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More on Comparing the Human and Chimpanzee Genome

dna1 — A schematic representation of DNA, concentrating on the nucleotide bases that encode biological information. (Click for credit)

How similar is the human genome to the chimpanzee genome? Since both genomes have been fully sequenced, you would think that would be an easy question to answer. Unfortunately, it is not. After all, how do you compare the genomes of two different species? You might think that the most straightforward way would be to simply line the two genomes up and see how much they overlap. If that’s the way you are comparing the genomes, then the answer is relatively easy. Based on the analysis done by the Chimpanzee Sequencing and Analysis Consortium, about 75% of the two genomes overlap well. There is an error rate of about 3% within that overlap, however, so the two genomes are 72% similar based on this kind of analysis.

The problem is that simply lining two genomes up and looking for overlap might not be the best way to compare them. After all, it seems that genomes have been designed to change. Genes and their regulatory agents can move around, be copied to different parts of the genome, etc. As a result, when you compare genomes between species, you might need to be a bit more careful in how you do it.

One popular means by which geneticists compare genomes today is by looking at chunks of DNA in one organism and comparing them to the genome of the second organism. One common way to do this is to use the computer program called BLAST (Basic Local Alignment Search Tool). This program takes a chunk of DNA from one organism and splits it into a series of short sequences called “words.” It then looks through the genome of the second organism, trying to find regions where there is a lot of similarity with the words generated from the first organism. If the similarity is above a specified threshold level, BLAST scores it as an overlap, keeping track of precisely how similar the two sections of DNA are within that overlap.

In other words, rather than looking for long stretches of DNA that overlap between two organisms, BLAST looks for smaller regions of overlap. This makes sense, of course, since a given gene or a given regulatory piece of DNA takes up only a small part of the total genome. By comparing small parts of two genomes rather than the genomes in their entirety, you are better able to find the functional units within the DNA that are similar.

So…when scientists use a comparison method such as BLAST, how similar are human and chimp DNA? Surprisingly, the jury is still out on the definitive answer to that question!

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Kisses From Katie

As most people who read this blog know, I spend a lot of time writing about science. However, I read a wide variety of books. Some are fiction, but most are nonfiction. When it comes to the nonfiction books, many are about science, some are about philosophy, some are about theology, some are about modern Christianity, some are about music, and some are about theater. Most of them have something useful to offer, and if I find one of them particularly interesting, I tend to blog about it, which is why I have an interesting books section. However, other than the Bible, most of the books I read do not have a deep, personal effect on me. I blogged about one notable exception to this general rule more than a year ago, and now it is time to blog about another one. Be forewarned. This is not going to be a typical blog entry. It has nothing to do with science, but it has everything to do with Jesus.

A few weeks ago, I saw a short video on Facebook about a young lady (Katie Davis) who, at the ripe old age of 16, decided that God was calling her to do mission work. She went to Uganda when she was a senior in high school and then again after graduation, and within a short time began adopting girls who had no caretakers. At the time of the video (roughly three years later), she had adopted a total of fourteen girls and was running a ministry that fed, clothed, and paid the school fees for hundreds of Ugandan children. The video was a promo for her book, Kisses from Katie. I decided to buy the book, and I thank God that I did.

In the promotional video, the author mentions Mother Teresa, who said that her role model (St. Therese of Lisieux) did:¹

small things with great love, ordinary things with extraordinary love

It’s fitting that the author looks to Mother Teresa, because she lives out St. Therese’s example better than anyone except perhaps Mother Teresa herself.

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Dr. Frank Logsdon and the NASB: Another Christian Myth

When I decided to start a blog, I wanted to devote a section of it to ideas that are popular in modern Christendom but are simply not true. I call these “Christian Myths,” and you can see the ones I have written about so far. Interestingly enough, one of those articles (Laminin Shaminin) is the most common article on this blog that people find via search engines. Even though the majority of my writing is devoted to scientific issues, I do keep a lookout for any Christian myths that need to be addressed.

A few days ago, someone left a comment that was a bit far away from the topic of the post for me to approve. However, I read it and replied to the commenter via E-MAIL, as I always do in such situations. The person’s comment included a discussion of Dr. Frank Logsdon, a man who claims to have been an integral part of the team that developed the New American Standard Bible (NASB). I tried to track down the primary source for the quote, but I could not find it. The closest I could come is an article by David Sorenson. Here is what that article says:

Dr. Frank Logsdon was the co-founder of the New American Standard Bible (NASB). He since has renounced any connection to it.

“I must, under God, renounce every attachment to the New American Standard Version. I’m afraid I’m in trouble with the Lord… We laid the groundwork; I wrote the format; I helped interview some of the translators; I sat with the translator; I wrote the preface… I’m in trouble; I can’t refute these arguments; its wrong, terribly wrong… The deletions are absolutely frightening. . .there are so many. Are we so naive that we do not suspect Satanic deception in all of this?

Upon investigation, I wrote my dear friend, Mr. Lockman (editor’s note: Mr. Lockman was the benefactor through which the NASV was published) explaining that I was forced to renounce all attachment to the NASV (editors note: This is the same as the NASB)…”

Now, of course, this sounds very bad for the NASB. If the “co-founder” of the translation – the man who wrote the format, interviewed and sat with the translators, and wrote the preface – denounces the NASB, it must be a terrible translation. Fortunately, it is almost certainly not true.

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Antiboitic Resistance Doesn’t Dissapear Quickly

sow_piglet — A piglet nursing (Image in the public domain.)

Those who are not very familiar with the phenomenon of antibiotic resistance often use it as evidence to support evolution. However, those who understand genetics and biochemistry do not. That’s because most antibiotic resistance arises from genes that have been around for a long, long time. For example, an interesting study published just this year showed that many of the genes involved in antibiotic resistance were around with the mammoths, long before antibiotics were available. This seems to indicate that rather than being a response to the human production of antibiotics, at least some antibiotic-resistance genes are necessary for the proper survival of bacterial populations.

A new study provides additional evidence for this idea. In the study, researchers analyzed pigs that were kept on a pig farm known to be antibiotic free for two and a half years. The results were not at all what they expected. You see, bacteria have two ways of storing DNA. They have their primary genome, which contains all sorts of genetic information. However, they also have small, circular strands of DNA called plasmids. An important difference between a bacterium’s primary DNA and its plasmids is that a bacterium can transfer plasmids to other bacteria. It cannot do so with its primary genome.

Because of this distinction, plasmids are generally thought to be “accessory” DNA. They contain lots of nice information, but since they are not a part of the bacterium’s primary genome, they are considered non-essential components. Since copying a plasmid each time the bacterium reproduces takes energy, it is assumed that bacteria get rid of plasmids that they aren’t using.

Well, it turns out that most known genes that confer antibiotic resistance to bacteria are found on plasmids. Since biologists assume that plasmids which aren’t used are lost after a few generations, it was assumed that if you get rid of antibiotics, a bacterial population would get rid of the plasmids that contained genes for antibiotic resistance in just a few generations. It turns out that they were wrong.

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Christopher Hitchens is Dead

Christopher Hitchens died yesterday at the age of 62. In 2010, he publicly stated that he was being treated for esophageal cancer. He ended up dying of pneumonia, which doctors said was a complication from the disease. He was a journalist and writer, best known for his caustic defense of atheism.

While he was a prolific author, I read only two of his books. The first, The Portable Atheist: Essential Readings for the Non-Believer, was actually a collection works from other writers. The authors ranged from Lucretius to Dawkins. As such, it was a rather hit-and-miss book. Some of the works (like those from Shelley, Hume, and Dennett) were quite good, and some (like those from Hardy, Sagan, and Dawkins) were quite bad. Hitchens wrote an introduction to each work, which gave me some idea of his views and the methods by which he came to them.

Based on that, I also read God Is Not Great: How Religion Poisons Everything. It contained very little of note, although Hitchens’s style did make it interesting to read. After finishing the book, I was left to wonder why some consider him to be such a powerful voice for atheism. There are very powerful voices in atheism, but based on what I have read, Hitchens doesn’t even register as a whisper compared to them.

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Certainty and Science Do Not Go Together!

Dr. Daniel Botkin holds a PhD in ecology and is currently Professor Emeritus in the Department of Ecology, Evolution, and Marine Biology at the University of California, Santa Barbara. He is best known for his books about nature, and has been called “one of the preeminent ecologists of the 20th century.” His website has a lot of good material, including an excellent FAQ regarding global warming.

The reason I am blogging about Dr. Botkin is that he authored a fantastic article in the December 2, 2011 issue of the Wall Street Journal. The article starts with an incredibly unscientific quote which comes (ironically enough) from NASA senior scientist Michael J. Mumma:

Based on evidence, what we do have is, unequivocally, the conditions for the emergence of life were present on Mars—period, end of story.

This kind of statement might excite people, but it does nothing to promote science. In fact, it does quite the opposite. As Dr. Botkin masterfully points out in his article, the phrase “period, end of story” should never be uttered by anyone who is trying to be scientific. The fact is that in science, we never have the end of the story. New information comes in constantly, and sometimes, it overturns old ideas, despite the fact that those ideas might be accepted by virtually every scientist on the planet. As the title of Dr. Botkin’s article correctly proclaims, absolute certainty is not scientific.

Dr. Botkin goes on to discuss how global warming advocates hurt their cause by making statements with absolute certainty, and I agree with his assessment. As I read his article, however, I couldn’t help but think about the hypothesis of evolution.

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The Debate Rages On…At Many Levels

I spend a lot of time discussing the creation/evolution debate. It is a popular topic on this blog, I have an entire series of young-earth creationist textbooks that discuss the debate, and I even discuss it among my own friends, many of whom are either atheists or theistic evolutionists. Every now and again, I even get the chance to publicly debate an evolutionist. This is a rare occurrence, however, as it is incredibly difficult to find an evolutionist willing to actually defend his or her view in a public debate. My last opportunity was in 2009, when I debated Dr. Robert A. Martin, vertebrate paleontologist and author of Missing Links: Evolutionary Concepts and Transitions Through Time. The debate was held at West Kentucky Community and Technical college. The audience was huge, and their response was enthusiastic. After the debate, I talked with many students, some of whom disagreed with me. Nevertheless, they all said that they appreciated the debate and were very happy that they attended.

Of course, the bigger question is whether or not such debates make any difference at all. Do any minds actually get changed as a result of a debate? I can tell you that mine did. I was an atheist at one time, and what led me down the road to accepting the truth of Christianity was an “Atheism versus Christianity” debate that I attended. The debate made me actually investigate the evidence for the existence of God, and when I did so, I found the evidence to be overwhelming. As a result, I ended up believing in God and, eventually, I came to realize that He is the God of the Old and New Testaments. However, I often wonder if a debate has changed anyone’s mind on the creation/evolution issue.

Well, I received an E-MAIL from a homeschool graduate who is now a biology major pursuing an MD/PhD. He says:

I was home educated from preschool all the way through high school and thoroughly enjoyed all of your science textbooks throughout high school…In fact your biology textbook was what got me interested in science in the first place.

It’s nice to know that contrary to what Dr. Jerry Coyne claims, good young-earth creationist textbooks do encourage students to study the sciences.

The reason I am blogging about his E-MAIL, however, is that he tells me from his own experience that a good debate about evolution can change people’s minds.

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Sea Ice and The Robustness of the Earth

As I have mentioned previously (here, here, here, and here), the earth has a wide array of negative feedback mechanisms that help it cope with change. This, of course, is exactly what you would expect for a system that was designed by an incredibly intelligent Designer. Unfortunately, many people who study the earth don’t understand these negative feedback mechanisms or don’t appreciate how incredibly powerful they are. As a result, they overstate the severity of certain trends that scientists observe. One excellent example of this comes from the observation that in recent years, the amount of sea ice in the Arctic has dropped significantly.

In the graph above, a 21-year average of Arctic sea ice extent is shown with the heavy gray line. The gray band that extends above and below that line shows the variation one would expect from random fluctuations. Now look at the green dashed line. That’s what was measured in 2007. Clearly it is far, far below the average, and it is well below what you would expect from random fluctuations. As a result, the drop in sea ice is probably the result of a systematic change that is occurring in the Arctic. Not surprisingly, some doomsayers went off the deep end when they saw such data.

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Another Goldilocks Planet?

kepler22b — An artist's rendering of Kepler 22b.
NASA image in the public domain.

More than a year ago, I discussed a planet named Gliese 581g. It was hailed as a “Goldilocks planet,” which means it is not too far away from its star and not too close to its star. Instead, it is at just the right distance, allowing it to receive the right amount of energy from the star so that stays warm enough to support life. Unfortunately, it’s not even clear that the planet really exists. One team of astronomers is confident that it does exist, but another team is confident that it does not. The latest analysis that I have seen adds more evidence to the “does not exist” side of the debate.

Well, the Kepler project has found another Goldilocks planet. I blogged about the Kepler project just a few days ago. It is a project designed to find planets that are roughly the same size as earth. They have found many, many such planets, and one of them, currently called Kepler 22b, is about 2.4 times the size of earth. What makes it special, however, is that it orbits a star similar to the sun, and it orbits that star at a distance which would allow it to receive just the right amount of energy to keep it warm enough to support life. Unlike Gliese 581g, there seems to be no doubt that the planet exists.

The popular media is abuzz with the news, and as usual, they aren’t being very accurate in their reporting. For example, here is how a space.com writer tells the story:

Kepler-22b’s radius is 2.4 times that of Earth, and the two planets have roughly similar temperatures.

Such a statement is nonsense, given what the Kepler team actually discovered.

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Plant/Fungus Symbosis Is A Real Relationship

mycorrhizae — The white fuzz on this root is a mycorrhizal fungus that lives in partnership with the plant. Click for credit.

If you have been reading this blog for any length of time, you know that I am fascinated by symbiotic relationships that are common throughout creation. Some of these relationships are between two specific species, others are between three specific species, and others are between many, many different species. Of all the incredible symbiotic relationships out there, one of the most ubiquitous is the relationship between plants and fungi. It is estimated that 90% of all plant species form a relationship with one or more species of fungus.¹ Because these relationships are so common, we give them a special name: mycorrhizae.

In this relationship, the fungus invades a plant’s roots and takes carbon-based nutrients from the plant. At first glance, you might think the fungus is a parasite that infects the plant and takes nutrients from it. If you look at the picture above, for example, you might be inclined to think that the root is infected with a fungal parasite. That’s not the case, however, because while the fungus does, indeed, take nutrients from the plant, it also supplies the plant with critical nitrogen- and phosphorus-based chemicals that the plant has a hard time extracting from the soil. Thus, this is a mutually-beneficial relationship, which is often called a mutualistic relationship.

Because mycorrhizae are common throughout creation, there are many species of plants and fungi that participate in them. Nevertheless, the details of how mycorrhizae work are poorly understood. A new study has started to unravel those details, and the results are truly fascinating.

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