Thinking Hard and Deep about the Very Small: A Review of Philosophy of Microbiology

I think it is generally true that all infectious disease physicians love microbiology. However, it is also probably true that most infectious disease physicians think of medical microbiology as their handmaiden — a powerful tool that allows them to make diagnoses, treatment decisions, and predictions. Microbiology as such is something that is often neglected not only by physicians but also by philosophers of science who are often focused on “bigger” entities when they delve into the philosophical questions posed by biology.


Philosopher Maureen A. O’Malley addresses these issues and much much more in an intellectually challenging and rigorous book aptly entitled Philosophy of Microbiology. O’Malley motivates her call for more attention to the philosophy of microbiology by calling to attention the fact that microbes are the “most important, diverse and ancient life forms on our planet. The science of these organisms, microbiology, is the science of the most significant living entities and their influence on all the rest of life.” Additionally if one looks at eukaryotes, it is the single-celled protists that dominate multicellular organisms.

The book provides great amounts of information on just how important microbial life is to all ote life and is full of facts that should be kept in mind such as the diversity of metabolic pathways possessed by bacteria, the role of cyanobacteria in the Great Oxidation Event, the oxygenation power of plants being derived from endosymbiont bacteria, conversion of carbon, nitrogen fixation, and much more.

One of the most fascinating discussions in the book is that on teleosemantics, “the philosophical study of how mental content can be explained naturalistically” and its relationship with magnetotactic bacteria, that “sense” the planet’s geomagnetic field.

There are also fascinating sections that deal with the implications of lateral gene transfer (LGT), phylogeny/classification, the pangenome, and microbial “communities.” Not only does the book prompt the reader to think harder about microbiology, it prompts one to consider well-established facts from a wider context.

It’s hard to do give O’Malley’s book the justice it is due in a brief blog post but it is really a clarion call to take microbiology much more seriously from a philosophical standpoint. As she writes:

“There are no eukaryotes without mitochondria, and (within eukaryotes) no plants without chloroplasts”

“The origins of life are exclusively microbial; life until recently was exclusively microbial; life in the future will most probably be exclusively microbial too. If there is indeed life on other planets in other galaxies, it is most likely to be exclusively microbial”

For those who want to think rigorously, endlessly, and deeply about microbiology, I highly recommend the book.

Getting Sour on Lyme: A Review of Lyme: The First Epidemic of Climate Change

I devour infectious disease books however the latest one has given me a bit of indigestion. I recently read Lyme: The First Epidemic of Climate Change by investigative reporter Mary Beth Pfeiffer. I came across this book after seeing it mentioned favorably in the premiere scientific journal, Nature. I don’t share their enthusiasm for the book.

For those who follow infectious disease news, the controversies and mythologies surrounding Lyme Disease are nothing new despite the fact that they seem to multiply, become more complex, and become more insoluble day-by-day.

Pfeiffer’s book is written from the viewpoint of someone who gives a lot of credence to alternative therapies for nebulous conditions that may or may not be related to Lyme infection. The best aspects of Pfeiffer’s book are its chronicling of the increasing geographic range of the Ixodes scapularis deer tick responsible for Lyme Disease transmission and explicitly linking it to suburban reforestation plans that put people into much greater contact with ticks.

She also deserves credit for cataloging the other important infections that can be spread by the deer tick such as Powassan virus, babesiosis, ehrlichiosis, and anaplasmosis — all of which are important for doctors to consider when evaluating someone with a potential tick-borne illness.

However there are several areas with which I strongly disagree with the book. Not surprisingly, much of my disagreement deals with her disparagement of the Infectious Diseases Society of America (IDSA) and major academic Lyme Disease researchers which she basically describes as a involved in a vast conspiracy to hide the truth about Lyme. This ire is focused almost entirely on the contentious subject of “chronic Lyme Disease” — an impossible to define concept that centers on the belief that ongoing damage-causing Lyme infection continues after sufficient antibiotic therapy and merits further antibiotics, hyperbaric oxygen, or other therapies.


In this brief review, it is impossible to rebut everything she asserts (with backing from certain physicians) but I would just point out that almost every patient I have seen who has this constellation of symptoms has no objective evidence of immune system response (i.e. C-reactive protein levels are completely normal) indicating that, even if remnants of the Lyme bacteria are present, there is no inflammation associated with and hence it does not make biological sense to attribute symptoms to something that the immune system itself is not attributing symptoms to. Furthermore, antibiotic therapy — which Pfeifer discounts the danger of — is not warranted.

One of my other problems with the book is how Pfeiffer conflates different diseases spread by ticks which could be confusing to the non-medical reader. While it is definitely the case that multiple infections with tick-borne pathogens can occur in the same person, it is not the usual case and lumping them all into the “Lyme” problem makes matters worse. For example, Borrelia miyamotoi does not cause Lyme Disease — it causes a distinct clinical syndrome — as does Babesia microti. The reader is left with dread feeling that every tick bite will unleash a Pandora’s Box of pathogens upon them and that of all infectious disease threats, this is the most pressing (while she discounts the arguably largest threat of antibiotic resistance fueled by antibiotic overuse).

I also have a lot of objections to what she writes about standard testing, its limitations, and the clinical diagnosis of Lyme by its characteristic rash.

I fear this book will make the field even more contentious and give patients, who desperately want answers for their symptoms, to continue down the wrong lane lined with those will not offer any evidence-based, scientific answers or therapies.

2 Years and 10 Questions: Remembering DA Henderson

It’s been 2 years since the founder of the Center for Health Security, DA Henderson, died. Like I wrote then and last year, it is an incalculable loss to the field of infectious disease that such a giant voice speaks no more. Personally, it’s rare that I go a day without thinking about him and the wisdom he always about all things infectious.


Last year to commemorate DA, and concretize how pressing public health and infectious disease issues are, I listed things that happened since he died that I — and the world — desperately needed his expert opinion about. So in that spirit, here are my new set of questions for DA.

1. What do you think about Russia and the current state of their former bioweapons program? There’s been a recent book about this topic and you personally debriefed some of the highest level defectors from the Soviet Union. Also, Putin has shown no qualms about using Novichok agents (as well as dioxin and polonium) so is their anything different about biological agents?

2. What’s your take on the number of food borne outbreaks? We had cyclospora and a big E.coli outbreak this year. Is it that surveillance is capturing what we never knew about or is the risk increasing or is it both?

3. The cholera outbreak in Yemen is the biggest ever and compounded by war. How would you tackle it? You dealt with conflict when you eradicated smallpox. Would you advise vaccines? Antibiotics? 

4. Back-to-back Ebola outbreaks have occurred in the DRC. The first one came and went but the second is a lot more scary because of the conflict zone in which it occurred. The vaccine seems excellent and was used in the ring vaccination manner — which you developed to beat smallpox — but they can’t find the contacts of cases so well in this 2nd outbreak. Should they just blanket immunize ? What priority should vaccination have when you can’t do contact tracing? 

5. Measles elimination in the Americas is no more. Venezuela and their totalitarian government have seen outbreaks of malaria, diphtheria, and now measles transmission for over a year. How can we fix this? You were never a fan of eradication and now it seems measles, which was on the list, is slipping away. 

6. We had a bad seasonal flu year and it had hospitals inundated. We seem no where near able to cope with a pandemic and H7N9 looms. I know you don’t have an easy answer but when this pandemic occurs not having you to lead will make it much worse.  

7. We have a new smallpox antiviral. I know you had issues with this drug and didn’t have a good idea for how it would be used and definitely opposed it’s research program being used as an excuse not to destroy the samples of the virus but it’s here now. How should we use it? Individual cases? The vaccine should still be the cornerstone of response, right? 

8. Horsepox was artificially synthesized in the quest for a better vaccine. I know you would  have something to say about that. The standard vaccine’s cardiac side effects weren’t something you thought was significant enough to scrap it and this is the reason cited for the horsepox version. There’s also the debate about this event lowering the threshold for those who want to synthesize smallpox. What do you think about all this? We really missed your voice on this.

9. Polio eradication is still faltering. Just Afghanistan and Pakistan have wild cases and it looks like type 2 polio is gone the way of 3 and we’re just contending with type I. The Taliban hasn’t stopped their anti-vaccine push either. People are getting hyper about vaccine-derived cases and we’re still using the Sabin vaccine in many parts of the world. I know you taught me to think of vaccine-derived cases entirely separately and I’ve been saying that to people. This is the way to do it right? Wild polio first then switch to Salk and deal with vaccine-cases separate, right?

10. What do you think about my Pandemic Pathogens report? I know this is my own vanity but I spent a lot of time thinking about this topic and really want it to impact the field. It hopefully would be something that would make you proud of the time you spent teaching me. 

As is apparent, DA’s intellect is needed just as much now as it was when he beat smallpox off the planet. I don’t know if humans will ever produce another DA. It seems like a dream that he existed, but we should all remember him and how the insoluble problems of infectious diseases fell away when his mind faced them. 

Why People Wore Penile Sheaths: A Review of Deadly Companions


I recently read a book that somehow escaped my attention when it was first released 11 years ago: Deadly Companions: How Microbes Shaped Our History. This book, by the University of Edinburgh's microbiology professor Dorothy Crawford, was just released in an updated edition. To someone like me who is completely obsessed with this subject, I increasingly approach books in this genre with a bit of apprehension because the value-added aspect of each additional books is less and less. However, Deadly Companions is a book which I found valuable. The book consists of 8 chapters plus a preface, introduction, and conclusion. Chapters are not organized around specific microbes, but forces that propel microbes to cause epidemics and disease such as crowding and famine; other chapters are devoted to explaining the dominance of microbial life on this planet. 

A few important tidbits that particularly stood out to me from the book include:

  • The use of penile sheaths to protect against schistosomiasis which was erroneously, but reasonably, thought to enter the body through the penile opening (it really enters via penetration of the skin)
  • An enlightening discussion of the fungal-caused potato blight responsible for the Irish famine
  • A great thought experiment concretizing the impact of travel on infectious disease: charting the travel patterns of your great-grandparents, grandparents, parents, and yourself

I recommend Deadly Companions for a short and enlightened -- but still comprehensive -- overview of infectious diseases of the past, present, and future. 

Where the Wild Things Are: Polio and Vaccine-Derived Polio are Distinct Issues

One of my major pet peeves with infectious disease reporting is the conflation of polio with vaccine-derived polio. While both conditions can be severe and paralyzing, there's an important distinction that is missing from headlines announcing the "return of polio." 

Vaccine-derived polio is a known and expected risk so long as the Sabin oral polio vaccine is used. The Sabin oral polio vaccine has many advantages that have favored its use: it's given orally (no needles), it's cheaper, and it's "live". This last is important since the vaccine is given orally and replicates in the GI tract -- just like the untamed wild strain of polio -- it more closely mimics natural infection. It is also shed in the stool and others are, in effect, vaccinated upon exposure. On the contrary, the injectable Salk vaccine does not prevent viral spread as the vaccinated are protected against paralytic polio but are still able to be infected with the wild virus, but only in their intestine, and are able to pass the virus along.


However, these advantages are a double-edged sword as the virus, which has been weakened, can mutate its way back to its original virulence level and paralyze someone (vaccine-associated paralytic polio, VAPP) In rare circumstances, the altered vaccine virus can circulate and cause outbreaks as a circulating vaccine-derived poliovirus (cVDPV) -- this last usually requires recombination with a non-polio enterovirus. Usually the impact of cVDPVs is delimited because of population immunity. This paper provides a great overview of the phenomenon. 

The risk of VAPP, in the US, became too much to bear and the US slowly changed recommendations and moved to an all injectable Salk regimen several years ago. The global eradication program will eventually phase out the oral vaccine as well.

What is missed by the recent headlines is the fact that so long as oral polio vaccine is used there will always be a risk of VAPP and the emergence of cVDPVs. I think that the eradication of polio should be restricted to the eradication of the wild virus -- something my mentor and smallpox eradicator DA Henderson insisted upon. cVDPVs and wild polio are distinct problems. Wild polio continues to spread in only two countries: Pakistan and Afghanistan, where a dozen cases have occurred so far this year. cVDPV outbreaks in the DRC, Somalia, and Papua New Guinea are important problems but should not, in my opinion, be considered on the same level as wild polio virus infections.