TWiV 178: T-Sharp on how tequila mosquito

The TWiValians meet up with Tyler Sharp for a discussion on the Epidemic Intelligence Service and controlling dengue.

Links for this episode:

Weekly Science Picks

Tyler - Co-infection with dengue and Leptospira (Emerging Inf Dis)
Alan - The Winged Scourge (YouTube)
Rich - Deepsea Challenge
Vincent - Why did a US advisory board reverse its stance? (Ed Yong)

Listener Pick of the Week

Sasha - Microfluidic Future
Adam - The Conversation
Jim -  ENIAC Programmers Project

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Sorting out Wesorts

None of the research blogging posts in my queue are quite ready yet, so it’s time for another update on the weird world of Wesorts. If you’re a Piscataway Indian reading that sentence, please don’t take offense – I’m talking about Wesort sailboats here, for the benefit of the six people in the world who’ve heard of them. And if you have absolutely no idea what any of this is about, hang on, because it’s going to get weirder.

First, a note about illustrating these posts. I wanted a picture of a Wesort to put here, but a search for “wesort” on Flickr returns a single hit that is a) fully copyrighted, b) related only to the Elmer Fudd interpretation of the term, and c) going to baffle the hell out of future digital archeologists.

And now, a Wesort history lesson from my dad, Tom Dove:

I can fill you in on the Wesort sailboat, having been present at its birth and development.

In the late 1950s, when the earth and I were both young, I was active in the sailing program at Indian Landing Boat Club in Millersville, Maryland, near the headwaters of the Severn river. We kids learned to sail in Penguins, a popular 11’6″ catboat which was well suited to our light, fluky winds. It was, and still is, a very good boat. The drawback to many of us was its cost, which ranged from about $150 for a battered, basic boat to over $500 for a new racing model. In 2011 terms, that range becomes about $1200 – $4000. That was a lot of money for a pre-teen to ask from parents. If you were a good woodworker, you could build one yourself, but it was a challenge with its compound curves and the performance would still not equal a professionally built boat.

Now I must tell you about two of my favorite lovable eccentrics: William H. Sands and “Willie”.

Bill Sands’ son, Bill Sands, was a childhood friend of mine, so I got to know the family pretty well. Bill Sands, Sr. was one of those fellows who worked hard to conceal his intelligence and education by affecting the style of a country bumpkin. While he was quite capable of holding forth on a detailed analysis of any of Shakespeare’s plays or analyz[ing] the vector forces on a mast, he loved to shuffle about the boat club and help kids learn to sail or to tinker in his workshop on some oddball project. One of these projects was the Wesort.

Bill Sands wanted to build the most economical junior training sailboat possible. He wanted it to be so simple that somebody with absolutely no knowledge of woodworking could build it out of standard size materials available at any lumber yard or could team up with a group of like-minded folks and turn out a dozen of them in one winter in assembly line fashion. The result was the Wesort, which could be built (less sails) for $50 – $100.

“Willie” was the caretaker of the Indian Landing Boat Club for as long as anybody could remember and nobody seemed to know how he got there. He lived in a little house on the premises and was paid a small salary in return for basic maintenance and tending the gate at the club. I believe that no more than a handful of members knew that he had a last name. He was absolutely gentle and universally loved.

Willie the caretaker was a small man who always smiled and hardly ever spoke. His ancestry was baffling. His features were neither Caucasian nor Negroid, but his coloration was somewhere between the two. I always thought he had a vaguely oriental look to his face. I knew him for a couple of decades and never heard him say anything more than, “Yeah,” which came out in an elongated form, something like “Yeaaaaah,” always with a smile and followed by a chuckle.

But Bill Sands knew Willie well and knew that he was a “We-sort”. That was a term a certain small, close-knit group in central Maryland used for itself to distinguish their kind from everybody else, whom they called the “They-sort.” They claimed to be descendants of the Piscataway Indians who had lived in the area for centuries and who greeted European settlers in the early 1600s.

And that is why Bill Sands named the boat the Wesort.

I’ll stop here and continue about the boat itself in another story.

I remember Willie quite well. He was always in the little gatehouse when we went in or out of the ILBC, which was just down the street from my grandmother’s house. The workings of the simple counterbalanced gate fascinated six-year-old me, as did this strange man who operated it and only seemed to know one word.

Dad, feel free to post the information about the boat in the comments, or email it to me and I’ll milk another blog post out of it.

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TWiV 177: Live in Dublin

A discussion of avian influenza H5N1 transmission experiments in ferrets and novel bunyaviruses at the 2012 Spring Conference of the Society for General Microbiology in Dublin, Ireland.

Links for this episode:

Weekly Science Picks

Connor - Wellcome Trust Science Writing Prize 2012
Vincent - Thoughts on academic scientists giving media interviews

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Finally, Some Beer in The Lab

We’ve been hearing for years about all the alleged health benefits of red wine, but researchers have left that other historic beverage largely untouched. I’m talking, of course, about beer. It’s not surprising – despite being one of the oldest human inventions and probably a major driving force in the formation of civilization, beer gets no respect. Now, though, a team from Belgium (perhaps the greatest beer-making culture in the world, by the way) has started to remedy that. As they explain in their paper:

Recent evidence suggests that hops-derived compounds positively impact adipocyte metabolism and glucose tolerance in obese and diabetic rodents via undefined mechanisms. In this study, we found that administration of tetrahydro iso-alpha acids (termed META060) to high-fat diet (HFD)-fed obese and diabetic mice for 8 weeks reduced body weight gain, the development of fat mass, glucose intolerance, and fasted hyperinsulinemia, and normalized insulin sensitivity markers.

Hops (Humulus lupulus) are an herb that serves as the main bittering agent in most beers, and the HFD mouse model is what happens when you put an ordinary lab mouse on an American-type diet. Apparently, the former can counteract some of the effects of the latter.

While I love my burgers and beer, though, we should take these new data with a dash of salt. The treatment in this paper consisted of spiking the animals’ high-fat food with 0.1 percent of the alpha acid analog these researchers are studying. Hops vary in their alpha acid concentrations, but even if you drink a strong IPA hopped with good Chinook and Cascade strains, your diet would have to be mostly beer to reach these levels. The same could be said about most red wine studies to date; the resveratrol that supposedly provides many of wine’s benefits is actually present in minuscule quantities in a typical glass of Merlot.

Nonetheless, I think there’s enough data here to warrant more research on beer. So let’s raise a glass to that.

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TWiV 176: Ave, magi virorum!

Vincent, Alan, and Rich answer listener email about MS, CFS, EBV, B cells, virii, influenza B, scientific papers, and more.

Links for this episode:

Weekly Science Picks

Rich - Alan Alda’s Flame Challenge (NY Times article, Science editorial)
Alan - ChronoZoom
Vincent - Academic Publishing is Broken by Michael P. Taylor

Listener Pick of the Week

Joel - Fighting a dengue outbreak by Tyler M. Sharp (parts one and two)
Sven-Urban - Fooled by Randomness and The Black Swan by Nassim Nicholas Taleb

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Some Advice for Stressed-Out Graduate Students

Brenna sent this link and email last night:

The link’s name is deceptive, but I thought you might like to comment on the state of depression and other mental health problems in graduate school. Is it just a sign of the times, something that was always around and not acknowledged? Or is it an indication of the need to remodel graduate education and training?

Glossing over the misspelling in the linked page’s headline, we get to an article by Piper Fogg that first appeared in 2009 in the Chronicle of Higher Education. It warms up with some cheery statistics:

Studies have found that graduate school is not a particularly healthy place. At the University of California at Berkeley, 67 percent of graduate students said they had felt hopeless at least once in the last year; 54 percent felt so depressed they had a hard time functioning; and nearly 10 percent said they had considered suicide, a 2004 survey found. By comparison, an estimated 9.5 percent of American adults suffer from depressive disorders in a given year, according to the National Institute of Mental Health. Meanwhile, nearly a quarter of the graduate students surveyed were not aware of mental-health services on the campus. And another Berkeley study recently found that graduate students were becoming increasingly disillusioned with careers in academe and did not view large research institutions as family-friendly workplaces.

Stress. Image courtesy BLW Photography.

Image courtesy BLW Photography.

The rest of the piece – which must’ve been a real pick-me-up to research and write – describes the experiences of several graduate students who’ve found themselves at wits’ end, and the strategies they’ve employed to cope. It’s an interesting line of discussion, even if the statistics underlying the argument are slightly suspect; the general public is the wrong control group to use. It would be more useful to know how depression and anxiety rates compare between graduate students in academic fields and, say, medical or law students. Any serious professional training is stressful, and stress can cause or exacerbate mental illness. Nonetheless, my intuitive guess is that at least the broad strokes of the story are correct: many aspects of grad school suck.

For me, the worst part was that moment, around the middle of my third year, when I suddenly realized what finishing my Ph.D. program would require. Sure, I knew the “requirements” already: completion of a thesis representing original scholarship yadda yadda yadda. But what hit me that morning was the magnitude of the job, and the terrifying fact that not only was there no guarantee I could do it, there wasn’t even a clear description of how to do it, nor could there ever be one. I’d felt insecure about my abilities as a scientist before, but now I saw that my insecurity wasn’t based on some imagined inadequacy. To graduate, I needed to discover something new about nature. It didn’t have to be a huge breakthrough, but it had to be new. And it’s nature – the raw, beautiful, terrifying, magnificent reality of the vast universe that humans have been trying to understand for millennia. The mists had lifted to reveal a sheer, rocky cliff to leeward. Who the hell was I to think I could discover anything new about that?

Anxiety and depression? Oh, yeah.

And that brings me to your questions, Brenna. My answers are “yes” and “moot,” respectively. For most students, graduate school means spending their young adulthood in strenuous study, with long hours and poverty-line (or negative) income, in the hope of eventually landing a job in academic research, a field that’s about as relaxing as Wall Street and as lucrative as Wal-Mart. It’s always been that way. So yes, the article is just acknowledging something that’s probably been true for awhile.

Does that mean we should we remodel graduate education and training? It doesn’t matter. We can’t. The entire modern research enterprise is built on the easy availability of cheap but highly-skilled and educated labor, namely graduate students and postdocs. Making graduate school easier and/or more rewarding financially would require rebuilding the world. Even then, we’d have to come back to that rocky cliff and acknowledge that ultimately, there’s no sugar-coating it. You’re doing a very, very difficult thing. It’s going to be stressful.

Still, nobody should have to tolerate abuse, and some of the stories Fogg relates are clearly over the line. Graduate school is inherently hard and can be lonely, but when you go to your advisor you should get help and encouragement, not bullying and discouragement. If you feel that you can’t discuss problems with your mentor, or that your department is placing unnecessary obstacles in your way, or that your colleagues are trying to undermine you, then you are in a toxic environment. Either find a way to mitigate it, or leave. Immediately. There are other schools out there that aren’t like that. A feeling of hopelessness and powerlessness may be common in graduate school, but it shouldn’t be a design feature of the program.

If the problem seems to be internal – your advisor is great, your colleagues are helpful, and your department is supportive but you still feel like you can’t go on – then beat a path to your university’s counseling office. Immediately. Let’s be clear: mental illnesses are as serious as physical ones, and they can kill you just as easily. They can also be managed or treated. Our society may attach an absurd and counterproductive stigma to mental illness (why is it okay to have heart disease but not social anxiety disorder?), but I assure you that the staff at the counseling center does not. It’s their job, after all.

Finally, remind yourself that you can do it. The breakers may sound loud on those rocks, but other people, no smarter than you, have navigated this route before. Even I got through it eventually.

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TWiV 175: More than one way to skin a virus

Vincent, Alan, and Matt discuss herpes simplex encephalitis in children with innate immune deficiency, and the local response to microneedle-based influenza skin immunization.

Links for this episode:

Weekly Science Picks

Matt - Phage and the Origins of Molecular Biology
Alan - Digital Imagine Institute
Vincent - iPad apps Goodreader and Notability

Listener Pick of the Week

Jane -Smoking Ears and Screaming Teeth by Trevor Norton

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Tools of The Trade: Zotero

If you read a lot of scientific papers, or do any other kind of academic study, you need a way to manage the mess. I’m talking about the piles of photocopies, books, and notes – or these days, gigabytes of PDFs, web links, and text files. Zotero is the best solution I’ve seen for this so far.

The genius of this little browser plug-in is that it automatically senses certain types of web content, such as research journal articles and bibliographic searches. It has a particularly profound understanding of PubMed, the main search engine for biomedical science. Zotero doesn’t flaunt its knowledge, though – it just adds an unobtrusive icon in the address bar when it understands what you’re reading. Click that, and you can add citations to a library the program maintains on your computer. There’s also an option to synchronize those citations across other devices, using Zotero’s server. All of this is free.

Zotero in action.

Zotero in action.

Once the citations are on board, you can get to work. The screenshot shows a paper I was reading today. The top part of the screen is the regular browser window, with a paper I was reading online. The bottom section is the interface for Zotero. With a click, I can make Zotero take up the whole screen, or open in a separate window, or go away entirely. To save clips of text from the paper, all I have to do is highlight some text, right-click to get a contextual menu, and then select “Add to Zotero note.” The clip gets stored alongside the citation for easy reference. Of course I can also add my own notes, and can export the notes, the citation, or both in a wide range of formats. There’s also a slew of collaboration tools that operate through the program’s web site.

As with any sophisticated tool, there’s a bit of a learning curve, but so far I’ve been able to figure out how to do just about everything I’ve wanted to with the application. If I find myself thinking “Zotero should be able to do that,” a few minutes of clicking around usually reveals that it can. There are other citation managers available, of course – Mendeley and CiteULike both have dedicated followings – but for what I do, Zotero has been a good fit.

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TWiV 174: Dog runs and mooing miRs

Hosts: Vincent RacanielloAlan Dove, and Rich Condit

Vincent, Alan, and Rich consider whether pet dogs might transmit human noroviruses, and an RNA virus microRNA that might be involved in oncogenesis.

Links for this episode:

Weekly Science Picks

Rich - NOAA Buoy Data
Alan - Autism’s False Prophets by Paul Offit
Vincent - Media Mining

Listener Pick of the Week

Mark - How the West fueled the AIDS epidemic
Henry - Regenesis
Rick - Biopunk: DIY scientists hack the software of life by Marcus Wohlsen

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Coney Island Snowstorm, January 2000

This gallery contains 8 photos.

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