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Monday, January 26, 2015

Not a CDC Coverup…A Case of Using the Wrong Analytical Method

Posted by jlwile on September 2, 2014

Sometimes, you can get the job done even when you use the wrong tool.  However, sometimes the wrong tool produces the wrong results.

Sometimes, you can get the job done even when you use the wrong tool. However, sometimes the wrong tool produces the wrong results.

The “news story” headline is astounding: “Fraud at the CDC uncovered, 340% risk of autism hidden from public.” The article says that data in a 2004 CDC study on the relationship between the Measles, Mumps, and Rubella (MMR) vaccine and autism were purposefully hidden so it could deny a relationship between the two. Those hidden data supposedly show that some who got the MMR vaccine were significantly more likely to become autistic than those who didn’t. According to the article, this shows that the original study is “fraudulent,” and there is now a petition to get the study retracted. It also calls into question the other studies that the CDC often cites to show that there is no relationship between vaccination and autism. And this article has to be reliable. After all, it is on CNN’s website, right?

Well, not exactly. If you go to the article, you will see “NOT VERIFIED BY CNN” at the top, and you will find a CNN producer note that this website is the network’s “user-generated news community.” So the article wasn’t written by someone at CNN. It was written by a blogger. Does that mean it’s not reliable? Of course not. I read several blogs regularly, and I find most of the articles written on them to be very reliable. In fact, I would say that some blogs are more reliable than some standard media outlets! The question, of course, is whether or not this particular blog article is reliable. When you look into the details, you find that it’s not.

The article’s big claim is that by including data which were supposedly covered up by the CDC, you can find that African American boys have a 340% increased risk of autism if they got the MMR vaccine. This conclusion, however, was “hidden due to pressure from senior officials.” Of course, to make such a claim, someone must have done some sort of study. The article itself tells you nothing about that study, but the CNN Producer Note at the top indicates that it was a study done by Dr. Brian Hooker (a bioengineer) and was published in a journal called Translational Neurodegeneration. An update to that note indicates that the journal has pulled the study, and the journal says this is “because of serious concerns about the validity of its conclusions.”

That doesn’t sound very good, but then again, maybe the journal has been pressured by the CDC to participate in their elaborate coverup. Fortunately, I was able to read the study before it was pulled, and I have to agree with the journal’s decision. The study’s conclusions are obviously wrong, because it used the wrong kind of tool to evaluate the data.

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It Did Sound Too Good to be True…

Posted by jlwile on April 2, 2014

These are stem cells taken from the embryo of a mouse.  The color is the result of a stain used to make them easier to see.  The embryo had to be killed to get the cells, but they can develop into almost any kind of mouse cell (skin, nerve, muscle, etc.).  (image in the public domain)

These are stem cells taken from the embryo of a mouse. The color is the result of a stain used to make them easier to see. The embryo had to be killed to get the cells, but they can develop into almost any kind of mouse cell (skin, nerve, muscle, etc.).
(image in the public domain)

Every once in a while, I run across a story in the scientific literature that seems just too good to be true. Such was the case when I was reading the February 22nd issue of Science News. In a story entitled “A little acid can make a cell stemlike,”1 the author reported on some amazing results that were published in the journal Nature. In the published studies, scientists from the RIKEN Center for Developmental Biology in Kobe, Japan claimed that they could take cells from various parts of a mouse (like the brain, skin, and liver) and transform them into stem cells by simply treating them with acid or other external stimuli!

This would be an amazing feat, because stem cells are able to develop into many different kinds of cells. Consider, for example, what happens when two mice successfully mate. The sperm from the male fertilizes the egg from the female, and the result is a single cell that will eventually develop into a new mouse. In order for that to happen, the cell begins making copies of itself. As more and more copies are made, the individual copies begin to start “specializing” so they can do specific tasks. Some develop into skin cells, others develop into nerve cells, others develop into blood cells, etc. This process of cells specializing into different types of cells is called differentiation.

Of course, the cells in the developing mouse don’t start differentiating right away. There has to be a group of cells that have the ability to produce all the different kinds of cells the mouse needs, and these cells are generally called embryonic stem cells. Examples of mouse embryonic stem cells are shown in the image above. They may look unassuming, but they are truly amazing, because they can produce any kind of cell that the mouse needs. Of course, in order to produce that image, the mouse embryo from which the cells came had to be destroyed. In other words, to get mouse embryonic stem cells, you have to kill the mouse whose cells you want. If you want human embryonic stem cells, you have to kill the developing baby whose cells you want.

This, of course, presents a problem. Embryonic stem cells have great potential when it comes to solving many medical issues. Suppose, for example, you have a heart attack. As a result, some of the cells that make up your heart muscle died. In most cases, the body can’t completely replace the cells that are killed, so you will probably have a weaker heart for the rest of your life. If stem cells could be used, perhaps they could differentiate into heart muscle cells and completely repair the damage to your heart.

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The More We Learn About Bone, The More Amazing It Is!

Posted by jlwile on March 31, 2014

This is the latest view of the microscopic structure of bone.  (click for credit)

This is the latest view of the microscopic structure of bone. (click for credit)

The bones that make up the skeletons of animals and people are a marvel of engineering. As one materials scientist put it:1

…bone properties are a list of apparent contradictions, strong but not brittle, rigid but flexible, light-weight but solid enough to support tissues, mechanically strong but porous, stable but capable of remodeling, etc.

More than three years ago, I posted an article about research that helps to explain why bones are so strong. The calcium mineral that makes up a significant fraction of the bone, hydroxyapatite, is arranged in crystals that are only about three billionths of a meter long. If the crystals were much longer than that, the strength of the resulting bone tissue would be significantly lower. What restricts the size of the crystals? According to the previous research, the tiny crystals are surrounded by molecules of citrate. It was thought that the citrate latches onto the outside of the crystal, stopping it from growing.

Some very interesting new research from the University of Cambridge and the University College London indicates that this is, indeed, what happens. However, it also indicates that citrate does much more than simply restrict the size of the crystals. It also helps to produce a cushion that allows bones to flex rather than break when they are under stress.

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More Evidence That Antibiotic Resistance Existed LONG BEFORE Antibiotics Were Developed

Posted by jlwile on March 3, 2014

This is a drawing of a bacteriophage, a virus that attacks bacteria.  (click for credit)

This is a drawing of a bacteriophage, a virus that attacks bacteria. (click for credit)

Many people know that bacteria have developed resistance to popular antibiotics. Indeed, it is a big problem in medicine, and it has caused many health-care providers to call for doctors to prescribe antibiotics only when they are necessary. The Centers for Disease Control calls this “antibiotic stewardship” and thinks it will improve medical care throughout the country.1 I have written about antibiotic resistance before (see here and here), because some evolutionists try to cite it in support of the idea that novel, useful genes can be produced by evolutionary processes. Of course, the more we have studied the phenomenon, the more we have seen that this is just not the case.

There are essentially two ways that a bacterium develops resistance to an antibiotic. One way is to have a mutation that confers the resistance. For example, a bacterium can become resistant to streptomycin if a mutation causes a defect in the bacterium’s protein-making factory, which is called the ribosome. That defect keeps streptomycin from binding to the ribosome, which makes streptomycin ineffective against the bacterium. However, it also makes the ribosome significantly less efficient at its job.2 So in the end, rather than producing something novel (like a new gene that fights the antibiotic), the mutation just deteriorates a gene that already existed. While this is good for a bacterium in streptomycin, it doesn’t provide any evidence that novel, useful genes can be produced by evolutionary processes.

There is, however, a second way that a bacterium can develop resistance to an antibiotic: It can get genes that fight the antibiotic from another bacterium. Bacteria hold many genes on tiny, circular portions of their DNA called plasmids. Two bacteria can come together in a process called conjugation and exchange those plasmids, which allows bacteria to “swap” DNA. If a bacterium has a gene (or a set of genes) that allows it to resist an antibiotic, it can pass those genes to others in the population, ensuring their survival.

Of course, the natural question one must ask is, “Where did those antibiotic-resistance genes come from in the first place?” Many evolutionists want you to believe that evolution produced those genes in response to the development of antibiotics. After all, antibiotics didn’t exist until 1941, when penicillin was tested in animals and then people. Why would antibiotic-resistance genes exist before the antibiotics?

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For Some Diseases, It Was Vaccination, Not Sanitation

Posted by jlwile on February 3, 2014

This is the logo of Project Tycho.  It depicts Tycho Brahe with his unique view of the universe. (click for credit)

This is the logo of Project Tycho. It depicts Tycho Brahe with his unique view of the universe.
(click for credit)

Dr. Wilbert van Panhuis and his colleagues have started an exciting initiative called Project TychoTM. In it, they are taking public health data that have been collected over the years and putting them into an easy-to-access digital system that is open to everyone. They describe the goal of their project in this way:

We aim to advance the use of public health data for the improvement of public health. Oftentimes, restricted access to public health data limits opportunities for scientific discovery and technological innovation in disease control programs. A free flow of data and information maximizes opportunities for more efficient and effective public health programs leading to higher impact and better health. Our activities are focused on accelerating the availability and use of public health data…

They named the project after Tycho Brahe, one of the more colorful 16th-century astronomers. Not only did he live an interesting life, he had a very interesting view of the universe. He made an enormous number of astronomical observations that he meticulously documented, and those observations convinced him that the planets must orbit the sun, not the earth. However, he couldn’t give up the idea of the earth being at the center of everything, so he produced what is probably the most interesting view of the universe ever. As shown in the logo above, he put the earth at the center of the universe, and he had the sun and moon orbiting the earth. The rest of the planets were then assumed to orbit the sun, as it moved in its orbit around the earth. While this view of the universe is clearly unworkable, it was incredibly original!

Why would a project involving public health data be named after this colorful character? Because his main contribution to science was the data he collected. While he couldn’t make heads or tails of his data, another astronomer, Johannes Kepler (who was once employed by Brahe) did. Kepler was able to use Brahe’s data to develop three laws of planetary motion that demonstrated all the planets, including the earth, orbit the sun. Sir Isaac Newton was then able to use Kepler’s Laws to develop his Law of Universal Gravitation, which describes how gravity works both here on earth and throughout the universe. Brahe’s data, then, were the foundation of some of the greatest advancements in the field of astronomy in the 16th and 17th centuries.

In Dr. van Panhuis’s view, the data he is collecting could end up being like Brahe’s data. It might be used by other scientists to better understand diseases and how to deal with them as they spread through populations. While I can’t say whether or not that will ever happen, I can say that these data make it easy for me to address a popular myth about vaccination.

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More Amazing News About Breast Milk

Posted by jlwile on January 27, 2014

This is an oligosaccharide - a molecule made up of a few simple sugars linked together. (click for credit)

This is an oligosaccharide – a molecule made up of a few simple sugars linked together.
(click for credit)

Approximately a year ago, I wrote about the bacteria in human breast milk. While that may sound like a bad thing, it is actually a very good thing. Over the years, scientists have begun to realize just how important the bacteria that live in and on our bodies are (see here, here, here, here, and here), and the bacteria in breast milk allow an infant to be populated with these beneficial microbes as early as possible. Not surprisingly, as scientists have continued to study breast milk, they have been amazed at just how much of it is devoted to establishing a good relationship between these bacteria and the infant who is consuming the milk.

For example, research over the years has shown that human breast milk contains chemicals called oligosaccharides. These molecules, such as the one pictured above, contain a small number (usually 3-9) simple sugars strung together. Because oligosaccharides are composed of sugars, you might think they are there to feed the baby who is consuming the milk, but that’s not correct. The baby doesn’t have the enzymes necessary to digest them. So what are they there for? According to a review article in Science News:1

These oligosaccharides serve as sustenance for an elite class of microbes known to promote a healthy gut, while less desirable bacteria lack the machinery needed to digest them.

In the end, then, breast milk doesn’t just give a baby the bacteria he or she needs. It also includes nutrition that can be used only by those bacteria, so as to encourage them to stay with the baby! Indeed, this was recently demonstrated in a study in which the authors spiked either infant formula or bottled breast milk with two strains of beneficial bacteria. After observing the premature babies who received the concoctions for several weeks, they found that the ones who had been feed bacteria-spiked formula did not have nearly as many of the beneficial microbes in their intestines as those who had been feed bacteria-spiked breast milk.2

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More Consequences of Anti-Vaccination Misinformation

Posted by jlwile on January 2, 2014

Even though the standard vaccines have been demonstrated to be safe and effective, many people decline to get them for their children, and the results can be serious. (public domain image)

Vaccines are a powerful means by which certain diseases can be prevented. Many scientific studies demonstrate that they are both safe and effective, but unfortunately, there are those who have been convinced by misinformation produced by anti-vaccination groups. As a result, some infectious diseases are beginning to make a comeback in the United States. One of those diseases is measles.

One reason measles is making a comeback in the United States is that there are several other parts of the world where measles has a stronghold. Since world travel is common, it is easy for someone to import the disease back to the U.S. In most cases, this isn’t a problem, because most travelers come into contact with people who have been vaccinated. As a result, the virus has a difficult time spreading, and the traveler is usually the only one who ends up suffering from the infection. Every once in a while, however, a traveler will come into contact with a group that has a very low vaccination rate. When that happens, the disease spreads quickly.

For example, in April of 2013, an unvaccinated person returned home to North Carolina after spending three months in India. Along with souvenirs and stories, the traveler brought home the measles virus. Two other unvaccinated family members got the disease, and in the end, there were 23 confirmed cases of the measles. The vast majority of them (18) were among unvaccinated people. Two of the measles cases were in people of unknown vaccination status, and three were in people who were fully vaccinated.

This, of course, brings up a very important point. When people refuse vaccination, they often think that the only possible consequences will be to them and their family, but that’s just not true. No medicine, including vaccines, is 100% effective. Thus, there will be a small percentage of people who get the vaccine but are not fully protected against the disease. When unvaccinated people provide a breeding and transmission population for the disease, this increases the risk to all people, even those who are vaccinated.

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The Benefits of Musical Instrument Lessons Last A LONG Time!

Posted by jlwile on December 19, 2013

A recent study shows that musical instrument lessons can provide lasting benefits to hearing.
(click for credit)

My parents thought it was very important for all their children to have piano lessons. I think they believed it would give us boys (I have no sisters) some culture, so in first grade we all began learning how to play the piano. My brothers quit as soon as they were allowed, but I really enjoyed those lessons, so I continued. At one time, I honestly thought I would become a concert pianist, but unfortunately, my fingers are too stubby. I simply cannot play many pieces of music properly, because I cannot spread my fingers wide enough to span more than an octave. I still play for church (mostly on the synthesizer), and anyone who watches me play can see that I am truly having fun. I thank God that my parents thought those lessons were important, because they ended up providing me with a long-term hobby that has brought me a lot of happiness.

Long after my brothers quit playing the piano, they complained that those piano lessons (as well as the practicing that went along with them) were a big waste of time. They understood that I really got something out of the lessons, but they were convinced they received nothing. However, a recent study indicates that they may be wrong. They might enjoy better hearing now because my parents forced them to take piano lessons when they were young.

It turns out that when you listen to someone else talking, your brain does an incredible job of interpreting the quickly-changing sounds associated with speech. Especially when the person speaking makes a transition between a consonant and a vowel, there is a rapid change in the properties of the sound wave that hits your ears. To be able to recognize such transitions, your brain relies on its ability to link the sounds the ears are receiving to the time at which the sounds were received. This is called neural timing, and as you get older, your brain’s neural timing deteriorates. This is one reason older people have trouble following conversations. They may be hearing just fine, but if their neural timing is off, they can’t understand the words they are hearing.1

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Some “Vegetative” Patients are Probably at Least Partially Aware

Posted by jlwile on December 11, 2013

An EEG image of a person in a vegetative state listening to a list of words that contains the word to which he is attending and a bunch of distractor words. (click for credit)

The Royal College of Physicians defines a vegetative state as:1

a clinical condition of unawareness of self and environment, in which the patient breathes spontaneously, has a stable circulation, and shows cycles of eye closure and opening that may simulate sleep and waking

When I read this definition, a question immediately arises: How do you know whether or not a person is aware of himself or his environment? You might ask him a serious of questions, but if he doesn’t have the ability to move his mouth or other parts of his body, how can he make you aware of his responses?

A few years ago, Dr Steven Laureys made headlines with his pronouncement that a man in a coma was able to communicate with people when given the aid of a keyboard and someone to support his hand as he typed. Based on Dr. Laureys’s work, it seemed that the man was describing exactly what you might think is going on in the mind of a person who is aware of himself and his surroundings but cannot communicate with the outside world. However, as skeptics started pointing out the flaws in Dr. Laureys’s method, further tests were done, and it turns out that the person supporting the patient’s hand was actually directing the patient’s hand. In other words, the patient wasn’t communicating; the helper was.

So what can we say scientifically about such patients? If they cannot do anything to communicate with the world, how do we know whether or not they are aware of it? A collaboration of scientists from Cambridge University, the University of California at Los Angeles, and the University of Western Ontario have gotten us a step closer to answering that question. They have published a study in the journal NeuroImage: Clinical that might help us produce a method by which an aware patient can communicate, even if he is not able to do so by traditional means.

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Astounding: Your Baby Can Heal You!

Posted by jlwile on October 30, 2013

This Facebook Meme is actually correct!

I avoided Facebook for a long time, but a few years ago, I finally gave in. Not long after I started connecting with long lost friends and finding out what everyone was eating, I learned the joys of Facebook memes. Every day now, I see lots of pictures with snarky sayings on them coming across my news feed. Some of them are funny, and some try to make a point. Many times, the ones that try to make a point are just dead wrong. They include either outright falsehoods or an incredibly mischaracterized fact. Thus, whenever I see a “science meme” or a “political meme,” I generally ignore it.

However, when the meme at the top of this article came across my newsfeed, I had to investigate it. If you have been reading this blog for a while, you might remember that almost two years ago, a talented writer named Amanda Read posted a story about how a baby’s cells reside in his or her mother long after the baby is born, and they may aid the mother in healing certain kinds of tissues. I was incredibly skeptical of the story, but when I did some investigation, I found out that it was true. Later on, I learned about a study that showed how a baby leaves DNA behind in his mother’s brain, and those “fetal remnants” might even fight against neurological disorders!

Since we are still barely scratching the surface in our understanding of the the amazing design behind pregnancy, I decided to pay attention to this Facebook meme. Of course, I knew that the statement on the left is true. All sorts of things pass through the placenta from the mother to the child, and that includes blood proteins which fight disease and shape the development of the baby’s B-cells.1 Those B-cells will affect the child’s ability to fight disease for the rest of his or her life.

I was, however, very skeptical of the statement on the right. Surprisingly, there is strong scientific evidence to back it up!

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