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Maggie Koerth-Baker at 3:50 pm • • 
About 20 years ago, the United States and a few other countries started using a different pertussis vaccine than had been used previously. The change was in response to public fear about some very rare neurological disorders that may or may not have had a relationship to that older vaccine (it couldn't ever be proven one way or the other).
The vaccine we use today was created to get around any possible mechanism for those disorders and, along the way, ended up having lower rates of the less-troubling (and far, far more common) sort of side effects, as well. Think short-term redness, swelling, or pain at the site of injection.
The downside, reports Maryn McKenna, is that this new vaccine might not be as effective as the old one. In fact, scientists at the Centers for Disease Control, Kaiser Permanente Medical Center in San Rafael, Calif., and Australia's University of Queensland’s Children’s Medical Research Unit, are raising the possibility that a less effective vaccine could be part of why we're now seeing a big increase in pertussis outbreaks.
In the most recent research, a letter published Tuesday night in JAMA, researchers in Queensland, Australia examined the incidence of whooping cough in children who were born in 1998, the year in which that province began phasing out whole-cell pertussis vaccine (known as there as DTwP) in favor of less-reactive acellular vaccine (known as DTaP). Children who were born in that year and received a complete series of infant pertussis shots (at 2, 4 and 6 months) might have received all-whole cell, all-acellular, or a mix — and because of the excellent record-keeping of the state-based healthcare system, researchers were able to confirm which children received which shots.
The researchers were prompted to investigate because, like the US, Australia is enduring a ferocious pertussis epidemic. When they examined the disease history for 40,694 children whose vaccine history could be verified, they found 267 pertussis cases between 1999 and 2011. They said:
"Children who received a 3-dose DTaP primary course had higher rates of pertussis than those who received a 3-dose DTwP primary course in the preepidemic and outbreak periods. Among those who received mixed courses, rates in the current epidemic were highest for children receiving DTaP as their first dose. This pattern remained when looking at subgroups with 1 or 2 DTwP doses in the first year of life, although it did not reach statistical significance. Children who received a mixed course with DTwP as the initial dose had incidence rates that were between rates for the pure course DTwP and DTaP cohorts."
You can read the rest of the story at Maryn's Superbug blog
A key thing to remember: This is a nuanced theory that may or may not turn out to be right. But, if it does turn out that this vaccine isn't as effective as we want it to be, that's not a dark mark against vaccines, in general. Sometimes, medicine doesn't work as well as intended. It's a risk of medicine. And the fact that it's major research institutions pointing this possibility out, should give people some comfort in the scientific process. If doctors and organizations who promote childhood vaccination are all in the pockets of an evil conspiracy then there would be no reason why they'd ever do research like this, or talk about it publicly.
Image: Day 59, Project 365 - 12.18.09, a Creative Commons Attribution (2.0) image from williambrawley's photostream
Maggie Koerth-Baker at 1:08 pm • •
Scientists aren't always right. In fact, individual research papers turn out to be wrong pretty often and scientists are the first people to tell you that they don't know everything there is to know. They're just working on it with more rigor than most of us.
But scientists are also people. And sometimes, they lie. At Ars Technica, John Timmer looks at some of the most famous cases of scientific fraud and comes away with 8 key lessons that show us how science's biggest scam artists got away with faking their data—sometimes for years.
1) Fake data nobody ever expects to see. If you're going to make things up, you won't have any original data to produce when someone asks to see it. The simplest way to avoid this awkward situation is to make sure that nobody ever asks. You can do this in several ways, but the easiest is to work only with humans. Most institutions require a long and painful approval process before anyone gets to work directly with human subjects. To protect patient privacy, any records are usually completely anonymized, so no one can ever trace them back to individual patients. Adding to the potential for confusion, many medical studies are done double-blind and use patient populations spread across multiple research centers. All of these factors make it quite difficult for anyone to keep track of the original data, and they mean that most people will be satisfied with using a heavily processed version of your results.
3) Tell people what they already know. Since you don't want anyone excited about your work, due to the likelihood they will ask annoying questions, you need to avoid this reaction at all costs. Under no circumstances should your work cause anyone to raise an intrigued eyebrow. The easiest way to do this is to play to people's expectations, feeding them data that they respond to with phrases like "That's about what I was expecting." Take an uncontroversial model and support it. Find data that's consistent with what we knew decades ago. Whatever you do, don't rock the boat.
Maggie Koerth-Baker at 2:10 pm • •
Over at Download the Universe, Ars Technica science editor John Timmer reviews a science ebook whose science leaves something to be desired. Written by J. Marvin Herndon, a physicist, Indivisible Earth presents an alternate theory that ostensibly competes with plate tectonics. Instead of Earth having a molten core and a moveable crust, Herndon proposes that this planet began its existence as the core of a gas giant, like Jupiter or Saturn. Somehow, Earth lost its thick layer of gas and the small, dense core expanded, cracking as it grew into the continents we know today. What most people think are continental plate boundaries are, to Herndon, simply seams where bits of planet ripped apart from one another.
The problem is that Herndon doesn't offer a lot of evidence to support this idea.
Once the Earth was at the center of a gas giant, Herndon thinks the intense pressure of the massive atmosphere compressed the gas giant's rocky core so that it shrunk to the point where its surface was completely covered by what we now call continental plates. In other words, the entire surface of our present planet was once much smaller, and all land mass.
I did a back-of-the-envelope calculation of this, figuring out the radius of a sphere that would have the same surface area as our current land mass. It was only half the planet's present size. Using that radius to calculate the sphere's volume, it's possible to figure out the density (assuming a roughly current mass). That produced a figure six times higher than the Earth's current density — and about three times that of pure lead. I realize that a lot of the material in the Earth can be compressed under pressure, but I'm pretty skeptical that it can compress that much. And, more importantly, if Herndon wants to convince anyone that it did, this density difference is probably the sort of thing he should be addressing. He's not bothered; the idea that the continents once covered the surface of the Earth was put forward in 1933, and that's good enough for him.
Read the rest
Maggie Koerth-Baker at 9:05 am • •
Yesterday, during a World Science Festival panel on human origins and why our species outlasted other species of Homo, geneticist Ed Green mentioned that there were thousands of sequenced human genomes, from all over the world, that had been made publicly available. Our code is open source.
But where do you go to find it? Several folks on Twitter had great suggestions and I wanted to share them here.
The 1000 Genomes Project—organized by researchers at the Wellcome Trust, the National Institutes of Health, and Harvard—is working on sequencing the genomes of 2500 individuals. The data they've already collected is available online. Read a Nature article about The 1000 Genomes Project: Data management and community access.
The Personal Genome Project is interactive. Created by a researcher at Harvard Medical School, the program is aimed at enrolling 100,000 well-informed volunteers who will have their genomes sequenced and linked to anonymized medical data. Everything that's collected will be Creative Commons licensed for public use.
The University of California Santa Cruz Genome Browser is a great place to find publicly available genomes and sequences.
Thanks to Eva Rose, Aatish Bhatia, and Edward Banatt.
Maggie Koerth-Baker at 5:30 am • •
Photo:Eric Niiler
I spent last weekend in the Harvard Forest, participating in hands-on science experiments as part of the Marine Biological Laboratory's science journalism fellowship. The goal was to give us an inside look at what, exactly, scientists actually do. When you're reading a peer-reviewed scientific research paper, where did all that data come from?
Sometimes, it comes from a swamp.
On Saturday, we walked into the Forest's Blackgum Swamp to take core samples out of the muck. There was no standing water in this swamp, at least not when we visited. But I wouldn't call the ground "solid", either. Instead, it was more like a moss-covered sponge. With every step, the ground beneath me would sink and smoosh. In some of the lower patches, that meant a shoe-full of water. In other spots, it was just a disconcerting sensation.
Taking core samples involves a little machine that's like a cross between a shovel and a straw. Made of heavy, solid metal, it has an extendable handle on one end. At the other, there's a hollow, cylindrical chamber that can be opened and closed by turning the handle counterclockwise. You drive the chamber into the ground, turn the handle, and then pull it back out. Once everything is back on the surface, you can open the chamber and see a perfect cylinder of earth, pulled up from below. That cylinder is removed from the chamber, wrapped in plastic wrap, labeled, and put in a long wooden box. Then you do all of that again, in 50 centimeter increments, until you hit stone. We got to about 475 centimeters—15 feet deep. By that point, you'll have collected 1000s of years of layered sediment.
This is not as easy as it sounds.
Read the rest
Maggie Koerth-Baker at 5:00 am • •
Every now and then, I get a glorious reminder of just how much the Internet has enriched my life. Fifteen years ago, if I had arrived at a conference center—as I did yesterday for my stint in the Marine Biological Laboratory Science Journalism Fellowship program—and seen a sign in the lobby announcing the presence of a "Xenopus Workshop" I could have, eventually, found out that a Xenopus was a frog frequently used as a model animal in medical research.
Thanks to the Internet, though, I was able to learn the following things in a remarkably short period of time:
Xenopus Fact: Xenopuses (Xenopodes? Xenopi? Freshman Latin was a really long time ago, you guys) were used in one of the earliest reliable pregnancy tests. That's because exposure even a tiny amount of the hormone human chorionic gonadotropin will cause a female Xenopus to lay eggs. Inject a female Xenopus with urine from a human female and, if the Xenopus lays eggs, it means the female human is knocked up.
Xenopus Fact: You know how some lizards can grow a new tail if you cut the old one off? Xenopuses can do that with the lenses of their eyes.
Xenopus Fact: Because Xenopuses are so widely used in laboratories, there's a whole industry of suppliers of Xenopuses and Xenopus accessories. Case in point, the "Xenopus enrichment tube" in the photo above—apparently, they like to have something to hide out in. Also, you can buy synthetic slime to replace your Xenopus' natural protective coating that is often lost through frequent handling.
Maggie Koerth-Baker at 11:34 am • •
Earlier today, David told you about a news story that's everywhere right now: The fact that the Kodak company ran a small nuclear facility at its research lab in Rochester, New York.
The facility closed down in 2007, but I can totally understand why this story interests people. It's nuclear! And it is really weird for a corporation to be sitting on 3.5 pounds of uranium. Like David said, this is unusual today. David did a good job covering this in a sane way. The TV news I saw this morning at the airport ... not so much. That's why I like the detail provided the Physics Buzz blog, where Bryan Jacobsmeyer explains, better than I've seen elsewhere, just what exactly Kodak was doing with their nuclear system. Turns out, it's really not all that odd for this specific company to own this specific piece of equiptment when they did. That's because of what Kodak was. We're not just talking about a corporation in the sense of middle managers and salesmen. We're talking about original research and development—a job for which a californium neutron flux multiplier is quite well suited.
In fact, these research reactors can be found on several university campuses, and they are operated under strict guidelines without any nefarious intentions.
Researchers working at Kodak wanted to detect very small impurities in chemicals, and Neutron Activation Analysis (NAA) proved to be one of the best techniques to find these impurities. During NAA, samples are bombarded with neutrons, and elemental isotopes from the sample will absorb a small fraction of these neutrons.
Many of these stable elemental isotopes will become radioactive after gaining a new neutron; consequently, they will emit gamma rays. With the right equipment, researchers can measure the precise energy levels of this radiation and narrow down which elements are in the sample.
Basically, it provided a way to sift through the components of a sample at a molecular level, and spot the things that shouldn't be there. Originally, the lab used just californium. Later, it added uranium plates that helped make the system more powerful.
Read the full Physics Buzz post
Image: IMG_7391.jpg, a Creative Commons Attribution (2.0) image from jameskarlbuck's photostream
Maggie Koerth-Baker at 2:26 pm • •
Last week, scientists used ice caves in Austria as a stand-in for Martian caves, testing spacesuits and rovers in the freezing chambers. This week: We go to the desert near Baker, California, where NASA is testing out its Curiosity rover. Curiosity is 86 days away from landing on the real Martian surface.
Gene Blevins / Reuters
Maggie Koerth-Baker at 9:24 am • •
The Eisriesenwelt—the "World of the Ice Giants"—is an Austrian cave that stays cold enough year-round to freeze any water that gets into it. As a result, the cave is full of massive ice formations. On April 28th, it was also full of people like physicist Daniel Schildhammer (seen above) who came to the cave to test out a wide array of space technologies, from protective suits to roving robots. It's all part of an international effort to prepare for a mission to Mars. Caves on Mars are likely place where bacteria and other forms of microbial life might be hiding out—the temperatures stay steady underground and the cave would protect those microbes from cosmic rays. Below: Another scientist tests out a rover meant to scale cliffs.
Images: REUTERS/Lisi Niesner
Maggie Koerth-Baker at 4:34 pm • •
When I was little, I read a Reader's Digest book of great disasters, which included a segment on the Black Death. One of the things the book tried to do was explain, on a child's level, why it wasn't easy to figure out that rats and fleas were the source of the plague. You couldn't just look for patterns, because there seemed to be no pattern. Half a household might drop dead while the other half only got a little sick, or remained entirely healthy. Plague doctors who handled the sick every day lived another 20 years. The real spread of disease wasn't like the movies, where one person coughing means everyone in close proximity is doomed.
One reason for the emergence of strange non-patterns like this is something called "super spreaders"—basically, some people spread disease more effectively than others. The infamous Typhoid Mary is the poster child for super spreaders, but the effect has been well-documented in a range of infectious diseases and it goes beyond the simple story of one woman who infected thousands. In fact, what makes the super spreader phenomenon so fascinating is that it isn't an anomaly at all. Super spreaders are the primary way some diseases spread. The Contagions blog—which is all about the history of infectious disease—has a great post up about this.
Eventually new models arose like the “20/80″ rule that says that 20% of cases are responsible for 80% of the transmission and formed a core ‘high risk’ group. This model works well for some diseases but not all.
For pathogens that do rely on super-spreaders, the majority of cases will not transmit the infection to anyone. This can lead to a sense of false security because it seems poorly communicated. As Galvani and May assert, “heterogeneously infectious emerging disease will be less likely to generate an epidemic, but if sustained, the resulting epidemic is more likely to be explosive”. Super-spreaders tend to beget more super-spreaders, although most of the cases they generate will still not transmit the infection to anyone. For example, a super-spreader begets 30 cases, 3 (10%) of which become new super spreaders. The rest may transmit to 0-1 people.
Super-spreading has been documented for HIV, SARS (Sudden Acute Respiratory Syndrome), measles, malaria, smallpox and monkeypox, pneumonic plague, tuberculosis, Staphylococcus aureus, typhoid fever, and a variety bacterial sexually transmitted diseases.
And that brings us back to medical mysteries because, the Contagion blog explains, we don't know exactly why some people are super spreaders and others aren't—or why some people are more vulnerable to infection than others. So far, what we have to go on is a list of well-established correlations.
Read about what makes a super-spreader at the Contagions blog.
Image: Thomas Bartholini's illustration of beak doctor from 1661. Via Wikipedia.
Maggie Koerth-Baker at 9:38 am • •
See the box in this photo? It's more interesting than it looks. This is a box that went to the Moon.
Astronauts used the boxes to collect and bring back to Earth nearly 50 pounds of moon rocks and soil ... Each of the boxes was machined from a single piece of aluminum, "seamless except for the lid opening, which had a metalized gasket that firmly sealed when closed."
The photo comes from the Y-12 National Security Complex in Oak Ridge, Tenn.—a research facility that participated in the Manhattan Project and later was involved in designing equipment for the Apollo Project. Journalist Frank Munger writes about Y-12 and other parts of the Oak Ridge National Laboratory for the Knoxville News Sentinel.
This photo, which he posted on his blog, is also interesting because nobody knows who the three guys in the photo are. Munger was hoping that Boingers might be able to offer some leads.
Maggie Koerth-Baker at 9:10 am • •
I recently had what I am pretty sure was foodborne illness. It arrived in the middle of a friend's birthday party, a sudden onslaught of misery that lasted for the next 8 hours, reminding me, horribly, of a similar scene in The Mask of the Red Death. It was followed by two days of pretty much constant sleep. I don't recommend it.
But if a growing body of research is right, that 48-hours of grossness might not be the end of your body's interaction with a foodborne bug. In fact, some people seem to have otherwise unexplained symptoms persisting for years after they thought they'd recovered from food poisoning. This is best documented in people whose food poisoning experience was much worse than mine—folks who ended up in the hospital or the doctor's office and were, thus, accurately diagnosed, so we know they had a foodborne illness and not, say, a stomach flu. But it's an interesting hypothesis.
Maryn McKenna, my favorite Scary Disease Girl, has a story about this at Scientific American, plus some extra information at her Wired blog, where she explains why this phenomenon is so difficult to study.
I start the story with the tale of a Florida teen named Dana Dziadul, who 11 years ago was hospitalized with Salmonella and now at 14 has what is called “reactive” arthritis. Her mother Colette struggled for years to figure out why this was happening to her daughter, but didn’t put the pieces together until she was asked to complete a survey of foodborne illness survivors, and spotted a list of possible after-effects — sequelae, technically — that the surveyors were curious about. That caused her to go back into Dana’s medical chart, where she realized that her daughter’s joint problems actually began while she was hospitalized as a 3-year-old.
The challenge of proving this connection is that our system for investigating foodborne illness is not set up for tracking victims long afterward. That’s first because state health departments, which bear the burden of identifying outbreaks, are most concerned with finding people at the time, not keeping track of them; and second, because many outbreaks are spread across multiple states, with only a few victims in each state — so that maintaining contact with former victims would require a shared effort that no one is set up, or funded, to do. (That’s not even to mention the complication of people moving from one jurisdiction to another. Myself, for instance, I’ve moved five times in the past 10 years.)
Read the full story at Scientific American.
Read Maryn's summary of the research, and extra info, at her Wired blog.
Image: X.L.D. Agar 1 - detail, a Creative Commons Attribution (2.0) image from nathanreading's photostream
Xeni Jardin at 11:47 am • •
Amazon founder and space entrepreneur Jeff Bezos announces on his blog that the Apollo 11 rocket engines which propelled Neil Armstrong and Buzz Aldrin to the moon in 1969—making them the first humans on the moon—have been found on the bottom of the Atlantic ocean by Bezos' research team. Next step? Finding a way to safely recover the long-lost engines, and bring them back to the surface.
Snip:
Millions of people were inspired by the Apollo Program. I was five years old when I watched Apollo 11 unfold on television, and without any doubt it was a big contributor to my passions for science, engineering, and exploration. A year or so ago, I started to wonder, with the right team of undersea pros, could we find and potentially recover the F-1 engines that started mankind's mission to the moon?
I'm excited to report that, using state-of-the-art deep sea sonar, the team has found the Apollo 11 engines lying 14,000 feet below the surface, and we're making plans to attempt to raise one or more of them from the ocean floor. We don't know yet what condition these engines might be in - they hit the ocean at high velocity and have been in salt water for more than 40 years. On the other hand, they're made of tough stuff, so we'll see.
Read more at his Bezos Expeditions blog.
Maggie Koerth-Baker at 9:48 am • •
We recently hosted an article by scientist and guest blogger Stephan Guyenet that explained how certain foods—those with a high calorie density, fat, starch, sugar, salt, free glutamate (umami), certain textures (easily chewed, soft or crunchy, solid fat), certain flavors, an absence of bitterness, food variety, and drugs such as alcohol and caffeine—could trip reward systems in the human brain. Those reward systems, then, encourage people to eat more of the foods that trigger the reward. The result, says Guyenet, is a cycle that could be the link between the American obesity epidemic and the rise of highly processed convenience foods, designed specifically to trip those neural reward systems.
This theory, and several related theories, are increasingly popular in the scientific community. This week, there's an opinion piece in the journal Nature Reviews Neuroscience that looks at the strengths and weaknesses of these theories and talks about what research needs to be done going forward. It's kind of a space for researchers to step back and say, "Okay, here's what we know, here's what's not lining up with what we think we know, and here's what we have to do if we want to understand this better." In the context of science, an article like this isn't really a slam against the ideas it analyzes. Instead, it's meant to summarize the state of the science and share ideas that could either strengthen the case, or lead down entirely new roads.
Sadly, you can't read this article unless you have a subscription to Nature Reviews Neuroscience (or pay them $32 for single article access).
Luckily, Scicurious, a neuroscientist and an excellent blogger, has read the article, and has a nice run-down of what it's saying and what you should know. Some of the ideas being discussed here overlap with Stephan Guyenet's research. Some don't. But this is connected enough that I thought you guys would be interested in reading more and getting more perspectives on this issue. Let me make this clear, though: Guyenet isn't doing bad science. As with a lot of scientific research, there's often more than one way to look at the same data. Scientists can disagree without one person having to be all-wrong and another all-right. In fact, having different scientists working on the same subject is a key part of getting the facts right.
As you read, you'll notice that an important place where Scicurious' perspective really differs from Guyenet's is in terms of connecting the idea of "addiction" to certain foods back to the idea of an obesity epidemic.
...is there a place for food addiction? The authors think so, and I am inclined to agree. However, it needs to be much more stringent than the current model of food addiction that many people want to embrace (the idea that sugar makes you addicted or that being overweight means you have a problem). Changes need to be made.
First off, it's important to separate food addiction from obesity. Binge eating does not necessarily mean you are overweight, and being overweight does not necessarily mean that you binge eat. Ranking by BMI is not going to work.
(Via the illustrious Ed Yong. Image: Fabio Berti, Shutterstock)
