The “Axis of Evil” in Astrophysics

The European Space Agency’s image illustrating two things that seem to falsify the cosmological principle. (click for credit)

A couple of days ago, I had a fun conversation with a student regarding astrophysics. He seemed very well-informed on the subject, so I begin using some physics “slang” to help move the conversation along. The student picked up on most of the references, but then we began discussing the cosmological principle, which is an assumption upon which the Big Bang model (and many other models of the universe) depends. It essentially states:

Viewed on a large enough scale, the properties of the universe are the same no matter where you are

The student was aware that most observations have never supported the cosmological principle, but he brought up the Cosmic Microwave Background (CMB), which he seemed to think supports it. I countered by mentioning the “Axis of Evil,” and he seemed to think I was joking. I was surprised that he didn’t get the reference, so I explained it to him. He was shocked that he hadn’t heard of it before, so he suggested that I write a blog post about it.

To understand the “Axis of Evil,” you first have to understand the CMB. When astrophysicists were working on the Big Bang model of the universe, which essentially says that the universe “exploded” into being from nothing, they realized that such an “explosion” would leave behind a signature: microwaves that appear from everywhere in the universe. The predicted details of these microwaves varied from paper to paper, but regardless of the details, everyone agreed that if the Big Bang happened, there should be a “background” of microwaves found everywhere in the universe. That’s what became known as the CMB.

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Directed Evolution Wins Nobel Prize

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

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

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

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

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

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No, We Won’t Have Dinosaurs in Two Years!

Even with a LOT of tinkering during embryonic development, only minor changes could be made in a chick’s skull.
(image from Bhullar et. al. article linked below)

A little while ago, I wrote an article about how silly “science journalism” can get. The article was about the popular media’s claim that scientists were about to bring mammoths back from extinction. I explained how the idea was based on real research, but the goal of the research was not to bring mammoths back from extinction. In addition, if anything concrete comes from the work, it will probably be decades from now. In response to that, a student sent me an even sillier article, which comes from that bastion of journalistic integrity, People. It states the following:

Famed paleontologist Dr. Jack Horner, who’s been a consultant on all four films and is the real-life inspiration for Jurassic Park’s dinosaur expert Dr. Alan Grant, believes we’re (optimistically) just five years away from genetically engineering a dinosaur.

This article was written back in 2015, so based on Dr. Horner’s optimistic projection, we should be just two years away from having dinosaurs roaming around in some laboratory.

So what is the source of Dr. Horner’s optimism? He thinks that birds evolved from dinosaurs, so he thinks that we could genetically “turn back the clock” and transform a bird into a dinosaur. He claims that this has already been done to some extent:

In what Horner calls a definitive “proof of concept,” a group at Harvard and Yale “just recently, within the last few weeks, were able to transform the head of a bird back to actually reverse-engineer the bird’s snout back into a dinosaur-like snout.”

There are so many things wrong with that statement, it is hard to know where to start. However, I will give it a try.

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Will Scientists Resurrect the Woolly Mammoth?

Model of a woolly mammoth at the Royal BC Museum in Canada. (click for credit)

One of my former students sent me an article from The Telegraph, a news outlet in the UK. The headline reads:

Woolly mammoth will be back from extinction within two years, say Harvard scientists

The article was written in February of 2017, so the student wanted to know if there would really be living woolly mammoths next year. The answer, of course, is absolutely not. This article is just another example of how many “science journalists” understand neither science nor journalism. Nevertheless, the actual scientific story is interesting, even though it isn’t nearly as sensational as what is indicated in The Telegraph‘s article, or articles found on other sites, such as here and here.

These articles are attempting to report on the Woolly Mammoth Revival Project, which is headed by Harvard professor Dr. George Church. As its website indicates, the goal is not to bring back the identical mammoth species again. Instead, its goal is to create some kind of elephant/mammoth hybrid that can live in colder climates. Why would it want to do that? For ecological engineering.

At some time in the past, woolly mammoth herds (and herds of other cold-adapted animals) roamed what are now the evergreen forests in the northern latitudes. This kept the growth of evergreens in check, making those areas more like grasslands. In addition, the mammoth herds would pack down and scrape away snow. Without this “land reshaping,” snow insulates the soil below, reducing the depth to which it freezes. As the deeper soil thaws, it releases greenhouse gases, and the worry is that those released greenhouse gases will accelerate global warming, aka “climate change.” Now please note that actual data indicate thawing soil will reduce greenhouse gases in the atmosphere, but most “climate change” alarmists aren’t interested in the data.

In the end, then, the Woolly Mammoth Revival Project hopes to populate the north with cold-adapted, elephant-like animals that will once again turn the northern evergreen forests into grasslands, packing down and scraping away the snow as they roam.

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

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

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

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

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Please Stop Believing Facebook, Especially When It Comes to Science!

A picture from a high school experiment that has been hyped on Facebook.

As I was scrolling through Facebook, finding my historical twin and learning what my friends are eating, I noticed a post on my wall. It was from someone I know only through Facebook, but I read her work from time to time, because she is a really good writer. Her post contained the picture above and linked to an article entitled, “WiFi Experiment Done By A Group Of 9th Grade Students Got Serious International Attention. THIS Is Why…” She asked if I knew whether or not the results were legitimate.

The experiment went like this: Students took 12 trays of cress seeds and put 6 of them in one room and 6 in another room. The six trays in one room were next to two WiFi routers, while the 6 trays in the other room were nowhere near a router. They tried to keep everything else (temperature, amount of water given, etc.) the same for all 12 trays. The article says:

After 12 days what the result spoke was clear: cress seeds next to the router did not grow, and some of them were even mutated or dead.

Obviously, then, WiFi routers produce something that kills (and apparently mutates) cress seeds.

I told my Facebook friend that the post reminded me of something that was popular a few years ago. It was an experiment where a person watered a plant with regular water and watered another plant with water that had been in a microwave oven. After several days, the one watered with microwaved water died, while the other one flourished. Obviously, then, microwave ovens are bad for you. Of course, the heart of science is being able to replicate experiments, and many people found that they couldn’t replicate the reported results. Indeed, the Mythbusters did an episode showing that microwaved water didn’t harm plants in any noticeable way.

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Resources for The Upcoming Solar Eclipse

The 1999 solar eclipse as photographed through a telescope (and then Photoshop enhanced) by Luc Viatour in France (click for full credit)

As most people are probably aware, there will be a total eclipse of the sun visible from many parts of the United States. It will occur on August 21st, but the exact times depend on where you are. I received a question about how to best enjoy it, so thought I would compile some resources to help people who are interested. First, you can find out exactly when to expect the eclipse by going to this website:

https://www.timeanddate.com/eclipse/in.html

If you put in your city and state, it will tell you when to start viewing the eclipse, when it will be at its maximum, and when it will end. In addition, it will tell you the magnitude, which is the fraction of the sun that will be blocked by the moon. If it doesn’t have your city, just add a comma and the full name of your state, and it will bring up several other cities in that state. Choose the one closest to you.

The next thing to make clear is that YOU SHOULD NEVER LOOK DIRECTLY AT THE ECLIPSE! The sun produces a lot of light; too much for your eyes to handle. As a result, when you look directly at the sun, the light-sensing cells in your eyes can be overwhelmed. If they are overwhelmed for too long, they can die. Even though the sun is a lot dimmer during an eclipse, it still produces too much light for your eyes. However, it isn’t as difficult to look at as the uneclipsed sun, so you don’t notice that you are overwhelming your light-sensing cells. This can lead to solar retinopathy, which can cause serious vision problems.

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When People Don’t Believe in God, They Will Believe Anything!

Some people actually think it is possible that we are living in a computer simulation.
(click for credit)

Malcolm Muggeridge, the British journalist who was largely responsible for bringing Mother Teresa to the world’s attention, once said:

One of the peculiar sins of the twentieth century which we’ve developed to a very high level is the sin of credulity. It has been said that when human beings stop believing in God they believe in nothing. The truth is much worse: they believe in anything.
(Malcolm Muggeridge and Christopher Ralling, Muggeridge Through the Microphone, British Broadcasting Corporation, 1967, p. 44)

I couldn’t help but think of that quote when a student asked me to read Scientific American’s article entitled, “Are We Living in a Computer Simulation?

Apparently, that question was the topic of a debate held at the American Museum of Natural History back in 2016. The debate was moderated by serial spreader of falsehoods Dr. Neil deGrasse Tyson, who is responsible for one historian asking if it’s okay to lie about history, as long as the lies support a good cause.

According to the article, Dr. Tyson made the evidence-free speculation that there is a 50/50 chance we are, indeed, living in a computer simulation. Why? Because as Muggeridge suggested 50 years ago, when you give up belief in God, you must believe in all sorts of wild ideas in order to make sense of the universe around you.

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Homeschooling and Socialization

Homeschooled children are better socialized than those in public and private school. (click for credit)

When I first started working with homeschoolers, lots of people were concerned about socialization. They wondered how children would “learn” to get along with other children and navigate difficult social settings without being in school. Even before I started researching the matter, I thought the concern was unfounded. After all, school is probably the most artificial social setting a child will ever experience. When are adults ever cloistered away in ghettos, surrounded by people who are the same age? Never. Thus, the idea that students can learn good socialization at school always seemed nonsensical to me.

Nevertheless, people did express concern, so I looked through the academic literature. Even back in the 1990s, there was a wealth of research available on the socialization of homeschoolers. Not surprisingly, the research showed that homeschoolers were better socialized than their publicly- and privately-schooled peers. Perhaps the most interesting study done back then was a Ph.D. thesis by Larry Shyers. In his study, he filmed children from public, private, and home schools in free and structured play. The behaviors of those students were then analyzed by clinical psychologists who didn’t know the schooling backgrounds of any of the children. When Shyers compared the analyses of the homeschooled children to those of the other children, he saw that in nearly all categories of social interaction, the homeschooled children were equivalent to the children from public and private schools. There was only one category in which the homeschooled students scored lower: problem behaviors. As Shyers wrote:

It can be concluded from the results of this study that appropriate social skills can develop apart from formal contact with children other than siblings.

Wow! What a shocker! Children can learn to get along with other people even if they aren’t cloistered away in ghettos, surrounded by people their own age!

Now as I said, even back in the 1990s it was well known that homeschooled students are, on average, better socialized than their peers. Why, then, am I writing about homeschoolers and socialization now? Because someone raised the issue in a Facebook group of which I am a part, and I decided to turn my response into a more detailed blog post.

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Can Courses Taken in Junior High Be Included on a High School Transcript?

Me and Savannah, a scientist in the making!
Me and Savannah, a scientist in the making!

I just got back from Ontario, California, where I spoke at the California Homeschool Convention. I gave a total of five talks over the three-day conference, and I had the chance to speak with lots of homeschooled students and their parents. Several wonderful things happened at the conference, but the highlight for me is pictured above.

On Friday, a young lady named Savannah came up to my publisher’s booth and asked if I was Dr. Wile. I said yes, and she proceeded to tell me that she loved my biology textbook and planned to major in biology at university. I tried to express how much that meant to me, and then she hesitantly asked if I would sign her copy of my book. I said, “Of course!” She didn’t have it with her, but she promised to bring it the next day. Late into the convention on Saturday, she returned with her book, and when she handed it to me, she said, “This is my favorite book in the entire world!”

I had no idea what to say to that. While a lot of students tell me that they love my textbooks, and many of them have also said that my textbooks have inspired them to study science at university, I have never had anyone tell me that one of my books is their favorite book in the entire world! I have lots of favorite books, and none of them are science-related! Don’t get me wrong, there are a lot of science-related books that I really love, but I wouldn’t list any of them as my favorites. When I think of my favorite books*, I think of fictional works like The Chronicles of Thomas Covenant (my all-time favorite series), The Lord of the Rings, and Armageddon’s Children. Not a single science-related book comes to mind. Needless to say, I was overwhelmed by Savannah’s words.

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