s saying a lot, given that it took me twelve pages to detail all of the errors I found in his book. I want to give you some idea of how egregiously wrong that statement is by just highlighting a few people I have met over the past six weeks.

Let’s start with the family pictured with me at the top of this post. The woman in the picture is a homeschooling mother. She has two young ones with her, but she wanted to tell me about her eldest son, who is in the fifth year of his MD/PhD program. Why is he getting two advanced degrees? Because he wants to do cancer research. To treat patients, you typically need an MD. Being trained to do original research typically involves getting a PhD. Thus, those who want to do original research in medicine often get both an MD and a PhD so they have all of the relevant training they need.

This mother’s son demonstrates in no uncertain terms how wrong Bill Nye is. I met her in Peoria, Illinois this past Friday, when I spoke at the APACHE homeschool convention. She came up to me at my publisher’s booth and told me that her son had asked her to inform me of two things: First, my science courses encouraged him to pursue medical research as a career. Second, they helped him excel at university so he could get accepted into medical school.

I am not telling you this to “toot my own horn,” even though a former pastor of mine says I play that particular instrument very well.^* I am telling you this because my courses are young-earth creationist courses, and this mother gave her son a young-earth creationist education. Far from suppressing “the basic human curiosity that leads to asking questions,” this young man’s creationist education encouraged him to continue to ask questions, explore the world around him, and make discoveries. He has, most certainly, already felt “the joy of discovery that science brings.” Indeed, I suspect he will be experiencing that joy for the rest of his career.

Now, if this justifiably-proud mother were the only person I met recently who demonstrated Mr. Nye to be wrong, I probably wouldn’t have posted about her and her son. However, the Lord has led several such people to me recently, and I want to introduce a few of them to you!

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More Disagreement Between Climate Models and Data

A promotional banner for the film "The Day After Tomorrow." (click for credit) — A promotional banner for the film “The Day After Tomorrow.” (click for credit)

The Day After Tomorrow was a 2004 film co-written, directed, and produced by Roland Emmerich. It depicted the destruction of a good fraction of the United States by a terrible weather calamity that had been brought about by global warming. While it was widely recognized as being scientifically inaccurate, it supposedly had a scientific premise. The idea was that global warming had caused so much polar ice to melt that it interrupted the North Atlantic current that transports heat around the world. As a result, outbreaks of violent weather occurred, causing terrible destruction. The media discussed the film a lot back then, and even Al Gore said that while it was fiction, it was a good starting point for a debate about climate change.

While no scientist would ever suggest that such a thing could happen as depicted in the movie (the timescale was way too short, for example), a study was published last year that suggested global warming has started disrupting ocean currents.¹ In particular, the paper suggested that the Atlantic Meridional Overturning Circulation (AMOC) was slowing down. Since the AMOC is a “conveyor belt” of currents that move heat around the globe, the study got the media once again talking about the 2004 film.

Much like the science in The Day After Tomorrow, however, the science in last year’s study was (at best) speculative. It relied mostly on computer models as well as some “reconstructions” of surface temperatures that went back to 900 AD. Using these speculative tools, the authors claimed that their study

suggests that the AMOC weakness after 1975 is an unprecedented event in the past millennium. [emphasis mine]

Not surprisingly, a study that suggested something “unprecedented” received quite a bit of media attention. Equally unsurprising, a recent paper demonstrates that actual measurements of the AMOC indicate that there is no evidence for any kind of weakness.

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Yes, Earth Is Unique, But This Study Doesn’t Demonstrate That!

The earth is sometimes called “the blue planet.” Just as Mars looks red when viewed from the earth, the earth looks blue when viewed from space. Why? Because of all the water. About 71% of the earth’s surface is covered by water, and that’s one of the many, many factors that allows life to flourish on this planet. Based on the limited observations we have, there is simply no other planet like earth. To me, that’s not at all surprising. God created this earth as a haven for life, so it makes sense that there isn’t another planet like it.

Based on my news feed from a few days ago, you would think that a recent scientific paper confirmed this idea. The Daily Mail, for example, proclaimed:

Earth really IS special: None of the 700 million trillion planets in our known universe are similar to our own, study finds

Other sources, such as Science Alert and Discover agree. The latest, most cutting-edge physics demonstrates that earth is unique.

Because these headlines peaked my interest, I decided to look at the scientific paper that describes this cutting-edge research. When I did so, I learned that once again, the media doesn’t bother to try to understand the science that they report. In fact, the researchers who wrote the paper didn’t find the earth to be unique. They estimate that there are about 2×10¹⁸ similar planets in our observable universe.

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A Spinosaurus and a “Pregnant” T. Rex at the Texas Homeschool Convention

A spinosaurus drawn by Hayley, a Texas student who has used my courses.

I love going to homeschool conventions. This past weekend, I spoke at the Texas Homeschool Convention, and it was a wonderful experience. I got to talk with a lot of interesting people, like the great granddaughter of Maria von Trapp. I also got a headache from discussing quantum physics, mechanistic naturalism, and determinism with two of the philosophers I mentioned in a previous post. Of course, I also got to talk with students who have used and are using my courses. One of those students was incredibly enthusiastic, asking me several questions about science. During the course of the convention, she drew me the wonderful picture you see above, which is of a spinosaurus. He is the villain in a story she is writing.

Speaking of dinosaurs, I got a very interesting question during one of my talks. A student who was obviously interested in science asked if I had heard about the pregnant Tyrannosaurus rex that had recently been found. I was surprised by the question for two reasons. First, I had not heard about it, and I try to keep up on the latest events in science. The fact that this student knew a current event in science that I had not heard about really surprised me. Second, it seemed strange that someone would say a Tyrannosaurus rex was pregnant, since all that we know indicates it was a reptile, meaning it laid eggs. I think the term “pregnant” refers to carrying a developing fetus, so it wouldn’t be applied to an egg-laying animal.

Due to the wonders of in-flight internet, I was able to investigate the student’s question on my flight home. Sure enough, there were a lot of news stories about a pregnant Tyrannosaurus rex (see this one, for example). However, when I found and read the scientific paper upon which the stories were based, it became clear to me that the news outlets were doing their typically less-than-stellar job of reporting on science.

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