Coyne and Embryonic Development…Wrong AGAIN!

A student recently sent me a question based on a statement made in Dr. Jerry Coyne’s book, Why Evolution is True. Since there doesn’t seem to be much written about it for a general audience, I thought I would summarize the issue. Here is Dr. Coyne’s statement:

One of my favorite cases of embryological evidence for evolution is the furry human fetus. We are famously known as “naked apes” because, unlike other primates, we don’t have a thick coat of hair. But in fact for one brief period we do – as embryos. Around sixth months after conception, we become completely covered with a fine, downy coat of hair called lanugo. Lanugo is usually shed about a month before birth, when it’s replaced by the more sparsely distributed hair with which we’re born. (Premature infants, however, are sometimes born with lanugo, which soon falls off.) Now, there’s NO NEED for a human embryo to have a transitory coat of hair. After all, it’s a cozy 98.6 degrees Fahrenheit in the womb. Lanugo can be explained ONLY as a remnant of our primate ancestry: fetal monkeys also develop a coat of hair at about the same stage of development. Their hair, however, doesn’t fall out, but hangs on to become the adult coat. And, like humans, fetal whales also have lanugo, a remnant of when their ancestors lived on land.1 (emphasis mine)

Note the strong words by Dr. Coyne. Embryos have “no need” for such hair, and thus its presence can “only” be explained as a remnant of our primate ancestry. Not surprisingly, Dr. Coyne is wrong on both counts.

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Synthetic Life Shows the Impossibility of Abiogenesis

Dr Craig Venter made the news last week in a big way. As The Guardian put it:

Craig Venter and his team have built the genome of a bacterium from scratch and incorporated it into a cell to make what they call the world’s first synthetic life form.

It’s an amazing feat of biotechnology, and the process he and his team produced might result in some incredible applications down the road. What I find interesting about the process, however, is how well it illustrates that life simply cannot come about as the result of random chemical reactions guided by some sort of selection process. In other words, this stunning achievement really demonstrates the impossibility of abiogenesis.

The scientific report of Venter and his team’s accomplishment can be found on the website of the journal Science1. I finally got around to reading it, and it is truly fascinating. When you look at the details of how they created their “synthetic” life form, you find that Venter and his team relied on already-living systems not once, not twice, but a total of three times. Without relying on these already-living systems, they would not have been able to produce their “synthetic” cell.

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I want to discuss more about Dr. Peter Borger’s excellent posts at Creation Ministries International’s website, because I really think he is onto something. As anyone who is remotely familiar with young-earth creationism knows, God designed specific kinds of organisms. Those organisms were created with the ability to adapt to changing environments, so the organisms we see today are those that descended from the various created kinds. The scientific pursuit dedicated to determining exactly what kinds of organisms were made and how the organisms we see today are related to those created kinds of organisms is called baraminology. This word comes from the Hebrew words bara, which means “created,” and min, which means “kind.”

So how did God give these created kinds the ability to adapt to changing conditions? According to Dr. Borger, He gave them baranomes, which are:

pluripotent, undifferentiated genomes with an intrinsic ability for rapid adaptation and speciation. Baranomes are genomes that contained an excess of genes and variation-inducing genetic elements, and the law of natural preservation shaped individual populations of genomes according to what part of the baranome was used in a particular environment.

In other words, the genome of each created organism was full of many genes, some of which the organism didn’t even need. These “excess genes,” as well as changes produced by the built-in elements that promote genetic change, were then acted on by natural selection (which he calls “natural preservation”) to produce the various organisms that we see today. In the article I linked above, Dr. Borger produces some powerful evidence to support this idea.

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Others Get E-MAIL

In my “Links to Investigate” section, I recently added Red Wagon Tutorials. This is a business set up by the most talented teacher with whom I have ever worked. Not surprisingly, he is a young-earth creationist, and he recently forwarded me an E-MAIL that demonstrates what happens when a great young-earth creationist teacher uses great young-earth creationist materials in class. Here is the E-MAIL:

Dear Mr. Rosenoff,

I was in your 2006-2007 TPS highschool Biology class and then in your 2007-2008 TPS highschool Marine Biology class. I am currently in my second year of college/senior year of highschool. I wanted to let you know how much taking your classes has helped me and shaped my career path. In my first year of college I took BI143, Marine Biology. I learned more in your class than I did in the college class. Also, without everything you
taught me about marine biology, lab procedures, and note taking, I wouldn’t have received one of the few A’s in the class. Currently I am taking BI102, cellular biology. So far everything has been review. The time you took to explain all the concepts, especially genetics, has really helped me excel in this class. My teacher is constantly shocked that I always know the answers or am one step ahead of the class because of what I remember from your biology class 3 years ago.

Also, because of how amazing your classes were, in the fall of 2011, I will be transferring to OSU to major in biology with a premed emphasis. I am also hoping to attend a medical school that has a joint M.D. / Ph.D. program so I can continue in biology. If all goes as planned, I will have my Ph.D. in biology by the time I am 28. Thank you so much for all the time you took to make biology fun and interesting to me. Your classes were the first time I had actually enjoyed science.

Note that this student is in her second year of college and her senior year of high school. Not only is she well ahead of most of her peers, she is clearly excelling in her college-level courses. While her own hard work and the fact that she is being homeschooled both play a large part in her success, note who SHE credits. She credits Mr. Rosenoff. That’s the power of an excellent teacher.

Of course, this kind of E-MAIL also shows how ignorant some evolutionists are when it comes to education. Remember that not too long ago, an AP news article discussed young-earth creationist science texts, including those that I wrote. Remember what Dr. Jerry Coyne said in that article:

“If this is the way kids are home-schooled then they’re being shortchanged, both rationally and in terms of biology,” Coyne said. He argued that the books may steer students away from careers in biology or the study of the history of the earth.

This E-MAIL clearly shows just how wrong Dr. Coyne is. This young lady was definitely not shortchanged when it comes to her science education. She is way ahead of her peers when it comes to science. In addition, far from steering clear of a career in biology, she is going for her MD/PhD.

It’s really too bad that people like Dr. Coyne are more committed to dogma than to science. If Dr. Coyne were really interested in producing excellent students who are excited about science, he would not make such ignorant comments about quality science textbooks!

Genetic Redundancy – An Amazing Design

Rotating Anmation of DNA
(Animation in the public domain)
As I mentioned previously, Dr. Peter Borger has an amazing series of articles on genetics over at Creation Ministries International’s website. He is putting together a very impressive interpretation of the genome based on what has been learned about genetics over the past few years. He starts his series with a discussion of genetic redundancy, which is truly incredible.

The article begins by discussing something that has been known for quite some time: It is possible to disable a gene so that it no longer produces the protein it is supposed to produce. This technique is called gene knockout, because it as if the gene has been “knocked out” of the organism’s genome. The organism is referred to as a knockout organism or just a knockout.

Why would you study a knockout organism? Well, imagine that you have identified a gene but don’t really know what it does for the organism. If you create a version of the organism with that gene knocked out, any negative effects that you see will most likely be the result of the missing gene, so that will give you some idea of what the gene does.

This is a great experimental procedure that has produced a lot of genetic understanding over the years. However, it has also produced a very interesting result: often a knockout organism is not significantly different from the standard (usually called wild-type) organism. In other words, some genes can be knocked out of an organism with little or no effect on the organism itself.

This might sound surprising to someone who is not familiar with the genetics literature, but it really isn’t. In fact, geneticists thought they had an explanation for this interesting result…until experiments over the past decade or so really upset the applecart.

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Signature of Controversy

Dr. Stephen Meyer’s book, Signature in the Cell is an enormous success. It was named one of the New York Times Times Literary Supplement books of the year by a well-respected atheist. It was on Amazon’s top ten science books of 2009. It has been called a “landmark in the intelligent design debate” by a prominent professor of medical genetics, “a ‘must read’ for all serious students of the origin-of-life debate” by an accomplished PhD in ocean chemistry, and a “decisive case based upon breathtaking and cutting-edge science” by a chemistry professor who is a member of the National Academy of Sciences.

Of course the real way you can see how successful the book has been is to read the hysterical reviews from those who disagree with its conclusions. Many of the reviews are quite comical. For example, on this blog I highlighted Dr. Francisco Ayala’s pathetic review where he not only displays his unfamiliarity with genetics, but he also displays the fact that he hasn’t even read the book.

Well, now you can go to one place to find many of these amusing reviews as well as how poorly they fare when they are evaluated based on science: the online book Signature of Controversy. This book is 105 pages of snarky (one section is called “Attack of the Pygmies”), detailed, and scientifically devastating arguments that show how poorly the critics of Signature in the Cell deal with the science related to the origins debate.

In some ways, this book is even better than Signature in the Cell. After all, the case made by Signature in the Cell is very impressive. However, while I was reading it, I kept asking myself, “What will the critics say about this?” After all, if you want to be truly educated on an issue, you must examine it from all sides. Well, with the help of this book, you can see what the critics have to say, and you can see how poorly what they say compares to science as we know it today.

Often, you can judge the quality and impact of a work based on what its critics have to say about it. The weaker and more desperate the critics’ arguments, the stronger and more important the work. Based on the criticisms leveled at Signature in the Cell, it is clearly one of the strongest and most important books related to the origins controversy.

Neanderthals Didn’t…Didn’t…DID Interbreed with People

The original reconstruction of Neanderthal Man (left) and a more realistic reconstruction of a Neanderthal child (right). Both images are in the public domain.

It’s not a really new story, but I was interviewed by an internet radio show about the sequencing of the Neanderthal genome1 and its comparison to present-day people, so I decided I would blog about it as well.

The first thing to discuss is how they sequenced the genome of something that no longer exists. In this case, they used three Neanderthal fossil fragments found in the Vindija cave in Croatia. Fossils (especially those belonging to genus Homo) are rare and very valuable, and this process required the destruction of the fossils, so the three fragments were chosen carefully. They were all fragments that contained very little anatomical information, so anything lost due to the destruction of the fossils was minimal. Based on some pretty good reasoning, it was concluded that the fossil fragments came from three different women, two of which may be relatives. According to scientifically irresponsible dating techniques, these fragments are supposedly around 40 thousand years old.

When they looked at the DNA in the samples they prepared from the bones, they found that between 95 and 99 percent of the DNA came from organisms other than Neanderthals, like bacteria that colonized the fossil. In other words, only 1-5 percent of the DNA found was DNA of interest. How did they get rid of the other 95-99 percent so they could focus on Neanderthal DNA? They used restriction enzymes that tend to cut only bacterial DNA.

So even though this is a remarkable achievement, there are a lot of potential errors in the derived genome sequence. After all, any time the “signal” you are looking at is 20-99 times weaker than the “noise,” it will be hard to determine exactly what the signal is. Keeping in mind these potential errors, what was learned? In short, it was learned that creationists have been right about Neanderthals all along.

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Smallpox and AIDS?

Components of a smallpox vaccination kit (image in the public domain).

The smartest person with whom I have ever worked sent me a very interesting article from Science Daily. She and I wrote several articles related to the science behind vaccination years ago, and this article is relevant to that issue. It reports on a study published in BMC Immunology, an open-access journal. The results of the study are worth noting.

The researchers studied peripheral blood mononuclear cells (PBMCs) and how susceptible they were to infection by HIV, the virus that causes AIDS. PBMC is the name given to any blood cell that has a round nucleus. Since red blood cells don’t have a nucleus, what this means is that the researchers were looking at certain white blood cells, which are a part of the body’s immune system. Obviously, the susceptibility of white blood cells to HIV is an important issue in the study of AIDS.

Here is the key: they looked at the PBMCs from 10 volunteers who had never been vaccinated against smallpox as well as the PBMCs from 10 volunteers who had been vaccinated against smallpox with a Vaccinia-based vaccine 3 to 6 months prior to the study. Vaccinia is a virus in the poxvirus family that is typically used to produce the immune response to protect against smallpox. Guess what they found.

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The RNA Virus Paradox

A diagram of HIV, which is a retrovirus (image in the public domain)

Dr. Peer Terborg has an incredible series of articles on genetics and the design of life over at Creation Ministries International’s website. The ones to which I refer begin with “Evidence for the design of life…” While I plan to write about many of the major concepts discussed in these articles, I want to start with sort of a “sidelight” that appears in part 3 of his series.

Not too long ago, I wrote about the fact that evolution (in the ‘goo to you’ sense) is, at best, an unconfirmed hypothesis. A commenter, Grant C, tried to convince me that it is something more by offering several lines of evidence for evolution. Of course, I attempted to educate Grant on what the evidence really meant, but after only a few exchanges, he stopped responding.

One of his major lines of evidence for evolution was endogenous retroviral insertions (ERVs) in the genomes of primates. If you don’t know what ERVs are, you need to first learn what a retrovirus is.

Continue reading “The RNA Virus Paradox”