Intelligent Design Archives : Page 10 of 17 : Proslogion

Octopuses Can Change the Products of Their Genes When Necessary!

Pareledone — An Arctic octopus (photo by E. Jorgensen, NOAA)

I have always been amazed at animals that live in very cold water. I can’t stand it when my shower gets lukewarm, but animals like the Arctic octopus (genus Pareledone) flourish in waters that dip below 0 degrees Celsius! How can they do that? Well, they have specific characteristics that allow them to deal with the water’s cold temperature – characteristics that I obviously don’t have. But what is the basis of those characteristics? Until reading a recent paper by Sandra Garrett and Joshua J. C. Rosenthal, I would have said that the basis of those characteristics is the genome of the animal in question. As reasonable as that answer sounds, however, it is not correct, at least not in some cases.

One of the most important things a cold-water animal must deal with is how the temperature affects certain proteins that govern the response of the nervous system. Cold temperatures tend to reduce the efficiency of those proteins. As a result, the colder the water, the slower the nervous system conducts signals. In very cold water, the slowdown would be so great that in the end, signals would not travel quickly enough to allow the animal to do what it must do in order to survive.¹ Thus, it has always been assumed (reasonably so) that many nervous system proteins in cold-water animals are significantly different from the corresponding nervous system proteins of animals that do not frequent cold waters.

Garrett and Rosenthal decided to determine just how different such proteins are by comparing the genes of an Arctic octopus (genus Pareledone) to that of a tropical octopus (Octopus vulgaris). Since genes tell the octopuses’ cells how to make the proteins they need, the researchers assumed that whatever differences exist in the nervous system proteins would show up in the genes that produce those proteins. Once again, this is a completely reasonable assumption. However, their study shows that the genes involved in producing these nervous system proteins are nearly identical between the species.² To confirm this, they injected the genes from the different species into frog egg cells, and they found that the frog egg cells used those genes to produce nearly identical proteins. So in the end, the genes that produce those nervous system proteins are essentially the same in both species. But that doesn’t make sense. The proteins have to be different.

Well, it turns out they are different, but not because of the genes that produce them!

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Could This Be a Clue About the Origin of Pathogens?

house_finch — A house finch, which is now susecptible to a new eye infection. (Click for credit)

The origin of pathogens is of particular interest to creationists. When God finished creating the world, he pronounced it “very good.” Now as I have pointed out previously, the term “very good” does not mean perfect. Nevertheless, it is hard to understand how disease-causing pathogens could fit into to a “very good” creation. So where did pathogenic organisms come from? One of the first steps toward an answer to that question came in 2003, when J.W. Francis proposed that microscopic organisms were created to serve as a link between macroscopic organisms and their physical environment. This link helped to channel necessary chemicals from the environment to the macroscopic organisms. However, when the Fall occurred, mutations began happening, and those mutations ended up turning beneficial microorganisms into pathogenic microorganisms.¹

This makes sense in light of certain forms of cooperation between organisms. For example, a while ago I wrote about a relationship that exists between a grass that flourishes in hot soils, a fungus, and a virus. Scientists don’t know the details of the relationship, but they know that in order for the plant to grow in hot soils, it must be infected by a specific fungus. However, that fungus will not do the plant any good unless it is infected by a virus. Obviously, the fungus supplies some necessary chemicals to the plant, allowing it to live in hot soil. However, in order for the fungus to be able to do that, the virus must be providing necessary chemicals to the fungus. So in this situation, you have a viral link between the environment and a fungus, and then a higher-level link between the fungus and the plant. Obviously, if one of those links was corrupted, it could turn a beneficial relationship into a deadly one.

Over time, other creationists have suggested ideas for the origin of other pathogens. Dr. Peter Borger, for example, has a very interesting hypothesis on the origin of RNA viruses. He suggests that the genomes of all creatures were originally created so that they could produce fast adaptations to changes in their environment. As a result, all genomes contain variation-inducing genetic elements – sections of DNA that are specifically designed to produce changes that will aid in adaptation. He postulates that RNA viruses have been produced as a result of a corruption in certain variation-inducing genetic elements. This idea is intriguing because it solves the the RNA virus paradox, a recognized problem in the evolutionary literature.²

The real question, however, is what are the specific mechanisms by which this might happen? Exactly how could a beneficial microorganism (or genetic element) become pathogenic? As I was perusing the scientific literature the other day, I ran across an article in PLoS Genetics that might help us begin to answer that question.

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Is This a Miracle Tree? Not Really – It’s Just the Result of Amazing Design!

Moringa oleifera (commonly called the “drumstick tree”) is probably one of the most useful plants on earth. It’s leaves and flowers are eaten in many parts of the world. When its fruit is still developing, it can be cooked in a variety of ways. Even its roots can be eaten. These parts of the tree are rich in iron, minerals, proteins, and vitamins B and C. Its seeds produce an oil that can be used for both cooking and lubrication, and to top it all off, the tree is very hardy. It withstands significant droughts, making it easy to grow and maintain. Finally, unlike many trees, it matures very quickly. It usually bears fruit during its first year of growth, which means it can be used as a very productive crop.¹ It’s no wonder that some sources call it “the miracle tree.”

It seems that the usefulness of the drumstick tree doesn’t end there, however. Back in 1987, Madsen and colleagues found that if you crushed the seeds of the drumstick tree into muddy water, the water would not only clear up, but it would also be free of most of the bacteria that were originally there.² As a result, they suggested that the seeds of the drumstick tree could be used to purify water in third-world countries where no other means of water purification existed. Since drinking bacteria-laden water is a leading cause of death in many third-world countries, this could be a major benefit in many parts of the world. Unfortunately, carrying around the seeds and crushing them into water is fairly inefficient if you want to clean water on a large scale.

Eventually, the “active ingredient” that produces the water-purifying properties of the drumstick tree was identified. It turned out to be a series of proteins that are fairly small (as proteins go, in any case) and have a strong, positive charge.³ These proteins were dubbed “MOCP,” which stands for “Moringa oleifera coagulant proteins.” In February of 2010, the journal Current Protocols in Microbiology published a step-by-step procedure by which MOCP could be extracted from the seeds of the drumstick tree to make it easier to use.⁴ All of this represented great progress, but the question still remained: How can we most effectively use MCOP so that it becomes a cheap, efficient means of water purification?

That question might have been answered.

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More Peer-Reviewed Papers Critical of Evolution

On August 4, 2004, an article by Dr. Stephen C. Meyer appeared in a rather obscure peer-reviewed journal entitled The Proceedings of the Biological Society of Washington,¹ and it quickly ignited a firestorm of controversy. It argued that the current view of evolution can never hope to explain life as we see it today. The editor of the journal was branded a heretic, and he was then targeted for retaliation and harassment. Not surprisingly, he is no longer the editor of that journal. The Scientific Inquisition, which strives to enforce scientific orthodoxy, probably thought that would be the end of it. Surely no other peer-reviewed journal would ever dare to publish an honest discussion of evolution.

Well, it turns out that the Inquisition was wrong. Another obscure peer-reviewed journal, the Baylor University Medical Center Proceedings, has published an article by Dr. Joseph A. Kuhn, a surgeon who is affiliated with the Baylor University Medical Center at Dallas.² The article brings up three main points:

1. There is no significant progress towards coming up with even a plausible Darwinian-style mechanism to explain the origin of life.

2. Cellular systems exhibit irreducible complexity, and thus cannot be explained by any kind of Darwinian-style mechanism.

3. There is no reasonable fossil evidence to indicate that any kind of Darwinian-style mechanism produced the diversity of life we see today. (Here, the author concentrates on the supposed evolution of humans from an apelike ancestor and the supposed evolution of amphibians from a fish ancestor.)

While the article itself is interesting, what I find more interesting is the response of at least one member of the Scientific Inquisition.

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The Appendix: More Evidence That the Creationist Prediction Is Correct

For many, many years, evolutionists have called the human appendix a vestigial organ. In their view, our supposed ancestors needed a large cecum for digestive purposes. Over time, however, we evolved so that we didn’t need such a large cecum anymore. However, mutation and natural selection never got around to completely removing the large cecum and, as a result, we have a leftover, useless, small version called the appendix. As one evolutionist put it:¹

…we have an appendix (a small remnant of a prior ancestor species’ intestinal sack) which not only is of no use to us but which can sometimes kill us when it gets clogged up and infected! What kind of god or other “intelligent designer” would design organisms with such useless, imperfect, wasteful, and sometimes even harmful physical features?

As I wrote previously, there is strong evidence that this evolution-inspired idea is incorrect. Evidence indicates that the appendix acts as a safe reservoir of the beneficial bacteria that usually populate your intestine. That way, when you have a disease that wipes out those bacteria, they can quickly repopulate your intestine so as to restore your normal level of health. This function conforms quite nicely to a creationist prediction made several years before this evidence began to mount.

Of course, a few pieces of evidence do not make a clear-cut case. As a result, it is important to test the idea that the appendix has a vital function in the human body by making predictions based on that assumption and then seeing whether or not the predictions are confirmed by the data. This has recently happened. In 2007, some medical scientists wrote a paper suggesting that the appendix served as a reservoir for the beneficial bacteria that live in our intestines.² As a result, they predicted that if specific intestinal diseases were investigated, it should be found that people who have those diseases are better able to fight them if they have an appendix.

Well, a study that tested this prediction was recently published, and the prediction was dramatically confirmed.

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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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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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Former Scientific Heretic Wins the Nobel Prize in Chemistry

Dr. Dan Shechtman is a courageous scientist. Starting in 1975, he was on the faculty at Technion, the Israel Institute of Technology. He taught in the department of materials engineering, which investigates how the atomic structure of a material affects its observable properties. Back in the early 1980s, he spent his sabbatical at Johns Hopkins University, where he studied rapidly-solidified alloys of aluminum, and he discovered something that was revolutionary. It was so revolutionary that when he first saw it, he said to himself:

Eyn chaya kazo

which is Hebrew for “There can be no such creature.” Nevertheless, the more he studied, the more he was convinced of what he saw.

What revolutionary thing had Dr. Shechtman discovered? He discovered a kind of crystal that the scientific consensus said could not possibly exist. Until Dr. Shechtman’s discovery, it was thought that when substances form crystals, their atoms form an arrangement that is both ordered and periodic. An ordered arrangement just means there is a discernible pattern to the arrangement, and a periodic arrangement is one that repeats the same pattern in all directions. Thus, once I find the basic unit of a crystal’s pattern (called the “unit cell”), I can tell you what the entire crystal looks like by just repeating that pattern over and over again in three-dimensional space.

Well, chemists have been studying crystals for a long, long time, and because of the way atoms pack together, the mathematics of an ordered, periodic arrangement of atoms has been thoroughly worked out. These mathematics produced an absolute statement: There are only certain possible patterns for crystals. Some crystals can be rotated by one-half and end up looking the same as they did before they were rotated. Others can be rotated by one-fourth and end up looking the same as they did before. Others can be rotated by one-sixth and end up looking the same as they did before. However, it is impossible, quite impossible for a crystalline substance to have a structure that can be rotated by one-fifth or one-tenth and end up looking the same as it did before. Such atomic arrangements, called quasicrystals, simply cannot exist in this universe.

Nevertheless, that’s what Dr. Shechtman saw. Some of the crystals he saw forming in his experiments were quasicrystals. They were ordered, but not periodic. As a result, they had a structure that could be rotated by one-fifth or one-tenth and end up looking the same as it did before. As is typical for most scientists, he was initially very skeptical. But as he continued his experiments, he became more and more convinced of what he saw. Thus, as is typical for most scientists, he decided to communicate his findings to others.

That’s when the trouble began.

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