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.

In ten days, I am in Atlanta at a poultry meeting. There might be 25,000 people there. Not at my talk. But there.

Much to my total pleasure, I have made happen a dinner with Bruce Levin, his wife Adriana, and Ashley and I. Bruce and I are sparring over a number of issues in drug resistance evolution. But I wanted to have a foursome dinner because he is never dull. He tells me in e-correspondence that he cares more about being interesting than about being right. Sean Nee, the most stimulating theorist of my generation, used to say that as well. So too JMS.

Avoid Boring People… the title of one of Jim Watson’s books. Think about it. It washes both ways. And Watson’s subtitle?: Lessons from a Life in Science. Lessons from life I reckon.

Ygritte knows what’s up.

The first time I really learned about qualifying exams, I was an undergrad in a class on comparative endocrinology at Berkeley. My professor was Tyrone Hayes. Every exam was a booklet of open ended questions, including one question where the answer was always simply “I don’t know.” If you want to drive a room of overachieving pre-meds crazy, this is a pretty good way to do it.

One class, shortly after an exam, Professor Hayes announced that one of our TAs had passed his qualifying exam with flying colors. More important than what the grad student knew, Professor Hayes said, was his willingness to admit what he didn’t know.

This was a lesson that was reinforced when I became a grad student and it was my turn to take a qualifying exam. It’s a hard lesson to learn. Especially because most classes aren’t set up like my comparative endocrinology class, so it’s a lesson that is rarely reinforced until relatively late in our academic lives.

It’s a lesson that I was reminded of when I heard this story on NPR today, about a man who has made it his goal to be rejected each day. By doing so, he put himself through a form of exposure therapy for rejection. I’m sure that scientists across the country heard this story while drinking their morning cup of coffee, and thought about all their past and impending rejections. I know I did.

But it also struck me that fear of rejection comes from the same place as the aversion to saying “I don’t know”. And like my professor tried to teach his endocrinology class, we are indeed better scientists – and probably better off as people – when we make our peace with these uncomfortable feelings.

If there was an insect-mass-rearing version of Godwin’s law, the screwworm* would be Adolf Hitler. The more anyone reads about insect farming, the more likely one ends up reading about the U.S.’s successful 1966 eradication of the screwworm via sterile releases. Using SIT (sterile insect technique) screwworms were not only eliminated from the continental U.S., but by 1984, all of North America, was screwworm-free. How did we do it? By mass rearing 150 million sterile screwworms a week in a screwworm factory in Mission, Texas. Before the program ended, there were over two billion sterile flies being released each year.

That is insane.

Lucky me got some free literature on screwworm eradication from a friendly Penn State librarian.

What is striking however, is that screwworms, are like mosquito malaria-vectors in that both require animal tissue or blood to complete their life cycle. For screwworms a successful replacement was developed over fifty years ago. For the mosquito, we still rely on donated human blood or live animals.

There are a lot of reasons why we might want to mass rear the mosquito like we mass reared the screwworm. For those of us who saw Mike Turrelli’s talk at the CIDD this past fall, it takes a lot of mosquitoes to spread an artificially reared mosquito with certain traits (or in his case infection status) into a natural population. Simple things cause problems, like roads. We need a lot more mosquitoes than we originally thought. We need millions.

How do we rear millions of mosquitoes?

How did we rear millions of screwworms? Edward Fred Knipling (“Knip”), a USDA entomologist, developed an “artificial” diet made from slaughterhouse waste (200,000 pounds of beef and pork lungs, 11,000 pounds of dried blood, 8,500 pounds of horse meat), and milk (2,700 pounds of non-fat dried milk). Those 150 million screwworms that were produced a week as a result, fit into a plant that measured 75,000 square feet. In field trials a population could be eradicated in as little as 6 months. Once released into the United States in 1957, the screwworm was eradicated in the Southeast by 1959, the Southwest by 1966 and all of Mexico by 1984.

If it was possible for the screwworm, it seems possible for the malaria vector. Maybe we can even do one better: save some milk, save some beef and come up with a truly “artificial” way to rear mosquitoes without mammalian hosts?

*The screwworm is a parasitic fly (Cochliomyia hominivorax) that feeds on live tissue of either livestock or human hosts. It’s cousin, Cochliomyia macellaria, is a friendlier version that feeds only on already dead tissues and is employed in maggot therapy for medicinal purposes and in forensic entomology to determine time since death.

As a p.s. to this post, my current obsession with insect mass-rearing has turned into a library exhibit I’ve set up in the display cases on the 4th floor of Paterno. I’ll give you a free tour if anyone is interested.

The Gerald Kuku chicken stand. Every time I pass it (twice a day) I wonder who Gerald is and why he never has any chickens.

In two days, I’ll be boarding a Swiss Air flight out of Dar es Salaam. All told, this visit to Ifakara has been relatively uneventful (which isn’t necessarily a bad thing). It’s the period of short rains right now, which is just enough to dampen down the dust on some days but for the most part it’s hot and sunny and dry as a bone. I haven’t been stuck in the mud even once this time. This isn’t to say that life hasn’t been interesting. Some of the things I’ve seen include:

Giraffes, elephants, a breathtaking diversity of insects. Mantises as big as my foot and one small enough to fit on the tip of my pinky. Tiny, bright blue birds that put North American blue birds to shame. An huge owl taking flight off a fence post.

A rooster trying to mate with a duck, and a man recording it on his cell phone. Demonstrating that people the world over will whip out their cell phones whenever animals start doing something freaky.

A man with broken basket of tomatoes on his bike, hundreds of tomatoes scattering across the width of the one paved road here. Four people riding one motorcycle. One of them was holding up the flag of the political party that has held the presidency in Tanzania since they gained independence in 1964.

Which reminds me, it’s election season here in Tanzania right now. The opposing party is much more popular, even at the local level. The other day I was out walking with one of the technicians and we stopped by the house of his “grandfather” (not actually his grandfather, just an older family friend). The grandfather gave us fliers for one of the candidates running for a village leadership position and they tell me, confidently, that even Obama endorses their party.

I hate talking about money. Mostly because talking about money is boring. People are either complaining that they have too little, that other people have too much or that it is distributed in all the wrong places.

Scientists seem to choose the distribution complaint. A few months ago, NPR posted a story “When scientists give up,” on how tighter competition for grants and a crunched funding environment is leading some scientists to give up on science. The two former PIs interviewed both dropped out of academia, one to start a liquor distillery, and the other to own a grocery store in California.

The more I read about science and funding the more I start thinking about the prospect of, say, grocery stores. But I also start thinking about the prospect of a world without money.

Money has been around for a long time and is a simple concept that saves us a lot of hassle writing out IOUs when we can’t think of anything good to barter. Money also gives us a lot of headaches. Minor headaches like remembering to pay rent, and major headaches like income disparity leading to social unrest.

Would it ever be possible to just not have it? No money, no cash, no credit cards, no ibeacon payment systems, no bitcoin, no bartering.

The alternative to a monetary system is something called a gift economy. In a future where we have Schweebs, self-driving cars, automation of most menial tasks, super nanobots for gene therapy, and houses built by 3D printers, why don’t we ever talk about our monetary system changing? Or consider that money might be a “back-in-the-2000s” figment of the past, something we will only teach to monkeys?

Without money maybe scientists wouldn’t worry so much about having it or not having it. We could all go to work in our human powered monorail system of rapid transit, give the gifts of our ideas and hope we get lots of NIH and NSF gift supplies.

I’ve recently attended two talks given by colleagues of mine. After each talk, I was asked to comment on the presentation and provide feedback.

Initially I felt a little funny about doing this. On one hand, I am a huge fan of these individuals and I want to be maximally supportive of their scientific endeavors. On the other hand, although I certainly have very strong opinions about what constitutes a good presentation …….. I’ve never actually vetted these opinions with the community.

I did share my thoughts with these individuals. In retrospect, the conversations were really useful for me, and I hope they were also helpful for my colleagues.

It’s occurred to me that this is something we could do better as a group. We should cultivate a habit of having critical, open, honest conversations about how we are communicating our research. I’m not exactly sure what the best way to do this is. Lab meeting is not the place for this. As Dave put it, “lab meeting is for trying our hardest to poke holes in our work and then figuring out how to make it better”. It’s not the place to practice presenting a finished product.

Despite my love affair with cold hard facts. I’ve been forced time and time again to acknowledge the (cold hard) fact that science is conducted by humans. And humans …… in accord with the splendor of nature……. are a complicated mix of logical thought and fervent emotion. Although I’m still figuring out how to do this ……….. I’ve realized that its not enough to present the facts. The facts are absolutely essential. Without them, I would have nothing to say. But if I am truly interested in communicating my research I also have to demonstrate why I am passionate about what I do.

Waiting in traffic caused by a washed out dirt road during the rainy season in Ifakara, Tanzania.

My most used, most valued skill at the moment is patience. Not in the long suffering sense of the word but in the sense that I have to be at peace with waiting. It’s hard to spend a two day traveling around the world to sit and wait, but it is a skill and I practice it daily.

My office is right next to the hospital and I envy the medical doctors I see passing by every day who, I imagine, spend the entire day busily saving lives and making a difference with their more useful skills: diagnosing, treating, operating, healing.

I’d really like to make a difference. It’s why I got into this business. If it was purely for the love of science, I’d work on butterflies or better yet, drosophila. I believe that the work here can make a difference but it requires technicians, builders, Tanzanian scientists who understand the system and speak Swahili, and I am none of those things.

Still, I can see that my presence alone spurs activity, even if there is very little that I can actually do myself. I have to believe that just by being here, something will be accomplished. Science by gentle irritation, like a grain of sand in an oyster. A difference that I will only see in retrospect.

So I sit and I watch the medical doctors go by. I practice my patience. I try to teach myself Swahili (habari kazi? Ngumu). And I try to make peace with being the annoying white foreigner.

‘Do you have any advice?’

‘Stay calm’.

‘Is that it?’

‘Yep.’

This an honest account of an exchange between Andrew and I that occurred a couple of weeks ago. I wanted to know how to make the most out of a short visit to Aaron King, a theoretical ecologist with whom I’ve been collaborating. For six months, we’d been trying to translate the within-host dynamics of malaria infections into equations. We’d done pretty well over Skype, got a model up and running, but the extent to which the eye of a MacBook can capture the shape of functions drawn in the air is limited. It was time to really make some headway, particularly on our model of the immune system. So off I flew to Detroit.

Evening 1 – We investigate the data. All very very exciting. There are plots with swirls on them! By combining two data sets, we come up with The Pattern in the data that our new model has to be able to explain. We have a beer and sleep on it.

Day 2 – We walk to work together. Fueled by slumber and coffee we come up with a couple of verbal models that might explain the data. Almost running in to his office, we draw the models out on the board. Two competing models. NO, one model. It looks like this! Two equations, two curves. We look at more data – Is the data from that other experiment consistent with the predictions of this model? Yes! It might work!

‘I LOVE SCIENCE’, I said.

An hour or so later, just as we were about to head out for a victorious lunch. ‘Why is that first curve shaped like that?’.

Huh.

‘That doesn’t work at all’.

I laughed to myself. Stay calm, he’d said.

So it is with collaborative projects, I’ve found. Together you gamble up the intellectual hill then, while one of you is tying their shoes, the other gets a glimpse of the surroundings and realizes you’ve got to trot back down a bit. Staying calm and slowing down from the start would certainly be less exhausting. That said, at least at the beginning, perhaps you need the fun of running with ideas together to motivate you through the inevitable less-exciting moments? Moreover, when somebody points out the place you’ve got to doesn’t look right, its a good indication that they’re thinking and are willing to speak up. A climb down (and importantly a re-ascent) can’t be bad for trust and delineating the problem, either. Im hoping that, just like an eventful Sunday walk in the hills that turns out well in the end, all this yoyoing’ll be good fodder for a laugh and a well-deserved beer, afterward.

I went hiking this weekend and got stuck in the snow. Ten days ago, the forecast had predicted sunny weather with temperatures in the upper-40s to low-50s, by five days that changed to cloud-cover with a chance of rain, by the night before, the weather forecast couldn’t make up it’s mind — maybe sun, maybe rain, maybe snow?

Beautiful autumn day for a winter hike? It’s Nov.2

It snowed and I am confident it is impossible to predict the weather.

I don’t like saying things are impossible. Most things that we can’t predict now, I’m optimistic we could predict in the future, but my possibilist tendencies stop with the weather. I don’t think we will ever be able to predict it: we can’t now and I don’t think we can in the future.

When I say we can’t now, we are very, very poor predictors. Even with fancy tools like doppler radar and satellites, we haven’t made improvements to forecasts beyond six days in the past 20 years. According to a blog by Josh Rosenberg, who analyzed the accuracy of forecasts made by Accuweather, we can more accurately predict the long-term weather forecast using historical averages than by using modern technological tools and complicated prediction formulas. The average person with climatic trends data is just as good as a weatherman at telling you if it will rain next week. That is incredible to me and has eliminated my confidence that we will ever improve longterm weather predictions. In the short-term predictions, technology has helped us, but Accuweather’s new 21-day forecast is like using tealeaves and coffee grounds. The significant difference in accuracy between Accuweather and historical averages goes away within 4-5 days of the date of interest. In that case it seems to me like using yesterday’s weather to weight historical averages could be just as good as the satellite-doppler approach.

I figure I might as well put my own predictive power to the test, so here is the weather for State College, according to me. It is cool and sunny today in State College. My weather prediction for tomorrow is cool and sunny. I’ll go ahead and say it will be cool and sunny for the next 21-days with colder temperatures later in the month and scattered snow flurries as we approach Thanksgiving, chance of showers sometime in between. In 21 days I think I’ll see if I fared better or worse than my iPhone weather app.

The world’s population is projected to reach 9 billion by the year 2050.  Using current food production methods, we cannot sustainably feed a population of this size.  Various solutions to this problem have been proposed; change over to a vegetarian/vegan diet, genetically modify existing food sources to increase yield or arable farmland, use insects as a food source, grow meat in a laboratory, panic, etc..  I’d like to suggest an alternative solution.  Farm bacteria.

“Bacteria” is a catchall term that can apply to a lot of different things (even moreso than usual as I include Archaea in the term), and so let me first clarify that I’m not proposing that we all start eating random prokaryotes that we happen to come across.  I’m suggesting that we start farming bacteria in much the same way that we originally started farming plants and animals — find a few species that seem alright to eat and start selecting them for desirable characteristics.  I imagine that safety during consumption, nutritional content, and taste would be the most immediately relevant traits to select on, but feel free to disagree.  After a year of selection (i.e. on the order of 10,000 bacterial generations), it is hard to imagine that we couldn’t make some real progress on any of our traits of interest.

There are numerous advantages to growing bacteria over growing plants.  To name a few, bacteria can be grown literally anywhere.  Bacteria have a natural ability to acquire and lose genetic elements in the form of plasmids — for example, if a vanilla flavor is desired, add a plasmid that encodes for vanillin.  Nutritional requirements for bacteria to replicate are minimal relative to agricultural plants.  Doubling times are extremely short relative to growth rates of plants and animals providing advantages in production.  And perhaps most importantly, many bacteria can grow in the complete absence of other organisms, whereas plants and animals rely heavily on bacterial and fungal microbiomes.  This ability to grow in a true monoculture simplifies the complexity of the system, greatly enhancing the potential for research and development on limited budgets.

I’ve told this idea to many people over the last 10 or so years.  The most common responses I get are “ew, gross”, and “wouldn’t the texture be weird”.  My immediate response is, “people eat tofu, people will eat anything”.  My more thought out response, however, is that the texture and color of bacteria are highly variable in nature (not all bacteria are beige), and so it is hard to imagine that a palatable combination of taste, texture, and color couldn’t be generated with a little effort.

But the Beige Revolution won’t happen unless someone actually makes the effort to implement it, and I’m not going to be that person.  So if you think it’s a good idea, I wish you good luck, and I’ll put in my pre-order for an E. coli steak now.

Spherification in Charlie and the Chocolate Factory (illustration by Quentin Blake)

I recently bought some sodium citrate from Amazon. In addition to giving club soda its signature tang, sodium citrate solves one of the major concerns in my kitchen. Namely, how do you get cheese sauce that is both flavorful and creamy?

The problem with cheese is that when it gets hot, like when you’re making a cheese sauce, the hydrophobic dairy fats tend to separate from the water soluble components and you end up with greasy mac and cheese. One solution is to use a béchamel sauce, flour browned in butter and cooked with milk, which acts as an emulsifier to keep the dairy fats mixed into your cheese sauce. But the problem with béchamel sauce is that it’s not a great emulsifier and the more you add in, the more you dilute the flavor of the cheese. This is why most home made mac and cheese recipes call for cheeses with strong flavors, to balance out the béchamel sauce.

Sodium citrate, on the other hand, is a great emulsifier. It’s so good that you don’t even need the béchamel sauce, you can just mix your cheese directly into a hot liquid. You can use milk, beer, or even water as the base of your sauce.

Another use of sodium citrate, the one that’s listed on the jar that I bought, is spherification. In addition to being a really sweet word, spherification is a molecular gastronomy technique that produces little caviar-like bubbles of liquid. Sodium citrate isn’t the main ingredient for this process, but it can be used to change the pH of acidic liquids to make them more amenable to spherification. Which means that you can spherify just about any liquid you can think of. Check out this blog for photos of spherified wine, whisky, and sriracha sauce.

If I’ve sold you on sodium citrate, you can order your own here. Even if you aren’t as enthralled as I am by the idea of spherification, you can still use it to make this mac and cheese recipe.

Last Friday I got a copy of an email from David Paccioli who is writing an article about Andrew and his research.  Since Andrew was on I-am-off-line-any-questions-please-email-my-assistant status, I looked into the email.  David was hoping to use the story as front cover article, and he was sending a picture of an insect (which he assumed was a mosquito) that he wanted to use on the cover of the magazine.

I looked at the photograph and wondered, “Hmm, is this really a mosquito, and if so, what kind?”  In high school in Venezuela we studied the anopheles because at that time there still was malaria in the country.  I vividly remember the image, and this “thing” didn’t look much like it.  However, I wondered if, due to evolution (it’s been forty years!) maybe nowadays those critters look different.  What do I know?

I printed out the picture (I have to mention in black and white for the benefit of the people I asked) and decided to find out.  The first person to cross my path was Matt Ferrari.  I stopped him and asked, “Matt, what kind of mosquito is this?”  Matt, almost indignantly, replied: “ I work with VIRUSES!!!”  I just laughed and said, “Oh well, excuse ME!”

Off I went to find someone else.  Monica was at her desk.  I showed her the picture and asked, “What kind of mosquito is this?”  She looked at the pic and said, “I have no idea,” and when I turned around and saw Dave she said, “And don’t ask him, he wouldn’t know either.”  Then she reconsidered, grinned and corrected, “Go ask him!”

I went to Dave and asked,  “Dave, what is this?”  He said, “A mosquito?”  I replied, “But what kind?”  Dave admitted, “I have no idea.  All I can tell it is NOT a chicken!”  At that time all of us were laughing.  But I added:  “Listen, guys, I am DEEPLY DISAPPOINTED in all of you.  You are supposed to work on malaria and don’t even know what the transmitting mosquitoes look like!!!”  (OK, Dave works on chickens, but anyway….)

So I thought:  Elsa = Artemisinin = malaria = mosquito.  Maybe she knows?  Answer:  No.  Katey happened to be in the office, and she looked up some pics of malaria transmitting mosquitoes… they didn’t look much like the picture.  Suggestion:  contact the people at the insectary.

That’s what I did.  Lillian replied to my email, “I am 99% sure this is a crane fly…”  Wow! I immediately forwarded that email to Dave who must have been quite happy to get the news.  Shortly thereafter Lillian emailed back confirming her identification and offered to have the photographer over to take some pics of the “real thing.”

I am a non-scientist and as such, I believed that people who research malaria would certainly know what the transmitter looks like.  I never cease to wonder at all that I don’t know and all that I think I know and isn’t correct!  I love working here because I learn so much.  My days here are filled with daily discoveries that, while amazing to me, may be common knowledge to others. It makes my work quite enjoyable.