Six ways to help scientific integrity in the government

by JoshBerglund19

Welcome to the OSTP Blog:
[Via OSTP Blog]

Welcome to the OSTP blog, a place where you can learn about and have real input into the policymaking process as it relates to science and technology. The art and science of crafting sound government policy has long depended on public input, but new technologies now allow the process of public input to be multidimensional and dynamic. Among other things, that means members of the public can start to have a conversation about policy. Please take responsible advantage of this new aspect of democracy—in this first instance by reading the President’s memorandum

on scientific integrity and considering how the goals in that document might best be met. Give the topic some thought (we’ve provided a simple question alongside each of the six initial scientific integrity sub-issues, to help get the conversation going). Then share your ideas, your concerns, and your hopes.

Rick Weiss
OSTP Director of Strategic Communications

The Office of Science and Technology Policy has started a blog! It even states that this is a way for the public to have a conversation, that new technologies allow this conversation “to be multidimensional and dynamic.”

I’m not quite sure what a multidimensional conversation in (more than 3-D? Are we talking about some sort of 12-dimensional speech? Wow!) but it sure sounds wonderful.

Anyway, the President released a memo in March about Scientific Integrity and the OSTP is beginning its public input section. You can read about the details in a factsheet.

The OSTP has provided an area on the blog for people to discuss each of the 6 subsections of the memo: the metrics used to determine a science candidate’s knowledge, credentials, experience, and integrity; the processes used to maintain scientific integrity; the organizational structures needed for assuring scientific reliability; the best ways for maximizing public release of scientific information; determining when scientific integrity has been compromised; and, the best ways to make sure the information is reliable.

I know I will have lots to say. Now is your chance.

Technorati Tags: Politics, Science, Social media

When the pressure is on

by wwarby
Conducting Research in Disease Outbreaks:
[Via PLoS Neglected Tropical Diseases: New Articles]

Conducting research in an emergency situation, such as an outbreak of disease, poses ethical challenges. These challenges differ according to the type of research: epidemiologic or clinical, and for the latter, whether the disease outbreak can be anticipated in advance. We address these three situations, proposing different potential solutions for each.

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This is a very nice discussion of what must happen in order to carry out research during a disease outbreak. There are many ethical considerations that are under enormous time pressures. Not everyone really thinks about these beforehand.

Obtaining the proper permission, getting regulatory approval, etc. usually take place in a timeframe of weeks and months. But during an outbreak, minutes can be critical. So there needs to be a process for dealing with these questions. I am sure we will see just how much we have prepared for these processes in the next few weeks.

Technorati Tags: Health

Could flies be the difference?

by Opo Terser
CDC Offers Theories on Disparities in Swine Flu Severity:
[Via Medscape Infectious Diseases Headlines]

The acting director of the CDC offered a handful of theories in a press conference today about why the swine influenza outbreak has produced fatalities in Mexico, but not so far in the United States or elsewhere.
Medscape Medical News
[More]

Things are moving really rapidly. The CDC has gotten new kits out to public health officials to check out flu cases. Lots of work being done to create new vaccines. And some of the anti-virals look like they will be effective.

So, why the difference in severity between cases in the US and in Mexico? The CDC provides some of the obvious ones that are likely to be correct.

But, I wonder about a couple of other, more speculative possibilities. Some officials in Mexico say the vector for spreading the disease is a biting fly from the area. Transfer by insects is not a normal route for transmission of influenza and there are not many papers that examine this possibility.

A paper from 2006 found another strain of influenza (an H5N1 rather than H1N1) in blow flies. A more recent paper detailed the identification of mosquitos carrying influenza virus. So insects can harbor the virus.

Not much work has been done to investigate the ability of insects to transmit the virus. But I wonder if blood-to-blood transmission of the virus by biting insects could increase the apparent virulence of an influenza virus. The virus would get directly into the bloodstream rather than have to get in through the lungs.

I’d feel a lot better if there was some more definitive work on transmission of influenza by blood-sucking insects. I figure we will hear more shortly.

Technorati Tags: Environment, Health

We are Dr. Frankenstein

by Olddanb
Swine-flu outbreak linked to Smithfield Foods:
[Via Gristmill]

According to Mexican press accounts, thedeadly swine-flu outbreak now spreading into the U.S. is linked to large-scale hog operations in Mexico run by industrial-meat giant Smithfield Foods. WHO officials warned Saturday that the outbreak could reach pandemic levels.

[More]

I have not written anything on the flu epidemic because so many things are still changing. But I thought this article was possibly interesting. The details may change a lot in the next few days but it is a cautionary tale of how our methods for raising livestock could be very harmful to us.

It may take more time to get the location of ground zero figured out. Just because local source says that is what happened does not make it so. A little skepticism is warranted right now.

But, the circumstantial evidence is very intriguing. This huge pig operation is exactly where one might find the sort of epidemic flu we may be seeing begin its spread. The fact that the possible epicenter for a pandemic flu contains all the things needed for such a virus raises a strong case to be made. Further investigation will be warranted.

And the unique nature of the influenza virus makes it likely that, like Victor Frankenstein, we could create a monster made up of bits and pieces from a variety of sources that will have a tremendous impact on our lives. We would be the creators of our own calamity.

Influenza is an unusual sort of virus. Its genetic material is not a single piece of DNA; it is carried on 8 different RNA segments, almost like very small chromosomes.

And multiple influenza viruses can infect a single cell. So what can happen when multiple viruses infect a single cell? You get reassortment where new virus particles contain a mixture of segments from each of the different viruses.

So just as in the book by Mary Shelley, the new virus is made up of pieces from a variety of bits of genetic material. In this case, from different viruses.

Influenza viruses infect birds and humans. But generally, the influenza viruses for each species do not infect the other species very well. The worry about so called avian flu is that it would be a bird flu that could directly infect humans. Luckily this is not very easy to do.

Pigs hold a special place for influenza epidemics. They can actually be infected by both bird flu and human flu, as well as swine flu. So they have historically served as a wonderful reservoir for reassortment between bird, swine and human influenza viruses, resulting in a novel virus that can infect humans even though it contains genes from a bird virus.

When this happens, the new virus often can not be effectively fought off by our immune systems. If the new virus then can spread human to human, we get a pandemic.

So, the pig has historically been the animal that allows bird influenza to enter the human population, or at least some of the bird influenza genes. And, historically, Asia has been the hotbed of influenza outbreaks because it has been a one place in the world where large numbers of birds (such as ducks) have been raised in close proximity to pigs with large numbers of humans around.

But any place where there are lots of pigs plus lots of birds, with substantial human contact, is a potential breeding place for novel influenza viruses.

There have been large scale outbreaks of influenza in Mexican fowls before, some quite deadly.There are also apparently lots of ducks in Mexico that have been settling down in the huge fecal lagoons that are found at every large scale pig factory (read this old article from Rolling Stone to get an idea of what this is like). Almost a million pigs were produced at this plant in Mexico last year.

So, we have huge, relatively unclean factories with incredible numbers of pigs, large numbers of birds that have been known to carry avian flu viruses and lots of humans. A perfect incubator for a pandemic flu.

Here is a quote from a paper on influenza viruses:

Avian influenza viruses in wild aquatic birds are spread by fecal-oral transmission through the water supply (10); initial transmission of avian influenza viruses to mammals, including pigs and horses, probably also occurs by fecal contamination of water. Scholtissek has postulated that the use of fecal material from ducks for fish farming in Asia may contribute to transmission of avian influenza viruses to pigs (11). Another direct method of transfer is by feeding pigs untreated garbage or the carcasses of dead birds. Raising pigs under chicken houses and feeding them dead avian carcasses has been observed on rare occasions in the United States; H5N2 influenza virus was isolated from pigs living under chicken houses in Pennsylvania during the outbreak in 1982. Both pigs and poultry are commonly raised on the same commercial farms. From the perspective of the control of interspecies transmission of influenza, this is undesirable, for it may facilitate interspecies transmission of influenza viruses. After transmission to pigs, horses, or humans, the method of spread of influenza is mainly respiratory.

The bitting fly might be the vector that is involved, although I’m not so sure it would have much to do with a epidemic. This virus does not need blood to blood contact. It is spread human to human. This could just be a red herring.

So all it takes for an easy creation of a pandemic influenza virus is for there to be birds with influenza virus that pass it to the pigs. Throw in a sick employee and you have a ripe mix for reassortment of a deadly virus from bird, pig and human sources.

Following reassortment in the pigs, the virus can be spread a lot of ways. Perhaps contact between employees and the infected pigs. Or perhaps from the fecal lagoons where the virus could be released in a multitude of ways (i.e. release of fecal water, aerosolized by spraying, etc.) Someone breathes this in, gets sick and starts the spread.

It would be very ironic if a pandemic influenza virus was created due to the factory farming practices we have developed. In the end, Dr. Frankenstein died still fighting his creation. I hope that is not what lies ahead for us.

I’m hoping that the movie version is more descriptive. The one with Karloff, where the monster is fairly stupid and easily manipluated, dying in a huge conflagration while Dr. Frankenstein lives on … awaiting the inevitable sequel but with a wisdom borne of strife.

Technorati Tags: Science, Sustainability

Torture hurt us

by publik15
‘We Could Have Done This the Right Way’
[Via Newsweek]

The arguments at the CIA safe house were loud and intense in the spring of 2002. Inside, a high-value terror suspect, Abu Zubaydah, was handcuffed to a gurney. He had been wounded during his capture in Pakistan and still had bullet fragments in his stomach, leg and groin. Agency operatives were aiming to crack him with rough and unorthodox interrogation tactics—including stripping him nude, turning down the temperature and bombarding him with loud music. But one impassioned young FBI agent wanted nothing to do with it. He tried to stop them.

[More]

This may make a great movie someday as it has all the elements we like to see – lone man standing up to authority, expertise initially overridden by expediency followed perhaps by vindication. The FBI agent was instrumental in the investigation of the Cole bombing, using his knowledge of the Quran to help change the views of the prisoners. He was able to do the same with Abu Zubaydah:

Last week Soufan, 37, now a security consultant who spends most of his time in the Middle East, decided to tell the story of his involvement in the Abu Zubaydah interrogations publicly for the first time. In an op-ed in The New York Times and in a series of exclusive interviews with NEWSWEEK, Soufan described how he, together with FBI colleague Steve Gaudin, began the interrogation of Abu Zubaydah. They nursed his wounds, gained his confidence and got the terror suspect talking. They extracted crucial intelligence—including the identity of Khalid Sheikh Mohammed as the architect of 9/11 and the dirty-bomb plot of Jose Padilla—before CIA contractors even began their aggressive tactics.

Using the same sorts of social engineering techniques as sometimes seen on TV, as well as fluency in the languages, and adding in the background to discuss religion in ways to turn a prisoner. Soufan accomplished what we all imagine an American interrogator could. He got valuable information simply by being smart, not by being brutal.

He even went to Gitmo to help training:

Soufan became a teacher for other interrogators. McFadden says that in early 2002, Soufan flew to Guantánamo to conduct a training course. He gave a powerful talk, preaching the virtues of the FBI’s traditional rapport-building techniques. Not only were such methods the most effective, Soufan explained that day, they were critical to maintaining America’s image in the Middle East. “The whole world is watching what we do here,” Soufan said. “We’re going to win or lose this war depending on how we do this.” As he made these comments, about half the interrogators in the room—those from the FBI and other law-enforcement agencies—were “nodding their heads” in agreement, recalls McFadden. But the other half— military intelligence officers—sat there “with blank stares. It’s like they were thinking, This is bullcrap. Their attitude was, ‘You guys are cops; we don’t have time for this’.”

When he stood up against CIA techniques, the final response was for the FBI to withdraw ALL its personnel from the interrogations. The guys with the most expertise in interrogating Muslim prisoners, who had a record of obtaining information that undoubtedly saved lives, were no longer involved.

Someone please explain how this helped us.

Technorati Tags: Politics

Bummer news

NOAA stunner: “Methane levels rose in 2008 for the second consecutive year after a 10-year lull,” CO2 up 2.1 ppm to highest levels on record “despite economic slump”:
[Via Climate Progress]

NOAA stunner: “Methane levels rose in 2008 for the second consecutive year after a 10-year lull,” CO2 up 2.1 ppm to highest levels on record “despite economic slump”

[More]

This is not good news. We hear about CO2 emissions a lot because the anthropogenic emissions of these are huge. BUt CO2 is not the most potent greenhouse gas.

Methane is 25 times more potent than CO2. It is trapped in the permafrost and in the ocean. Warming temperatures release this methane into the atmosphere.

It is this release by a warming climate that has many scientists very concerned. If this methane is released, it can start a new climate regime with a much warmer climate – one that will stay hot, no matter how much we lower carbon emissions.

This is the real worry of climate change, that the pumping of huge amounts of CO2 into the atmosphere alters climate enough that new feedbacks prevent us from stabilizing it by reducing CO2 emissions.

So, increasing methane in the atmosphere is not good news at all.

Technorati Tags: Environment

Some call it denying, I call it fiddling

by bjortklingd
Industry spin on climate is still working on media:
[Via Gristmill]

New York Times reporter Andy Revkin has a blockbuster story showing that the Global Climate Coalition, the main industry group that spent much of the 1990s seeking to sow doubt in journalists’ and politicians’ minds about the reality of climate change, knew all along that it was real and dangerous.
[More]

Why are the guys ever listened to? They lied and misled 10 years ago. Many are still doing it today. Have they no shame at all?

Their own scientists told them that climate change was real and needed to be dealt with. And they were ignored.

This Coalition actually had the information to know that they were wrong, that their stalling tactics would imperil the rest of the world. All so they could keep making money. To quote Timothy: “For the love of money is the root of all evil: which while some coveted after, they have erred from the faith, and pierced themselves through with many sorrows.”

Unfortunately, they may have pierced the rest of us also.

And the media still keeps repeating their deceptions. I’m sure these guys in Nero’s time would have said “We can’t be certain the town will burn down and besides, if it was on fire, would the Emperor be playing such lovely music on the lyre?”

And the press would have written “Fire in Rome? Opinions differ.”

Technorati Tags: Environment, Science

Like a coyote

An icy Antarctic paradox:
[Via CEJournal]

The ozone hole is masking the impact of global warming in Antarctica

This image from NASA’s Aura satellite shows the extent of severe ozone depletion over Antarctica in September of 2008. (Image: NASA Earth Observatory Image of the Day)

Climate skeptics got their undies all in a bundle this past weekend over publication of an article in [...]

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For some reason, deniers of science think that if they can find one segment of a theory or model that is wrong, then the whole thing is invalidated. Because of this, they often grasp at anything, even something misleading, to provide this inconsitency.

Unfortunately for them, this is not how science works. A single fault does not usually destroy the framework. It often simply results in a modification or a whole new area of research.

Here, the misleading premise – that increasing ice in Antarctica means global warming is wrong – is simply wrong. As the article states, the ozone hole is modifying the effects on warming.

The ozone hole, the first real manifestation of humankind’s effect on the climate, is likely masking effects on another manifestation. That is a very nice explanation that can be easily be examined.

As opposed to simply howling “Wrong!” at the moon. And about as effective.

Technorati Tags: Environment

Stupid is as stupid does

Speaking of Texan doomism…:
[Via Bad Astronomy]

… I don’t know what to make of this clip of Texas Congresscritter Joe Barton (who once said that taking action against global warming is “absolute nonsense”) asking Secretary of Energy (and Nobel Laureate) Steven Chu about the origin of gas and oil in Alaska.

Is he denying global warming? Is …
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Explain petroleum geology and plate tectonics in 6 seconds. Nice question. Then he tweeted that he had stumped the Nobel Prize winner with that question.

Grandstanding politicians are one thing. BUu we can now all see ow they abuse science and scientists. Its one thing if they use sophisticated rhetoric to make a point (as detailed at Climate Progress).

This is about as far away from sophisticated as one can get. About on level with “I know you are but what am I.” Luckily Chu has obviously dealt with really stupid questioners and knows how to deal with them.

Anyway, Chu is a very droll subject. I love his answers detailed here.

Technorati Tags: Politics, Science

Conference presentations

from Wellcome Library
Black hole spews water vapour:
[Via BBC News | Science/Nature | World Edition]

Astronomers have found the most distant evidence of water in the Universe, a major conference has been told.

The vapour is thought to be present in a jet ejected from a supermassive black hole at the centre of a galaxy that is billions of light-years away.

The discovery, by a US-European team, was announced at the European Week of Astronomy and Space Science meeting.
[More]

Nice to see that this was done with Earth-bound technology. The Hubble’s pictures usually overshadow most everything else because they are so detailed and awe inspiring. (See this discussion of just one recent photo).Masers are not quite as sexy as lasers (I don’t think one has been used in a James Bond movie) but are interesting nonetheless.

This work was actually first revealed back in December. This latest article appeared because the data were presented at a conference. This would be one of the first times for other scientists to see the work themselves and ask questions about it.

Such public displays of a researcher’s work are often a critical part of the vetting process. Any bias or weakness in the data can be revealed and examined, usually in the Q & A segment.

I’m sure these researchers had little difficulties presenting their work. It is reasonable straightforward and probably not subject to harsh questioning by the audience.

That is often one of the fears that many presenters at conferences – that there is a heretofore unseen flaw in the scientific rigor of the project that will be revealed by careful, devastating probing of the audience, holding the speaker up to public ridicule.

That is why we are all trained in the tools of a politician at a difficult town meeting: obfuscation, answering a question that was not asked, misunderstanding the question, dropping the mike, stepping off the stage, fainting, etc.

While it does not happen often (fear of public humiliation is a strong stick to help ensure rigor), we are all aware of when a particularly hard question has been asked and the presenter dances around the question, trying to delay things until they can say “Well, why don’t we discuss this later so we don’t take up anymore time from the other speakers?”

But sometimes the most fun, for an unbiased audience member, is when two bitter rivals dance around each other like a classic Saturday Night Live routine.

It’s why I always love the Q & A part of a meeting. It has historically been the first time many scientists have had to state their support or objections to a line of research. So I can gather an idea for how the scientific community feels about a line of research.

Now, we can do a lot of this online (even the ‘ignorant slut’ part), with blogs and such. But I still like to see the real-life give and take of a good Q & A after a presentation. Those are the things that make memories at the pub afterwards.

And often produce beer stained doodles detailing new lines of research.

Technorati Tags: Science

How about ‘Save Our Butts’ Day?

by woodleywonderworks
Let’s Dump “Earth Day”:
[Via Climate Progress]

Affection for our planet is misdirected and unrequited. We need to focus on saving ourselves.

Last year, I wrote a piece for Salon, “Let’s dump ‘Earth’ Day.” It was supposed to be mostly humorous. Or mostly serious. Anyway, the subject of renaming Earth Day has been on my mind for a year now – and all the more so today because the NYT magazine just published an interview with our Nobel-prize winning Energy Secretary, Steven Chu, in which he says:

I would say that from here on in, every day has to be Earth Day.

Well, duh! Heck, we have a whole day just for the trees – and we haven’t finished them off … yet. So if every day is Earth Day, than April 22 definitely needs a new name. So I’m updating the column, with yet another idea at the end, at least for climate science advocates:

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As has been stated many times, the Earth will do just fine, no matter what we do, as will life on Earth. This is all about trying to maintain a climate on Earth that is close to the one we have evolved, both physically and socially, to thrive in.

We created the INdustrial Revolution in part to solve the problem of exponential population growth vs. arithmetical agricultural increase. Now we are having to deal with the fallout of Industrial Age approaches, while again dealing with the exponential vs. arithmetical.

Again, we do have the tools to fix this. Will we have the strength and foresight? I believe so but I would feel a whole lot better if the climate changes we are seeing were significantly less than predicted by the models. At the moment, the models have been underestimating the changes seen in the climate.

Technorati Tags: Environment, Sustainability

This could work

Switch and bait:
[Via Crooked Timber]

As I mentioned previously on this blog, I had a somewhat unfortunate experience a few months back. I was working in my office, when a work-study knocked on my door with a brand new MacBook Pro, which he told me had been sent over from my school’s technology program. I was nonplussed, and told him that he must be wrong, that I hadn’t ordered one etc, but he insisted, and indeed my name was on his work-order form. So I finally acquiesced, on the grounds of gift-horses, and the wisdom of not inquiring too closely into the dental conditions thereof, and unpacked it. 2 hours later, I was completely hooked – more rational and altogether nicer than my Windows box, while much smoother than my Ubuntu installation. I would have wanted to take it home and marry it, if I wasn’t married already. 3 hours later, I discovered that of course it had been a mistake, and that it was in fact intended for a colleague with a vaguely similar name (the person preparing the work order had not unreasonably gotten confused). And I had to give it back.

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He went out and bought a Mac shortly thereafter.

So his suggestion is for Apple to ‘accidentally’ send a Mac to unsuspecting Windows people. Let them have it for a few days. Then show up and film their response when it is explained that it was a mistake , that Apple is there to take back the computer.

They could even have Justin Long and John Hodgman show up to discuss the ‘error’ with them. I bet they would get some great responses. Especially when they told them that they could keep the Mac if they really wanted ;-)

Technorati Tags: General, Technology

It helps to read them out loud

Sheesh:
[Via In the Pipeline]

Readers may have seen the recent sting operation on Coast IRB, an institutional review board company that’s in the business of monitoring clinical trials. They signed off on a trial of a nonexistent product from a bogus company, which doesn’t…

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Its like an article from the Onion. Some of the names are dead giveaways- Phake Medical Devices, April Phuls, etc. The company involved says it has updated it procedures. Hope so.

IRBs are really important to make sure safe and ethical procedures are being done. I’ve been on a few of these and the people involved take the responsibility very seriously. I would hope that commercial IRBs would take things just as seriously.

Technorati Tags: Health, Science

But will Milton Bradley sell it?

by Hello Turkey Toe
Brown researchers create novel technique to sequence human genome:
[Via Eureka! Science News - Popular science news]

Since the human genome was sequenced six years ago, the cost of producing a high-quality genome sequence has dropped precipitously. More recently, the National Institutes of Health called for cutting the cost to $1,000 or less, which may enable sequencing as part of routine medical care.

[More]

While this is still very much in the research phase, it is a pretty intriguing technique. Will it be scaleable and cheap enough to sequence the human genome (3 billion bases) rapidly? And with what error rate?

Hard to say but I love the vision of using magnetic tweezers to pull the DNA though a hole. Kind of like a high tech game of Operation, only this time we want the DNA to interact with the sides of the hole.

Technorati Tags: Science

Just one thing

by Stuti ~
Eating your veggies doesn’t have to be scary:
[Via Gristmill]
[Crossposted at Path to Sustainable]

Save some moolah (and Ma Earth) by snarfing beans instead of burgers once a week.

[More]

Please be careful, though. While most people produce gaseous carbon dioxide, nitrogen and hydrogen, up to a third produce methane (no one knows exactly why the difference but it probably has to do with different intestinal flora). Methane is a much more powerful greenhouse gas than carbon dioxide.

So, if you are a methane producer (here is a way to tell) make sure you use Beano or similar before eating beans. I have found that a good soaking in water, several hours to overnight) helps a lot. Just remember to discard the water and use fresh water to prepare the beans.

Here is my recipe for Red Beans and Rice:

1 pound of red kidney beans
2-3 bay leaves
1 yellow onion (diced)
2 tablespoons olive oil
1 pound andouille sausage (cut into quarter inch pieces)
2-3 cloves of garlic (chopped)
1/2 teaspoon each of back, white and red pepper
Prepared white or brown rice

1. In large dutch oven, cover beans with water and let soak for 2 hours (1 hour will work and so does overnight). Remove any beans that float. Drain the beans and rinse with cold water. Add bay leaves, cover with 2-3 inches of water, set on high heat and bring to a boil.

2, While the water is heating up for the beans, put a frying pan on medium heat. Add the olive oil and diced onions. Cook until the onions become tender.

3. Add the sliced andouille sausage, garlic and pepper. Heat through for 3-5 minutes, with occasional stirring. Add mixture to dutch oven when water has begun to boil.

4. Cover, lower heat and simmer for 2-3 hours, adding water to keep mixture from sticking to the bottom. After 2 hours or so, you can remove the lid and let the mixture reduce somewhat. Keep stirring every so often to keep it from sticking and prepare some rice (white or brown).

5. Once the red beans has gotten to a nice thick consistency, it is ready. Put a scoop of rice on a plate followed by a scoop of the red bean mixture.

I like to mix everything up together and dig in. Sometimes a little shredded cheese on top is nice and garlic bread is always a treat.

And never any toots!

Technorati Tags: Environment, Science