Disease, insects and broadaxes – a tale of an old book

By Jonas Waldenström

With three kids, and the youngest a toddler, there isn’t much room for daring adventures. At least not for a few more years. But I don’t mind, in fact I have learned to appreciate the adventures that take place on a smaller scale. Instead of twitching a rare bird in a remote place, I do patch birding in the garden. Instead of climbing steep mountains (as if I ever did), I climb up and down ladders painting and repainting old windows. But the best for sure is to see the world through the kids’ eyes, where a strangely shaped little rock, a big spider or a bee can be absolutely enthralling.

One thing we do, however, is to visit flea markets. One our favorite is in a nearby village, just 15 minutes by car from our summerhouse. The kids skim through the baskets with old toys, my wife scouts for various decorative things, and I search for old everyday stuff, such as forged nails, handmade wooden planes or broadaxes. (Especially broadaxes, but they are rare). Today was no exception, and after half an hour we have gathered a little hoard of stuff that appealed to our various interests. In my pile was a hundred years old pitchfork, some wrought hooks and a little book with the title Insekter och sjukdomar.

That book turned out to be a nugget. It was originally published in 1910 by the entomologist Rennie W. Doane, and my copy was a translation published in Swedish in 1912 by Ivar Trägårdh. The full title is Insects and Disease – A Popular Account of the Way in Which, Insects May Spread or Cause Some, of Our Common Diseases. Perhaps not a title for everyone, but for me that do research on infectious diseases it had much promise. And yes, better than expected, reading this book turn out to be a fantastic journey back in time to when modern medicine was in its infancy. I was mesmerized, and read it in one go, cover to cover.

Rennie W Doane (downloaded from XXX)

Rennie W Doane (downloaded from Bishop Museum’s list of dipterist, [hopefully under fair use])

You see, we tend to take things for granted, and although we know that things change and new knowledge unfolds, it is still far too seldom we think about how the world was just a hundred years ago. Yes, we read about WW1 in school, and yes, we sort of understand that it was poorer, more rural, more potatoes and turnips, but we (or at least I) don’t really think about the state of medicine around the turn of the second last century. There are exceptions, of course, such as the growing literature on the Spanish Flu, or Maryn McKenna’s excellent texts on pre-antibiotic medicine. And I have through my teaching read up a little on the old scholars, such as John Snow (the founder of epidemiology, the Broad Street pump-handle remover), or Edward Jenner and variolation of cowpox and smallpox, but there is so much more to reread and learn.

So what does this book tell us? Written in 1910 it was published in a time when great medical breakthroughs came one after the other. The idea of foul air, or miasma, as cause to diseases had lost to the germ theory some decades before. Bacteria and protozoa could be studied under the microscope and the experimental and critical thinking inspired by Koch’s postulates led researchers to discover more and more etiological agents to diseases. Anthrax and tuberculosis were known, and the life cycles of the blood parasites Plasmodium (malaria) and Trypanosoma (sleeping sickness and nagana) had been studied in detail (although they seemed not to have realized the asexual schyzogony part that takes place in the liver).

The most striking part is actually what is not in the book. Today we know that viruses cause some of the worst insect borne diseases, such as Dengue, Yellow fever, or Chikungunya – but there is not a single description in the book of an insect borne viral disease. Yellow fever is discussed in length, but the causative agent was not identified; it was by many presumed to be bacterial, but the author raise the hypothesis that it may be a protozoan, perhaps related to spirochetes (which is, in the rearview mirror a double fault, as spirochetes such as Borrelia are indeed bacteria, and the causative agent of Yellow fever the aptly named Yellow fever virus). It has to be remembered that virology is one of the youngest medical disciplines, viruses were simply too small to be seen with the microscope. Actually, Tobacco Mosaic Virus – the first described virus in 1898 – was described based on the fact that it was infectious after being filtered through a porcelain filter that excluded bacteria. They couldn’t see TMV, but they could observe the disease it caused in tobacco leaves and prove that it was contagious. It wasn’t until 1927 that Yellow fever virus was identified and described.

Another notable thing in the book is the very strong belief in science as a way of reducing the suffering of mankind. Scientific progress didn’t come lightly, and many of the scientist that tried to identify and find cures to diseases actually succumbed to the very disease they studied. Moreover, human ‘volunteers’ – often convicts – were used to establish disease causality. The methods were grizzly and morally questionable (even in that time), involving exposure to sneezes, coughs, bodily fluids, blood or vomits from sick patient to healthy study people. Abhorring methods, but they stemmed from believed necessity in a time when infectious diseases caused devastating outbreaks, and where no counter measures except quarantine and hygiene were available.

And even in our age there are lessons to be learned from 1910. In the last century humanity invented vaccines and antibiotics to fight disease, and pesticides to fight the insect vectors. It worked brilliantly to start with, but the once powerful tools became blunt when the pathogens and the insects evolved resistance. It is interesting to be reminded that the Yellow fever scourge that stopped the Frenchmen to build the Panama Canal was effectively fought by rather simple means by the Americans later on. Knowing that it was an insect borne infection (but without knowing the causative agent), clear-cutting the forest around the canal and targeting the specific mosquito that transmitted it by limiting standing water sources in and around houses, Yellow Fever could be managed down to a very low level. These are methods that work well today too, for instance for West Nile virus eradication in the US, or for limiting malaria transmission in rural Africa. When the big guns don’t work, we need to look for other means.

Finally, and a clear example of a rapidly changing world, I found out that the book has been digitalized and can be accessed for free. Go ahead; download it to your computer, or even your Kindle. And the next time you go to a flea market, don’t forget to look for books. And broadaxes.

One cannot simply have too many axes...

One cannot simply have too many axes…

 

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A paper a day keeps the doctor away – advice for surviving in academia

The academic sea can be rough at times. (Photo by the Royal Navy under an Open Government License)

The academic sea can be rough at times. (Photo by the Royal Navy under an Open Government License)

By Jonas Waldenström

As a teacher and supervisor I meet many ambitious students that want to pursue an academic career. But how should you navigate your boat through the rough and stormy sea of academia? What lessons can be learned from earlier travelers?

This is my list for you:

  1. Don’t listen to advice (or at least filter them). This is the first and probably most important advice – kind of the Fight Club rule of academia. But why? The truth is, there is no single road to the Ivory Tower (if that’s where you’re aiming). Yes, there are some patterns, but everyone up there came through a different route; a path unique to them. On top of that, those whose advice you so eagerly seek were students in another time. Some things may have stayed the same, but other things have changed. Think of it this way: they (and me) are dinosaurs and you are a furry mammal.
  2. If you read this you have already failed to follow the first advice. That’s good, you’re learning to be independent. Keep on reading if you want, but don’t say I didn’t warn you.
  3. Find your balance. Don’t work yourself to pieces. Deep inside I think we all know if we work too much. Listen to that voice, and you’ll live happier. People will pretend they work hard ALL THE TIME, but no one can do that for longer stretches of time. It’s just impossible.
  4. Publish where you want. Use your own criteria for determining the target journal for your manuscript. If you are pro open access, weigh that in. If you aim for highest possible impact journal, do that, it is all fine. Many professors talk about ‘society journals’ as a publication therein has an intrinsic value. But who knows how the publishing world looks in the future, with all the novel publishing initiatives such as PLOS, PeerJ, Peerage of Science, and F1000 to rock the scene? My best advice is to read the aims of the journal before submitting, and format the manuscript as they say you should. And write well. That’s time well spent.
  5. Try not to be an ass. For your own sake, and for others. Life in academia would be much better without the rivalry between colleagues.
  6. Don’t be bitter. Please.
  7. Don’t drink too much. You’d be surprised how much alcoholism there is in academia.
  8. Keep up with the literature, but don’t bring home a pile of papers each night. Actually, ‘one paper a day, keeps the doctor away’ is a good slogan.
  9. Have fun.
  10. Read number 1 again, and heed it this time.
A cohort of prospective students wishing to embark on an academic career.

A cohort of prospective students wishing to embark on an academic career.

In case you wonder, I have not adhered strictly to this list myself. I have definitely been an ass a few times, and regretted it. I have tried to work long hours, but blessedly having three kids stopped that. I was very journal-obsessed, but that has dwindled with time. I read less than I should, but am working on it. I have fun, and really, really try to stem feelings of bitterness when things don’t work out as I had hoped.

Live long and prosper, folks.

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My, my, hey, hey – (I wish) natural history was here to stay

Is natural history heading down the Dodo track? ("Dodge the dodo" by Elian Chrebor at Flickr, used under a CC BY-NC-ND 2.0 license).

Is natural history heading down the Dodo track? (“Dodge the dodo” by Elian Chrebor at Flickr, used under a CC BY-NC-ND 2.0 license).

By Jonas Waldenström

We all love our Darwin. The quiet little man who changed the way we perceive the world around us. A bearded gentleman who laid forth the simple, but elegant principles of evolution by means of natural selection. What is less known is that he spent years studying barnacles, classifying the shells of specimens sent to him from collaborators around the world. Partly, I guess, because he liked these strange animals – but also because that in Victorian England you proved your worth in science by careful natural history studies, and preferentially studies of marine animals.

Goose barnacles. (Picture from Wikimedia Commons by M. Buschmann used under a Creative Commons Attribution-Share Alike 3.0 license).

Goose barnacles – delightful kritters that Darwin studied. (Picture from Wikimedia Commons by M. Buschmann used under a Creative Commons Attribution-Share Alike 3.0 license).

Who study obscure animals these days? Is there a career in a more descriptive science? Who measures the sizes of thousands wasp genitalia, surveys the distribution of barklice in the boreal forests, or studies the nesting behaviors of Eiders? Not too many it seems. Natural history is slowly vanishing at the universities, and even though there are many scientists pointing out that natural history research is the foundation of most other scientific disciplines, there is still a long-term downward trend. There are cooler things for a prospective graduate student to work with. If you can sequence a genome in a day, why bother characterizing the everyday life of isopods under rocks for four years? When only a fraction of every PhD cohort makes it all the way to faculty positions, natural history research often end up on the wrong side of the cut. Natural history research is under-funded, collections at universities are not managed (or are even tossed out, or given away), and less and less of a biology student’s curriculum is devoted to identifying species and how to make notes on natural phenomena.

Actually, natural history isn’t doing very well in ordinary society either. We see an increasing ‘biological illiteracy’. When Swedes on the street were asked to identify the leaves from the most common deciduous trees – like ash, oak and birch – most people got them wrong. This was especially true for younger people. Perhaps it is inevitable that urbanization puts people more and more at distance with nature – but as someone interested in birds, plants and animals it is a disheartening trend.

So what can be done? At a structural level funding needs to be secured, and universities need to realize that taxonomy, field ecology and identification are important skills to teach and research in. Specialists are needed, and they need to have funds and means to conduct their research. However, at a personal level – as non-natural history scientists or amateurs – we can also do our part. I started my science track at a bird observatory – a great way of learning a lot about birds – which led me to write several studies on bird migration phenology, habitat preferences, and moult patterns during my early years at the university. I got great help from more experienced scientists, and valuable training in the arts of science. In turn I nowadays help young birders with their studies, either at the bird observatory, or as a supervisor for undergraduate students. If you are in a position to help students, you should do that. Perhaps in the process you are nurturing a coming star in science.

And if you are a birdwatcher, an amateur herpetologist or a botanist, put your observations in one of the growing data repositories (for an example see Artportalen – a Swedish database for observations), where they can be accessed by others. And don’t forget, bring your kids, friends and foes with you when you go to the field – perhaps you can inspire someone to become more interested and knowledgeable in nature. For in the end of the day, what is nature if we don’t know what it is we see? A mere postcard.

For more on natural history, read this editorial in Nature, or jump to the Natural History Fridays initiative by Alex Bond at The Lab and Field (where you also can learn how thick Murre eggs really are).

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The rise and fall of avian flu research

By Jonas Waldenström

You’d be surprised how much of science that goes in and out of fashion. A certain topic may become hot for a time, go through a burst of development and then either stagnate, branch out in a new direction, or just vane into oblivion. These trends can be broad and slow, as say for instance a shift from behavior ecology to conservation biology, or very narrow from one bacterial protein to the next. Examples of recent trends in biology include epigenetics and CRIPRs, that currently seem to grow exponentially.

The figure below is a good illustration to a thought that has lingered with me for some time: have we reached peak avian flu? It comes from a recent PLOS ONE paper by Sarah Olson et al that investigate sampling strategies and biodiversity patterns in avian influenza viruses. It is a very nice paper, and I hope to return to it in a future post. But for now I stick with this single figure (actually it was hidden in the supplementary files), as I find it highly interesting.

Decline in subtyped AIV sequence submissions to GenBank in both poultry and wild birds. From Olson et al. 2014 PLOS ONE.

Decline in subtyped AIV sequence submissions to GenBank in both poultry and wild birds. From Olson et al. 2014 PLOS ONE.

So what does the figure say? It looks like a population fluctuation plot of the introduced reindeers on St. Matthew Island; a sudden increase followed by collapse (for a great comiv see here). But it is not. It is a graph that shows the variation in the number of sequences with know sample years submitted to Genebank from 1979 to 2012 divided on wild birds and poultry. As can be clearly seen, flu sequences from the early years are few. In fact, they don’t start to rise in numbers until 2004/2005. Then there is a massive peak followed by a large decline. Interestingly, these trends follow the natural history of H5N1, which is also depicted in the figure.

If you remember your flu history, you will recall that H5N1 hit Europe in 2005, making a very swift journey from SE Asia through Russia to Europe, and then south to Africa. But it didn’t start then – the first cases occurred in Hong Kong already in 1997, but for the first couple of years it was an all Asian affair, that didn’t involved western research labs. Our mallard study started in 2002, quite timely if you look at it in retrospect: before the big boom, so to speak. In the first years our research on low-pathogenic avian influenza viruses (the milder cousins to H5N1) mainly interested those already in the field, but after 2005 the interest exploded. Avian flu was hot, and our research was highly warranted – not only by researchers, but more so from policymakers, governmental bodies, and media. It was a raving storm for a time.

At that time many labs jumped onto the bandwagon and for some years many things happened at once. The European Union funded surveillance schemes in all member countries, the US and Canada launched big schemes as well, and even Africa became involved, with sampling in several sub-Saharan countries orchestred through the French research body CIRAD. Everyone was looking for H5N1, but few found it. Fortunately, they found a lot of low-pathogenic viruses and some great studies were made (and some less great, too) but as time passed the bars for publication became higher, funding agencies were more reluctant to give out money, and many scientists left for greener pastures elsewhere.

Having spent time in different research fields, such as ecology, parasitology and virology, it is striking how often the virology field jumps from one virus to the next. During my time we have seen SARS, H5N1, Bluetongue, Schmallenberg, Ebola, MERS, and Chikungunya. It remains to see what happens in the years to come. H5N1 is not gone – it is endemic in parts of Asia and in Egypt – but not at present occurring in the EU or the Americas. And during the last two years new avian influenza viruses have caused human infections in Asia, and it is clear that there is much more we need to understand regarding this extremely important zoonotic pathogen. And especially, we need to study the viruses before they pop up in the human population.

Link to the article: Olson SH, Parmley J, Soos C, Gilbert M, Latorre-Margalef N, et al. (2014) Sampling Strategies and Biodiversity of Influenza A Subtypes in Wild Birds. PLoS ONE 9(3): e90826. doi:10.1371/journal.pone.0090826

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