Review of Evolution: Still A Theory in Crisis

Dr. Michael Denton's latest book
Dr. Michael Denton’s latest book
Back in January, I read that Dr. Michael Denton was about to release a new book on evolution. I ordered it right away and started reading it as soon as I could, because I thought that his previous book, Evolution: A Theory in Crisis, was amazing. For a long time, I considered it the best discussion of evolution that was available to the general public. However, like all books on scientific issues, much of the information became outdated over the years, so I was really excited that he was releasing a new book on the same subject.

Dr. Denton earned an M.D. from Bristol University and a Ph.D. in biochemistry from King’s College London. After earning his Ph.D., he was appointed to the faculty at La Trobe University in Australia. He then did pathology work in England, Canada, and Australia. Eventually, he ended up on the faculty at the University of Otago in New Zealand. Currently, he is a Senior Fellow at the Discovery Institute’s Center for Science and Culture, which tells you he is a member of the “intelligent design” community. His dual training in medicine and biochemistry, as well as his experience working in several different countries, gives him an interesting perspective on science in general and evolution in particular.

Like his previous book, this one is encyclopedic. It covers a wide range of topics, but unlike his previous book, it is focused on the difference between structuralism and functionalism. The way he constructs the two positions, all Darwinists fall into the functionalism camp. They believe that structures develop in nature because they are functional. After all, natural selection is constantly weeding out poor adaptations and preserving useful ones. As a result, whether or not it is functional determines whether or not it exists in the biological world. Denton, however, argues for structuralism, a view that was quite in vogue in the 18th and 19th centuries. In this view, there are certain structures that are inherent in the world, and life makes use of those predefined structures. As Denton writes:

It is hard to imagine two scientific frameworks as diametrically opposed as structuralism and functionalism. Where functionalism suggests that function is prior and determines structure, structuralism suggests that structure is prior and constrains function. (Kindle e-reader, Chapter 1: Introduction)

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Jupiter May Not Shield Earth from Comets

An image of Jupiter as captured by the Hubble Space Telescope.
An image of Jupiter as captured by the Hubble Space Telescope.
Years ago, I was editing an elementary-level science text, and I ran across a statement that didn’t make a much sense to me. The author said that Jupiter acted as a “shield,” protecting earth from comets that could hit it. I am not an expert in orbital mechanics, but I couldn’t understand how that would work. It’s true that Jupiter is quite massive; therefore, its gravity would tend to attract comets towards it. However, it seemed to me that its gravity could just as easily attract comets toward the inner solar system (where the earth is) as deflect them away from it. Thus, I didn’t see how Jupiter could do what the author suggested.

So I did a little research, and I found a paper from 1995 that seemed to support the author’s contention. The focus of the paper was the hypothetical formation of gas giant planets like Jupiter, but one thing it noted was:1

…terrestrial planet systems physically similar to ours may be abundant but hazardous unless protected by gas giant planets.

This seemed to support the idea that Jupiter “protects” earth from comets, so I didn’t suggest any changes to the author’s statement. However, I still avoided making such a statement in my own textbooks (as least I think I did), because the physics of the claim still did not make any sense to me.

Well, yesterday I attended two lectures by Dr. Kevin R. Grazier at Anderson University, where I am an adjunct member of the faculty. Dr. Grazier is a planetary scientist at NASA’s Jet Propulsion Laboratory, but that’s not why I wanted to listen to his lectures. He is also a science consultant for television shows and movies, and I wanted to learn more about how that works. I have served as an unofficial science consultant for one yet-to-be-produced screenplay, but I was really interested to learn how the process works in productions that are actually being made.

The more he talked about his experiences, the more interested I became, because I learned that he has consulted for some of my favorite television shows. He was the science consultant for Eureka, Defiance, Falling Skies, and the reboot of Battlestar Galatica. Aside from the first series (which I never really got into), those are some of my favorite television shows! In fact, had Battlestar Galatica ended more reasonably, I would probably call it the best science fiction series that has ever been on television. Because of its awful ending, however, I rank it just under Babylon 5, which every science-fiction fan should watch in its entirety. He also was the science consultant for Gravity (one of the more scientifically-accurate space movies) and will soon start working on Pirates of the Caribbean: Dead Men Tell No Tales.

While his experiences with films and television shows were fascinating, and while he did confirm my thoughts regarding “scilebrities” Bill Nye and Dr. Neil deGrasse Tyson, it was something he said about his scientific research that inspired this post.

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Review of Shadow of Oz

shadow_ozDr. Wayne D. Rossiter earned his Ph.D. in ecology and evolution from Rutgers University in February of 2012 and is currently an assistant professor of biology at Waynesburg University. His book, Shadow of Oz, has already caused me to write two blog posts (here and here). In one of those posts, a commenter called Rossiter’s book a “must read,” and I have to agree. While I have issues with some of the content, on the whole it is a valuable addition to the wealth of information that has already been written on the subject of origins. As a result, I encourage you to read this book and seriously think about its contents.

In some ways, the main thrust of his book is obvious: the standard view of Neo-Darwinism (random mutations filtered by natural selection) is incompatible with the Christian faith. I don’t know many people who would disagree with that statement. Nevertheless, the way Rossiter makes that point is rather profound. Early on in the book, for example, he gives five extended quotations from different authors regarding the history of the universe. The first and fourth are from Dr. Carl Sagan (atheist), the second is from Dr. Richard Feynman (atheist), the third is from Dr. Richard Dawkins (atheist). The fifth is from Dr. Karl Giberson (Christian who is a staunch evolutionist). The passages are indistinguishable, and that’s the point. As Rossiter says:

I could have chosen any number of brief atheistic accounts of the history of the universe, and not one of them would differ in any functional way from the one offered by Giberson. (p. 25)

Rossiter’s discussion of Dr. Kenneth Miller’s views on origins is equally insightful and perhaps even more damning. He shows that, like Giberson, the “creation” account that Miller believes is indistinguishable from that of an atheist. Further, he shows in rather stark terms just how confused Miller is when it comes to what he believes. For example, Rossiter quotes Miller as saying that he tells his students that he believes in Darwin’s God. However, as Rossiter makes clear, that statement is pure nonsense:

…as Miller admits earlier in his book, Darwin was not a believer in God. He became a staunch agnostic, who demanded strict naturalistic answers for life’s workings. As so, it’s quite appropriate that Miller should claim to share Darwin’s view. (p. 163)

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Universal Genetic Code? No!

The basic process by which proteins are made in a cell. (click for credit)
The basic process by which proteins are made in a cell. (click for credit)

I am still reading Shadow of Oz by Dr. Wayne Rossiter, and I definitely plan to post a review of it when I am finished. However, I wanted to write a separate blog post about one point that he makes in Chapter 6, which is entitled “Biological Evolution.” He says:

To date, the National Center for Biotechnology Information (NCBI), which houses all published DNA sequences (as well as RNA and protein sequences), currently acknowledges nineteen different coding languages for DNA…

He then references this page from the NCBI website.

This was a shock to me. As an impressionable young student at the University of Rochester, I was taught quite definitively that there is only one code for DNA, and it is universal*. This, of course, is often cited as evidence for evolution. Consider, for example, this statement from The Biology Encyclopedia:

For almost all organisms tested, including humans, flies, yeast, and bacteria, the same codons are used to code for the same amino acids. Therefore, the genetic code is said to be universal. The universality of the genetic code strongly implies a common evolutionary origin to all organisms, even those in which the small differences have evolved. These include a few bacteria and protozoa that have a few variations, usually involving stop codons.

Dr. Rossiter points out that this isn’t anywhere close to correct, and it presents serious problems for the idea that all life descended from a single, common ancestor.

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New Study Indicates Chimp DNA is 88% Similar to Human DNA

A chromosome-by-chromosome comparison of human and chimp DNA.  The bars show the percent match on the chimpanzee chromosome to the corresponding portion of human DNA. (figure from the study being discussed)
A chromosome-by-chromosome comparison of human and chimp DNA. The bars show the percent match on the chimpanzee chromosome to the corresponding portion of human DNA. (figure from the study being discussed)

NOTE: Based on comments below by Glenn (who is mentioned in the article) and Aceofspades25, there are questions regarding the analysis used in Dr. Tomkins’s study, upon which this article is based. Until Dr. Tomkins addresses these questions, it is best to be skeptical of his 88% similarity figure.

More than two years ago, Dr. Jeffrey P. Tomkins, a former director of the Clemson University Genomics Institute, performed a detailed, chromosome-by-chromosome comparison of human and chimpanzee DNA using a widely-recognized computer program known as BLAST. His analysis indicated that, on average, human and chimpanzee DNA are only about 70% similar. This is far, far, below the 95-99% numbers that are commonly cited by evolutionists, so once I read the study, I wrote a summary of it. Well, Dr. Tomkins has done a new study, and it invalidates the one he did two years ago.

The new study was done because last year, a computer programmer of financial trading algorithms (Glenn Williamson) discovered a bug in the BLAST algorithm that Tomkins used. This bug caused the program to ignore certain matches that should have been identified, which led to an artificially low similarity between the two genomes. As any responsible scientist would do, Dr. Tomkins took this issue seriously and did a detailed analysis of several different versions of the BLAST program. His analysis showed that most of the newer versions of the program were bugged, including the one used in his study two years ago.

As a result, Dr. Tomkins redid his study, using the one version of BLAST that did not contain the bug. His results are shown above. As you can see, every chromosome in the chimpanzee genome, with the exception of the Y chromosome, matched a corresponding region of the human genome by somewhere between 85% and 90%. The overall similarity between the human and chimpanzee genomes was 88%. While this is still far lower than the 95%, 98%, or 99% similarity touted by many evolutionists, it is much higher than the 70% found in his previous study.

To make sure that these new results aren’t an artifact of some other unknown issue in the BLAST computer program, Dr. Tomkins also did his analysis with two other programs: nucmer and LASTZ. The nucmer program’s results agreed with the unbugged BLAST results: on average the human and chimpanzee genomes are 88% similar. The LASTZ program produced a lower average similarity (73%), which indicates that perhaps LASTZ has a bug or is not optimized for such comparisons, since its results are very close to the results Dr. Tomkins got with the bugged version of BLAST.

I think this is the most comprehensive comparison of human and chimpanzee DNA that has been done, so I am inclined to take the results (88% similarity between human and chimpanzee DNA) as the best number we have to date. Of course, I said something similar about Dr. Tomkins’s previous study (which turned out to be wrong), so take that statement with a grain of salt! [later addition:It might not be the best number we have to date. See note at the top of the article.]

Homo naledi: Human Relative? Probably Not.

A composite skeleton of Homo naledi, surrounded by other fossils from the same find (click for the full picture and credit)
A composite skeleton of Homo naledi, surrounded by other fossils from the same find
(click for the full picture and for credit)

PLEASE NOTE: Based on subsequent analysis, I have changed my mind on this fossil. Please find my new thoughts here.

Social media has been abuzz with reports of a newly-discovered ancient relative of people. Named Homo naledi, this “new species” is supposed to shed light on the supposed evolution of human beings. One news report said the discovery “…may alter ideas about the human family tree.” Of course, we’ve heard that before. It seems that every major discovery related to the supposed evolution of humans is said to radically change our view of how humans came to be. While this discovery is very, very interesting, I seriously doubt that is has anything to do with people.

One of the things that makes this find so interesting is where the bones were found. They were found in a cave more than 80 meters from its entrance. Even more intriguing, the chamber in which the fossils were found was accessible only through a narrow chute. The chute was so narrow that most paleontologists couldn’t fit through it. Indeed, in order to excavate the fossils, the lead investigator (Lee Berger) had to put out an advertisement on social media. It called for “…tiny and small specialised cavers and spelunkers with excellent archaeological, palaeontological and excavation skills.” There were 57 people who answered the ad, and six women were chosen from that group. They excavated the bones, while the other members of the expedition watched on video.

In the end, the paleontologists think they found fragmentary remains of at least 15 individuals. The picture above shows a partial composite skeleton that was made from these different individuals. In one of the two scientific papers written about the find1, they say that this composite skeleton represents the remains of a new species. Why? Because it contains a lot of traits associated with the genus Australopithecus, which is supposed to be an early ancestor of human beings. However, it also contains traits that are more like those of modern humans. Because of this mix of “primitive” and “modern” traits, it is thought to be a new species in the supposed evolutionary history of people.

While there is certainly a mixture of traits found in these fossils, I seriously doubt that they belong in the genus Homo (the genus that contains human beings), and I seriously doubt they are related to us in any way.

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Dawkins Demonstrated to be Wrong….Again

This is the center panel from a stain-glassed window entitled, 'Education.'  Found in Yale University's Linsly-Chittenden Hall, it shows religion and science working together to educate people.
This is the center panel from a stain-glassed window entitled, ‘Education.’ Found in Yale University’s Linsly-Chittenden Hall, it shows religion and science working together to educate people.
(click for credit)

In 1989, Dr. Richard Dawkins wrote the following in a book review for the New York Times:

It is absolutely safe to say that if you meet somebody who claims not to believe in evolution, that person is ignorant, stupid or insane (or wicked, but I’d rather not consider that).

He has since added to that remark, writing:

By far the largest of the four categories is ‘ignorant’

Like much of what Dr. Dawkins writes, however, the actual evidence says something completely different.

Consider, for example, a new study that has been published in the journal American Sociological Review. The authors, Dr. Timothy O’Brien and Dr. Shiri Noy, examined people’s views on religion and science, correlating them with their actual knowledge of science. They found lots of interesting things, but I want to focus on just two of them.

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UndeNYEably Uninformed

This is the cover of Nye's error-filled book.
The cover of Nye’s error-filled book.
Bill Nye calls himself “The Science Guy,” but he sometimes acts in ways that can only be described as anti-science. For example, in a video he stated that creationism shouldn’t be taught to children. This, of course, is blatantly anti-science, because scientific progress is built on the competition of ideas. If you say that an idea shouldn’t be considered because you don’t like it, you are working against science, not for it. In addition, he narrated a video about global warming that contained a faked experiment! Faking experiments is definitely not pro-science! Nevertheless, Nye obviously loves science, which leads me to wonder why he sometimes acts against it.

After reading Nye’s book, Undeniable: Evolution and the Science of Creation, I think I understand. He simply doesn’t inform himself on scientific issues. As a result, he really doesn’t understand science and doesn’t understand why some of his actions are so anti-science. Consider, for example, what he writes about kids who are taught creationism:

Not only that, these kids will never feel the joy of discovery that science brings. (p.10)

This, of course, is demonstrably false. Had Nye bothered to inform himself about kids who are taught creationism, he would find that they often do better in science than their peers who were not taught creationism. In addition, he would have learned that many kids who were taught creationism are now studying science at the university level or are already professional scientists. I have several students, for example, who say that the reason they decided to become scientists was because of my creationist textbooks (see here and here, for example)!

Of course, the fact that Nye is utterly uninformed about creationism leads to all sorts of problems with his book, which I have detailed in the PDF document at the end of this review. What really surprised me, however, is that his book shows that he hasn’t really informed himself about the science related to evolution, either. As a result, much of what he says in the book is utterly false.

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Bill Nye Makes a Prediction

Bill Nye is known as "The Science Guy," even though some of his behavior is rather anti-science. (click for credit)
Bill Nye is known as “The Science Guy,” even though some of his behavior is rather anti-science.
(click for credit)
Despite the fact that Bill Nye is known as “The Science Guy,” some of his behavior is rather anti-science. He doesn’t think certain scientific ideas should be debated, despite the fact that conflict between competing theories is one of the most important aspects of science. He also narrated a faked experiment, demonstrating his lack of understanding of basic climate science along the way. Nevertheless, he is an interesting (and funny) guy. In addition, he debated Ken Ham on the creation/evolution issue. Even though the debate was not all that interesting, it was nice to see him engage in it. That’s more than most evolutionists will do! As a result, I like to keep up on what Bill Nye is doing and saying.

He was recently in Canada to attend the 65th International Astronautical Congress. While there, he was interviewed on The Morning Show. You can see the entire interview here. Not surprisingly, I disagreed with much of what he had to say, but I want to highlight two of his statements here. The first is a prediction. When speaking of creationists, Nye said:

In another 20 years, I claim, those guys will be just about out of business. That’s my claim.

I am willing to make exactly the opposite claim. I predict that in 20 years, creationism will be stronger than ever. I expect more scientists will be creationists, creationism will be more openly discussed in academic settings, and there will be more groups dedicated to communicating creationism to the general public. This will be true not only for the U.S., but for most countries in the world. After all, contrary to a previous statement Bill Nye made, creationism isn’t something unique to the U.S.

Barring some unforseen tragedy, Mr. Nye and myself should both be alive in 20 years. It will be interesting to see whose prediction is the more accurate one.

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Strike Yet Another Vestigial Organ

This drawing illustrates the skeleton of a baleen whale.  The small pelvis is circled.  (click for credit)
This drawing illustrates the skeleton of a baleen whale. The small pelvis is circled. (click for credit)

Evolutionists love to talk about vestigial organs. Consider, for example, the human appendix. This wormlike tube connected to a person’s cecum looks something like the cecum that you find in some herbivores. Since there is some similarity between the two organs, and since a person can live an apparently normal life without his or her appendix, evolutionists long thought it was a vestigial organ – a remnant of our evolutionary history. Most evolutionary sources said it was useless in people, but we now know that isn’t true (see here and here). Others claimed it wasn’t necessarily useless, but it was still vestigial. They said the appendix is definitely the remnant of a herbivore’s cecum, but as it shrank, it developed a new purpose. We now know that’s not true, either.

Of course, there are many other organs that evolutionists claimed were vestigial but we now know aren’t (see here, here, here, here, and here). It seems we can add another to that list: the pelvis in a whale. Like the appendix, most evolutionary sources say that the whale pelvis is useless. For example, the book Life on earth says:1

During whale evolution, losing the hind legs provided an advantage, better streamlining the body for movement through water. The result is the modern whale with small, useless pelvic bones.

We now know that this is simply not true.

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