Proslogion : Page 66 of 112 : Thoughts from a scientist who is a Christian (not a Christian Scientist)

Human and Chimp DNA Only 70% Similar, At Least According to This Study

human_chimp — A chromosome-by-chromosome comparison of chimpanzee and human DNA. The chimp DNA was cut into slices of varying lengths (see legend on the right), and a similar sequence was searched for on the relevant human chromosome, which is shown on the horizontal axis.
(Copyright Answers in Genesis, published at http://www.answersingenesis.org/articles/arj/v6/n1/human-chimp-chromosome in a study by Jeffrey P. Tomkins)

PLEASE NOTE: The results of this study are known to be wrong due to a bug in the computer program used. A new study that uses several different computer programs shows an 88% overall similarity.

I have written about the similarity between human and chimpanzee DNA three times before (here, here, and here). It’s an important question for creationists, intelligent design advocates, and evolutionists alike, since the chimpanzee is supposed to be the closest living relative to human beings. As a result, a comparison of chimp DNA to human DNA gives us some idea of what the process of evolution would have to accomplish to turn a single apelike ancestor into two remarkably different species like chimpanzees and people.

Early on, it was widely thought that human DNA and chimp DNA were 99% similar. As I discussed in my first post on this subject, that was based on a very limited analysis of only a minute fraction of human and chimp DNA. Now that the entire set of nuclear DNA (collectively called the “genome”) of both humans and chimpanzees have been sequenced, we now know that the 99% number is just plain wrong. Interestingly enough, however, even though both genomes have been fully sequenced with a reasonable amount of accuracy, no one can agree on exactly how similar the two genomes are.

Why is that? Because comparing genomes is a lot harder than you might think. While we know the sequence of the chimp and human genomes really well, we don’t understand the DNA itself. Indeed, there are large sections of DNA that seem to be functional, but we simply have no idea what they do. As a result, comparing the genomes of two different species can be very, very tricky.

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Some People’s Beliefs About Climate Change are Blowin’ in the Wind

gw_views_temp — This graph shows the likelihood of New Hampshire residents agreeing with the statement, "Climate change is happening now, caused mainly by human activities" based on party affiliation and the average temperature. The gray fields represent the error associated with the data.
(The graph is from the study being discussed.)

If you have read this blog for any length of time, you probably know that I am skeptical of the idea that human activities are changing climate on a global scale. I don’t think the data support such a notion. Climate is certainly changing, but that’s nothing new. The data strongly indicate that around 1000 AD, the Northern Hemisphere was significantly warmer than usual; this is generally referred to as the “Medieval Warm Period.” About 650 years later, the Northern Hemisphere was significantly cooler than usual, and that period is often called the “Little Ice Age.”¹ The important question is whether or not the changes we are seeing today is unusual compared to events such as those. Based on the data I have seen, my answer would be, “No.”

At the same time, I hasten to add that global climate is incredibly complex, and we are not close to fully understanding how it works or even how to measure it in a detailed fashion. Indeed, there are various methods used to determine the “average global temperature” and how it has changed over time, and they each produce different results. So while I think that the data show there is nothing unusual about the way climate is changing right now, I think a lot more study needs to be done.

But what do most people think? When it comes to climate change, their beliefs vary over time. The percentage of Americans who think the earth is warming has been falling since 2007. Interestingly enough, however, there seems have have been a recent rebound, at least when the phrase “climate change” is used. What drives these changes? Are the data changing significantly? Are the proponents of one side “getting their message out” better?

Unfortunately, a recent study has provided insight into why some people change their mind on the climate issue, and the results are rather depressing.

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Even Shark Embryos Detect Electric Fields

I have always been fascinated by sharks. In fact, of all the times I have been scuba diving, the dive I remember the most occurred off the coast of South Africa. I went with some marine biologists who had been studying sand tiger sharks (Carcharias taurus). As I initially sunk down into the water, I leveled out just a few feet from the bottom, and as I was checking my gauge to determine my depth, a 2-meter (6-feet) long shark swum right underneath me! We ended up seeing more than a dozen sharks of various sizes on that dive. It was incredible.

One of the things that is fascinating about sharks is the way they hunt. While they use their sense of smell (and to some degree their sense of sight), one of their main hunting techniques involves using their electrical sense. Yes, sharks can sense electrical fields, and they are quite good at it. As a recently published book on sharks says:¹

They can detect the minute electrical currents generated by the nervous systems of prey by using electrical sensors called the ampullae of Lorenzini…These sophisticated sensors are very useful in finding prey buried under the sand.

Interestingly enough, these sophisticated sensors often develop while the shark is still an embryo. Is that just to get the shark ready for hunting its prey when it is fully developed, or could there be some use that the embryo has for sensing electrical fields? It doesn’t need to hunt, so for what purpose could it be using its electrical sensors?

Some Australian scientists decided to investigate this issue, and what they found is fascinating!

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Sockeye Salmon Use Geomagnetic Details to Guide Them Home

Salmon have an incredible lifecycle. They hatch in freshwater streams, eat and mature a bit, and then they make their way into the ocean. They do most of their growing and maturing in the ocean, and when they are ready to reproduce, they return to the very stream from which they hatched to find a mate and begin the cycle all over again.

A lot of research has been done trying to figure out how the salmon know the way back to the specific stream from which they hatched. Well, each stream has it own mix of soil, rocks, and other environmental elements. As a result, each stream has its own specific mix of chemicals. Most of the data indicate that a salmon remembers the specific chemical makeup of its original stream. Once it gets back to freshwater, then, it starts following a “chemical trail” that will lead it back to the stream from which it hatched.¹

While this is rather impressive, it doesn’t really tell us about the most difficult navigational aspect of the journey. The salmon spends a long time in the ocean growing and maturing. As a result, it often ranges far from the place where it entered the ocean. How does it find its way back to the correct freshwater inlet that will lead to the correct stream? It seems hard to believe that it could follow a “chemical trail” that far! Since we know that salmon are equipped with biological machinery that allows them to sense the earth’s magnetic field, it has been thought for some time that salmon use magnetic guidance to get them to the proper freshwater inlet.²

While that’s a reasonable conclusion based on what we know, there hasn’t been a lot of evidence to back it up. However, a recent study published in Current Biology has begun to remedy that situation.

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Cosmos, Bios, Theos

Dr. Henry Margenau was the Eugene Higgins Professor Emeritus of Physics and Natural Philosophy at Yale. He died in 1997, but five years before that, he and Roy Varghese, an international journalist, teamed up to edit a book entitled Cosmos, Bios, and Theos: Scientists Reflect on Science, God, and the Origins of the Universe, Life, and Homo sapiens. I came across an old review of the book some time ago, and it sounded intriguing, so I decided to put it on my reading list.

Margenau and Varghese contacted some of the most important scientists of the twentieth century and ask them about their views regarding God and the subject of origins. In the end, they got responses from 60 prominent scientists, 24 of whom had won the Nobel Prize. Most of them responded to six questions that Margenau and Varghese asked:

1. What do you think should be the relationship between religion and science?

2. What is your view on the origin of the universe: both on a scientific level and – if you see the need – on a metaphysical level?

3. What is your view on the origin of life: both on a scientific level and – if you see the need – on a metaphysical level?

4. What is your view on the origin of Homo sapiens?

5. How should science – and the scientist – approach origin questions, specifically the origin of the universe and the origin of life?

6. Many prominent scientists – including Darwin, Einstein, and Planck – have considered the concept of God very seriously. What are your thoughts on the concept of God and the existence of God.

As you might expect when 60 deep thinkers are asked such serious questions, the answers were varied and incredibly interesting. Before I discuss them, however, it is important to make two points. The first one is made in the preface of the book:

Cosmos, Bios, Theos makes no pretension to being a statistically significant survey of the religious beliefs of modern scientists. (p. xiii)

So the reader should not use the responses contained in this book to infer the general attitude among scientists toward the existence of God or the question of origins.

The second point is that not all the scientists responded to those six questions. Instead, some simply wrote a few pages of general thoughts about the topics of God and origins. Others permitted the use of interviews that had already taken place between them and Roy Varghese.

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Hippopotamus “Sweat”

hipposweat — This circus poster promoted the myth that hippos sweat blood. (Public domain image)

I am currently in Thailand, speaking at a family education conference. There are a lot of incredibly wonderful families here, and not surprisingly, some of them feel a bit overwhelmed at homeschooling their children in Asia. To all those homeschoolers in the United States: be thankful for all the support that exists where you live. Home education is difficult enough when there are support groups, easy access to curriculum, and homeschooling conferences that showcase multiple speakers and vendors. Imagine trying to homeschool with without such luxuries. That’s what these families do every day.

Because I am one of the few speakers at this conference, I have been giving a lot of talks. However, my favorite thing to do is answer questions. As a result, one of my scheduled times with the parents was simply a question/answer session. It went really well, and I hope I helped these parents with their unique situations. I was also scheduled for two sessions with the teens, and I made one of them a question/answer session as well.

When you offer a one-hour time slot for questions and answers, there is always a risk. What if the attendees have no questions? What if they have a couple of questions, but not nearly enough to last for an hour? I honestly didn’t think this would be an issue for the parents, since they face so many challenges homeschooling where they are. However, I did worry about the teens. While I was sure they had lots of questions, I was afraid they wouldn’t be “brave” enough to ask them in a group setting. To reduce the risk, then, I offered free candy for every question. Not surprisingly, the teens ended up having plenty of questions.

One of the reasons I love answering questions is that I often learn something new in the process, and this conference was no exception. The second question I got from the teens was:

What is the color of hippo sweat?

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Even More Impressive DNA Storage

dnastore — DNA can store incredible amounts of information (montage of public domain images)

A few months ago, I wrote an article about a group of scientists who stored a book that contained words, illustrations, and Java script on DNA. It was an amazing technical achievement, and it demonstrated the incredible storage capabilities of this marvelous biomolecule. Well, another team of scientists has gone even further: they stored words, pictures, and audio on DNA!

Yes, the team encoded all 154 of Shakespeare’s sonnets, a photograph of the European Bioinformatics Institute (where the scientists work), and a 26-second audio clip from Martin Luther King’s famous “I have a dream” speech.¹ Also, in a very fitting symbolic gesture, they added the famous James Watson and Francis Crick paper that first revealed the structure of DNA.²

This new achievement was noteworthy for more than just the fact that the scientists stored audio on DNA. While the method that the previous team used to store the book worked well, it was difficult for instruments to retrieve the information from the DNA once it was stored there. Thus, the time it took to retrieve the book from DNA storage was fairly long. The scientists who produced this study used a different method to store the information, which made it much easier for instruments to read it back. As a result, not only was everything retrieved from DNA storage with 100% accuracy, the time it took to get it back was significantly reduced.

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Dr. Jay is AFK

For those of you who do not speak nerd, “AFK” means “Away from Keyboard.” I will be traveling for the next three weeks, and for much of that time, I will not have internet access. That means I will not be able to moderate or respond to your comments. However, please feel free to leave your comments. When I have internet access, I will try to do what I can to moderate the comments and answer any questions you might have. I will also try to post new articles, but it’s not clear whether or not that will happen. It’s possible that there won’t be a new article posted for as many as three weeks.

Being Degenerate Can Be Very Good!

dna1 — DNA uses four nucleotide bases taken three at a time to code for an animo acid (click for credit).

The genetic code is degenerate, but that doesn’t mean it is immoral or corrupt. In fact, in the case of the genetic code, degeneracy is a good thing! Let me explain. One of DNA’s jobs is to tell the cell what proteins to make and how to make them. As a result, it stores “recipes” for proteins, and we call those recipes genes. Well, a protein is produced when smaller chemicals, called amino acids, are linked together in long chains that then fold into intricate shapes. So in order to tell a cell how to make a protein, a gene needs to list a string of amino acids. If the cell puts those amino acids together in the order specified by the gene, the correct protein can then be produced.

How does a gene list the amino acids? As shown in the illustration above, it does so by using the four nucleotide bases known as cytosine (C), guanine (G), thymine (T), and adenine (A). A group of three nucleotide bases codes for a specific amino acid. For example, when a gene has three thymines in a row (TTT), this means “use the amino acid called lysine.” When it has three guanines in a row (GGG), it means “use the amino acid called proline.” So by grouping its four nucleotide bases three at a time, a gene specifies which amino acid should be used in building a protein.

Here’s the catch: There are only 20 amino acids in the standard proteins of life. As a result, there need to be only 20 codes to specify them. However, there are 64 possible ways you can group four nucleotide bases three at a time. Thus, there are 64 different possibilities for how a gene can specify an amino acid, but there are only 20 amino acids the gene needs to specify. As a result, most amino acids are specified by more than one set of three nucleotide bases. As I said above, a sequence of three thymines (TTT) means “use the amino acid called lysine.” However, two thymines followed by a cytosine (TTC) means the same thing. This is why we say the genetic code is degenerate. It has multiple ways it can specify most amino acids.

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Poop Transplants Treat Clostridium difficile Infections!

cdifficle — *Clostridium difficile* from a stool sample, magnified 3,006x (public domain image fron the CDC)

Clostridium difficile is a bacterium that produces toxins which can kill intestinal cells and cause severe inflammation of the intestinal walls. Mild infections from this bacterium can cause diarrhea, while severe infections can cause death. Over time, C. difficile infections have gotten worse. As one medical resource states:¹

C. difficile infection has transformed from a nuisance into a potentially life-threatening illness with an attributable mortality rate of up to 16.7%.

The typical treatment for severe cases of C. difficile infection is a round of strong antibiotics, but that doesn’t always work. A significant number of patients end up experiencing one or more recurring infections within 60 days.² As a result, medical researchers are trying to come up with new ways to treat this infection.

In a recent study published in the New England Journal of Medicine, researchers tested an…interesting…approach. They took 43 patients who had a C. difficile infection and split them into three groups. The first received the standard antibiotic treatment (in this case, 500 milligrams of vancomycin four times per day for 14 days). The second received the standard antibiotic treatment plus a bowl lavage 4 or 5 days into the treatment. In case you aren’t familiar with the term, a bowel lavage involves flushing out the intestines. It is usually done to prepare the intestine for medical imaging. The third group was given a shortened round of antibiotics (500 milligrams of vancomycin four times per day for 4 or 5 days), a bowel lavage, and then a poop transplant.

Yes, you read that right. After the bowel lavage, the patients were given a mixture of water, salt, and the feces from a healthy donor. Now don’t worry. They didn’t have to eat or even smell the stuff. It was sent into their intestine through a sterile tube that went up the nose, down the esophagus, through the stomach, and into the start of the small intestine. While the process sounds incredibly gross, the results were amazing!

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