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How Meaningful are Genome Comparsons?

dna — The information in DNA is stored in specific sequences of the nucleotide bases adenine (A), thymine (T), cytosine (C), and guanine (G). (Click for credit)

We hear a lot about how similar the human genome is compared to the chimpanzee genome. As I have discussed previously, if we compare the genomes one way, they are 72% identical. If we compare them another way, they more than 95% identical. If we compare them yet another way, they are 88-89% identical. That’s a wide range of results! Why can’t we say definitively how similar the human genome is to the chimpanzee genome? There are probably several reasons for this, but I want to highlight a basic one. Even though the human and chimpanzee genomes have been sequenced, we still don’t know them as well as you might think.

To understand why we don’t know these sequenced genomes very well, you need to know a bit about how DNA stores information. As most people know, DNA is a double helix. Each strand of this double helix has a sequence of chemical units called nucleotide bases. There are four different nucleotide bases: adenine (A), thymine (T), cytosine (C), and guanine (G). Taken three at a time, these four nucleotide bases code for a specific kind of chemical called an amino acid. The two strands of the double helix hold together because the nucleotide bases on one strand link up with the nucleotide bases on the other strand.

As shown in the illustration above, the way the nucleotide bases link up is very specific. Adenine (A) links only to thymine (T), and cytosine (C) links only to guanine (G). Because of this, if you know the sequence on one strand of DNA, you automatically know the sequence on the other strand. After all, A can only link to T, so anywhere one strand has an A, the other strand must have a T. In the same way, C can only link to G, so anywhere one strand has a C, the other strand must have a G. So the two strands of the DNA double helix are held together by pairs of nucleotide bases.

As a result, we count the length of a genome in terms of how many base pairs there are. The illustration above, for example, has 14 base pairs (the black G is hiding a C behind it, and the black A is hiding a T behind it). Obviously, then, the larger the number of base pairs in the genome, the longer the genome is. Believe it or not, even though the human and chimpanzee genomes have been sequenced, we don’t know for sure how long either of them are!

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Jesus Talks to Pilate After the Resurrection?

I have a little-used category on this blog called “Christian Drama.” It is there because from time to time, I write dramas that are performed at my church. Back in January of 2011, for example, I wrote a 25-minute drama based (very loosely) on the end of John Newton’s life. It turned out pretty well, and I posted the video here so that others might enjoy it. Since then, I have written a few dramas for church, but I didn’t consider any of them worth posting.

Yesterday, of course, was Easter Sunday, which I consider to be the most important Sunday worship service of the year. I was asked to come up with a short drama for the service, and I agreed – with some hesitation. The problem with writing a drama about Easter is that it’s hard to come up with something new. The account of Jesus’ resurrection is so important to the Christian church that it has been written about, preached about, and depicted in all sorts of different ways. How do you come up with something that is original and at the same time meaningful?

Well…here’s what I did. I decided to present a fictional (but maybe plausible?) presentation of Easter from Pilate’s point of view. Pilate was governor of Judaea at the time, so it fell on him to order Christ’s crucifixion. His wife warned him to “have nothing to do with that righteous Man; for last night I suffered greatly in a dream because of Him” (Matthew 27:19), but he felt pressured by the crowd to order Christ’s execution. I suspect that as time went on, he regretted that decision. I wondered how he might deal with that regret. I then wondered how Jesus might have helped him.

Below the fold you will find a wholly made-up encounter between Jesus and Pilate shortly after the resurrection. This is not meant to have even the slightest hint of historical accuracy. It is just meant to communicate the gospel’s message of forgiveness. I hope you enjoy it.

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Just How Evil Is This “Evil Twin”?

Lophelia — This cold-water coral flourished in acidic waters once it was given time to adapt. (Click for credit)

Ocean acidification has been called the “evil twin” of global warming. That’s because rising carbon dioxide levels are not just supposed to result in an overly-warm world. They are also supposed to result in an overly-acidic ocean. How does carbon dioxide in the air affect the acidity of the ocean? Well, the ocean absorbs a large fraction of the carbon dioxide that is in the atmosphere. Some of that carbon dioxide then reacts with the water in the ocean, producing carbonic acid. The more carbon dioxide there is in the atmosphere, the more carbon dioxide the ocean will absorb. As the ocean absorbs more carbon dioxide, more carbonic acid will be made. Thus, rising carbon dioxide levels will lead to a more acidic ocean.

Unlike the link between rising carbon dioxide levels and global warming, the link between rising carbon dioxide levels and ocean acidification is straightforward and has already been seen to some extent. As you may remember from high school chemistry, acidity can be measured using the pH scale. A pH of 7 is neutral. A pH greater than 7 indicates a basic solution, while a pH lower than 7 indicates an acidic solution. The key for this discussion is as follows: the lower the pH, the more acidic the solution. Well, according to the Ocean Studies Board of the National Research council:¹

The average pH of ocean surface waters has decreased by about 0.1 unit—from about 8.2 to 8.1—since the beginning of the industrial revolution, with model projections showing an additional 0.2-0.3 drop by the end of the century, even under optimistic scenarios

Now this might not sound like a big change, but the pH scale is logarithmic. That means if the pH decreases by 1 unit, the acidity has increased by a factor of 10! Thus, a drop in pH of 0.1 is actually a change of 26%. This means the ocean is 26% more acidic than it was before the beginning of the industrial revolution. If the models are correct (and who knows if they are), the ocean will increase in acidity by an additional 58 to 100 percent by the end of the century!

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The Christian Home Educators of New Hampshire Convention

chenh — The view from my room at the Christian Home Educators of New Hampshire Convention.

On Friday and Saturday, I spoke at the Christian Home Educators of New Hampshire convention. It was held at a very nice resort in the town of Laconia, New Hampshire. The resort was right on a lake, so the views were beautiful. Indeed, my Saturday talks were held in a large room that had huge windows and a great view of the lake. I expect people were enjoying the view more than my talks! Even so, there were some great questions, and because it was a smaller convention, I got to spend a lot more time talking to people one-on-one.

The conference started on an incredibly memorable note. I was sitting at a table in the vendor hall waiting for my first talk to begin, and a young woman who was in her 20’s came up to me and asked if I was Dr. Wile. When I told her that I was, she introduced herself, giving me her married name and her maiden name. I seemed to recognize the maiden name, but I couldn’t place it. Then she told me her story. Back when I owned a publishing company, I used to have a “Science Question of the Week” competition on the company’s website. I would post what I thought was a challenging science question, and I would invite students 18 or younger to answer the question. After 12 questions, whoever had the most correct answers got to choose from a list of four prizes, typically bought from the Edmund Scientifics catalog.

This young lady told me that she was a past winner of the contest. That, of course, told me why I recognized her maiden name. She said that she chose a Galileo thermometer as her prize and had treasured it for many years. Well, not too long ago, she was cleaning the shelf where it was stored and broke it. Even though she is now an adult with young children of her own, she actually sat down and cried over the loss! Her grief must have been evident, because her husband ended up buying another one to replace it.

Her story meant a lot to me. I thoroughly enjoyed my time working on the Science Question of the Week, but I had no idea that it meant so much to (at least some of) the students who participated in it. It just goes to show that when you work with students, you never know how you will touch them. Never in a million years would I have thought that the contest meant so much to a student that even as an adult, she would be emotionally affected by the loss of a $30 prize. Teachers and homeschooling parents, take this as a lesson. The things you do that you think are small and insignificant might affect your students in an incredibly powerful way!

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The Evidence from Mercury: Inconclusive

Mercury is a difficult planet to study because of its proximity to the sun. As a result, there are only two robotic spacecraft that have visited it. Starting on March 29, 1974, the Mariner 10 spacecraft flew by Mercury a total of three times, but it never entered orbit. Then, on March 18, 2011, the spacecraft known as MESSENGER (MErcury Surface, Space ENvironment, GEochemistry and Ranging) settled into a comfortable, near-polar orbit of the planet and has been studying it in detail ever since.

As a scientist, I am always excited to learn new information about God’s creation, so I have been watching MESSENGER’s progress with interest. As a young-earth creationist, however, my interest in MESSENGER was somewhat heightened, because its mission included collecting data on Mercury’s magnetic field. The young-earth model of planetary magnetic fields had made a prediction about what MESSENGER would find once it collected those data, so I was naturally very interested in the results of the measurement.

Since the previous measurement of the field was made more than 35 years ago, and since the young-earth model predicts that all planetary magnetic fields should decay fairly rapidly, the young-earth model predicted that Mercury’s magnetic field should have decayed by roughly 4 percent since Mariner 10’s previous measurement. By contrast, the old-earth model predicts no measurable change at all. Because the young-earth model has been successful in three other predictions,¹ I was hoping that MESSENGER would provide a fourth.

Unfortunately, that didn’t happen.

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The 2012 Southeast Homeschool Convention

Last Thursday, Friday, and Saturday, I spoke at the 2012 Southeast Homeschool Convention in Greenville, South Carolina. It was the first of the Great Homeschool Conventions, and I enjoyed myself immensely. I got to “catch up” with several of my colleagues who also work with home-educating families, but most importantly, I got to speak with homeschooling students and parents. The very first time I spoke at a homeschooling convention, I noticed a distinct difference between homeschooled students and their publicly- and privately-schooled peers. While most publicly- and privately-schooled students actively avoid interaction with adults (especially adults who are teachers), most homeschooled students actively seek out such interaction.

I will never forget an experience at that first homeschooling convention. I was sitting in my booth, and a teen came up to me and said, “You’re a scientist, right?” I told him, “Yes. I am a nuclear chemist.” His eyes brightened up, and he said, “Great! I need to ask you something.” He then sat down and asked me a very detailed question about the nature of light. While he had some misconceptions about the subject (don’t we all?), I was pretty impressed with his knowledge. More importantly, however, I was impressed with how he sought me out and was perfectly comfortable discussing science with me for what ended up being well over half an hour. In addition, he was very careful to avoid monopolizing my time. If someone else came to my booth, he would indicate to me that I should pay attention to this new person, and he would wait until I was free again.

Since then, I have come to expect such interactions at homeschooling conventions. This one was no exception. I ended up having a long talk with a teen who really wanted to understand how gravity can affect the passage of time. He had read about the strong evidence indicating that time passes more slowly in the presence of strong gravitational fields and more quickly in the presence of weak gravitational fields, but he wanted to understand why it actually happens. Of course, without the appropriate mathematics, it is rather hard to understand, but I explained it to him as best I could. He seemed to get it in the end, and he was very appreciative of my time.

I talked with homeschooling parents as well. One set of parents came by my booth and told me that their daughter was pursuing a PhD in biology. They said she credits my books with sparking her interest in science and preparing her to excel at university. Obviously, that made my day! I asked them what her PhD thesis would be about, and as near as I can tell, she is working on the phenomenon of horizontal gene transfer between organisms from different biological kingdoms. It sounds like fascinating work, and if my experience with homeschool graduates is any indication, she will probably be incredibly successful at it.

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La Presidenta and Other News from Costa Rica

Last week, my wife and I went to see a friend who is currently living in Costa Rica. It’s a beautiful country that I find significantly more pleasant than most other Central American countries. We could drink the water in Costa Rica without experiencing any digestive issues. In addition, we actually ate food that people were selling on the side of the road, and we experienced no problems whatsoever. In fact, my favorite Costa Rican dish was queso palmito. It is essentially a ball of incredible cheese, and we bought it from a roadside vendor. Also, even though there is poverty in the country, it is not nearly as extreme as the poverty I have seen in other parts of Central America.

During our visit to this wonderful country, we actually got to meet the President, Laura Chinchilla Miranda! We were touring the main governmental building in San José and were allowed into a press conference that the president was having. It was all in Spanish, of course, so I didn’t understand a word. However, I will have to say that I was incredibly impressed with how the president handled herself. A member of the press would ask a 1-2 minute question, and the president would reply with a 5-10 minute answer. She did this with no notes or teleprompter. She had two advisers with her (the Vice President and her press secretary), but she rarely referred to either of them. My impression was that she was giving detailed answers to the questions off the top of her head. It was definitely a lot different from the kind of press conferences U.S. presidents give!

After the press conference, the president was kind enough to come down from the stage and meet us. She even let us take a picture with her (shown above). When I told her what an honor it was to meet her, she told me (in perfect English) that it was an honor for her to meet me. Obviously, she was simply being gracious, but once again, I doubt that I would see such graciousness from a U.S. president. While I know nothing of her political stances, I have to say that after that day, I became a fan!

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The Gorilla Genome Falsifies Another Evolution-Inspired Idea

There is a vast gulf between humans and the great apes. While we share some superficial similarities with them, they are dwarfed by significant differences. For example, most (but not all ¹) evolutionists think that our closest living relative is the chimpanzee, because our genomes are the most similar (72%-95% similar, depending on how you make the comparison). Nevertheless, there are distinct anatomical and behavioral differences between humans and chimpanzees. Indeed, nearly every bone in the chimpanzee body is individually recognizable as chimpanzee and not human simply by its shape and size. Humans and chimpanzees also have different postures, different means of moving around, and different methods of obtaining food. Of course, the biggest difference between chimpanzees and humans is that of intelligence. People have a level of intelligence not seen anywhere else in creation, and it is apparent through our ability to create amazing technologies, produce breathtaking works of art, develop philosophies, and communicate across the generations.

But wait a minute. Haven’t experiments shown that apes can communicate in a very sophisticated way? If you read too much of the popular press, you might think that’s true. However, consider the words of Dr. Jonathan Marks, Professor of Anthropology at UNC-Charlotte and an expert on communication in apes:²

For all the interest generated by the sign-language experiments with apes, three things are clear. First they do have the capacity to manipulate a symbol system given to them by humans, and to communicate with it. Second, unfortunately, they have nothing to say. And third, they do not use any such system in the wild…There is in fact very little overlap between chimpanzee and human communication. (emphasis mine)

So what is it that produces the remarkable difference between apes and humans when it comes to communication? Evolutionists thought they might have at least a partial answer to this question. If you look in detail at human genes and chimpanzee genes, you see some remarkable differences among those genes that deal with hearing. As a result, it has been widely suggested that the human lineage experienced “accelerated” evolution in its hearing genes, which in turn produced our ability to utilize language, which in turn produced our ability to communicate in a sophisticated way.

Not surprisingly, additional data have falsified this evolution-inspired notion.

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Interaction Interruption?

I am currently on my way to Costa Rica. I will be there for a week, and within about 36 hours of when I get back, I will be off to Greenville, South Carolina for the first Great Homeschool Convention of the season. Because of this, I am not sure how much time I will have for blog-related activities over the next couple of weeks. This means my blog might be significantly less interactive than usual for a while. On the bright side, since my travel season is starting, there will be more Notes From The Road entries.

In the meantime, please enjoy this nighttime video from the International Space Station. It starts out dark, but eventually shows you lights from cities, clouds, lightning strikes, and auroras, all from above. The thin, curved line is the haze of earth’s atmosphere, and the brightness that approaches intermittently marks when the space station is moving into the sunlit side of earth. It is well worth watching!

Octopuses Can Change the Products of Their Genes When Necessary!

Pareledone — An Arctic octopus (photo by E. Jorgensen, NOAA)

I have always been amazed at animals that live in very cold water. I can’t stand it when my shower gets lukewarm, but animals like the Arctic octopus (genus Pareledone) flourish in waters that dip below 0 degrees Celsius! How can they do that? Well, they have specific characteristics that allow them to deal with the water’s cold temperature – characteristics that I obviously don’t have. But what is the basis of those characteristics? Until reading a recent paper by Sandra Garrett and Joshua J. C. Rosenthal, I would have said that the basis of those characteristics is the genome of the animal in question. As reasonable as that answer sounds, however, it is not correct, at least not in some cases.

One of the most important things a cold-water animal must deal with is how the temperature affects certain proteins that govern the response of the nervous system. Cold temperatures tend to reduce the efficiency of those proteins. As a result, the colder the water, the slower the nervous system conducts signals. In very cold water, the slowdown would be so great that in the end, signals would not travel quickly enough to allow the animal to do what it must do in order to survive.¹ Thus, it has always been assumed (reasonably so) that many nervous system proteins in cold-water animals are significantly different from the corresponding nervous system proteins of animals that do not frequent cold waters.

Garrett and Rosenthal decided to determine just how different such proteins are by comparing the genes of an Arctic octopus (genus Pareledone) to that of a tropical octopus (Octopus vulgaris). Since genes tell the octopuses’ cells how to make the proteins they need, the researchers assumed that whatever differences exist in the nervous system proteins would show up in the genes that produce those proteins. Once again, this is a completely reasonable assumption. However, their study shows that the genes involved in producing these nervous system proteins are nearly identical between the species.² To confirm this, they injected the genes from the different species into frog egg cells, and they found that the frog egg cells used those genes to produce nearly identical proteins. So in the end, the genes that produce those nervous system proteins are essentially the same in both species. But that doesn’t make sense. The proteins have to be different.

Well, it turns out they are different, but not because of the genes that produce them!

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