TWiV 183: Bats out of hell

Connor joins the TWiV team to discuss bats as hosts for major mammalian paramyxoviruses.

Links for this episode:

Weekly Science Picks

Connor - Microbiology Twitter journal club
Alan - 
Where the Wild Types Are (YouTube)
Rich - May 14th: Smallpox vaccination day
Dickson - Searching for pore-fection (Science)
Vincent - RRResearch

Listener Pick of the Week

Stephen - Every Major’s Terrible (xkcd)

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The NEC-4 Security Scam

A few decades ago, scientists at Lawrence Livermore National Laboratory (LLNL) in California developed a computer program called the Numerical Electromagnetic Code, or NEC. This set of algorithms allowed researchers to build computer models of radio antennas so they could make realistic predictions about a given antenna design’s performance. As has happened in many other fields, this computer-aided approach drastically accelerated research and development. Instead of building working prototypes and trying them out on elaborate antenna test ranges, then repeating the whole process dozens of times to arrive at a final product, designers could now test and refine their plans on the computer first, and spot-check the results on the final product. LLNL describes the program this way:

NEC (Numerical Electromagnetic Code), written by Gerald Burke, is a popular antenna modeling code for wire and surface antennas and scatterers. Models can include wires buried in a homogeneous ground, insulated wires and impedance loads. The code is based on the method of moments solution of the electric field integral equation for thin wires and the magnetic field integral equation for closed, conducting surfaces.

Like all good algorithms, NEC has grown over the years. The latest release is version 4.1, and it incorporates a huge array of variables that allow users to model all sorts of antennas over realistic terrain. Whether you’re a cellular phone company, a physicist, or an amateur radio operator, this is a tremendously powerful tool.

Antenna Tower. Image courtesy Razvan Caliman.

Antenna Tower. Image courtesy Razvan Caliman.

As computers became faster, smaller, and cheaper, other programmers extended NEC, porting it to platforms beyond its original mainframe implementation and building user-friendly front-ends for it. Many of these ports and interfaces came from hobbyists who released their code for free, a tradition that continues today – the latest open-source Mac version, for example, is here.

However, if you download one of those excellent open source implementations, or even a commercial antenna design package built on NEC, you may notice a discrepancy in the version number: all of these programs use NEC-2, not the much more sophisticated NEC-4. That’s because LLNL, citing export-control regulations, forbids software developers from including NEC-4 in their products. Instead, anyone who wants to use the more advanced version of the algorithm has to submit an application and pay a fee directly to LLNL. The folks at Livermore will then provide a copy of the NEC-4 code, with the stipulation that the applicant can’t give it to anyone else.

I understand and support the need to keep America’s enemies from exploiting American research, and that’s what export-control laws are supposed to do. But it’s very hard to see how LLNL’s licensing policy accomplishes that. Take a look at the NEC-4 application form (PDF). There’s a lot of legalese telling the applicant that the code comes with no warranty, and that he/she/it is not to redistribute this software. Then there are blanks for the applicant’s information: name, address, phone, email. And that’s it. It’s clear that the most important – probably the only important – part of this form is “attach payment.”

How much? Well, NEC-4 will set you back $300 for an individual or academic institution, $500 for non-U.S. academic institutions, $1,100 for American companies, or $1,500 for non-U.S. companies. Considering that the software was developed on U.S. government grant funding, and that much of the heavy-lifting of interface design and code porting was done by others for free, exactly what is this money for? It’s certainly not for a thorough background check – LLNL isn’t collecting enough information to do one, at least not on the main form for U.S. citizens. You don’t even have to enter your Social Security number.

But wait, there’s a separate “Customer Screening” form (PDF) that non-U.S. entities have to fill out. Let’s take a look at some excerpts from it to see what kind of heavy-duty security screening the foreigners are getting:

Is your facility involved in any of the following activities?

Research on or development, design, manufacture, construction, testing or maintenance of any nuclear explosive device or components or subsystems of such a device? [] Yes [] No

Will the item(s) requested for export be used in the design, development, production or use of missiles? [] Yes [] No

Will the item(s) requested for export be used in the design, development, production, stockpiling, or use of chemical or biological weapons? [] Yes [] No

The rest of the form is in the same vein. I’m pretty sure that even the world’s stupidest terrorist would know not to check “yes” to any of these items. Even if that level of understanding escaped them, or if their mailing address seemed likely to arouse suspicion (e.g. “Hidden Base, Afghanistan”), they could simply find a U.S. citizen willing to fill out the form and forward the CD-ROM, perhaps in exchange for a small bribe.

It’s hard to see how LLNL is accomplishing anything with this silly sham, besides scamming the public out of some money and preventing legitimate users from accessing a useful tool. The cumbersome but pointless licensing process for NEC-4 is actively hindering innovation, as many users who might otherwise be able to contribute to the development of the next generation of antennas can’t afford the extra tax LLNL has chosen to levy on them. Even those who can pay the fee may run up against technical problems, such as the need to compile the code from source. If NEC-4 were available as openly as NEC-2, developers could not only do the compiling for their users, but also improve the code’s integration into antenna modeling packages.

I think it’s high time to channel some of this geek rage toward changing the situation. The first step is to unmask the scam. Who wants to take up a collection to submit a transparently bogus license application (with a valid payment) and blog about the results anonymously, to prove that LLNL isn’t doing background checks? I’ll put up the first $20.

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TWiV 182: One flu over the ferrets’ nest

Hosts: Vincent RacanielloRich ConditAlan Dove, and Michael J. Imperiale

Michael joins the TWiV crew to discuss the recently published influenza H5N1 transmission paper and how it was viewed by the NSABB.

Links for this episode:

Weekly Science Picks

Alan - 18th century shipping mapped
Rich - Brave New World by Aldous Huxley
Vincent - Air France 447 (Telegraph)

Listener Pick of the Week

Josh - Vaccines course by Dr. Paul Offit

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One of the two H5N1 influenza papers that fueled this brouhaha has finally seen the light of day. Rather than rehash what others have already said so well, I refer readers to the excellent summaries by Vincent Racaniello and Ed Yong.

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Tools of the Trade: Timestamps and Text Editors

Quoting people accurately is a mundane but crucial task in my daily work. Over the years, I’ve tried a variety of approaches, but I think I’ve finally evolved the most efficient system for handling it. When I’m conducting an interview or attending a presentation at a research conference, I take copious notes. These used to be on paper, using a complicated note-taking technique I developed in college, but after discovering the amazing capabilities of Emacs (the One True Text Editor), I’ve switched to doing it on a computer.

My notes are not strict transcripts. I tried doing transcripts, but it was more hassle than it was worth, and I found that there’s a conflict between transcribing someone’s words accurately and actually understanding what they’re saying. Instead, I note the important parts of the conversation as if I were attending a lecture, and periodically insert a semi-transcribed snippet if they start saying something I think might be quotable. Such a snippet might read “thr’s bn a lotta contrvrsy n th fld abt this, bt itot tht th mech is rly simpl.” With that sort of primitive shorthand, I can transcribe even relatively quick talkers with about 90% accuracy in short bursts. But I want 100% accuracy.

To get that, I record all of my interviews and conference sessions. Yes, recording phone conversations is completely legal everywhere, as long as you ask permission first. The notes plus the recording give me all the information I need, complete with 100% accurate quotes. To streamline the process, though, I added one more piece: timestamps. As I’m taking notes, I hit a keyboard shortcut, and my computer inserts the elapsed time since I started the recording. When I’m writing, I can look through my notes to find the quote I want, then zip to that time in the recording, play back the tape, and check the quote. Cumulatively, this can shave hours of tedious rewind-play-forward-play searching on a long assignment.

Unfortunately, most word processing software doesn’t offer elapsed time stamps, and because the popular choices are either closed-source (Word, Pages) or mind-bogglingly complicated open source (OpenOffice), it’s not trivial to add this feature. You could sort of work around the problem by using real-time stamps, then calculate the elapsed time between when you started the tape and when you got to a particular point, but that could take as long as just searching the recording blindly. Instead, I suggest switching to a proper text editor (a choice that has a lot of other benefits, too). Once you’ve done that, there are at least two ways to add the elapsed time feature.

For Emacs users, the solution – like the solution to every other Emacs need – is to modify your “.emacs” customization file. It’s not hard. Here’s the bit that does the actual work:


;;; Elapsed time and realtime stamp functions
(defun clock-start ()
"Starts a clock which can then be used by
`clock-insert-elapsed' to insert elapsed time into the current buffer."
(interactive)
(setq clock-start (current-time)))

(defun clock-time-elapsed ()
"Returns the elapsed time since the clock was started with `clock-start'."
(interactive)
(setq elapsed-time (time-since clock-start))
(format-time-string "%T" elapsed-time t))

(defun clock-insert-elapsed ()
"Inserts the elapsed time since the clock was started with `clock-start'."
(interactive)
(insert (clock-time-elapsed) " ")
(newline))

(defun timestamp ()
"Insert string for the current date and time."
(interactive)
(insert (current-time-string) " ")
(newline))

To link that to some convenient shortcut keys, also add these lines:


(global-set-key [(hyper f8)] 'timestamp)
(global-set-key [(hyper f7)] 'clock-start)
(global-set-key [f8] 'clock-insert-elapsed)

That’s it. Now, hitting command-f8 inserts a real-time stamp, while command-f7 starts a stopwatch and f8 by itself inserts the elapsed time since the stopwatch started. Whenever I start recording a phone call or conference talk, I simply hit command-f7 right after pressing the “record” button. Whenever the source says someting potentially interesting, f8 then bookmarks it for later access. These keys are convenient on a Mac – if they’re already assigned to something else on your system, simply choose different shortcuts. Once you’ve used them a few times, they’ll become second nature.

For other text editors, I use a pair of Bash scripts that I can call from a general system-wide shortcut. These are incredibly primitive scripts, and I’m sure there’s a more elegant way to do this, but here’s my approach. First, we have a script to start the clock, creatively named starclock.sh:


#!/bin/bash

if test -e ~/Desktop/clock
then
rm ~/Desktop/clock
fi

echo $(date +%s) > ~/Desktop/clock

That saves a file to my desktop with the current time, in seconds since the Unix epoch date (don’t ask – it works). The other script, etime.sh, looks like this:


#!/bin/bash

BEFORE=$(cat ~/Desktop/clock)
AFTER=$(date +%s)

# Calculate elapsed time in seconds and subtract 19 hours (68,400 seconds)

ELAPSEDSECONDS=$(expr $AFTER - $BEFORE - 68400)

echo -e $(date -r $ELAPSEDSECONDS +%H:%M:%S)

That reads the clock start time from the desktop file, then calculates and returns the elapsed time since the clock started. Set a pair of keyboard shortcuts (such as command-f7 and f8) to call these two scripts and insert the result of the latter into your text document, and you’re all set. This has worked well for me in both Vim and the free version of Smultron, but any text editor that can call command-line scripts should be able to handle it.

Yes, I understand how useless this post will be to most of my readers. If you’re a scientist working in the lab, you probably have no need of timestamps or interview recordings. If you’re a journalist, you probably have no clue how to make a text editor execute a script, how to modify your .emacs file, or even whether any of this is safe. However, I hope it provides a good example of why you might want to learn those things. For modern writers, editing text on a screen is a fundamental job skill, and the software we use to do it is an essential tool. If you’re limiting yourself to corporate-oriented word processors, you’re like a photojournalist trying to shoot an assignment on a crappy camera phone. It might be possible, but it won’t be easy. Text editors are the digital SLRs of writing, and learning how to use and modify them is time well spent.

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TWiV 181: ORFan poxviruses and nIRFing prions

Hosts: Vincent RacanielloRich Condit, and Kathy Spindler

Vincent, Rich, and Kathy discuss Cotia virus, a new poxvirus, Orf virus infections associated with handling goats and lamb, and the innate immune response to prions.

Links for this episode:

Weekly Science Picks

Kathy - Astronomy Picture of the Day (especially this and this)
Rich - Tom Lehrer Element Song (YouTube)
Vincent - Albert B. Sabin Archives

Listener Pick of the Week

Mark - Netter’s Infectious Diseases by Elaine C. Jong and Dennis L. Stevens
Richard - Germs, Genes & Civilization by David P. Clark

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TWiV 180: Throwing IFIT at flu and holding a miR to HCV

Hosts: Vincent RacanielloAlan Dove, and Rich Condit

Vincent, Alan, and Rich review association of an interferon-induced protein with severe influenza, and stabilization of HCV RNA by a microRNA.

Links for this episode:

Weekly Science Picks

Alan - Micro Empire (Vimeo)
Rich - Census of marine life
Vincent - Pinterest

Listener Pick of the Week

Mark - The Secret Life of Plankton (YouTube)

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Trade Wind Tree, South Point, Hawaii

Trade Wind Tree

Trade wind tree, South Point, Hawaii, May 2000.

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TWiV 179: Was ist ein virus?

Hosts: Vincent Racaniello, Alan Dove, Rich Condit, and Gertrud Radu

Gertrud joins the TWiVoners to review how dengue virus infection of mosquitoes alters blood feeding behavior, and gene therapy as practiced by parasitoid wasps.

Links for this episode:

Weekly Science Picks

Gertrud - Bat on a plane! (MMWR)
Alan - The Rings of Earth (YouTube)
Rich - Giant Magellan telescope
Vincent - Hepatitis C new drug pipeline

Listener Pick of the Week

Ricardo - Evolution: The Natural History of Animal Skeletons
Peter - Self-assembly line (YouTube)

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Colony Collapse Disorder: Dead Bees and Sloppy Science

A flurry of recent scientific papers, and a blizzard of subsequent news hype, has led a lot of people to conclude that the mystery of colony collapse disorder (CCD), which causes beehives to die suddenly, has been solved. Indeed, a Reuters reporter recently proclaimed exactly that in an editorial published on the wire service’s site.

All of these reports have converged on a single culprit: neonicotinoid insecticides, a category that includes some of the most widely-used chemicals in agriculture. According to this story, the pesticides aren’t present in high enough levels to kill the bees right away, but low-level exposure over a period of weeks slowly poisons them.

Beehive

A beehive. Image courtesy artethgray.

Of course the pesticide industry hasn’t been taking this lying down. Agrochemical giant Bayer, for one, has been issuing testy press releases faulting the new studies. Bayer is a leading supplier of imidacloprid, a very popular neonicotinoid compound that is used in both agricultural and home pesticides.

Imidacloprid was also the focus of the most recent scientific study to pin CCD on pesticides, and in this case, at least, Bayer may have a point.

I’ve found this new study, by Chensheng Lu of the Harvard School of Public Health and two collaborators from the Worcester County Beekeepers Association, particularly interesting – and not in a good way. The press release about the paper has been the source of most of the news coverage, so I suppose it made a better impression on other science journalists than it did on me. Here’s how it starts off:

The likely culprit in sharp worldwide declines in honeybee colonies since 2006 is imidacloprid, one of the most widely used pesticides, according to a new study from Harvard School of Public Health (HSPH). The authors, led by Alex Lu, associate professor of environmental exposure biology in the Department of Environmental Health, write that the new research provides “convincing evidence” of the link between imidacloprid and the phenomenon known as Colony Collapse Disorder (CCD), in which adult bees abandon their hives.

The study will appear in the June issue of the Bulletin of Insectology.

“The significance of bees to agriculture cannot be underestimated,” says Lu. “And it apparently doesn’t take much of the pesticide to affect the bees. Our experiment included pesticide amounts below what is normally present in the environment.”

Let’s take this a little bit at a time. First, we’re being told the “likely culprit” has been found in a condition that’s baffled researchers for several years. That’s an extraordinary claim, so I’m expecting extraordinary data to back it up. Apparently the new paper will contain just that, because it’s supposed to be “convincing evidence.” Anyone setting the bar that high is either sitting on rock-solid results, or full of shit. In my experience the latter is much more common, so my skeptic senses are already tingling.

Then things really start to go pear-shape. The Bulletin of Insectology? I try to avoid being a journal snob, but come on, insectology? The name of the field is entomology, and a quick Google search confirms that “insectology” appears nowhere else in science except for the title of this journal. Their web site doesn’t exactly scream “high publication standards,” either. If you’re a fan of impact factors, the B of I scores a whopping 0.371, so apparently it’s not going to be rivaling Nature for citations anytime soon, either.

Then it gets even worse. The press release came out in early April, with no embargo, but the paper is scheduled to be published in June. Nor is this an “advanced online publication” situation – this paper really isn’t out yet in any format. This is truly science by press release. Maybe we should just move on, forget we ever saw this, and also ignore the absurdity of the author’s quote (he didn’t really say “cannot be underestimated” did he?).

The subsequent media storm was deafening, though, so I felt compelled to dig in. Emailing Dr. Lu, I got a prompt and courteous reply with an attached PDF of the paper – or at least a “corrected proof.” After confirming that it was okay to discuss it even though it wasn’t slated to be published for two more months (a question I gather he hadn’t been asked yet), I started reading.

It wasn’t as bad as I’d expected.

I realize that’s faint praise given the foregoing, but working my way through the paper a picture started to emerge. This project seems to have begun as an earnest effort to do good science. Then, somewhere along the line, someone decided to push the data out the door in a big hurry, bypassing the revisions that a competent peer reviewer would have demanded. Perhaps it was because two other publications about neonicotinoids and bees had just come out in Science (Henry et al. and Whitehorn et al.). Or perhaps the collaboration fell apart, or the team decided that some of the additional experiments they needed would take another year to do and they were sick of waiting. Whatever the reason, the final publication suffered.

Nonetheless, the experiment – there’s only one in the paper – had a lot of potential. Hypothesizing that imidacloprid sprayed on corn crops could contaminate the high-fructose corn syrup (HFCS) that’s fed to commercial beehives, the researchers decided to see what eating sub-lethal doses of the pesticide would really do to bees under field conditions.

They placed five newly constructed and stocked honey bee hives on each of four field sites, for a total of twenty hives. The field sites were more than 12km apart, so the bees from different sites would forage on independent territories. Following conventional apicultural practices for commercial hives, the team fed HFCS to all of the bees to supplement their honey stores during the winter. Four hives on each site ate HFCS spiked with various doses of imidacloprid, while the fifth hive was a control, receiving unadulterated HFCS. At the end of the winter, fifteen of the sixteen imidacloprid-fed hives – and one of the four control hives – had died.

The authors claim that the hives’ deaths resembled CCD, but that may be a bit of a stretch. For one thing, they report seeing dead bees on the ground near the hive entrances, which isn’t typical of colony collapse. They also didn’t see any of the pathogens that often correlate with CCD, such as varroa mites, iridoviruses, and the unicellular parasite Nosema ceranae. In addition, these experiments all took place in Worcester County, MA, just east of where I live, during 2010 and 2011. That was an absolutely horrific winter, breaking all kinds of records for snowfall, ice accumulation, and cold. It was hardly representative of the way traveling commercial hives spend their winters (they go to Florida). Of course the usual numerical objection also comes up; this was a very small experiment that clearly lacked the statistical power to extrapolate to an entire industry.

The biggest problem, though, is that the work is full of provocative but completely unsupported speculation. The authors discuss imidacloprid use on corn in some depth, and outline a plausible route by which it could end up in HFCS – but that’s entirely theoretical. Nowhere do we see data or a reference showing that the pesticide was ever actually in the sweetener that commercial bees ate, or measuring its levels.

Even if we assume, without a shred of evidence, that imidacloprid routinely contaminates HFCS, that would raise a whole new problem. Control bees also got HFCS. That means the controls also would have been eating some unknown amount of the chemical, and the experimental bees would have gotten a double dose, rendering the result meaningless. To do the experiment right, one would have to test the HFCS for the pesticide to confirm the levels, and also find some source for uncontaminated HFCS for the controls. If I were reviewing this paper for publication, I’d demand those data, and would also insist that claims of “convincing evidence” be edited to more cautious language – which, I suppose, might drive the authors to send the paper elsewhere.

We should see whether low levels of imidacloprid are contributing to CCD. It’s an entirely plausible hypothesis. Unfortunately, it remains untested.

Lu, C., Warchol, K., Callahan, R. (2012). In situ replication of honey bee colony collapse disorder, Bulletin of Insectology (in press).

Henry, M., Beguin, M., Requier, F., Rollin, O., Odoux, J., Aupinel, P., Aptel, J., Tchamitchian, S., & Decourtye, A. (2012). A Common Pesticide Decreases Foraging Success and Survival in Honey Bees Science DOI: 10.1126/science.1215039

Whitehorn, P., O’Connor, S., Wackers, F., & Goulson, D. (2012). Neonicotinoid Pesticide Reduces Bumble Bee Colony Growth and Queen Production Science DOI: 10.1126/science.1215025

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