Category Archives: Rant

York, PA Ebola worries!

Presentation1Spoilers! Ebola worries are non-existent for us in South Central Pennsylvania. However, according to an email I received this week might lead one to believe that the risk is far, far worse. A notice to staff, faculty, and students at York College requires that anyone planning on traveling anywhere outside of the United States through the beginning of March 2015 self identify themselves to the Health Center, and monitor their temperature for the 3 week Ebola Hemorrhagic Fever incubation contagious period. The notice also contains several editorialized Ebola facts, which unfortunately convey a sense about the risks of contracting Ebola virus that are perhaps a bit exaggerated.

A posting in the Atlantic Monthly gives a concise summary of our current understanding. There is no indication today, and there never has been, any evidence to support the hypothesis that Ebola viruses can be transmitted between humans via any indirect means. Ebola virus is what is known as an enveloped virus, and contains a genome made of RNA; consequently, intact virus particles with these characteristics are unable to survive in an infectious state outside of a mammalian host. As a result, in contrast to many bacterial pathogens, inanimate objects (fomites) in the environment are very poor reservoirs for these types of viral pathogens, although virus shed via sneezing does pose a temporary risk.

Distinction between droplet and airborne transmission, via the Virology Down Under blog

The one study that examined the possibility of airborne transmission found that transmission between infected pigs and non-human primates can occur in specialized situations. This study has a big caveat (and indeed was followed up with an additional study to address this), in that in pigs Ebola virus has a hugely significant lung involvement, resulting in massive amounts of the virus in respiratory secretions. This doesn’t happen in primates, which show mainly hemorrhagic disease. The followup study looking at primate to primate aerosol transmission found no infection between test animals. Because of the very nature of Ebola virus in comparison to many respiratory viruses, we are not likely to see a change in these properties.

What about the risk to York College community members who are planning on traveling overseas in the near future? The Centers for Disease Control and Prevention and the Pennsylvania Department of Health remain the best sources of information to assess the risks of this scary disease to the general public. The CDC in fact has a page devoted to precautions that are recommended for college students planning travel abroad. All of these precautions are directed towards travel to those countries where the Ebola outbreak is occurring (Guinea, Liberia, Sierra Leone). The CDC also has a page which clearly indicates epidemiological risks for contracting Ebola virus for use in evaluating whether an individual has potentially been exposed.  Class 4–No Identifiable Risk is indicated for persons traveling to a country without widespread Ebola virus transmission–this includes travel anywhere besides Guinea, Liberia, and Sierra Leone. Persons traveling to the Democratic Republic of the Congo should practice enhanced precautions, however the CDC risk assessment is very low for travel there. The Pennsylvania Department of Health echoes all of the CDC guidelines, and as of 27 October 2014, is monitoring a total of 105 residents of the Commonwealth who are considered “at some risk” for exposure to Ebola virus, due to recent travel to one of the afflicted countries. These individuals are being monitored for potential exposure to Ebola by local and state health officials.  As indicated on the PA Department of Health page, travel into Pennsylvania from any other international origin is NOT considered a risk factor for Ebola exposure.

There is an awful lot of poorly cited information circulating and straight out disinformation about this epidemic at present. Advocating unwarranted steps in screening for potential exposure when the risk is non-existent creates an atmosphere of uncertainty, and this can be damaging in the long run. I urge all BIO230 students to follow the links they see on the Internet, and check to see whether they represent experimentally-supported science, or merely reflect someone’s opinion.


Keeping viruses at bay

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!”

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 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.

Measles, now at epidemic levels

I saw this story at, 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!

No commentary necessary

ImageVia the I (really, really) Love Science Facebook page. If you find this amusing, then follow that page, and additionally follow the web comic Saturday Morning Breakfast Cereal, because it is awesome.

Science denialism

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.

Brushing your teeth is still controversial

A pretty graph

All time BIO230 blog stats since mid-2011. The two peaks to the right are due to two days only, November 30 and December 1, 2013.

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.


Biofilm (Photo credit: AJC1)

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!

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