Jay L. Wile's Blog, page 16

What’s Really Causing Coral Bleaching?

The soft coral colony at the center of the picture is bleached. The corals to the right are not. (click for credit)

Coral are amazing animals. They live in a mutualistic relationship with algae, giving the algae a safe home in exchange for some of the food that the algae make through photosynthesis. The variety of colors seen in a coral reef are a result of this relationship. However, coral sometimes expel their algae, turning white. This is called “coral bleaching,” and it generally happens when the water is warmer than usual. the Australian Marine Conservation informs us:

Coral bleaching is a global crisis, caused by increased ocean temperatures driven by carbon pollution.

This has become a common mantra in the “global warming is going to kill us all” movement, because coral reefs are so fundamentally important to the health of ocean ecosystems. Indeed, it has become so important that if you question what the global-warming alarmists say, it can lead to dire consequences.

Consider, for example, the case of Dr. Peter Ridd. Some of his colleagues at James Cook University published work indicating that Australia’s Great Barrier Reef was on the verge of collapse because of global warming. Dr. Ridd dared to question that narrative, pointing out the data that indicate there is nothing unusual about the bleaching events that have been occurring at the Great Barrier Reef and that the reef has about the same amount of healthy coral as it did back in 1985. For that transgression, he was fired. While a court has ruled the firing unlawful, the university plans to appeal the ruling. Regardless of what happens at appeal, it is clear that the firing was anti-science. Criticism of data, even data related to sacred cows such as global warming, is the hallmark of good science. To squelch such criticism is a direct assault on the progress of science.

Of course, the real question is whether or not global warming is a threat to the oceans’ coral reefs. The answer remains unclear, but the balance of the evidence indicates that it is not. For example, one study of the Great Barrier Reef shows that bleaching events were more common several hundred years ago. According to that study, bleaching events hit their peak in the 1850s. There is also some indication that bleaching is an adaptive mechanism and is not necessarily bad for the health of a coral reef.

With all that in mind, consider a new study that looked at the Looe Key reef in the lower Florida Keys. The study examined all sorts of data related to coral and water conditions over three decades, and they found something rather interesting: high water temperatures were not enough to cause large amounts of coral bleaching. Since we know bleaching is tied to warm water temperatures, marine biologists define something called the “bleaching threshold,” which is when the water temperature reaches at least one degree above the monthly average for that region. It is thought that any temperature above the bleaching threshold can lead to a bleaching event.

Surprisingly, the researchers found that the bleaching threshold was exceeded many times, but there was rarely a mass-bleaching event. In fact, the only mass-bleaching events that occurred were when the bleaching threshold was exceeded AND there was a lot of runoff from the Everglades. Specifically, they found that when a bleaching event occurred, the amount of dissolved inorganic nitrogen (DIN) and soluble reactive phosphorus (SRP) in the water had increased. Both DIN and SRP are elevated when there is an excessive amount of runoff.

Here is how the researchers put it:

Although water temperatures at Looe Key exceeded the 30.5 °C bleaching threshold repeatedly over the 3-decade study, the three mass bleaching events occurred only when DIN:SRP ratios increased following heavy rainfall and increased Everglades runoff.

So while warm water temperatures are necessary for coral bleaching, they weren’t the critical factor for Looe Key. Instead, the amount of water pollution was key. Please note that we already know sunscreen in the water can be very bad for coral larvae, so water quality is obviously a serious factor to consider when trying to protect the health of the ocean’s reefs.

Unfortunately, I don’t think the “global warming is going to kill us all” crowd will pay much attention to inconvenient data like these.

Something I (and Most Scientists) Have Taught for Many Years is Probably Wrong!

One of the problems that science textbook authors face is the fact that science is constantly changing. As we learn more about the Creator’s handiwork, we find that the science we have taught as fact is actually incorrect. Sometimes, this is because the experiments upon which those facts are based were in error. Sometimes, it’s because our interpretations of those experiments were in error. Sometimes, it’s a result of making conclusions that go beyond what the experiments actually tell us. The practical upshot of all this is that some of the things you are reading in your science textbooks are wrong.

I recently found out that something I (and most other authors) have taught about DNA is probably wrong. Most people know that DNA is a double helix. As shown in the illustration above, those two helixes wind around each other, with the information-bearing units (called nucleotide bases) inside. In order for cells to use the information in DNA, those helixes have to be separated so that the sequence of the nucleotide bases can be read. That means the helixes need to be held together when DNA is not being used, and then they must be separated when it is time for the cell to read the DNA.

How does that happen? Well, according to most textbooks (including mine), it is because the nucleotide bases form hydrogen bonds with one another. Hydrogen bonds are weaker than true chemical bonds, but they can hold things together. As I say it in my textbook, Exploring Creation with Chemistry, 2nd Edition:

…the attraction between the atoms in hydrogen bonding is about 15% as strong as the attraction between two atoms that have a true chemical bond linking them. Thus, the hydrogen bonds in DNA are strong enough to keep the two chains together in a double helix, but they are significantly weaker than a true chemical bond. Since they are weaker than a true chemical bond, it is rather easy for the two helixes in DNA to unravel.

This sounds great, but a recent study indicates that it’s probably not true. If nothing else, it doesn’t tell the entire story.

The researchers showed that you can unravel the two helixes in DNA without forcing the hydrogen bonds to break. Instead, all you have to do is change the environment in which the DNA exists. If DNA is in an environment that is mostly water, the two helixes hold together nicely. This is because DNA is hydrophobic, which means it is repelled by water. The DNA stays together in order to avoid the water molecules as much as possible. However, if you add a chemical that makes the DNA’s surroundings more hydrophobic, the DNA will relax, because it doesn’t need to avoid as many molecules. If you make the environment hydrophobic enough, it will relax to the point that the helixes unravel.

Based on their results and results from other researchers, the authors suggest that there are enzymes in the cell’s nucleus that do exactly that. When the DNA is not being read, it is surrounded by a lot of water molecules, so the helixes stay tightly wound around one another to avoid the water molecules. When the cell needs to read a section of DNA, enzymes are brought near that part of the DNA. Those enzymes are partially hydrophobic, and the DNA relaxes. This allows the helixes to unravel so that the information can be read.

This research really surprised me, since I have used the textbook explanation over and over again throughout my years as a science educator. Because of this, I contacted a molecular biologist who is a part of my extended family. I don’t like to bother him too often, because he is retired, but he is one of the most accomplished, brilliant, and humble scientists I have ever met. I asked him if he would take a break from fishing and hunting to let me know what he thought of this “surprising” research.

He basically said that he didn’t find it terribly surprising. He said that years ago, his lab saw that adding a chemical called formamide significantly lowers the temperature at which you need to heat DNA to unravel the helixes. This was good for them, because they wanted to heat the DNA as little as possible. They assumed it was because the formamide was making the DNA’s surroundings more hydrophobic and therefore allowing the DNA to relax, reducing the energy needed to pull the helixes apart. They just never investigated the process to see if they were right.

Now this doesn’t mean the hydrogen bonds between the nucleotide bases in DNA are not important. They allow the bases on each helix to pair up properly, and they may aid in holding the two helixes together. However, the textbook explanation that they are the main reason DNA holds its double-helix shape when it is not being read is almost certainly wrong.

Science is a wonderful way to gain knowledge about God’s creation, but by its very nature, it is tentative. You must always be willing to reevaluate what you have been taught about science, because much of what you have been taught will eventually be shown to be wrong.

And Now For Something Completely Different

A while back, I posted a very creative test answer given to me by one of my former students. I want to post something else that she wrote. It’s not what you normally see on this blog, but I enjoyed it immensely. I hope you do, too.

A Tale of Two 19th Century Gentleman Scientists Living in the 21st Century in Six Short Scenes

By Eden Cook

~January 21, 20—~

It has been said, though by whom I cannot say, that every good story starts with a bad decision, and that is precisely what a certain Mr. Tobias Newton was thinking he had made in accepting the chairmanship of the S. O. O. S. S. Like so many societies of its kind, the Something-or-other Science Society had been founded with the best of intentions. It was to be a society for the local pursuers of all branches of scientific knowledge to aid one another by exchanging ideas, hypotheses, and data, and for some time this was what it had been. In past times Newton had brought those who were flagging in their scientific zeal to the society meetings and it almost never failed to invigorate their studies, but now it had fallen into disrepair due to that same lack of zeal on the part of its leading members. It could now be best described as a meeting of rather glum persons, mostly men and mostly chemists, who came together to complain of the weather, their health, and the lack of available Cesium. Newton had hoped to be able to revive the society that he had enjoyed so much in the past by accepting the position of chairman, but he found that instead of influencing the members for good, their persistent pessimism was wearing away his resolve.

Hence it was a rather dejected Mr. Tobias who arrived back at his extensive Edwardian abode. It was a house with that strange sort of charm peculiar to antiquated buildings which have not yet been allowed to fall into disrepair. But to one so accustomed to its premises as Newton, these finer qualities were for the moment swallowed by his many other preoccupations. Not the least of these other worries was the guests he had coming to stay with him. His cousin, Rutherford—a chemist—was coming to visit Newton later that week. In general Newton felt inept at entertaining company, but he was always at his ease around his cousin. The trouble was not (as it so often was) Rutherford, but his much younger lab assistant who simply went by Tertius. Newton knew next to nothing about the young scientist, but in all probability he would be a sorry addition to their customary twosome. But whether he really was or not, Newton needed to try to make his cousin’s assistant feel welcome, and we will leave him to attempt that very thing.

~January 25, 20—~

It snowed heavily the on the day that Rutherford and Tertius arrived at Newton’s residence. The weather drove them quickly indoors to the front room where a large fire helped to thaw the travelers, and where hot tea (Rutherford’s customary beverage) awaited the company. Introductions were quickly made by Rutherford who introduced Tertius as a “capital fellow” and Newton as “my better in everything.” To which remark Newton protested that he was not and would never be a chemist. After a brief pause Rutherford inquired, “Say, do you still go to those wonderful little meetings? There were quite a few chemists there.”

“Yes, I do,” Newton replied hesitantly.

“You were made chairman a little while back weren’t you? Capital society.”

“Yes, I am the chairman, but I must say the society days are coming to an end. I really think I could manage better without them.”

“Well I’m sure you’re the brightest of the lot, but it can’t be all that bad. It is just the kind of thing that Tertius here would like—what say you to us dropping in on the next meeting?”

Newton deliberated a little before replying, “I don’t think it is at all the kind of thing to interest your young companion.”

“Nonsense, it is highly interesting; they are a capital lot.”

“I am sure that anything Rutherford finds interesting, I would not be bored by,” input the heretofore silent Tertius.

“We may give it a try, but do not hold high expectations. I must seem strangely reticent to you, Rutherford, but indeed the society has fallen on bad times,” said Newton.

“Well, we shall see on Tuesday, assuming they still meet on Tuesdays. In the meantime we will put away a subject that makes you so unusually unenthusiastic, and inquire after Laska,” spoke Rutherford with a genial finality, turning to a subject that seldom fails to please anyone—the wellbeing of their dog.

~January 28, 20—~

“I understand now why you were so unenthusiastic,” granted Rutherford as our three scientists exited the Tuesday meeting of the S.O.O.S.S.

“We are not in our heyday,” replied the unhappy chairman.

“I would say not. I would have thought that Bascome though, he ought to have been above such trivialities as all that. He was rather renowned in his day… ”

“Trivialities have been the favorite object of the society for some time now.”

“Well it really is a shame how it turned out. I hope you can find some way to turn things around for the better. You have a knack for inspiration.”

For the sake of my long-suffering and worthy readers, I will fill out the picture put before you. Our Scientists had indeed attended that Tuesday’s society meeting. Newton had known what the gathering would be like, and Tertius had nothing but vague expectations, but to Rutherford, who had fond prior memories of the society, recalling it as a place of excitement and scientific ardor, the meeting was particularly disappointing. However, we will not dwell long on this disappointment, but rather turn to the other events of our story…

~February 1, 20—~

It was the day before Rutherford and Tertius were scheduled to leave when the accident happened. Tertius was taking notes for Newton on an experiment he was conducting, and Rutherford had gone to remedy the lack of tea and some such sundry things. At around 2 p. m. the telephone rang. Having attained a somewhat secretarial position in the house, Tertius answered. When he came back, an anxious Tertius related that Rutherford had managed to land himself in the hospital.

“That is just like him,” answered Newton. “What did he do this time?”

“I think he was in a small car collision, and broke one of his wrists. He said it was a bad break, but not much besides the wrist.”

“Well, it certainly could have been worse, but we ought to see what help we can offer.”

The friends of the unfortunate arrived at the hospital in all haste and after waiting nigh on an hour found Rutherford almost without difficulty.

“Well, I see they’ve beat you up cousin,” commiserated Newton upon seeing the harried Rutherford.

“I’m afraid they have,” Agreed the invalid. “It was good of you to come, and you too Tertius.”

“We could hardly have done anything else. How did it happen?” inquired a concerned lab assistant. And as is the fate of most who have received visitors in the hospital, Rutherford commenced a retelling of his mischance, not for the first time, and not for the last. “It isn’t all that bad, but it is terribly annoying… It is very annoying. It means no work for quite some time, and what am I to do without work? And it means Cecil…well, never mind about Cecil.” He concluded letting his last phrase trail off.

“Cecil will understand.” Answered Tertius, while Newton wondered why he hadn’t heard of the said Cecil before.

“But it is so annoying,” reiterated Rutherford in frustration.

“Nothing keeps you down for long. I am sure this is no exception. In the meantime, we will be of what service we can,” chimed in Newton with optimism.

“Well if you are in earnest, it would be capital if you could get a real cup of tea. The only kind they have here is that nasty, pre-packaged, green stuff.” Once the request was issued it was scarcely two minutes before Tertius and Newton were on the trail of some

“real” tea.

“Mr. Newton,” Tertius ventured once they were out in the hall, “I gather that you suppose Rutherford is irritated by his overall lack of mobility and the changes that will make in his general daily life, but in fact there is a much more specific reason why he is so bothered.”

“Is it this Cecil? I have never heard of him, who is he?”

“He is a recent acquaintance, who had cause to come to Rutherford for help. You see, Rutherford has promised to get him certain lab results by a certain time, and will now be unable to.”

“Can the fellow not wait?”

“I understand that it was rather important. I do not know all the particulars. I am just a lab assistant, but I know that it vexes Rutherford sorely to have to rescind a promise.”

“What else is there to do, though?”

“Perhaps if you were to ask some of the science society members, they could help. I know what experiments need to be done, and I understood that many of them were chemists.”

Newton’s brow lowered a little at this suggestion. “Maybe the two of us could do it ourselves.”

“But I do not think that your lab has all of the equipment for the experiments.”

“And you don’t think that a physicist could do it anyway,” replied Newton, correctly reading Tertius’ mien. “You can try what you may to get one of the society fellows to help, but do not expect great results. As soon as you confront them with what is in fact real research that requires some work they will mow you down with half a dozen excuses. They are in fact more suited to philosophy than the sciences.”

~February 3, 20—~

Newton had no trouble in assembling a group of society members soon after. He had invited ten of the members and eight of them appeared, but he had expected fewer. After a brief introduction, Newton allowed Tertius to explain the dilemma and lay down his proposition.

“I believe that all of us here are acquainted with my friend Rutherford,” the assistant began. “Yesterday, he broke his wrist in a car accident. Fortunately, there was little real damage, but he will be unable to use his left hand for weeks.” There was very little reaction to this, and after an awkward silence Tertius continued, “Before all of this happened Rutherford had promised to run an experiment for a friend of his, who needed the results by the end of this week. But, now, he will be unable to finish it, and hence, unable to fulfill his promise.”

“Well, I’m sure we’re all very sorry for ‘im, but what has this got to do with us? Asked one of the more prominent (and vocal) members, a certain Archibald Scrubb.

“My friend is more upset about not being able to finish his work than he would like to admit. It would mean a lot to him if some of us could finish it for him. It is tedious, but not particularly challenging if you have the equipment.”

“Well, that is another thing. These setbacks happen, but you can’t get all worked up about them. Everyone has promises they can’t keep, and it doesn’t mean that everyone else has to go and make it right, does it?” replied the same Mr. Scrubb.

“But you are a scientific society. This is what you do. You help each other with your scientific pursuits! Why is this any different?”

“I understand it is a bad lot, but you can’t come to others to fix your problems. And it wouldn’t work anyway. You—being an assistant—would like to lump us all in as chemists, or worse, scientists. What you don’t see is that we are all different species of chemist and that it would be almost impossible for us to all work together. I am a Geochemist, very different from the others here. Jones here is a biochemist, and Mr. Miller is a nuclear chemist, while Bascome over there is really just a pseudo chemist.” (Bascome made some small interjection here, but was largely ignored.) “We ‘aven’t much at all to do with each other. You can give Rutherford our sympathies, but I’m afraid there isn’t much more I can spare.”

“And is this how all of you feel?” asked Tertius, not without some annoyance.

“I am sure we would love to help in some other way, but I think Scrubb is right. We couldn’t work together,” put in Jones apologetically. There was murmured assent from the rest of the group, confirming Newton in his hypothesis.

“Well, in that case I suppose there is not much more for me to say,” said Tertius, looking deflated. It did not take long for the meeting to adjourn, as it had already grown so uncomfortable. And again Newton and Tertius were left alone.

“I have always thought it better to be a physicist,” was all that Newton had to offer.

~February 7, 20—~

Rutherford and the very loyal Tertius were scheduled to leave the next day, as there had been no complications with Rutherford’s injury, and, while he had very little use of that hand, he had been able to adapt quite nicely. Not for the first time (and we shall hope not the last) were the three assembled in the front room enjoying a large fire and “real tea”. All pretense of a conversation had dropped as each sank into his own thoughts. At a violent knocking on the front door all three started and reverie was banished. Tertius’ face lighted up and he quickly offered to see who the visitor was.

“I wonder who he could be expecting,” said Newton more to clear away the silence than for an answer.

“I don’t think he could be expecting anyone. He doesn’t really know anyone around here, does he?” answered Rutherford.

In answer to his question, into the room walked four thoroughly bundled figures of varying heights, with Tertius at their heels. It was not until they had divested themselves of their outer layers, that they were recognizable as Messrs. Scrubb, Jones, Miller, and Bascome of the S.O.O.S.S.

“Good evening, Chairman,” greeted Scrubb, “Sorry to drop in on you this way—all of a sudden, I mean—but we had a bit of business with your friend here before he leaves.”

“With my cousin?” asked Newton incredulously.

“Yes, sir, with ‘im,” replied Scrubb, relapsing into his habit of clipping his “h’s”.

“Capital! It is very good to see all of you again,” put in Rutherford.

“Well to get right to point, you see, we all ‘eard how you were injured from this young man here, and ‘e asked us to do something to ‘elp. At first we all thought it was none of our business and that there really wasn’t anything we could do. But I went ‘ome and I went to thinkin’ a bit, and I thought how bad it would be if that young man, a mere sapling in the sciences, thought that all of us were old and past our prime and not up to anything of real purport. And Jones was a’thinkin’ the same. So, the point of it is,” repeated Scrubb wringing his hands a little,” that the four of us have gone and finished some work of yours, that we understood you were unable to do, so there it is,” finished Scrubb in a hurry.

“Well, I don’t really know what to say,” answered Rutherford in genuinely perplexed, “what work was it?” He asked, as if he could not tell whether they had written a treatise or washed his car.

“It was the work for Cecil,” Answered Tertius, “We all finished it together, and I wrote up the report.”

Rutherford made no attempt to conceal his astonishment and Tertius hurriedly continued his explanation. “It’s all done, but it turned out rather differently than you were expecting.” Tertius continued to explain the details of the experiment to Rutherford, while Newton arose and came towards the four dissimilar chemists.

“This is very decent of you,” he began, but was quickly interrupted.

“Oh, don’t start that, chairman,” said Scrubb.

“We are leading members of a scientific society. What else could we do?” added Bascome.

“Well, I hardly expected it.”

“You mean to say, you hardly expected it from us… Well, maybe we’ve given you reason to doubt us. We’ve been a bit cantankerous at times, and really haven’t held up our edge of the table,” conceded Scrubb.

“It was difficult at first, since we hadn’t done much scientific work lately, but we all had such a good time of it, that it made me sorry I ever stopped that kind of work,” put in Jones.

“We’ve all agreed to give it our best in the future. Ahh, but I am not fit for this kind of schoolboys’ penitence,” said a somewhat flustered Scrubb.

“I am very glad of it, and congratulate you heartily. The Something-or-other Science Society has a brighter future now.”

“And since we had such a good time, we wanted to invite you to come with us tomorrow. We’ve pooled what potassium we have and are going to toss it into a retaining pond tomorrow. It will be great fun, even for a physicist.”

I need not inform my readers that Rutherford was profusely grateful and that he and Tertius traveled back with eased minds on account of the finished work. As for the society, it is resuscitated for the moment, and seemingly doing well. It remains to be seen if it will last. The moral of this story? Why, surely not every story must have a moral. But you may come to the conclusion that the moral is when trying to get out of homework, land yourself in the hospital, so I see I have no choice but to provide one. This story lacks much depth, but if you wish to find any, it is this: when in need of help and encouragement, helping others can be the best medicine. And with that I bid you adieu.

This “Junk DNA” Confirms a Creationist Prediction!

How DNA is arranged in the nucleus of a cell when it’s not in the process of reproducing. (click for credit)

When a scientist refuses to see the design that is so obvious in nature, it can lead to all sorts of incorrect conclusions. Consider, for example, transposable elements in DNA. Often called “transposons,” they jump around in an organism’s genome. In other words, they are in different places in different cells of the same organism. Those who have their naturalist blinders on initially thought that they were useless – part of the “junk DNA” that represents all the evolutionary “flotsam and jetsam” that has accumulated over hundreds of millions of years. Dr. Leslie Pray, writing in Nature Education, puts it this way:

Transposable elements (TEs), also known as “jumping genes” or transposons, are sequences of DNA that move (or jump) from one location in the genome to another. Maize geneticist Barbara McClintock discovered TEs in the 1940s, and for decades thereafter, most scientists dismissed transposons as useless or “junk” DNA. McClintock, however, was among the first researchers to suggest that these mysterious mobile elements of the genome might play some kind of regulatory role, determining which genes are turned on and when this activation takes place.

Of course, we now know that these supposedly useless stretches of DNA have widespread functionality throughout the genome. However, a recent study demonstrated that one set of transposable elements (the HERV-H subfamily) has a particularly interesting function, which indicates that a creation scientist’s prediction I wrote about nine years ago has been confirmed.

Let’s start with what the HERV-H subfamily is. The “ERV” part stands for “endogenous retrovirus.” When a retrovirus infects a cell, its RNA is converted into DNA, and that DNA is then inserted in the cell’s genome. That way, the retrovirus is replicated as a part of the cell’s DNA. As long as the cell stays alive, that stretch of DNA stays in the genome. If the cell reproduces, each of its progeny also has that DNA sequence. So these stretches of DNA are thought to be the result of retrovirus infections that happened in our evolutionary past. The first “H” stands for human, because this particular group of DNA sequences is found in humans. The last “H” is a category that separates this HERV family from other HERV families.

You can see why most scientists dismissed ERVs as useless. They came from an infection in our primate ancestors, so we have no use for them. I distinctly remember my university biology professor specifically indicating that HERVs are excellent evidence for evolution. ERVs are “obviously” useless, and yet we have many in common with apes. While similar stretches of DNA that have purpose can be understood in terms of common design as well as common ancestry, similar stretches of DNA that are useless are best explained by common ancestry. Of course, now that we know how functional HERVs are, they can also be explained by common design.

But that’s not the point of this post. In the study I am writing about today, the authors determine one of the things the HERV-H subfamily does: It helps to change the way the DNA is arranged in the nucleus of the cell, which allows each type of cell to be as efficient as possible. Remember, every cell has the same DNA (barring some mutation or chimeric effect). However, once a cell is mature, it has a specific job to do, like being a skin cell. To do its job efficiently, it must use its DNA differently than another type of cell, like a nerve cell. As a result, the DNA in each cell’s nucleus is arranged to maximize its efficiency.

You can see that by looking at the image above. Each chromosome has its own “territory” in the nucleus. Each colored region on the left represents a chromosome’s territory. Within each territory, the DNA of the chromosome is not spread out evenly. There are areas called topologically associating domains (TADs) that have to interact quite a bit. Those areas are placed so that they can interact easily, while the areas that don’t need to interact much are “pushed away” near the territory’s edge. Each type of cell will have its own arrangement of TADs, since each type of cell uses its DNA differently.

How does the cell know how to arrange its TADs? That’s where the study comes in. The authors show that the HERV-H subfamily is at least partially responsible for TAD arrangement.

Here, by interrogating chromatin reorganization during human pluripotent stem cell (hPSC) differentiation, we discover a role for the primate-specific endogenous retrotransposon human endogenous retrovirus subfamily H (HERV-H) in creating topologically associating domains (TADs) in hPSCs.

Now remember, human pluripotent stem cells are cells that have the ability to become many different kinds of cells. So as a stem cell matures into whatever cell it is going to be, the HERV-H subfamily helps to arrange the DNA in the nucleus so the mature cell can do its job efficiently.

How does this confirm a creationist prediction? In April of 2009, Dr. Peer Terbor wrote about ERVs. In the article, he develops a hypothesis for the origin of certain viruses. To develop that hypothesis, he specifically redefined ERVs as “Variation Inducing Genetic Elements” (VIGEs): parts of the genome that are designed to change the DNA when change is needed. What is the HERV-H subfamily doing? It is inducing variation in the DNA. Now Dr. Terbor was specifically talking about the variation you see from one generation to the next, but implicit in his definition is that HERVs have a specific function: they produce changes in the DNA that help the organism to survive. That’s what the HERV-H subfamily is doing, so his prediction has been confirmed.

If you have heard the lie that creationism cannot make useful predictions about the way the world works (a necessary component of any scientific theory), you should know that this is just one of many confirmed creationist predictions. You can read about others here.

Cool Video of a Soft Dinosaur Cell

A dinosaur fossil (left) and a cell that came from a different part of the same fossil assemblage (right)
(Images copyright Mark Armitage. Click for source)

A couple of years ago, I wrote about the remarkable dinosaur research being done by microscopist Mark Armitage. The story discussed two scientific articles he wrote about finding soft dinosaur cells in a Triceratops fossil. Well, Armitage is continuing his research at the Dinosaur Soft Tissue Research Institute in the state of Washington. The pictures above represent some new results: soft bone cells from a Nanotyrannus fossil.

Now whether or not there is such a thing as a Nanotyrannus is actually a matter of debate. Some paleontologists think the fossils are really from a juvenile Tyrannosaurus. So it might be a different species, or it might just be a juvenile form of an already-known species. Regardless of which is correct, it is well accepted that these fossils have been found in Cretaceous rock that is supposed to be about 65 million years old. It’s hard to understand how any cellular material could have survived for that long without being fossilized. Nevertheless, the cells that Armitage has extracted from the fossil are soft, as shown in the video below.

Of course, it is always possible that the cell is not really from the dinosaur. However, that’s a bit hard to believe. It came from a bone, and it has all the visual characteristics of an osteocyte, which is a bone cell. I can’t think of any possible contaminant that has the size, shape, and filipodial extensions that you see in the video. Also, remember that Armitage previously extracted soft bone cells from a Triceratops fossil. Thus, if this is a contaminant, it must be common to two completely separate fossils (or somehow introduced by Armitage’s process, which once again, is hard to believe).

I think it is reasonable to conclude that Armitage is, indeed, isolating soft dinosaur bone cells. He plans to make a presentation at Lower Columbia College in Longview Washington, on October 5th 2019, at 7 pm. In that presentation, it looks like he will also discuss how the soft tissues from which his cells are isolated react to stains for DNA and RNA. I won’t be able to make it, but I sincerely hope that it is recorded and that Armitage eventually writes another article about his continuing research!

Large Study Indicates Genetics Has Little Influence on Sexual Orientation

I don’t normally write on topics like this, because studying human behavior is a tricky subject. There are all sorts of different explanations for a given behavioral characteristic in people, and trying to isolate a specific cause is difficult, to say the least. However, there has been a lot of news about the recent study that concluded there is “no gay gene,” and I have gotten several questions about it. As a result, I decided to read the study and share my thoughts.

First of all, it’s not surprising that there is no gay gene. In fact, researchers have said that for years. If there were a single gene that heavily influenced whether or not a person is homosexual, it would have been easy to find and discovered years ago. Also, even something as simple as the color of your eyes is governed by at least eight different genes. Thus, to think that something as complex as sexual behavior is governed by one gene is naive at best. So that specific result of the study is not even interesting, much less newsworthy. What makes the study newsworthy is its size, its scope, and the fact that its conclusions are very weak.

The study is massive in two ways. First, the main study looked at 477,522 individuals, but then it repeated the study using three smaller datasets that were composed of 15,142 individuals. Whenever you study people, the more people you have, the less uncertain your results will be. Thus, the sheer number of individuals in the study makes it important. Second, the study compared the entire genomes of the individuals. In other words, they looked at all the DNA found in the nucleus of the individuals’ cells. That’s a massive amount of data for a massive number of people!

What it tried to do is compare single nucleotide polymorphisms (SNPs) among the individuals to see if they could be correlated with sexual behavior. If you aren’t familiar with the term, SNPs are the most common variation between sets of human DNA. Genetic information comes in sequences of DNA building blocks called nucleotide bases. There are roughly three billion nucleotide bases in one strand of human DNA. An SNP is a change in one of those nucleotide bases.

The entire genomes of the individuals studied were available to the researchers, as were answers to several questions about behavior. One of those questions was whether or not the individual had ever had sex with another member of the same gender. When they tried to find SNPs associated with people who answered “yes” to that question, they found five, none of which were on the sex chromosomes. When they replicated the study with the three smaller samples of people, they could only confirm three of those five.

However, all of these SNPs were very, very weakly correlated with the individual’s answer to the question. One of them, for example, made a male 0.4% (four tenths of one percent) more likely to have answered “yes” to the question. That’s an incredibly small effect. Given the weak effect of those SNPs, the researchers concluded that there must be many, many genes associated with sexual behavior, which is not surprising.

As a result, they decided to just look at the similarity in the genomes of the people who answered “yes” to the question. This is called a “heritability” study, and it is typically used to estimate the contribution that DNA makes to a specific trait. When they did that, they found that genetics can only account for 8-25% of whether or not a person answered “yes” to the question. This is significant, since behaviors that have been linked to genetics typically have much higher heritability results. For example, current studies on alcoholism indicate that 40-60% of whether or not a person is alcoholic is determined by genetics. A score of 8-25% indicates that genetics has a tiny effect.

There were two other interesting aspects of the study. First, they looked at the genetic similarities among the people who answered “yes” to the question and tried to correlate them to other traits like alcohol use, anorexia, autism, loneliness, etc. They couldn’t find any genetic correlation with most of the traits, but they did see a genetic correlation with risky behavior, smoking pot, schizophrenia, ADHD, loneliness, and having a large number of sexual partners.

This highlights the main weakness of the study’s focus. Answering “yes” to the question of whether or not you ever engaged in sex with the same gender doesn’t really probe your sexual orientation so much as your willingness to try new things and the culture with which you are engaged. I would think it is rather obvious that if you get high a lot, you are more likely to try a homosexual experience than if you never get high. In the same way, if you have a lot of sexual partners, it makes sense that you might decide to try at least one of the same gender. That’s what the correlation seems to be saying.

This brings us to the second interesting aspect of the study. The authors tried to address this weakness, but it was difficult. For most of the individuals, they had data related to how common homosexual experiences were for them. Among those individuals, there was a wide range of variation from mostly engaging in heterosexual experiences (but making rare exceptions) all the way to being exclusively homosexual.

If they looked at the genetic similarities they had already found and tried to correlate them with the percentage of homosexual encounters, they found weak correlations that had an enormous amount of error and were different between the sexes. The correlation was 0.72 +/- 0.55 for men and 0.52 +/- 0.68 for women. A “0” would mean no correlation, and a “1” would mean perfect correlation. The “+/-” indicates the error involved. In other words, the error involved is almost a much as the correlation found for men and more than the correlation found for women. Once again, this indicates that if an effect is there, it is very, very weak.

If this study’s findings are confirmed by other studies, it means that genetics plays a very small role in determining a person’s sexual orientation. This is important, since the same kinds of studies indicate that genetics plays a much more significant factor in other behavioral traits, such as alcoholism and ADHD.

Excessive Screen Time Linked to Poor Psychological Health in Children and Adolescents

A child playing with an Apple iPad

(click for credit)

Screens are everywhere. It’s very hard to avoid them. However, many health organizations recommend that parents limit the amount of screen time children and adolescents have. First, the health effects of excessive screen time have been well documented. Children who watch TV, computer, phone, and tablet screens a lot don’t exercise much. That leads to some very poor health outcomes, such as obesity. Second, a recent study indicates that there are significant negative psychological effects associated with a lot of screen time.

Psychological research is difficult for many reasons. Whenever you deal with people, you have to try to control for all sorts of variables that affect each subject, and those variables are often significantly different in different subpopulations. In addition, some of outcome measures are subjective, at best. As a result, psychological studies often have conflicting results. However, this one seems to do a good job getting over those hurdles. It contains a lot of subjects (40,337) who were randomly selected, leading to an averaging-out of at least some of the variables. Also, it used the results of the National Survey of Children’s Health (NSCH), which was done in 2016. This survey was given to the people who know the subjects best: their caregivers. It also asks a lot of fairly objective mental health questions, such as whether or not the subject was ever diagnosed with anxiety or depression.

The survey also asked the subjects’ caregivers the following questions:

a) On an average weekday, about how much time does [child’s name] spend in front of a TV watching TV programs, videos, or playing video games?

b) On an average weekday, about how much time does [child’s name] spend with computers, cell phones, handheld video games, and other electronic devices, doing things other than schoolwork?

The researchers added the results of both questions to get the total amount of screen time the subject has each weekday. They then correlated that number to the mental-health-related questions on the survey. The results were rather alarming.

Consider, for example, the question about whether or not the subject has ever been diagnosed with anxiety or depression. Here are the results of that question, graphed against the subjects’ screen time:

The graph is busy, but good graphs usually are. The y-axis represents the percentage of subjects who had ever been diagnosed. The grey lines represent an anxiety diagnosis, while the black lines represent a depression diagnosis. Solid lines are for ages 14-17, while dashed lines are for ages 11-13. The vertical lines are error bars. They represent the range of statistical error for each point. Essentially, each point could be anywhere along its error bar.

Now look at the solid, black line. This is for subjects aged 14-17 who have been diagnosed with depression. There are huge statistical errors associated with teens who have no screen time, less than 1 hour of screen time, and one hour of screen time each day. That means there are very few teens like that, and it also means we can’t really draw any conclusions from those data points. However, once you get to teens with 2 or more hours of screen time each day, the error bars become manageable. If any parts of different error bars end up having the same value, we say the error bars overlap and we can’t draw any real conclusions when comparing those data points.

Now, if you follow the black line, you will see that as screen time increases, the percentage of teens diagnosed with depression increases, and the error bars don’t all overlap. The bottom of the error bar on the point that represents 4 hours, for example, is clearly much higher than the top of the error bars on 2 and 3 hours. Looking at the graph, then, you can see that after 2-3 hours of screen time each weekday, subjects with more screen time are more likely to be diagnosed with anxiety or depression.

There are several graphs like that one, and they all show that after a certain number of hours per day, more screen time means a higher likelihood of poor psychological outcomes. In the end, the authors state:

Children and adolescents who spent more time using screen media were lower in psychological well-being than low users. High users of screens were significantly more likely to display poor emotion regulation (not staying calm, arguing too much, being difficult to get along with), an inability to finish tasks, lower curiosity, and more difficulty making friends. Caregivers also described high users as more difficult to care for and as lower in self-control. Among adolescents, high (vs. low) users were also twice as likely to have received diagnoses of depression or anxiety or needed treatment for mental or behavioral health conditions. Moderate users were also significantly more likely than low users of screens to be low in well-being and, among 14- to 17-year-olds, to have been diagnosed with depression or anxiety or need mental health treatment.

I think this conclusion is justified based on the data, and it should motivate parents to limit their children’s screen time!

Another High-Profile Defection from Darwinism

Yale computer science professor Dr. David Gelernter (click for source)

The High Priests of Science continue to assure us that there is no debate when it comes to the validity of evolution as an explanation for the history of life. As the National Academy of Sciences says:

…there is no debate within the scientific community over whether evolution occurred, and there is no evidence that evolution has not occurred. Some of the details of how evolution occurs are still being investigated. But scientists continue to debate only the particular mechanisms that result in evolution, not the overall accuracy of evolution as the explanation of life’s history.

The problem, of course, is that such dogmatic statements are not consistent with the data that is supposed to guide scientific inquiry. When people honestly evaluate such data, many see how wrong the High Priests of Science are. Nearly two years ago, for example, I wrote about a world-renowned paleontologist who put up a display in his museum showing how there was no controversy about evolution. The problem, of course, is that he had never investigated all the data. When he got up the courage to actually read books written by scientists who point out the many flaws in evolutionary thinking, he ended up being convinced by the data and defected away from Darwinism. This cost him his job, but at least his scientific integrity remained intact.

Now there is another addition to the list of high-profile academics who had the courage to investigate all the data. His name is Dr. David Gelernter, and he is a professor of computer science at Yale University. In May of this year, he wrote a very interesting article for The Claremont Institute. I encourage you to read the article in its entirety, but I cannot help but add a bit of “color commentary.”

He starts out by discussing the beauty of Darwin’s theory, which is one of the reasons I think it is still so widely believed despite the wealth of data indicating that it doesn’t work. He also says that he believed it simply because he was told it was true and never bothered to investigate it for himself. However, he eventually read Darwin’s Doubt by Dr. Stephen Meyer, and everything changed. As he states:

Darwin’s Doubt is one of the most important books in a generation. Few open-minded people will finish it with their faith in Darwin intact.

Now Dr. Gelernter is quick to point out that he cannot agree with Intelligent Design as a replacement theory for Darwin (as Dr. Meyer suggests in his book), at least not as it exists right now:

An intelligent designer makes perfect sense in the abstract. The real challenge is how to fit this designer into life as we know it. Intelligent design might well be the ultimate answer. But as a theory, it would seem to have a long way to go.

As a result, he joins the ranks of intellectuals like Dr. Thomas Nagel who are willing to recognize the fact that Darwinism cannot hope to explain the diversity of life we see on this planet but are unable to accept any of the alternatives that have been presented. It’s this kind of honest, data-driven inquiry that has always led to scientific revolutions. As long as it is alive and well in some academics, there is hope that science will progress.

Dr. Gelernter’s most insightful comment comes near the end. After discussing the discoveries of modern science that indicate the significant failings of Darwin’s theory, he writes:

It can hardly be surprising that the revolution in biological knowledge over the last half-century should call for a new understanding of the origin of species.

Unfortunately, many biologists cannot seem to grasp this simple, yet profound statement.

Of course, those who desperately cling to the dogma promulgated by the High Priests of Science will tell you that Dr. Gelernter’s defection from Darwin isn’t important. After all, he isn’t a “real” scientist. He is a computer scientist. In some ways, however, computer scientists are the ones who are best suited to understand many of the issues related to the origin and diversity of life. Sure, they don’t know all the ins and outs of mutation, selection, regulation, etc. However, they understand in detail how to take information and transform it into an active process. Fundamentally, that’s what life is. It’s an active process that is built on information. Computer scientists know how such things happen in the digital world, and perhaps they can help biologists understand how it happens in the natural world.

There Is Nothing Unusual About the Fires in the Amazon

Fire in the Stanislaus National Forest (not the Amazon region) in 2013 (click for credit)

I had another blog post planned for today, but I decided to put it off because over the weekend, I got three questions regarding the fires in the Amazon. People are concerned, mostly because of irresponsible articles like this one:

Brazil’s Amazon rainforest is burning at a record rate, research center says

It’s the classic example of a story that is technically true but absurdly misleading. Indeed, the National Institute for Space Research has never seen the number of forest fires that it is currently seeing in the Amazon. However, as the article notes, that research program started in 2013. So yes, over the past six years, this is the worst year yet. However, if you just broaden your scope a bit, you will see that there is nothing unusual about this year.

While the National Institute for Space Research has only been collecting data about forest fires since 2013, researchers at the Global Fire Emissions Database have been studying them since 2003. That’s almost three times as long. What do their data tell us? Well, all you have to do is go here. It gives you a handy graph that shows you the total count of fires in the Amazon region by year.

To make it stand out, I thickened the green line, which represents this year. As you can see, this year is pretty much dead center compared to the past 16 years. If you go to the link itself, you can put your cursor over the year listed under the graph, and you can see each year clearly. If you do that, you will see that 2003-2007 were all worse than this year, with 2005 setting the record. The data are actually more detailed than this. You can click on areas of the Amazon region on the left part of the website and see data for each region. If you click on “Amazonas,” for example, you will see that a few days in 2019 did set the record in that region.

It’s probably worth noting that many of these fires are caused by people…deliberately. Natural forest fires don’t happen in the Amazon region very often. Most of the fires are being set to clear land for agriculture, and most of them are not in the heavily-forested regions. Also, while you might be worried about deforestation in general, you needn’t be. The latest research indicates the earth has been getting greener since 1982.

Postmodernism Redefined

The cover of Dr. Lawler’s book

I am not a fan of postmodernism, at least as it is generally defined. Because of this, I have written a couple of posts (here and here) that portray it in a negative light. A frequent commenter on this blog, Jake, took issue with my negative portrayal and suggested that I read Postmodernism Rightly Understood by Dr. Peter Augustine Lawler.

Since I appreciate Jake’s excellent comments and have learned from him on more than one occasion, I wanted to read the book, but it took me a while to get to it. I finally did read it last week. It was an interesting book that discussed several important authors and their ideas. Some of the authors (like Walker Percy, Alexis de Tocqueville, and Allan Bloom) were familiar to me, but others weren’t. As a result, I learned a lot and was exposed to several new ideas. However, I think the book misses the mark.

Now, of course, I am practicing philosophy without a license, while Dr. Lawler is a trained philosopher with lots of experience. Thus, you can take this criticism for what it is worth. Nevertheless, I don’t think this book is a defense of postmodernism. It is more of a discussion of anti-modernism, and based on Lawler’s obvious admiration of Walker Percy (who definitely deserves admiration), it is more a defense of Thomism.

Of course, it’s easy to get lost in the language of philosophy, so let’s make sure we are all on the same page. When it comes to philosophy, modernism suggests that we should ignore traditions (both religious and social) and the inherent biases that come with them, and we should try to judge the world critically. The more unbiased we can be in our judgments, the better. If we do that, we will be able to control our own destiny.

Dr. Lawler defines modernism a bit more narrowly:

By modern thought I mean the attempt to master or overcome nature through action directed by thought. Modern thought, roughly speaking, can be called pragmatism. The point of thought, as Karl Marx said, is not to understand the world but to change it. (p. 1)

I have no problem with that definition of modernism, and Lawler deftly shows that it is an untenable view. As a result, he says, any reasonable philosopher must be a postmodernist. That’s where I have a problem. I would say that any reasonable philosopher must be an anti-modernist, not a postmodernist.

I say this because while postmodernism is, by its very nature, difficult to define, one of its core tenets is to be very skeptical of universal meanings or universal truths. I may accept certain truths, but those truths are far from universal. Other individuals from other cultures or other backgrounds might have very different truths, and there is no way to argue whose “truths” are more or less reasonable than mine. One person’s “truths” are just as valuable as another person’s “truths.”

Dr. Lawler seems to be too good a philosopher to believe that kind of nonsense, so he chooses to redefine postmodernism. As his book’s title suggests, he thinks that the best postmodern philosophy is realism:

Realism, Christopher Lasch and Walker Percy agree, is postmodernism rightly understood. (p. 179)

I am not familiar with Lasch, and I have clearly not read as much Percy as Dr. Lawler, but I would be skeptical that Percy would consider himself a postmodernist. Once again, he is definitely an anti-modernist, but not a postmodernist. Instead, he is clearly a Thomist.

What is Thomism? It is a school of philosophical thought inspired by the works of St. Thomas Aquinas. He was a committed Roman Catholic and accepted the truths as taught by the Roman Catholic church. However, he was convinced that there were other sources of truth as well. Indeed, he thought that even pagans like Aristotle could express truths, and the Christian’s job is to “examine everything carefully; hold fast to that which is good” (1 Thessalonians 5:21). St. Thomas Aquinas incorporated truths from Greek philosophers, Roman thinkers, and Jewish theologians into Christian thought. Those who are guided by that approach are called Thomists.

A Thomist is a realist, so that part of Lawler’s statement is correct. Walker Percy rejects modernism and accepts realism, which posits that truths exist independent of our preconceptions. At the same time, realists also admit that our understanding of those truths is not complete. Obviously, Christians should believe those things, so Thomists are also realists.

Perhaps Dr. Lawler has decided that if you reject modernism, you must be a postmodernist. In my opinion, however, that’s not true. Premodernists (those who believe we learn objective truths based on Divine revelation) also reject modernism, but there is no way to call them postmodernists, since their view predated modernism. Indeed, I would think that the realism espoused by Percy has much more in common with premodernism than anything remotely postmodern.

That’s why I entitled this article “Postmodernism Redefined.” Dr. Lawler has redefined postmodernism to mean realism. I don’t think that’s reasonable, since by the standard definition, postmodernism is pretty much anti-realism.