Boing Boing 

Lake Vostok bacteria: It's something new. No, it's not. Yes, it is, maybe.

Let's just play this safe and assume that, until more samples have been collected and detailed DNA analysis has been done, the real answer to the question, "Is bacteria found in Antarctica's Lake Vostok actually new to science or just contamination from the drilling?" is "We don't really know." This is a great example of why making scientific pronouncements from the field, before you've had time to do the really in-depth analysis that goes into writing a peer-reviewed research paper, can be problematic. Right now, you've got different camps of researchers making totally contradictory claims. Who is right is, so far, anybody's guess.

Sucking up to shrimp

Say you're a marine biologist and you want to study the little bitty creatures of the sea — shrimps and worms and things like that. How do you go about capturing them?

Why, with an underwater vacuum, of course.

At the PNAS First Look blog, David Harris writes that this "SCUBA-tank powered vacuum, called an “airlift,” inhales shrimp, sand fleas, marine worms, and 'things that would swim away if they had the chance.'"

Science and gun violence: why is the research so weak? [Part 2]

Part 2 of Science and gun violence: why is the research so weak?

The town of Macapá is in the north of Brazil, on the coast, where the Amazon River flows into the Atlantic.

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Wikipedia and libraries: a match made in heaven

John Mark Ockerbloom's "From Wikipedia to our libraries" is a fabulous proposal for creating research synergies between libraries and Wikipedia, by adding templates to Wikipedia articles that direct readers to unique, offline-only (or onsite-only) library resources at their favorite local libraries. Ockerbloom's approach acknowledges and respects the fact that patrons start their searches online, and seeks only to improve the outcomes of their research -- not to convince them not to start with the Internet.

So how do we get people from Wikipedia articles to the related offerings of our local libraries? Essentially we need three things: First, we need ways to embed links in Wikipedia to the libraries that readers use. (We can’t reasonably add individual links from an article to each library out there, because there are too many of them– there has to be a way that each Wikipedia reader can get to their own favored libraries via the same links.) Second, we need ways to derive appropriate library concepts and local searches from the subjects of Wikipedia articles, so the links go somewhere useful. Finally, we need good summaries of the resources a reader’s library makes available on those concepts, so the links end up showing something useful. With all of these in place, it should be possible for researchers to get from a Wikipedia article on a topic straight to a guide to their local library’s offerings on that topic in a single click.

I’ve developed some tools to enable these one-click Wikipedia -> library transitions. For the first thing we need, I’ve created a set of Wikipedia templates for adding library links. The documentation for the Library resources box template, for instance, describes how to use it to create a sidebar box with links to resources about (or by) the topic of a Wikipedia article in a reader’s library, or in another library a reader might want to consult. (There’s also an option for direct links to my Online Books Page, if there are relevant books online; it may be easier in some cases for readers to access those than to access their local library’s books.)

From Wikipedia to our libraries (via Making Light)

(Image: library card, a Creative Commons Attribution (2.0) image from raqkat's photostream)

How will the Sequester affect science

Basic science — the kind of research done for curiosity's sake, in order to better understand how parts of our world work — is the foundation of applied science — research that's aimed at developing a product, or tool, or achieving a goal. In the United States, the federal government is, by far, the number one funding source for basic research. So what happens to that investment in our future when things like the Sequester come along? Obviously, funding goes down. But the details are what's important here. Tom Levenson explains the short-term and long-term impacts.

A brief history of space monkeys and spies

In the late 1950s, American scientists very publicly readied a crew of monkeys for a series of trips into Earth orbit and back. As far as the researchers knew, Project Discoverer was an actual, honest-to-Ike peaceful scientific program. Naturally, they were wrong about that. In reality, their work was part of an elaborate cover-up masking a spy satellite program. At The Primate Diaries, Eric Michael Johnson reports on some fascinating space history.

Take a survey to help scientists improve indoor air quality

Researchers at the Lawrence Berkeley National Laboratory are studying how the seemingly innocuous things we do in our homes and offices can have big impacts on our health. One of those things is cooking, because the way we cook can affect the air we breathe. Scientists are trying to figure out how to make houses safer, but to do that, they need to understand how people use houses — what we cook in them and how we cook it. You can help by taking this quick, anonymous survey.

Lead and violent crime — why a good hypothesis isn't proof

We know that lead exposure can be dangerous. We know that it can cause brain damage. But what levels are dangerous. How does that damage express itself? And how do you separate the effects of lead poisoning from a whole host of other potentially dangerous, damaging factors? Last week, Mother Jones had a well-done article about research that is drawing connections between leaded gasoline and the crime wave of the mid 20th century. That's a hypothesis. It's a hypothesis with a lot of correlational evidence. But it's not proof. I recommend reading public health researcher Scott Firestone's excellent article that delves into the details of the studies from the Mother Jones story. It's a great look at the lines between public health as a science and public health as activism and it helps shine some light on why seemingly airtight cases aren't always immediately acted upon.

Science, confidential

We've talked here before about the crazy things you can find when you read the "Methods" section of a scientific research paper. (Ostensibly, that's the boring part.)

If you want a quick laugh this morning — or if you want to get a peek at how the sausages are made — check out the Twitter hashtag #overlyhonestmethods, where scientists are talking about the backstory behind seemingly dry statements like "A population of male rats was chosen for this study".

A toast to physics

You will be pleased to note that multiple physicists are at work on the problem of why a piece of falling toast tends to land with the butter side down.

It's time to start asking serious questions about the safety of lube

The stuff you use to make sex a little more smooth might have some serious drawbacks. Nothing has been proven yet — most of the data comes from disembodied cell cultures and animal testing, which doesn't necessarily give you an accurate picture of what's happening in humans — but several studies over the last few years have drawn connections between lubricant use and increased rates of STD transmission. (It also looks like some lubricants might kill off natural vaginal flora — the good bacteria that live "up there" and make the difference between a healthy vagina and, say, a raging yeast infection.)

Some of these studies have provided evidence suggesting that the ingredients in lubricants damage the cells lining the vagina and rectum — which would explain why those lubricants might facilitate STD transmission.

At Chemical and Engineering News, Lauren Wolf has a really well-researched, well-written story that will give you the low-down on this research without hype and without fear-mongering. Her story is easy to understand and explains what we know, what we don't know, and why this matters (besides the obvious, lubricants have been proposed as a possible means of applying topical anti-microbial STD preventatives).

Right now, the Food & Drug Administration doesn’t typically require testing of personal lubricants in humans. The agency classifies them as medical devices, so the sex aids have to be tested on animals such as rabbits and guinea pigs. Rectal use of lubricants is viewed by the agency as an “off-label” application—use at your own risk.

Questions about lubricant safety arose nearly a decade ago when micro­bicide developers were testing whether the detergent nonoxynol-9 could block HIV transmission. Manufacturers had been incorporating the compound into spermicidal lubricants for years because of its ability to punch holes in the cell membranes of sperm. In 2002, however, a Phase II/III clinical trial of a nonoxynol-9 vaginal gel failed to protect women from HIV infection. Not only that, but the detergent actually increased the risk of HIV infection in the sex workers tested—women living in countries such as South Africa and Thailand who used the product three or four times per day.

Lab work eventually revealed the reason for the paradoxical increase: Nonoxynol-9 is so good at punching holes in cell membranes that it not only bores into sperm but also into the cells lining the vagina and rectum. The mucosal lining of the vagina is a good barrier to infection all by itself, says Richard A. Cone, a biophysicist at Johns Hopkins University. But if that barrier gets compromised, all bets are off, he explains. After nonoxynol-9—still used on some condoms today—went from promising microbicide candidate to malevolent cell killer, scientists like Cone began to question the safety of other supposedly innocuous spermicide and personal lubricant ingredients.

Read the full story

Via David Kroll

Image: Beer Lube?, a Creative Commons Attribution (2.0) image from 28096801@N05's photostream

Gun lobby has opposed research on effects of gun ownership/gun laws

Photo: Shutterstock

Last week, after giving myself an initial overview of the scientific research on how gun ownership and gun laws affect violent crime, I told you that it seems like there's not a solid consensus on this issue. At least not in the United States. Different studies, of different laws, in different places seem to produce a wide variety of results.

On the one hand, this is kind of to be expected with social science. People are hard to pin down. Harder, often, than the Higgs Boson particle. And you can't just do a clean, controlled laboratory study of these issues. Instead, you're left trying to compare specific places, laws, and enforcement techniques that may not be easily comparable, in an attempt to draw a broad conclusion. That's hard.

But, it seems, the National Rifle Association has gone out of its way to make this work even more difficult than it would otherwise be. Since the early 1990s, NRA-backed politicians have attacked firearms research they believe is biased against guns. Alex Seitz-Wald at wrote a piece on this back in July, after an earlier mass shooting. He describes how a vaguely worded clause has lead researchers to avoid doing firearms studies at all, for fear of losing their funding.

The Centers for Disease Control funds research into the causes of death in the United States, including firearms — or at least it used to. In 1996, after various studies funded by the agency found that guns can be dangerous, the gun lobby mobilized to punish the agency. First, Republicans tried to eliminate entirely the National Center for Injury Prevention and Control, the bureau responsible for the research. When that failed, Rep. Jay Dickey, a Republican from Arkansas, successfully pushed through an amendment that stripped $2.6 million from the CDC’s budget (the amount it had spent on gun research in the previous year) and outlawed research on gun control with a provision that reads: “None of the funds made available for injury prevention and control at the Centers for Disease Control and Prevention may be used to advocate or promote gun control.”

Dickey’s clause, which remains in effect today, has had a chilling effect on all scientific research into gun safety, as gun rights advocates view “advocacy” as any research that notices that guns are dangerous. Stephen Teret, who co-directs the Johns Hopkins Center for Gun Policy and Research, told Salon: “They sent a message and the message was heard loud and clear. People [at the CDC], then and now, know that if they start going down that road, their budget is going to be vulnerable. And the way public agencies work, they know how this works and they’re not going to stick their necks out.”

In January, the New York Times reported that the CDC goes so far as to “ask researchers it finances to give it a heads-up anytime they are publishing studies that have anything to do with firearms. The agency, in turn, relays this information to the NRA as a courtesy.”

Read the rest

Via Dave Ng

Image: IMG_0362, a Creative Commons Attribution Share-Alike (2.0) image from neontommy's photostream

What science says about gun control and violent crime

Does gun control mean fewer guns on the street and less violence? Does encouraging gun ownership mean better protected people and less violence?

I don't think it's too early to be asking questions like this. When you're faced with a tragedy like what happened today at Sandy Hook Elementary School, it's reasonable to start asking questions about violence prevention. It's part of the bargaining stage of grief — wondering if there's something we could have done that would have prevented all those needless deaths. And let's get one thing straight: Everybody wants to prevent what happened today.

So what can be done about it? And what does the science say?

I've been trying to get a handle on that for the last hour or so and here are three things it seems we can definitively say:

• It would be completely accurate for someone to tell you that studies in places like Australia and Austria found that implementing more stringent gun control laws reduced deaths from gun-related suicides and violent crime.

• It would also be accurate to say that a study of the effects of the Brady Handgun Violence Prevention Act in the United States showed no big reductions in gun-related deaths, except for suicides among people older than 55.

• And it's also true that a 2003 study of conceal-carry laws in Florida found that they seemed to make no difference one way or the other — neither increasing nor reducing rates of violent crime.

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How experimental design can create conflicting results

Is coffee bad for you or good for you? Does acupuncture actually work, or does it produce a placebo effect? Do kids with autism have different microbes living in their intestines, or are their gut flora largely the same as neurotypical children? These are all good examples of topics that have produced wildly conflicting results from one study to another. (Side-note: This is why knowing what a single study says about something doesn't actually tell you much. And, frankly, when you have a lot of conflicting results on anything, it's really easy for somebody to pick the five that support a given hypothesis and not tell you about the 10 that don't.)

But why do conflicting results happen? One big factor is experimental design. Turns out, there's more than one way to study the same thing. How you set up an experiment can have a big effect on the outcome. And if lots of people are using different experimental designs, it becomes difficult to accurately compare their results. At the Wonderland blog, Emily Anthes has an excellent piece about this problem, using the aforementioned research on gut flora in kids with autism as an example.

For instance, in studies of autism and microbes, investigators must decide what kind of control group they want to use. Some scientists have chosen to compare the guts of autistic kids to those of their neurotypical siblings while others have used unrelated children as controls. This choice of control group can influence the strength of the effect that researchers find–or whether they find one at all.

Scientists also know that antibiotics can have profound and long-lasting effects on our microbiomes, so they agree on the need to exclude children from these studies who have taken antibiotics recently. But what’s recently? Within the last week? Month? Three months? Each investigator has to make his or her own call when designing a study.

Then there’s the matter of how researchers collect their bacterial samples. Are they studying fecal samples? Or taking samples from inside the intestines themselves? The bacterial communities may differ in samples taken from different places.

Read the full story at The Wonderland blog

Image: Apples & Oranges - They Don't Compare, a Creative Commons Attribution (2.0) image from thebusybrain's photostream

The kids dig minor keys: How pop music has changed since 1960

While 85% of Billboard Top 100 songs of the 1960s were written in a major key, that preference no longer holds true today. Minor key songs have become the majority, representing about 60% of modern hits. Scientific American's Helen Lee Lin delves into this, and other documented changes in musical preference. The research is totally interesting, even if the scientists don't seem to have a good idea of what it means. Maybe we're depressed. Or maybe we're just trying to sound more mature. Here's the original paper. (Via ScienceGoddess)

You, too, can be a guinea pig for pot

Sometimes, it's hard to find people interested in playing the role of guinea pig for the sake of science. And, sometimes, that job is not so hard. Like when what you want the guinea pigs to do is get real high. That's a good example.

Pot-based research isn't all fun and games. Given the interest in medical marijuana for cancer patients and people with AIDS, some of the studies require volunteers to, you know, have cancer or AIDS. Others are interested in the sociology — these scientists want to talk to you about your pot use and collect data about how it may or may not have affected your life.

But the mythical opportunity to "get high for science" really does exist, writes Brian Palmer at Slate.

The National Institutes of Health maintains an online database of clinical trials that are in the recruitment process. As of this writing, there are approximately 100 marijuana studies currently enrolling patients. Each listing contains inclusion criteria (the types of people the researchers are looking for) and exclusion criteria (characteristics that will remove otherwise qualified people from contention).

... there are a few trials that might interest someone looking for a free high. Consider the University of Iowa’s “Effects of Inhaled Cannabis on Driving Performance.” Participants will be dosed with varying amounts of alcohol or vaporized cannabis, then placed into a driving simulator to measure their performance. There are some restrictions. You must be a social drinker and marijuana user already, but you can’t have an addiction. People who are susceptible to motion sickness are out, and you must live near the driving simulator in Iowa. Keep in mind that getting into the study doesn’t guarantee free marijuana—two control groups will get no THC whatsoever. (Previous studies have shown that low doses of marijuana have little to no impact on driving performance.)


Image: Getting your head above the parapet..., a Creative Commons Attribution Share-Alike (2.0) image from kevenlaw's photostream

How to: Read the abstract of a scientific research paper

Abstracts are summaries — the short paragraph that usually explains the question a study was asking and the answers it found, plus a brief overview of what methods the researchers used. Because most peer-reviewed scientific research papers sit behind big, awkward pay walls, abstracts are often the only part of the paper that you, the general public, can easily read. That's why it's important to know what to look for in an abstract and how to interpret the information you read there. Noah Gray, a senior editor at the journal Nature, put together an introduction to abstracts. It's online at The Huffington Post.