Antiboitic Resistance Doesn’t Dissapear Quickly

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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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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Another Goldilocks Planet?

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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Life Isn’t All That Special?

Dr. Seth Shostak has a B.S. in physics from Princeton and a PhD in astronomy from the California Institute of Technology. Obviously, then, he knows a thing or two about astronomy. His original research started out using radio telescopes to measure the motion of distant galaxies, but for quite some time now, he has been involved in the search for extraterrestrial intelligence (SETI). He is currently the senior astronomer at the SETI institute.

In a recent report, CNN interviewed him to lead off a discussion about the possibility of extraterrestrial life. Here’s what he said:

…one thing that strikes you is that every time we learn something new about the universe, what we learn is that our situation doesn’t seem to be all that special, and that suggests that life is not all that special, either.

When I heard that statement, the first thing I wondered was, “How can such a well-educated astronomer say something that absurd?” Really? Our situation isn’t all that special? We live on a special planet that orbits a special star (at just the right distance) that resides in a special part of the galaxy. Yet our situation isn’t all that special?

And then there’s the last part of the statement. Life isn’t all that special? Really? Even with all our technology, we can’t come close to making it. Indeed, single-celled organisms can stitch DNA together better than we can. Despite a lot of looking, we haven’t found life anywhere else in the universe. Nevertheless, according to Dr. Shostak, it isn’t all that special.

I was hoping that the rest of the video would explain how in the world anyone could consider such a statement to be even remotely reasonable. However, it never did.

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Former Scientific Heretic Wins the Nobel Prize in Chemistry

Nobel Laureate Dr. Dan Shechtman (Click for credit)
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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Hummingbirds Can Shake Their Heads at 34g!

Most birds aren’t very active in the rain. They can fly in the rain if they have to, but they prefer not to. After all, the longer they are in the rain, the soggier they get. This adds to their weight, meaning they have to work harder to generate the lift necessary to stay in the air. So in general, birds tend to wait out the rain. Like most rules in biology, however, this one has an exception. The activity of hummingbirds is not significantly affected by most rainfall.1

How these incredible birds can fly even after being in the rain a long time was a bit of a mystery to scientists, but thanks to some artificial rain and high-speed photography, we now know that hummingbirds regularly dry themselves off by shaking like a dog.2 The shaking propels the water off their feathers so that the tiny birds don’t get too waterlogged. If you watch the video above (which comes from the referenced study), you can’t help but be reminded of a wet dog coming in out of the rain. Of course, the dog isn’t flying at the time, but the similarity is remarkable.

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Yet Another Failure of “Geological Column” Reasoning

Skeleton of the titanosaur Epachthosaurus at the National Museum, Prague, Czech Republic. Note the plant, a cycad, in the display. (Click for credit)

If a display of dinosaurs or dinosaur skeletons includes plants, it usually shows the dinosaurs walking among ferns or cycads, like the picture shown above. There usually aren’t any grasses in the display. Why not? Because according to the geological column, grasses and dinosaurs didn’t live at the same time. After all, dinosaurs mostly died out by the end of the Cretaceous period, which was supposed to have closed about 65 million years ago. According to You Are Here: A Portable History of the Universe, grasses didn’t evolve until much later:1

Rabbits and hares appear 55 million years ago. The Himalayas begin to rise 50 million years ago. The face of the earth looks recognisably as it is now, except that Australasia is attached to Antarctica. Bats, mice, squirrels, and many aquatic birds (including herons and storks) appear during this period, as do shrews, whales, and modern fish. All major plants make their appearance and grasses evolve.

Notice how certain the author is. He is telling you the story of the history of life as if he is watching it happen. According to his “observations,” grasses didn’t evolve until about 50 million years ago, long after the dinosaurs went extinct.

This kind of certainty is rampant in evolutionary writings. For example, The Encyclopedia of Earth tells us:

The evolution and spread of grasses UNDOUBTEDLY resulted from their ability to adapt to seasonally dry habitats created as tropical-deciduous forests developed in the Eocene (58 to 34 mya, million years ago). Considering their importance and taxonomic diversity, grasses have a relatively poor fossil record. While the earliest potential fossil grass pollen was described from late Cretaceous sediments, the oldest reliable megafossil grass fossils were spikelets and inflorescences from the latest Paleocene (about 58 mya). These were PRIMITIVE proto-bamboos with broad leaves, QUITE UNLIKE the narrow-leaf modern grasses of desert grasslands and deserts. (emphasis mine)

Of course, as is often the case, current research is demonstrating just how wrong this evolution-inspired reasoning is.

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Science Will Survive. In Fact, It Might Even Improve…

Steven Newton is the Programs and Policy Director at the National Center for Science Education. He has a B.A. in History from the University of California at Berkeley and a M.S. in Geology from California State University at Hayward. Most importantly, he is a fervent believer in evolution. Because of this, he tends to watch trends in science education as well as the scientific community. His observations recently led to a very interesting article in New Scientist.

The article discusses the fact that young-earth creationists have been presenting at scientific conferences and publishing in the peer-reviewed scientific journals. Since he is a geologist, he is focused on meetings of the Geological Society of America (GSA), where young-earth geologists have presented papers and led field trips in recent years. While he thinks that this is a bad thing, he rejects calls to ban them from the meetings. He says:

Scientific organisations will continue to experience creationist infiltration; this week’s GSA meeting will include several presentations by creationists. But it is important for scientists not to overreact and to remember that science is far stronger than any creationist attempts to undermine it.

While his reasoning is deeply flawed, his final conclusion is correct. As a result, we should at least give him partial credit for his endeavors.

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When You’re Desperate, Anything Is Plausible

A commenter left this link on an unrelated post. Since the commenter has, in the past, tried to support several unscientific positions, I assume he or she thought that the experiment demonstrated the plausibility of abiogenesis, the the idea that life might have emerged through a series of incredibly unlikely interactions between nonliving chemicals. Of course, such an idea contradicts everything we know about the study of life, since all life we have ever studied comes from other living things. I have written several articles (here, here, here, here, here, and here) that demonstrate how the data speak against abiogenesis, but those who want to ignore the scientific evidence desperately hope for some special time in the past when all our current evidence doesn’t apply and life could actually spring from nonliving chemicals.

One of the many, many problems associated with any naturalistic origin-of-life scenario is that of stereoisomerism. As I explain here, there are certain biological molecules that can be formed in two different ways. They have the same chemical formula and form mirror images of each other. However, these mirror images are not identical. Think about your hands. When you hold them palms together, they are mirror images of one another. However, no matter how you tilt or turn it, you cannot make your left hand look identical to your right hand. If you put the palm of one hand on the back of the other hand, for example, one hand’s thumb will be where the other hand’s pinky finger is. So while your hands are mirror images, they are not identical. There are many biological molecules that are like that, and we call them chiral molecules. The two mirror images that are formed by a chiral molecule are called enantiomers.

All origin-of-life scenarios start with simple molecules that do not form enantiomers. We call these achiral molecules, since they cannot form two mirror images that are different from one another. This is a problem, because in the lab, when achiral molecules react to form a chiral molecule, an equal amount of each enantiomer is formed. As a result, you end up with a mixture that is 50% one enantiomer and 50% the other enantiomer. We call this a racemic mixture. The problem is that life isn’t like that. In most chiral molecules of life, only one of the enantiomers is used. We call this an enantiopure compound, since it is purely one enantiomer, without any of the other. So any origin-of-life scenario has to figure out a way of producing just one enantiomer, or it has to figure out a way to get rid of the other enantiomer once it has formed.

This is a major problem, of course, and the link that the commenter left claims that a “plausible” solution to this problem has been found. Of course, when you look at the actual paper you find that the process is anything but plausible in an origin-of-life scenario.

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Making Something 100% Efficient Is No Problem For God!

A model of ATPase. The rotor portion (purple) turns as H+ ions pass through, and the synthesis portion (green) uses that energy to force two molecules (ADP and P) to join together to make ATP. (click for credit)
When you eat food, your body digests it, sending chemicals from the food to your cells. When your cells receive simple sugars like glucose, they are burned for energy. However, that energy is mostly produced in one part of the cell: a small organelle called the mitochondrion. The cell needs energy in many different locations, however, so the energy that comes from burning simple sugars is “packaged” into smaller units that can be distributed throughout the cell. The units are stored in molecules called ATP. When the cell needs energy, it breaks down the ATP, releasing the energy that has been stored there.

So a cell takes the energy that comes from burning simple sugars and stores it in small units that are held in a molecule called ATP. The ATP is then shipped to where the cell needs it, and when that part of the cell requires energy, ATP is broken down so that the energy is released. The two molecules into which it is broken down (ADP and P) eventually make their way back to the mitochondrion, so that they can be put back together to store another unit of energy. The process by which all this is done is mind-bogglingly complex. Ask any biochemistry student who is required to memorize all the chemical reactions that take place in order for this to happen in a cell!

Now we know that this process is not only mind-bogglingly complex, but part of it is nearly 100% efficient!

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