I like weighted maps and infographic maps in general for their instant impression and information they convey.

This example below shows deaths from malaria in 2011. The world malaria day website says that Nigeria and the DRC account for around 40% of malaria deaths out of the 97 countries where malaria transmission still occurs.

Alternatively, this infographic displays the wealth of nations. Malaria prevention and treatment costs money. Something to keep in mind.

Just back from the outstanding Evolutionary Medicine meeting in Phoenix, Eleanor’s inspired waffle post reminds me of one of the messages rap artist Baba Brinkman delivered at the meeting in the debut performance of his new album The Rap Guide to Evolutionary Medicine [I know, what are scientific meetings coming to?].

Performance, feedback, revision…. That is why science works. It is also the recipe for how to get better at doing science – and, evidently, waffle-making. And, by coincidence (?), it is also how natural selection works.

The newest additions to my kitchen.

A good friend of mine recently sent me this book, titled “Will it waffle? Yes it will!”. I love this book. In addition to the recipes for waffled tostones, waffled sweet potato gnocchi, waffled squid salad, and waffled waffles, I love the optimism inherent in the title and honestly, in the very premise of this book. An optimism that runs through the last section, where the author closes with:

“Is there anything that won’t work in a waffle iron?” I get this question a lot. I’m not sure how to answer it. Sure, there are things that won’t work in the waffle iron. Soup. Daquiries. Ice cubes. But more than anything else, this is what won’t work in the waffle iron: giving up. Some of these recipes didn’t work the first time I tried them. Or the second. The ice cream sandwiches fell apart or were hard as bricks. The maple butter burned. The waffled fries were neither very waffled nor very much like fries. That’s why we test recipes – again, and again, and again – to get them right. When it comes to trying your own recipes, persevere. I’ve had epic meltdowns – so have my waffles irons. The only thing all of these mistakes had in common was that they didn’t stop me from trying again.

Words to live by, both insides and outside the kitchen. Maybe next time that science gets me down, I will find inspiration in these words. And if not, I can always bury my sorrows under waffled apple pie.

Sometimes I poll people on questions I don’t have an answer to because (1) it is an easy way to crowd-source my internal moral dilemmas and (2) it makes for more interesting conversation than talking to someone about the weather. My most recent poll question of interest: which is worse smoking a cigarette or eating a slab of meat? The results are very one-sided. Everyone I’ve talked to says the cigarette is worse*.

This confuses me. Smoking meat-eaters say the cigarette is worse. Smoking vegetarians say the cigarette is worse. People that abstain from both practices say the cigarette is worse. I thought the question would generate multiple answers but instead it was unanimously answered with the same answer. Chose the meat.

I thought maybe people would ask what metric I was considering: Environmental health? Personal well-being? Degree of venial sin? No one asked because no one cared. Everyone seemed to think that always, all the time, regardless of serving size or frequency, cigarettes are bad and meat is good. It feels a bit like grading student quizzes and everyone answers the question “wrong” with the same “wrong” answer. Are they cheating or am I missing something?

I am probably missing something.

Cigarettes are bad for your lungs. Yes.

Cigarettes are also bad for life expectancy, the cardiovascular system and littering sandy beaches. With the exception of the sandy beaches, sitting down for extended periods carries most of the same risks. If we consider other bad habits that we humans love, smoking seems on par with death risks and the healthcare burdens associated with not exercising, food overindulgence, stimulant use, driving too fast on interstates and being stupid.

What about meat-eating? Last year an article in Cell metabolism reported that people who eat high-protein meat-based diets have a “75% increase in overall mortality and a 4-fold increase in cancer death risk” based on data from middle-aged Americans. Yet meat-eaters don’t experience social stigma for their dietary choices.

Meat eating also is associated with tremendous amounts of water waste, methane production, and according to an FAO report accounts for “65 percent of human-related nitrous oxide, which has 296 times the Global Warming Potential (GWP) of CO2.”

It would take a lot of second-hand smoke to release the same amount of atmospheric pollutants. So why do we hate on cigs but support the beef?

My best answer is media brainwashing: ads that relate to cigarettes are sponsored by organizations like the American Cancer Society and meat ads are sponsored by the meat industry.

*One exception was a respondent who replied: “Both sound good.”

Thanks for all of the great suggestions in response to my last post. I plan to pull most of these books from the library’s shelves. That is, excepting “Adaptation and Natural Selection”. I have ordered my own personal copy of this book so that I can mark up the margins with impunity.

I have two new officemates today.  Apparently, my previous officemates  failed to return their keys, and so my new officemates won’t have keys until new ones are made.  How long does it take to make a key?  The estimate was two months.  Two months.  For a key.  Seriously.

I could probably sculpt a working replica of my own key out of stone faster than that.  And it would probably be cheaper for the University.

Below is an excerpt I lifted from the most recent issue of The Sun Magazine, which is an interview with Daniel Lieberman, a biology professor who studies why the human body looks and functions the way it does.

Jaw size develops in response to use, and similarly, Lieberman suggests that the immune system grows to meet demands as well. My question: How much immune exposure is too much? If you’re sick all of the time, when do you have the time or resources to grow? This “use it or lose it” theory must come with some moderation and with balance. Also, does this demand change with age? (Are older people less exposed to germs and become more sick as a result??).

(below: credit to The Sun Magazine, March 2015)

Frisch: In your book you say that “to grow properly, almost every part of the body needs to be stressed.” What do you mean by “stressed”?

Lieberman: When you’re born, your body doesn’t yet know how much it should develop any particular organ. How large should your liver be? How strong should your bones be? How much muscle should you have? How big should your heart be? There’s a normal range of variation for each, of course, but we can’t predict in advance from a person’s genes exactly how everything will turn out, because our bodies grow in response to stress, by which I mean excess demand on the system. The body adjusts its capacity according to demand. […] Your immune system, too, responds to demand, and when you decrease that demand — as we have done by creating relatively germ-free environments — the system loses capacity. If you’re not using something, your body sort of “decides” you don’t need it, and gives it fewer resources. With all the modern conveniences that we’ve created for ourselves, we’ve reduced demand to the point where we have weak hearts, weak bones, and various other problems.

We also process our food so much — grind it, purée it, cook it — that we chew less. When we don’t use our jaws as much, they don’t grow as long. Over time our faces have actually shrunk.

Frisch: Is that why people don’t have room for their wisdom teeth?

Lieberman: That’s right. There’s just no room for the last teeth to come in because we don’t chew our food as much. We’ve done experiments in which we’ve raised animals on soft diets and shown that their jaws don’t grow as long. There’s no question that impacted and crowded teeth are more common today because we eat so much cooked, chopped, and ground-up food.

I am interested in reading some good books on the theory of evolution. In particular, I am looking for good candidates for my night stand.

It seems that the natural place to start is at the beginning …… but before surrendering myself to Darwin’s tome, I thought I would canvas the group for suggestions.

One esteemed colleague of mine recommended “The Beak of the Finch” by Jonathan Weiner. The virtue of this book is that it provides a bird’s eye view of the landscape of evolutionary theory. Although it is a popular science book, and so won’t discuss the finer points, it should give a nice road map and help me plan where I would like to stop and explore the theory in more detail.

I have placed a hold on this book and look forward to some enjoyable nights of reading.

What are your favorite books on evolutionary theory?

I am often fascinated by how similarly everybody thinks.  For example, people have a harder time comparing fractions than comparing decimals.  If I asked which is larger, 3/25 or 7/56, you would almost certainly have to think before answering, whereas you likely wouldn’t be challenged at all if I had asked the same question in decimal form (0.12 vs 0.125).

My more recent fascination comes from an observation in games like charades and pictionary.  Why is it so easy to depict an adjective (for example, blue or happy) but so hard to depict an adverb (for example, quickly or sadly)?  How much of this difference is cultural and how much of it is hard-wired into the way humans think?  Would an intelligent alien species have the same bias?  Apple’s advertising slogan used to be, “think different”.  I wonder if it might be possible to train people in science to instead “think differently”.

Around this same time last year I wrote a blog on the subject of whether drug resistance evolves as readily against whole plant medicinals as it does in response to single component drugs — “Before drug resistance was there plant resistance?”

My question has been partly addressed by findings PNAS published in December (Elfawal et al.): “using the whole plant (Artemisia annua) from which artemisinin is derived can overcome parasite resistance and is actually more resilient to evolution of parasite resistance; i.e., parasites take longer to evolve resistance, thus increasing the effective life span of the therapy.”

Steve Buhner has touted that whole plant medicinals act as the original combination therapy for years. Perhaps a more surprising result would be to find a case where the opposite is true — anyone know of a plant where efficacy of an active component might be masked in whole plants because of the presence of antagonists rather than agonists?

Artemisia is not the only plant that herbalists have argued could be acting as combination therapy and this presents an interesting idea that Dave and I were discussing at the bar last night: why should plants contain more than one compound that acts against a human parasite?

My best answer is that perhaps plants that are better suited for treating malaria (i.e. wormwood, cinchona bark) are plants that have evolved defenses to plant-infecting protists that are like a plant-version of malaria.  Plants that are used as herbal antibiotics may be the plants that historically were more likely to succumb to bacterial infections and thus have multiple defensive compounds that target bacteria, whether human-infecting or plant-infecting. How many human infections may have a look-alike plant infection? And could understanding which plants are exposed to and have defenses against certain plant diseases help predict which plants will best function in fighting a complementary human disease?

I’m reading more of Steve Buhner to try and gauge the extent to which this could be true. If anyone else is interested, I’m happy to lend a few of his books: Herbal Antibiotics and Plant Intelligence and the Imaginal Realm.

Fun fact about Buhner: his great-grandfather, an herbalist from Indiana, became the Surgeon General of the United States under Eisenhower and Kennedy.

I want to bring attention to the recent measles outbreak. Pennsylvania is one of the 14 states where measles is spreading right now. This map is from February 2nd, 2015, only 4 days ago.

I imagine these numbers have changed already, and will continue to increase.

The “epicenter” for this 2015 outbreak is Disneyland in California, a tourist destination.

There’s a lot of emotion about vaccines. This physician’s impassioned blog communicates these feelings and also why not everyone can be protected by vaccination. Age is common reason – those under 1 year old have weakened immunity and can’t receive the MMR vaccine. That’s roughly 120,000 kids in PA, or roughly 4,360,000 kids in the USA. To count this many kids by saying numbers aloud would take more than 100 days with non-stop counting day and night. That’s a lot of people who can’t be vaccinated against measles.

To establish herd immunity we need enough converts to get vaccinated. Pennsylvania is ranked the second worst vaccination rate for the MMR vaccine in the country, roughly 10 percentage points lower than the 95% required for herd immunity.

On my mid-morning visit to the post office last week, I met a former student of mine. We greeted each other enthusiastically, I was really pleased to see him. Despite not being a star student, he had nevertheless really tried – just the attitude you want. For weeks in a row, he had come to my office hours with good questions and talk of his ambitions to be a neurologist. The first question I asked him in the queue was, ‘So, are you doing research?’

I doubt he was surprised. Just as when I worked in a library, it was my mission to convert just one child from free DVDs to free books, when I TA a laboratory section I aim to get a few of my students doing research. The first time you mention it, they look at you like you’re crazy. But I try to make the idea of undergraduates doing research normal. When we review micropipetting I teach them ‘tips and tricks that would be really useful if you join a lab’. I introduce new topics by referring to Penn State faculty that work on the subject ‘if anybody’s interested in finding out more’. Particularly with the students that struggle, I tell them that research would increase their confidence. Now, come the fourth week of the semester, students have started to hang behind after class or send me emails to ask me about getting involved with research. The main things they say are ‘I don’t know how to go about it’ and ‘Is it too early/too late to start?’.

The last question is easily answered with a quick ‘absolutely not’, though I’m of the belief that the earlier a student starts working in a lab, the better. And how to get into research? It seems so simple: just google ‘Penn State’ and the subject you’re interested in, read the faculty members’ blurbs, choose one, make sure they don’t have an ‘undergrads not welcome’ sign on their door and send them a short email. The problem is that most of these students can’t imagine what ‘research’ looks like, let alone think it’s for them. They are astounded when I tell them that really, it’s as simple as that. Some of my students just need to hear what my Mum always told me, ‘Go for it! The worst they can do is say no’. The thanks I receive from students for doing the googling step for them and emailing along the results, are incredible. In terms of the time-invested: satisfaction ratio, this ranks pretty highly.

And so to the guy in the post office. He was queuing up to send off an application for a summer research project at another university. Just the previous week, he’d started working with a professor whom I rate very highly and was due to start running an experiment with him, working one on one, that weekend. In this student’s case, I don’t know if I had a role in making this happen but I was delighted, anyway. One more for research!

Last week, Matt forwarded me an e-mail for a “careers in tropical medicine” type event that is being hosted, of all places, on Twitter. Given Matt’s general opinion on social media, the idea that he would recommend anything on Twitter was surprising. Naturally, this raised the question of when we can expect @MattThomas to make an appearance on Twitter and I have to report that it seems unlikely to happen any time soon.

After a brief perusal, Matt said that he would consider joining if I could show him some tangible benefit from being on Twitter. There are some relatively well-known and respected people in the field who are active on Twitter, and a few have written about why they find Twitter useful. But I doubt that there’s a single instance where Twitter has made a substantial difference in somebody’s career. If anybody has an example please let me know, I’d be interested to hear about it.

As for myself, I’m a Twitter agnostic. I maintain a presence because it’s easy enough to do and it’s an additional avenue to maintain a professional presence on-line, but I don’t derive any particular enjoyment from it. For maintaining a non-professional (but I like to think not un-professional) social media presence, I actually prefer Facebook. In this preference, it turns out that I’m showing my age.

So why Tweet? As a Twitter agnostic, I’m not going to try to change your mind one way or the other, but I will say that I see it as the electronic equivalent of attending conference happy hours. It’s a way to maintain connections to people you already know and maybe make some new contacts, but it’s highly unlikely that someone is going to offer you a job on the spot.

“This would be a good country,” a tourist says to me, “if only you had some water.”
He’s from Cleveland, Ohio.

Edward Abbey opens a chapter of his book Desert Solitaire, with a short conversation that really encapsulates the remarkable situation that characterizes the Southwest: massive cities, massive populations; both arising on arid, water deprived land – a stupefying, unnatural demand for such an environment.

I recently saw a talk given by Glen MacDonald, a Professor of Geography at UCLA, and what he said and how he said it, staggered me. I’ll quickly remark here that important issues necessitate good speakers, and if there was ever a reason for a graduate student to improve their skill in giving talks, this is it. Important issues will not resound with the public unless they are presented with shattering clarity. I’m glad climate change and water resources in the Southwest have a speaking voice through Professor MacDonald.

Lake Mead, a reservoir that holds water which flows to big cities in the Southwest.

The water situation in the Southwest is more than dire.  We are currently amidst a major drought that has taxed the Colorado River basin to its limits in its ability to provide water for cities in Arizona, California and Nevada. Lake Mead, a reservoir in Nevada that serves as a gauge for water availability, is nearly at a level that would require the federal government to initiate a mandatory rationing program in some states in the Southwest. The drought is not fueled by decreases in precipitation, but rather increases in evaporation due to climbing temperatures. Surprisingly, it’s not Jacuzzi’s and perfect manicured lawns that suck water from Lake Mead. According to Dr. MacDonald, 80% of water use (at least in Los Angeles) is used for agriculture maintenance.  Feeding our population is heavily water intensive.

Dr. MacDonald went on to say that predictions on the length of the current drought are fraught with uncertainty, but if history can tell us anything, it is that droughts can last an immensely long time, and they have done so in the past. The question remains, what happens when these long term droughts hit now, when we have such massive developments? I think we need a massive rethink on how we are managing our water.

As scientists, we certainly have an obligation to present our field of research well and with passion, but I also think that we have a certain obligation to keep ringing the bells on important issues. This is important. I say we keep talking about it. We may not be experts as infectious disease evolutionary biologists, physicists, statisticians or biochemists, but as scientists and people who inhabit the earth, we need to be interested in how we mange it.

I recently discovered that a poet, whose verses were forever floating around my childhood home, is responsible for a geometric solution of a cubic equation.  Digging a little deeper, I learned that Omar Khayyam is a celebrated polymath who made significant contributions to astronomy, math, poetry and philosophy.

Pretty cool.

“Here with a Loaf of Bread beneath the Bough,
A Flask of Wine, a Book of Verse – and Thou
Beside me singing in the Wilderness –
And Wilderness is Paradise enow.”

Excerpt from “The Rubaiyat” by Omar Khayyam.

Laura Pollitt is giving the department seminar today at Silwood. We were discussing some disease theory (as we do) and stumbled across a photo in Grenfell and Dobson’s Ecology of Infectious Diseases in Natural Populations.  Who is this guy?

For an avian malaria parasite, bites from uninfected mosquitoes increased Plasmodium parasite numbers bird blood, demonstrated in this recent paper. Birds not bitten by mosquitoes didn’t have this increase. (This was during the chronic phase of infection).

What time of day is mosquito happy hour? And does malaria go to the same pub?

I found this paragraph interesting (the hyperlinks to the embedded references should work): “..the periodicity of malaria may have evolved as a way to maximize the availability of mature gametocytes when mosquitoes feed [75]. Although this hypothesis remains controversial [76], [77] our approach could help identify the conditions that may promote the evolution of cell cycle coordination in malaria as a response to daily fluctuations of vector availability.”

There’s some evidence that malaria may cycle with vector abundance seasonally, but what about daily?

Furthermore, if mosquitoes that bite humans are shifting biting patterns from indoor to outdoor, and late evening to early evening, perhaps because of increased indoor control (LLINs and IRS), will this change anything about how Plasmodium parasites cycle in humans?

What do you all think?

“Ahh we look like big blue condoms!” I exclaimed as Chris helped fit us into our sterile blue synthetic onesies outside of the chicken houses in the crisp cold. There were murmurs of agreement. Hopefully the chickens wouldn’t mind the casual resemblance.

I had decided to forego my work for the day on the charismatic malaria parasite in exchange for inhalation of only the finest chicken dust in the state. There is a separate mad cult within our malaria dominant ranks that studies Marek’s disease in the chicken industry, with the aim of learning its basic epidemiology and evolutionary drivers. Despite hearing myths of said farms and feathery creatures, this was my first time coming face to face with the process and place that spills the data onto the lab benches and computers of my fellow lab-mates.

Chris sporting the much needed beard net.

The sight was staggering. We (myself and another CIDD member) were expertly guided by the young and bearded Chris Cairns into three houses holding numbers of chickens that made me question the accuracy of my sight. Still fairly young (only two weeks old), Chris described the masses as being in that “awkward teenage stage”. The chickens certainly looked slightly disconcerted, sporting small tufts of down that asymmetrically covered their bodies, having not yet formed full feathers yet.  Amazingly, their adolescence would be short-lived, with these birds only living about 35 days before being sent to the dinner table. We circled each house, collecting dust that would be tested later for Marek’s virus, chatting idly, bombarding Chris with questions.

Snow glare threatened immediate blindness as we emerged from each house and removed our protective clothing. I was left thinking on the ride back about how separated we are from the industries and processes that make our food, having once been so intimately connected to the plants and animals we consumed. I was also left thinking, when are we going to get viral vision? I want goggles that illuminate viral particles! It’s 2015, come on now.

Amazon has just calculated that I am their 12,620,896th most useful reviewer. That number is almost exactly 1000-times more than the number of citations I have on Google Scholar.