What is a Virus?

Typical Bacteria (Wikipedia)

With the recent Ebola outbreak in Africa, I’ve had a number of individuals question me as to what exactly a virus is. When I ask them what they think it is, they usually say a very small organism related to a bacteria. In actuality viruses are quite a bit different from bacteria and trying to understand the difference can be quite a task for those without a biology background. In this post I’m going to walk you through it by placing viruses in the larger context of life on Earth.

Most people are familiar with cells. These are the living building blocks of plants and animals. Cells are self-contained structures (due to their outer cell membrane). They take in nutrients from their surroundings and convert these into energy, store hereditary material (DNA), and are capable of duplicating themselves. The human body has trillions of cells, all working together to provide complex function and the ability for us to heal when injured. Cells can exists independently of each other and some of the smallest organisms are just that – single cells that have their own lives. They take in nutrients, create energy, and divide, creating more of themselves. The figure above and to the left shows an example of a single-celled bacteria. Bacteria are everywhere and we know that some can be very beneficial (the Escherichia coli in your gut) while others can pose health hazards (Bacillus anthracis which causes Anthrax).

It’s relatively easy to view bacteria as being “alive” since they, all by themselves, take in nutrients, convert nutrients to energy, store heritable material like DNA, and reproduce. Bacteria also make sense in the larger spectrum of life as they help the decomposition of matter (dead animals, plants, etc.) and they are also food for larger single-celled organisms and small crustaceans. These organisms are, in turn, food for larger organisms and the trend continues all the way up to humans which consume a wide variety of plants and animals. Bacteria are quite small (between 0.5 and 5 micrometers). Viruses, on the other hand, are 0.02 – 0.4 micrometers in size. So, viruses are generally smaller than bacteria and it’s natural to assume they fall below bacteria on the “food chain.” Perhaps bacteria feed on viruses and so on. However, the reality is somewhat different.

Typical Virus (Wikipedia)

Viruses are not cells. They consist of heritable material (DNA or RNA) surrounded by a protein coat, which is in turn surrounded by an envelope of lipids (fats). A typical virus can be seen in the picture to the right. Left alone viruses cannot take in nutrients from their surroundings and convert them to energy, nor can they reproduce themselves. The gut reaction when people first hear this is…viruses aren’t alive? It’s actually generally accepted that viruses are alive because once they infect a host’s cells (or the host cell if the host is just one cell like a bacteria), they use the cell’s machinery (organelles) to generate energy and reproduce. Viruses can infect bacteria, plants, animals. Nothing is immune. A virus infects a cell and highjacks the the cell’s normal infrastructure for living in order to support a rapid reproduction of itself, which then results in the destruction of the host cell. For single-celled organisms, this kills them, for multicelled organisms like humans, it causes cell death in our bodies which we can sometimes recover from (a Cold) and other times have a very hard time recovering from (Ebola).

From an evolutionary perspective viruses are very confusing. We don’t really know how they arose. We also don’t really understand their “purpose.” It’s much easier to see the purpose of almost every other organism as they tend to do something constructive like generate oxygen, breakdown decaying matter, or at least, they are food for other organisms. You might look at humans and think, well we are somewhat of an exception as well. We don’t really have any predators and can certainly do more harm than good to an ecosystem if we aren’t careful. For a “circle of life” view you might think of viruses preying on humans, as they can certainly kill us, but it’s still a bit forced as viruses infect everything, not just humans, and nothing really preys on viruses to complete the cirlce. So, even today, viruses are still a bit of a mystery. They are exquisitely designed to infect other organisms and propagate themselves at extremely high rates/numbers. We know much more about viruses today compared to when they first came across our radar in the late 1800s, but there is clearly still much more to understand.

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Pull-Ups or Chin-Ups?

When I train my clients one of the questions I often get asked by them is, when performing a pull-up, does the grip (or orientation of the hands on the bar) matter? Specifically, they are asking the difference between having their palms facing away from them versus having their palms facing them. The palms facing away grip is known as a Pull-Up, whereas the palms facing you grip is known as a Chin-Up. You can see an example of each below as taken from Youdas et al., 2010:

Pull-Up, Palms facing away (pronated)
Chin-Up, Palms facing you (supinated)

There actually is a difference in the exercise depending on which grip you use to pull yourself over the bar. This difference has been known for a while now and to highlight it, I have chosen an older work – Youdas et al., 2010.

The Takehome: Using EMG and motion capture analysis the authors of this study showed that when you do a pull-up (palms facing away from you) your back muscles (specifically, infraspinatus and lower trapezius muscles) tend to have a greater activation. If you switch your grip for a chin-up (palms facing you), then your chest (pectoralis major) and arms (biceps brachii) are more maximally activated. When my clients are just getting started, I don’t have them worry about which grip they use. I let them choose whichever is most comfortable because, either way, they will be getting a good upper-body workout. However, for those more advanced in their training, this distinction can be important; you can choose your grip to focus more on developing the anterior (front) of your body with a chin-up or to focus more on developing the posterior (back) of your body with a pull-up. Assuming an individual doesn’t have any pre-existing muscle imbalances, mixing both grips into one’s training routine is a good way to be well-rounded.


The Experiment:

  • Electromyography (EMG) was used to measure motor unit activity within muscles.
  • The authors compared the pull-up, chin-up and The PerfectPullup(TM) device, the latter of which I do not discuss.
  • 7 muscles were examined with EMG – lower trapezius, latissimus dorsi, infraspinatus, erector spinae, pectoralis major, external oblique, and biceps brachii.
  • Motion analysis was combined with EMG data to link muscle activation to specific parts of the exercises’ range of motion.
  • 21 men and 4 women in their 20s were used in the study.

The Results:

  • The lower trapezius and infraspinatus had greater activation in the pull-up compared to the chin-up.
  • The pectoralis major and biceps brachii had greater activation in the chin-up compared to the pull-up.
  • Differences in elbow joint sagittal plane range of motion between chin-ups and pull-ups were statistically ambiguous.

The Limitations:

  • The participants (the study sample) were heavily biased towards men. It would have been better to have the study just use men since an equal mix of men and women was not possible.
  • The finish position for each trial had the participant just reaching their nose above the bar. Pulling such that the entire chin was over the bar or so that the bar touched below the clavicle (chest), would have been more challenging and might have resulted in different muscle activation patters. It is interesting that they did not take this approach given that they did try to compare elbow joint sagittal plane range of motion (which turned out to be statistically ambiguous).
  • The authors highlight some statistical differences in the text of their paper that do not match the indicators in the Figures of the paper (which may be a result of clerical error).
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Publication Bias – Null Results Are Rarely Published

Publication bias is something that continually plagues science. It is most apparent in the types of data the get published. Data that is not positive (that did not prove the researchers’ hypothesis) is rarely published. Such “null result” data indicates that no effect was found or no difference exists (within the study’s design limitations of course). Part of the rationale behind this is, if you didn’t see an effect, there might still be one if you performed the experiment differently. Perhaps if you used a higher dose of drug, looked in a different age group, or used a different animal model, an effect would in fact be there. Allowing for this possibility, scientists don’t like to flood the literature with null results. But how big of an issue is this really? In a recent article from the journal Science, researchers examined this bias in the social sciences.

The authors followed 221 research projects and found:

  • 96% of the experiments that produced positive results were then written up and submitted for publication.
  • Nearly two thirds of the experiments that produced null results were simply filed away (not prepared or submitted for publication).

The fact that nearly 65% of null studies weren’t even written up is surprising. This represents a lot of time, money, and work that is not seeing the light of day. Many people feel that all results from all studies should be made available. This way a bigger picture can be formed, but also having this data available would help prevent other researchers from conducting the same experiment in duplication – wasting time and money only to get the same null results. In clinical drug trials the demand for a release of all data (in the form of a completed manuscript) has been the greatest as it would give doctors and patients more information from which to base opinions. For example, with just two successful positive trials showing an effect there is little reason to not use the drug. But humans are genetically very diverse and history has shown that over time many approved drugs ultimately show side-effects that were not anticipated. Currently, many experiments in animals with null results don’t have to be published at all and negative results in human clinical trials only need to have the simplest data set released to an NIH registry; researchers do not have to write the full human study up for publication. If instead the two successful trials were available, but so were 5 other experiments that showed no effect in different models (animals, humans) and different age groups. This might temper the decision of doctors and patients towards trying a new drug.

There is no simple answer to this problem of publication bias. Many researchers insist that null results should not be given the same weight as positive results and thus do not want the literature flooded with such studies. At the same time, studies with null results give valuable information. Many are now calling for a public database in which scientists can deposit their null results so that everyone can make better informed decisions going forward. What do you think? Should all results be written up and made available to the public?

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Product Recommendations Page Launches

If you haven’t checked out the Product Recommendations page, which had a soft launch several months ago, have a look now. Today is the official launch of the page which has been created in response to numerous requests from my readers. The page gives the rationale behind my offering this service, the initial two companies I am recommending, as well as instructions for submitting other candidates for the page. Let me know what you think!

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Effect of Gut Bacteria on Exercise Performance

Bacteroides Fragilis
from the National Review of Medicine

The human body contains numerous microorganisms (bacteria, funji, etc.) residing in locations such as the intestinal tract (gut), mouth, and skin. Many believe the number of of these microorganisms (microbes) exceeds the number of cells we have on our bodies. Some microbes are known to have an important beneficial role to human health (see my prior article for an example of what can happen to your digestion if you disrupt them), but for the vast majority, we don’t fully understand what role they have in human health.

Studies have indicated that gut bacteria are important for digestion, energy production and energy storage. In addition, studies have shown that gut bacteria can affect anti-oxidant production; anti-oxidants are compounds that protect against free-radical tissue damage which occurs, in part, from the pathways your body uses to obtain energy. Since exercise causes an increased demand for energy and this potentially increases free-radical tissue damage, it is possible that gut microbes are moderators of exercise performance through regulation of energy production and anti-oxidant activity. Using this line of thought, the authors of Hsu et al., 2014, in a recent article from the Journal of Strength and Conditioning Research, performed a study to examine the effect of intestinal bacteria on exercise performance.

The Takehome: This study had two main questions. The first was whether gut microbes affected exercise ability, specifically time to exhaustion in swimming mice. The second was whether they simultaneously affected anti-oxidant production, thereby linking the effect on exercise exhaustion to anti-oxidants. The study indicated that a normal disease free mouse (Specific Pathogen-Free) had the most swimming endurance and that if you use a mouse who has no normal gut microbes (Germ-Free) the endurance is notably worse. The third mouse group was “Germ-Free with added Bacteroides Fragilis” which is a “rescue” group. Here the investigators gave the Germ-Free mice one beneficial gut bacteria and, as expected, they had better endurance than Germ-Free, but not quite as much as the Specific-Pathogen free mice which had multiple types of gut microbes. Thus, endurance exercise appears linked to a healthy gut microbe population. The second story, trying to link this to anti-oxidants, was not as convincing. Some anti-oxidant levels were higher in the normal disease free mice (Specific Pathogen-Free), some were lower, and some were identical. That these levels were measured in different sites (blood, liver, etc.) also complicates the story. So, we must reserve judgement on the anti-oxidant effect, but the exercise effect is interesting. Would a similar effect be found if the mice were resistance trained (jumping, climbing)? This would make for an interesting follow-up study.

The Experiment:

  • 12 week male mice were used. Groups were “Specific Pathogen-Free” (no infectious microbes), “Germ-Free” (all microbes absent), or “Germ-Free with added Bacteroides Fragilis” (a beneficial gut microbe found in mice and humans).
  • Exercise was administered to mice in the form of a swimming test which recorded time to exhaustion.
  • 48 hours after the swimming test, organ measurements were taken and blood measurements were taken. This included general descriptive data as well as antioxidant activity in tissue and blood serum.

The Results:

  • All groups had identical body weights, but the proportion of liver, muscle and fat was higher in the Specific Pathogen-Free mice.
  • Swimming time to exhaustion was different for all three groups with the Specific Pathogen-Free mice being able to swim the longest, Germ-Free being able to swim the shortest amount of time and the Germ-Free with added Bacteroides Fragilis being able to swim for an intermediate length of time.
  • Germ-Free mice had the highest levels of uric acid and urea nitrogen in their blood.
  • Germ-Free with added Bacteroides Fragilis had the lowest levels of total cholesterol and triglycerides in their blood.
  • Antioxidant activity of glutathione peroxidase, and catalase in blood, was greatest in Specific Pathogen-Free mice.
  • Antioxidant activity of superoxide dismutase in blood was lowest in Germ-Free with added Bacteroides Fragilis mice.

The Limitations:

  • This study was conducted in mice, so application to humans is limited.
  • Mice where swam to exhaustion (near drowning) which is an extremely stressful form of exercise that may not translate to exercise that most humans would conduct to stay healthy.
  • This study does not address the possible effects of resistance exercise.
  • The decline in exercise ability from Specific Pathogen-Free mice to Germ-Free mice, which was then partially recovered using Germ-Free with added Bacteroides Fragilis mice does not match the anti-oxidant data. That is, although Germ-Free with added Bacteroides Fragilis mice were better swimmers than Germ-Free, they had either similar or lower anti-oxidant levels to Germ-Free mice, making the link between exercise and anti-oxidant levels weak at best.
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Video Post – 5 Tools Everyone Should Own

In today’s video post, I talk about 5 tools everyone should own to assist in daily maintenance and recovery of their bodies – specifically their muscles, which can get very tight from non-deal lifestyle factors, sports, or training. Be sure to go to Science for Fitness’ YouTube channel and subscribe if you haven’t already.

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Tooth-Organ Relationships

Several months ago my mother started feeling out of it and began to develop lower back pain around her sacroiliac (SI) joint. She’s always fairly active, tap dancing and going to the gym, but she had no choice other than to take it easy. After a month or so I visited her and examined her movement patterns. The pain was particularly bad when she got up from sitting down. I noticed she was bending her torso very far over to get up. This was her body’s way of mechanically compensating for weak hip flexors. I had been working with her on getting her legs stronger, but with the onset of the lower back pain, things were coming undone. I speculated that the excessive forward torso lean was now overworking her erector spinae muscles (the muscles that stabilize your lumbar spine). I had her rise from sitting by keeping a more vertical back, driving through her heels, and pressing with her hands on the arm rests as an assist. It worked very well and she was now able to rise from sitting without serious pain. I told her to keep using this approach to let her lower back muscles rest.

Time continued to pass, the lack of energy worsened and the pain was still there during movements of her lower back. I decided too much time had passed for a muscle strain injury and was about to call my parents to suggest seeing a specialist. Before I could call them up, my father called me and said that one of my mother’s molars was dying. The nerve was shot and giving her excruciating pain. They both new she needed a root canal, but it was late in the night. After discussing interaction effects (or lack thereof) of over-the-counter pain killers, I suggested she call her dentist at his home and set up a visit for the next morning – an emergency root canal seemed required. It turned out to be exactly what was required. The tooth had 3 nerves and all of them were dying. One of the three was particularly buried and in the dentist’s search for it he found a serious infection. The infection was so buried, he didn’t notice it in previous encounters even though he said it must have been there a while since it was so far along. He told my mother that the infection had likely leaked into her entire body by now, which would explain why she felt so terrible. He said it also likely explained her excruciating back pain. After removing the tooth and nerves, he put my mother on antibiotics. The very next day she felt substantially better. Her energy levels were not to be believed.

Click to zoom

What are we to make of all this? The dentist had a chart on his office wall similar to the one to the left. The chart indicates a relationship between the teeth of the body and the health of other organs. But my literature review of how tooth health may affect the health of other organs was largely unsuccessful. Indeed, the chart has origins from Acupuncture suggesting that the connection may have its roots from observations within the Traditional Chinese Medicine (TCM) paradigm. Still, web searching reveals many individuals who experienced pain in various parts of their body, only to have it disappear after a root canal. Given that root canals are almost always paired with antibiotic treatment, it’s unclear whether the mere removal of the dead nerve or the antibiotics are relieving the pain. Personal observation seems to suggest both are possible and at least one study gives support for the role of antibiotics in improving back pain. Although a terrible experience for my mother, this turned out to be quite eye-opening for all of us. It was a great reminder. Even though science can explain a great deal, there are still major gaps in our understanding. In addition, for those that treat, train, or coach others, we must remember that the body is an exquisitely interconnected structure; just because a problem presents itself in one region of the body does not mean that region is also the root cause of the problem.

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Science For Fitness Newsletter

A number of my readers requested that I create an email mailing list so they can more easily keep tabs on when new content is posted. Everyone is busy these days and checking websites constantly doesn’t help things much. In addition, there is no guarantee you will see an Science for Fitness post on your Facebook pages feed. Therefore, I have launched an email newsletter for Science For Fitness! It won’t be a weekly mailing (so you won’t be inundated with emails), but it will be regular enough for you to keep up to date with things. The newsletter format will also enable me to offer some more varied content. I will be able to update everyone on what I’m working on, comment briefly on certain news items, share some fun things like quotes and of course, I will end with a listing of the most recent website and YouTube posts so you won’t miss any of those. You can opt-in or out of the newsletter at any time and I will NEVER share the email list with third parties.

To sign up for the newsletter, just fill out your information in the form that appears to the right of the website, or if you’re on the Science for Fitness Facebook page, click the “Newsletter Signup” tab.


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Fructose Content in Popular Beverages

From Wikipedia

Last year I posted a review of a conference abstract looking at the sugar (carbohydrate) content of soft drinks. You can view the original post here. The abstract was a summary of work in progress with only preliminary findings. As such, there was no way to know how the full study would turn out. Recently, the authors completed and published the full study so now we can see how they compare.

The study centers around the sugar Fructose which is somewhat controversial. I discussed Fructose in detail previously, but the essence of the controversy is that Fructose is metabolized preferentially by the liver and as part of this process there is the potential, if conditions are right, for the sugar to more readily build fat. Fructose has been linked to obesity, fatty liver disease, and other health problems. It’s because of all this that many people are scrutinizing foods and drinks with high levels of fructose. And of course when foods with high fructose corn syrup (HFCS) are brought up, well, the name alone suggests a potential problem. Of course, what many people don’t realize is that most HFCS doesn’t have notably more fructose than glucose. Or does it? Since companies are not forced to list the final ratio of fructose to glucose on product labels, there is no way for the consumer to know. And so, the authors of Walker et al., 2014 wanted to find out for themselves.

The Takehome: The results of this full study supported the authors’ original conference abstract findings. Even using two additional independent methods, higher than expected levels of fructose in sweetened beverages were found. Specifically, the 5 most popular HFCS-sweetened beverages (Coca-Cola, Pepsi, Dr. Pepper, Mountain Dew, and Sprite, which comprise ~90% of the annual beverage market share) had fructose to glucose ratios of ~60:40 which means they contained 50% more fructose than glucose. Remember, sucrose (table sugar) has a ratio of 50:50 and HFCS-55 is 55:42. In addition, beverages had ingredient errors such as Mexican Coca-Cola having a high fructose content despite no source of free fructose being listed and Pepsi listed sucrose as an ingredient but none was found after analysis by the authors. There are many possible causes for all these discrepancies including production methods that allow for hydrolyzed syrups (loss of sucrose content), use of juice concentrates (which may have high fructose contents), and bleeding of HFCS-55 with higher syrups like HFCS-90. All of these methods are allowed in beverage production and do not have to be indicated on labels. Regardless of the sources of discrepancy, and regardless of whether or not manufacturers are intentionally creating products with sugar levels higher than claimed, the data suggest that sweetened beverage ingredients are not what they seem. Thus, according to the result of this study, estimates of society’s fructose intake are likely being underestimated.

The Experiment:

  • In addition to the original measurement data using liquid chromatography (LC), two different approaches were used to measure sugar content: 1) a metabolomics-type (MET) approach based on mass spectrometry combined with liquid and gas chromatography and 2) gas chromatography (GC) by itself.
  • The different analyses were performed by separate companies and both companies were blinded as to the identity of the samples they were testing in order to prevent bias.
  • 14 popular sodas/teas were analyzed (e.g., Dr. Pepper, Pepsi, Sprite, Mountain Dew, Coca-Cola) along with 19 juices/juice-like drinks (e.g., Minute Maid Apple Juice, Kool-Aid Jammers, V8 Splash Berry Blend).
  • Product sugar measurements were compared against standards with known concentrations of glucose, fructose, sucrose, and maltose (and also galactose and lactose for the GC analysis).
  • The amount of each sugar present in the tested sodas and juices was obtained from the NCC Food and Nutrient Database, USDA Nutrient Data Laboratory, data in the scientific literature, and food manufacturer’s information.

The Results:

  • Results were consistent across all three methodologies for % fructose, glucose, sucrose, and maltose. In addition, free fructose content was consistent across all the three methodologies.
  • Mexican Coca-Cola consistently contained 49% of total sugar as free fructose even though neither HFCS nor fructose was listed on the label.
  • Pepsi Throwback, Gatorade and Sierra Mist (none of which list HFCS or fructose as ingredients) contained fructose as 59, 40, and 8 percent of their total sugar, respectively.
  • Beverages listing HFCS as an ingredient had a mean fructose to glucose ratio of 59 while those not listing HFCS had a mean ratio of about 50.
  • Sprite, Dr. Pepper and Pepsi had free fructose accounting for 60% or more of total sugar.
  • Pepsi listed sucrose as an ingredient, but no sucrose was detected as an ingredient using gas chromatography.
  • Minute Maid and Juicy Juice 100% Apple Juices had the highest ratios of fructose to glucose of all the juices measured (67.1 and 67.3, respectively).

The Limitations:

  • Some values for sugar amount claimed/known to be in beverages were missing and a probable value had to be created using statistical procedures.
  • A variety of sources were used to obtain the claimed/known amount of sugar in beverages and we do not know how the authors handled different values being reported in different sources (if any).
  • This study would have been enhanced with a variety of control beverages such as those that are artificially sweetened and those with minimal ingredients and low sugar amounts (such as Honest Teas and Inkos Teas).
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Video Post – How to Make Almond Milk

In today’s video post, I team up with Nieves, owner of Sexy Batch Baking Company to show you how to make your own Almond Milk. It’s quick, simple and healthy. Be sure to go to Science for Fitness’ YouTube channel and subscribe if you haven’t already.

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