Category Archives: Rant
Well, it’s heading into flu season, and what’s a Micro prof to do? Get a flu shot, that’s what. As part of the YCP Wellness Fair on Monday during Fall Break, I went over to the Grum and received my flu shot from a very competent nurse, and now am ready to say “Bring it on, Influenza!”
— David Singleton (@drsingleton) October 13, 2014
The same day that I did this positive step for public health, I came across a little bit of craziness about the Ebola outbreak, via the science blog io9.com. Writer Mark Strauss spent some time among the seedier conspiracy theory websites over the weekend, and documented that in addition to the hysteria and mistaken information that is available, there is also some outright disinformation about the Ebola outbreak. Members of the anti-vaccination network have proposed that the spread of Ebola to Texas is part of a concerted government effort to shift attention away from a discredited “whistleblower,” who was going to make a statement about a vaccine/autism link that supposedly had been covered up by the CDC. Another site claims that the initial outbreak of Ebola in discrete regions in Guinea is indicative of a deliberate release of the virus by pharmaceutical companies, so that they could test a secret antidote on an unsuspecting population. Finally, the Vaccine Information Network doesn’t seem to believe that Ebola virus is real, and that the reports in the media are attributed to purposeful misinformation on the part of authorities ultimately “to poison us with drugs and vaccines.”
So after we all take a deep, cleansing breath to clear our minds after that, here’s a bonus opportunity. Simply do as I did up above–go get a flu shot. Document it if you can as I did, by tweeting it or posting it on Instagram with hashtag #ycpmicro, and paste the link in the comment thread below. Offer goes through the end of October, when we should all have gotten our flu shots anyway.
I saw this story at io9.com, which summarized a news alert from the Centers for Disease Control about the ongoing outbreak of measles in the US. In the year 2000, measles was determined to essentially eliminated in this country, following an aggressive vaccination campaign during the second half of the 20th century. Prior to the introduction of the vaccine, there were over 500,000 cases each year, with a death rate of about one per 1000 cases. Because of the perceived low rate of death due to measles, there is a public perception that it is not a very serious disease, however there is actually a high risk of complications from measles that can lead to extensive medical care. Up to 30% of measles cases have one or more complications, with pneumonia being the most frequent cause of death in children due to complications of measles. In countries where malnutrition is prevalent, death due to measles occurs in 25% of the cases.
The graphic above was published by the CDC this week, and documents the rise in measles cases over the past decade+ since the disease was declared “eliminated” in 2000. This year marks the highest number of cases in over 20 years, and this milepost has been reached by the end of August, not the end of the calendar year. The CDC attributes the spike in cases solely on failure of parents to vaccinate their children; essentially all of the cases in this year’s outbreaks have been in unvaccinated individuals. In the majority of the cases this year, a cluster of cases were observed–an outbreak–where a single patient infected unvaccinated people around them, resulting in many cases of the disease.
The CDC strongly recommends that all individuals be immune to measles through vaccination. Because of the high threat of complications, the added cost to society through lost wages and healthcare, and the highly contagious nature of the disease, it is important to not become complacent about its threats. Additionally, certain segments of the US population (the very young, others with specific sets of underlying medical conditions) are not immune to measles, and therefore are significantly at risk due to exposure by others. The United States along with other partners in the World Health Organization have pledged to eliminate this disease for good by 2020. If we all do our part, we can see this happen!
The last posting on the potential effects of poor vaccine coverage has led me to think about public perceptions on science. Although generally the public feels that science in general has an overall positive effect on American society, a National Science Foundation survey from several years ago indicates that people do not have a very good idea of exactly what it is that science does, or who scientists really are. Indeed, many public science advocacy groups such as the NSF linked above, as well as private professional societies (such as the American Society for Microbiology which I belong to) have turned to having pretty significant public outreach and education efforts as part of their overall mission. Even with these efforts, there remains significant public distrust towards the motives of scientists and and the practice of science for specific issues. This distrust span a range of topics, including very broad ones such as the analysis of historical and geological climate change or the role of biological evolution in producing the diversity of life, to rather narrow ones such as the effectiveness of vaccination on public health or the benefits/dangers of genetically modified foods. I think that distrust of ANY of these topics reflects two failures; one on the part of scientists to not properly frame topics adequately in a more generally approachable manner, and one on the part of the public to be educated on the basic principles of the scientific method, and a failure to distinguish between the concepts of causation and correlation.
I am actually OK with this to some degree; misunderstanding of what I do as a scientist can be addressed through conversation and explanation. In the case of the anti-vaccination movement, I think that much of the perceived public resistance comes about from the failure to understand causation and correlation. This is prompted by real fears drawn from personal experience–we have all seen commenters in various public forums describing how a family member suddenly “changed” after receiving a shot. Although anecdotal evidence has its place, these observations generally only relate one single incident with one single outcome, and neglect the many other variables that may also have led to the outcome. The challenge then is to convince people that causation can only truly be determined in conjunction in blinded, controlled studies that allow the manipulation of only a single variable.
I also looked at the other extreme of science distrust–these would be the extreme outliers in the Pew Study linked above–and did some simple Google searching for conspiracies relating to vaccination. I won’t link back to any of the sites I scanned, however it quickly became apparent that rational discourse is likely not to be very effective. The main arguments seem to be two-fold: governmental agencies are constantly working to exceed their bounds essentially in a move to keep the population under control through vaccination, and the pharmaceutical industry seeks to maximize profit margins by selling vaccines. One site I found spent several pages detailing the lack of evidence supporting the premise that variola virus is the causative agent of smallpox, minimized the health risks of smallpox outbreaks, and ridiculed the eradication effort using attenuated vaccinia virus. This type of denialism towards vaccination fortunately doesn’t carry much weight in the general public, however I am frequently dismayed reading the Letters to the Editor in the newspaper by local correspondents who put forward the same types of motives in their arguments in opposition to climate change proposals.
My hope to all who come into BIO230 is that we think carefully about things we hear, and ask lots of questions when we come across something that we don’t understand. I find intuition is frequently helpful–I may not know the particulars about a given subject, but I can sometimes sense that something doesn’t seem right. Consider the evidence that is used to back up claims that you may see being made, and think of an experiment that might disprove those same claims. And I think the best experiment is one that immediately leads you to think of the next experiment–you are truly thinking then.
Thanksgiving Break is generally a quiet time around the BIO230 blog site, as the major visitors are spending time away from the Internet and Microbiology to spend time with their loved ones. Imagine my surprise to open my email over break and see that there were multiple comments to the blog! Student engagement! Discussion! Microbiology talk even when a grade isn’t on the line! However, when I scanned the comments in moderation, I didn’t recognize any of the names, and furthermore they were all for a posting that I had put up almost 3 years ago. What had happened was this: @joedevon who is tech writer and developer based in California came across my posting from 2011 describing the competing commensal relationships between different Streptococcus species in the human mouth.
In the article, I was trying to point out that the web of interactions between microbes is complex, but we could conceivably tweak the interactions in our favor to promote good oral health. @joedevon found my posting via a Google search, and posted the link to the web headline aggregator Hacker News. This lead to an approximately 1000-fold increase in the number of people visiting the blog. The previous best day was in November 2011 on a day that had both a lab report due and a bonus opportunity on the blog, and there were about 120 hits from students that day and I have never come close to that number a second time. November 30, 2013 had almost 12,000 people, several of whom left comments on the blog.
Two commenters remarked about the tenacious nature of biofilms, and the difficulty of removing them. From Craig:
There’s a perfectly good, and reasonablylow-tech, way to break up dental biofilms: using irrigators like Waterpik, or similar gizmos made by Panasonic, Phillips and others. These things are really needle-jet pressure washers that blast apart biofilms that toothbrushes or floss can’t touch, on even the most unexposed dental surfaces.
and from Clay:
Green Tea is the best thing you can do other than floss and brush and maybe use an H2O2 mouthrinse. Green Tea basically disolves the plaque, and does so very effectively indeed.
Biofilms are indeed difficult to remove, and the act of physically brushing does indeed work to break them apart.
Several commenters remarked on the hold that Big Dental has on Western Society, offering insights into the controversy that public health measures bring. From Transfire:
This has been worked out before at the university of florida. It has been possible to all but eliminate cavities for ten years, but $ talks, cures walk.
and these from GogglesNinetynine and Smokes:
There is little evidence that consumption of fluoride increases tooth strength or promotes enamel growth. This is junk science that is forced on citizens because the “nanny” knows best.
…google truth about water flouridation.. it destroyes our teeth…fortunately there are companies now that started making toothpaste without flour in it…
I would point out to Smokes that gluten-free toothpaste is very important for our friends with Celiacs disease. Wait, I don’t think that’s what he meant. I’m sorry guys, but there is a phenomenal body of epidemiological data supporting that small amounts of fluoride promote dental health. The conspiracy argument suggesting that the money involved in prophylactic fluoridation campaigns is somehow lucrative just doesn’t hold water. Look, your average dentist will make far more money from extensive oral reconstruction than he or she does with a twice yearly polishing.
One commenter who passed my moderation test actually spoke to the topic which the original blog post was about; that is, is it feasible to tweak the complex interaction of microorganisms in the mouth to our advantage? Here is a link back to my conversation with Jonathan in the original post. His comment about the diffusion barrier that a biofilm presents is an interesting concept to think about. I think that small molecules might easily pass in and out of a biofilm, however larger molecules might have more of a problem.
This then shows a difficulty with one approach I put forward 3 years ago, where the use of an enzymatic mouthwash to dissociate biofilms that have formed requires that the enzymes have access to the biofilm material. If the biofilm represents a diffusion barrier for large molecules, the enzymes in the mouthwash would need to chew up the biofilm from the outside in, which might not be the most efficient method. Regardless, the tried and true methods of biofilm dissociation likely remain the best options for the foreseeable future.
BONUS: for those that have read down this far, list an organism (at least to the Genus level) that is part of the normal microbiota of the human oral cavity, and include a link to where you got that information. UPDATE! I have finished adding points into Blackboard, so I am calling time, thank you for playing!
I spotted this article in the Health Section of the New York Times; an extensive retrospective study published in the journal Clinical Infectious Diseases has found no correlation between receiving the seasonal influenza vaccine and developing the serious neurological condition Guillain-Barré Syndrome (GBS). This finding gave me great joy, and also gives me an opportunity to link back to one of my favorite Rage Stroke®-inducing BIO230 postings. The possibility for correlation arose from the 1976 Swine flu vaccine, in which the Centers for Disease Control and Prevention reported a slightly increased risk for developing GBS following receiving that vaccine, with the risk being approximately 1 case of GBS per 100,000 vaccine doses. This measurable increase led to a moratorium and reformulation of the vaccine.
An extensive investigation by the Institutes of Medicine (IOM) confirmed the increased risk of developing GBS with the 1976 influenza vaccine, and although several theories were put forth to explain the potential correlation, the cause remains unclear. One possibility hypothesized in the IOM study linked above suggests that the clear association between developing GBS and infection with the bacterium Campylobacter jejuni might be to blame. Campylobacter is an ubiquitously distributed organism, however it does infect chickens, and eggs are used to produce the influenza virus used to produce the vaccine. The increased incidence of GBS with that year’s vaccine therefore might have been due to contaminating Campylobacter antigens present in the killed vaccine preparation.
The study described in the New York Times article recounts an extensive retrospective analysis of patients from a California health care system, and data examined covered more than 30 million person-years worth of medical records. In that data set, 415 cases of Guillain-Barré were observed for a total annual incidence of approximately 1 in 90,000 people in the population, a number that is very much in line with what is reported by the CDC. Out of those 415 confirmed cases, 25 of them had a reported influenza vaccine in the 6 weeks prior to developing GBS symptoms. Most of the cohort had received a flu vaccine at some point in their medical history, but had additionally had a large variety of other vaccines. The researchers recognize that the very limited number of GBS cases in relation to the large number of records examined limits the statistical power of their analysis, however no apparent correlation between first receiving a seasonal influenza vaccine and then developing GBS could be demonstrated. The researchers further affirm that during the 1976 outbreak there was a causal link between the swine flu vaccine and developing GBS, but as vaccine formulations have been modified, no further link exists. The much more likely culprit causing Guillain-Barré Syndrome is an underlying infection, most likely due to Campylobacter, which can be easily prevented by properly cooking food and washing your hands.