Baranomes

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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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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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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Gut Microbes and Obesity

An obese mouse next to a normal mouse (image in the public domain)

A very interesting study was published in the April 9, 2010 issue of Science.1 In this study, Matam Vijay-Kumar and colleagues experimented with mice, trying to find out how their immune systems interacted with their body weight. Scientists have known for a while that obesity and the immune system are related, but most scientists have thought that obesity causes immune system disorders.2 That might, indeed, be true. However, this study shows that, most likely, immune system disorders can also cause obesity!

Mice (and most vertebrates, including people) have two levels of immunity: innate immunity and adaptive immunity. Innate immunity refers to the mechanisms in the body that protect against general threats. Adaptive immunity refers to the mechanisms in the body that protect against specific threats. So the mechanisms in the body that fight against all bacterial infections are a part of the body’s innate immunity, but when the immune system is attacking a specific species of bacterium, the adaptive immune system is at work.

Matam Vijay-Kumar and colleagues investigated a very specific part of the innate immune system and its effects on obesity in mice. The results were quite surprising.

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Babies and Morality

Is morality something that is a part of our very being, or is it something that is learned from our culture? From a scientific point of view, that is a hard thing to answer. Data exist that could support either argument, so often the conclusion that is drawn from the scientific evidence tells us more about the interpreter than the data. A very interesting article in the New York Times illustrates this in very stark terms.

Before I start discussing this article, there are two things I want to make clear. First, I got this article from PZ Myers’s blog. As anyone who reads this blog probably knows, he is my favorite atheist. More than anyone else, he demonstrates how the atheistic worldview is based on irratonaility. As I have written before, there are serious scholars who are atheists, and their arguments need to be heeded. There are also hacks that are atheists, and their arguments make it very easy to be a theist. PZ Meyers is, indeed, one of the hacks. Nevertheless, I read his blog because it is fun to see the mental gymnastics through which a scientist must go in order to be an atheist.

The second thing I want to make clear is that I do not think that the argument from morality is a reasonable argument for the existence of God. While there is ovewhelming scientific evidence for the existence of God, the argument from morality simply isn’t one of them. Indeed, in my experience, some of the most immoral people I know call themselves Christians, and their “morality” is put to shame by many atheists.

So…while I don’t think the argument from morality holds much weight, I do think that the interpretation of any data related to morality (like the interpretation of many other kinds of data) is heavily influenced by whether or not you think God exists. This New York Times story demonstrates that in no uncertain terms.

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Leaf Miners and Amazing Symbiosis

This is the ADULT form of a leaf miner. Image from:
http://en.wikipedia.org/wiki/File:Cameraria_ohridella_8419.jpg
I ran across a short article on Creation Ministries International’s website that really intrigued me. It was about “green islands” on decaying leaves, which are patches of green on a leaf that is otherwise dead. I have seen these “green islands” many times, and I just assumed they were the result of areas in the leaf where the majority of chlorophyll just hadn’t completely decayed away. Perhaps that region was chlorophyll-rich and thus would take longer to lose its chlorophyll than the rest of the leaf. However, when the green spot is strongly localized, it is probably the result of the larval version of a leaf miner insect.

This really intrigued me, so I spent some time looking into leaf-mining insects, and what I found was truly incredible. First, there are a lot of leaf miners. Some are moths, some are flies, some are beetles, and even some are wasps. The adult lays her eggs in within the tissue of a leaf, and when the eggs hatch, the larvae begin eating the insides of the leaf. This, of course, protects the larvae, because they are not exposed to predators. They stay inside the leaf until they are ready to pupate (start metamorphosis into their adult form).

Now, of course, if a larva is “unlucky” enough to hatch shortly before or after the leaf falls from the tree, this could be a problem. After all, the larva is eating the living tissue inside the leaf and therefore needs the leaf to stay alive while it is feeding. What happens if the leaf dies before the larva is ready to pupate? Well, that’s where the “green islands” come in. It seems that the larva can keep the portion of the leaf it is eating alive so that it can continue to eat and develop, and that’s why the area around the larva stays green!

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With Enough Faith You Can Believe Anything!

The fish in the above public-domain photograph is a ninespine stickleback fish. It gets its name from the nine spines that stick up from its back. A similar fish, the threespine stickleback, looks very similar but (you guessed it!) has only three spines sticking out its back. Both fish have two spines sticking down from their pelvis, but those spines are typically larger in the threespine stickleback. These similar species of fishes have shown us more examples of the failed predictions of evolution.

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Antony Flew Dies

With apologies to Gregory Maguire (author of Wicked), there are atheists, and then there are Atheists. Hacks like Richard Dawkins and PZ Myers are atheists, and scholars like Thomas Nagel and Bradley Monton are Atheists.

Well, one of the greatest Atheists of all time, Antony Flew, recently died at the ripe old age of 87. Interestingly enough, he didn’t die an Atheist. Why? Because he was convinced by the evidence that God must exist. In his own words:

There were two factors in particular that were decisive.  One was my growing empathy with the insight of Einstein and other noted scientists that there had to be an Intelligence behind the integrated complexity of the physical Universe. The second was my own insight that the integrated complexity of life itself – which is far more complex than the physical Universe – can only be explained in terms of an Intelligent Source.  I believe that the origin of life and reproduction simply cannot be explained from a biological standpoint despite numerous efforts to do so.  With every passing year, the more that was discovered about the richness and inherent intelligence of life, the less it seemed likely that a chemical soup could magically generate the genetic code.  The difference between life and non-life, it became apparent to me, was ontological and not chemical.  The best confirmation of this radical gulf is Richard Dawkins’ comical effort to argue in The God Delusion that the origin of life can be attributed to a”lucky chance.” If that’s the best argument you have, then the game is over. No, I did not hear a Voice. It was the evidence itself that led me to this conclusion.

Now don’t get the wrong idea – Flew did not become a Christian. After a lifetime of arguing against the existence of God, however, he was forced to concede that the evidence clearly indicates that God does, indeed, exist. To him, this God is not necessarily a personal God, but He is an all-powerful Creator. In the end, Flew was probably best described as a Deist.

Flew was a rare man, indeed. As an Atheist, he was a formidable foe. As a philosopher, he had enough integrity to follow the evidence to its logical conclusion, even if it meant repudiating his life’s work and finally admitting that God exists. As an Atheist-turned-Deist, he was a powerful demonstration of just how strong the evidence for God’s existence is.

He will be missed.

Wasp Pharmacology

A beewolf wasp
From http://en.wikipedia.org/wiki/File:Wasp_August_2007-12.jpg
Beewolves are solitary wasps that typically prey on bees. The females dig tunnels and then drag their bee prey into the tunnels, where they lay their eggs on the bee. That way, when the larvae hatch, they have a ready source of food. There are several species of beewolves, but one in particular, Philanthus triangulum, loves to prey on honeybees, which makes it a pest for beekeepers.

Scientists from both the Max Planck Institute for Chemical Ecology and the University of Regensburg studied the reproductive process of this species, and they found an amazing thing: the female uses a cocktail of antibiotics to protect her young.1 Where does the female get those antibiotics? From bacteria that she cultures in her antennae!

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Bacterial Batteries?

A schematic of the bacterial flagellum.
Image in the public domain.
The bacterial flagellum has become a symbol of the intelligent design movement, and rightly so. After all, bacteria are commonly recognized as the “simplest” organisms on the planet. Nevertheless, these “simple” organisms can make an amazingly well-designed locomotive system. Well, it turns out that the flagellum isn’t the only example of the amazing things that bacteria can construct. It seems that they can construct batteries as well!

I saw a blurb about this in the March 1, 2010 issue of Chemical and Engineering News, so I went online to find more information. I found this article on Nature News. According to the article, Lars Peter Nielsen of Aarhus University (in Denmark) did some experiments to see how bacteria are able to consume organic compounds and hydrogen sulfide in sediments that have very little oxygen. You see, in order to use these compounds, the bacteria have to oxidize them, which means that have to remove electrons from them. In order to remove electrons from the chemicals they consume, however, the bacteria have to “put” those electrons somewhere else. In most organisms, the electrons go to oxygen molecules. This process, reasonably enough, is called oxidation, and it is the reason you and I breathe. We take in oxygen so that we can oxidize our food, which produces energy for us to live.

It is very easy to understand how most organisms oxidize their food, because most organisms are exposed to a reasonable amount of oxygen in the air they breathe or the water in which they swim. However, there are lots of sediments (on the sea floor, for example) that are low in oxygen underneath the surface of the sediments. Nevertheless, bacteria in those oxygen-poor sediments seem to oxidize organic compounds and hydrogen sulfide just fine. Nielsen wanted to know how they accomplish this feat.

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