More like a hothouse

Ebola and the henhouse:
[Via Effect Measure]

When an Ebola virus related lab accident in German occurred, special pathogens researchers girded themselves for bad news. Working with agents for which there is currently no treatment of vaccine requires high containment laboratories, often touted as being virtually fail safe. While engineering and procedural controls can be instituted to minimize accidents, the wild card is always the human element, so accidents in these laboratories happen. There has already been an Ebola related death in such circumstances, and when the German woman pricked her finger with a needle containing Ebola virus, there was fear of another. While there is no vaccine for Ebola currently in use, several are in development, and one was tried on an emergency basis. The incubation period is now past and the lab worker remains healthy. Was it the vaccine that saved her would she not have developed Ebola in any event? Helen Branswell (Canadian Press) takes it from there:

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It is good to hear that the women is okay. It can be a tough waiting period for something like Ebola. The best that can usually be done is to keep the patent alive until their body fights off the disease.

Of course, this opens up a question about doing this sort of research – the greatest danger for hot pathogens to appear in a populated area may be due to infection of a lab worker.

Read The Hot Zone. It described lab workers who could easily have been infected with Ebola walking around in public. Luckily for us, that particular strain did not infect humans.

In this case, the woman knew she had stuck herself . And perhaps a new vaccine helped her survive (You can read the original paper describing this use of the vaccine in a post-exposure regimen). But if she had not noticed, she might have been able to walk out the door in an infected state.

That is the reason all smallpox stocks worldwide were supposed to have been destroyed – with smallpox, eradicated the greatest chance for another epidemic would have come from lab workers.

Now these are not likely scenarios but all it takes is one. And there are a lot of such labs worldwide working on a host of diseases. Should there be a set number that can work on each particular hot virus?

There are a lot of these labs in the US, perhaps too many. But it would be hard politically to reduce them very far in number.

And I would think that for national security reasons it would be hard to convince countries to curtail research simply because too many other labs in the world were working on the same pathogen.

This may be a bigger Pandora’s Box than we imagine.

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Irony abounds

cooperateby tomsaint11
Science IS imagination:
[Via Bad Astronomy]
“The mind that’s afraid to toy with the ridiculous will never create the brilliantly original…”

–David Brin, Brightness Reef

People don’t understand science.

And I don’t mean that your average person doesn’t understand how relativity works, or quantum mechanics, or biochemistry. Like any advanced study, it’s hard to understand …

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I’ll get to the ironic is a second.

I feel like taking a shower after reading the article linked to by Bad Astronomy, the one published in the Vancouver Sun. The author takes an interesting approach – using a word that was pretty much the provence of pejorative attacks on science

Like calling evolutionary biology Darwinism, calling the process of science Scientism allows for easier name-calling and strawmen creations. But it does little to further any real discourse (just label anyone who disagrees a follower of scientism).

Phil Plait’s response covers some of the important aspects of the other article. One thing I wanted to point out, is that the article in the Vancouver Sun discusses Lynn Margulis as an example of someone who expands her mind beyond scientism:


The truth is that many scientists are slowly becoming more open to at least discussing the possibility that elements of purpose, not just chance, are inherent in the evolutionary process.

They include the noted biologist Lynn Margulis, the first wife of the late astronomer Carl Sagan, and their science writer son, Dorion Sagan.


The article tries to make out that this is an example of how evolution has not been explained and why other ideas, such as creation by outside agencies, should also be allowed to be included. See, there are 12 different ways evolution could work besides Darwin’s.

But Margulis’ theory, a least from what I have read (actually Margulis taught a class I took at CalTech when she was visiting one semester. It is where I first learned about endosymbiosis), deals with the creation of new species by cooperation rather than competition, that symbiosis is an important driver of evolution. This does not really seem to go against the idea that random mutation provides a wealth of choices that natural selection reduces.

It is all about what drives the greater selective advantages of an organism, competition or cooperation. But both are just strategies used by organisms to survive and spread their genes to other generations.

Now to the ironic. On the same page as the diatribe about Scientism, there is a little box entitled “Related Stories From Around the Web”. It contains a link to an interesting story.

The title says it all and really undercuts the attempt to say that cooperative behavior is not a part of evolution thought – Cooperative Behavior Meshes With Evolutionary Theory. And the fact that they did this in yeast only makes the proposition stronger.

Helping others, even when they do not help you, can still be a useful strategy for survival. Turns out that even if there is only a 1% advantage for an individual that is performing a cooperative behavior, one that helps all members (even the ones who cheat) then the population of cooperators will expand. Eventually, there is an equilibrium that is reached between cooperators and cheaters.

So cooperation even with very little overall benefit for the cooperator can be successful. Competition is not all. Even in yeast. Current theory is able to encompass cooperation as a strategy.

So, on the very page someone discusses all the theories that are not covered by evolutionary science, suggesting that a theory based on cooperation is non-Darwinian, there is also a link to another article demonstrating that there is no real dichotomy there, that cooperation meshed with competition.

Would this count as a massive fail?

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Science stick figures

Stick figure science contest!:
[Via Bad Astronomy]

Can you draw? Yeah, me neither. But don’t let that stop you from entering the Florida Citizens for Science Stick Science contest!

The concept is simple:

Contest for ages 13 through adult:

Your job is to create a cartoon that can be used to educate the general public and especially decision makers …

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Now we can really see who can do some edumacating! Of course, the comments reveal who would probably win, if he decides to submit anything.

Actually, it can be pretty difficult to simplify everything down so that stick figures can be used. And there has to be some angle for a comedian when the idea is to use stick figures to educate decision-makers.

Maybe hand puppets would be another contest to have?

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Watching data on a sphere

[Crossposted at A Path to Sustainable]

The Wonders of SphereCasting:
[Via The Intersection]

Yesterday, as previously mentioned, I was at the magnificent National Weather Center at the University of Oklahoma in Norman, giving a speech to this conference about science communication. I’m hoping that the talk—which covered anything from the work of the 18th century French philosophe the Marquis de Condorcet to the unfortunate depictions of science in Hollywood films—will eventually be available online. Meanwhile, though, I’d like to remark on a spectacular encounter I had at the event. We tend to complain and critique on blogs; this post will be the opposite.

science on a sphere

In the first floor lobby of the airy National Weather Center, where the tornado investigating devices “Dorothy” and “TOTO” are on display, there’s also a large suspended globe which acts as a spherical screen. Four projectors flash onto it simultaneously, so that it is possible to fully project the entire globe’s weather as provided by satellites. It’s called SphereCasting, NOAA’s “Science on a Sphere” program, and I can only call it magnificent. If there’s a better technology for explaining science to the interested public, I can’t think of it. And apparently there are now 30 such spheres in existence.

The sphere doesn’t merely allow one to display weather everywhere all at once. You can pretty much project anything onto it with the right program. You can make the sphere into Mars, or Jupiter, or Titan, or the Sun. The woman who gave me a brief tour of how it works even said she was waiting for the program that would let her turn it into the Death Star. And it’s hard to see why one couldn’t also project the results of global climate models up there. Frankly, the possibilities are vast, if not endless.

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One of the major difficulties discussing global warming arises from the problems dealing with the data sets. They are large, often multidimensional yet seldom placed into context on a globe.

This is a relatively cheap way to show very rich data sets to a large group of people. In fact, to my knowledge, this method of displaying 3-dimensional planetary data was first demonstrated over 25 years old during a presentation of vital military data.

Actually, I am really taken with the similarity in the two pictures, one a representation of someone’s fantasies and the other an actual presentation. I am also curious with how this sort of presentation will change the relationship of the presenter with their audience.

Currently, most presentations are linear, with a speaker standing in front of the data and facing an audience. Like a play, there is a linear focus of attention. In fact, the speaker is often placed on a stage so that everyone can see them speak. This acts to separate the speaker from the audience.

But here, as in theater in the round, the audience surrounds the data as well as the presenter. In fact, this presentation is strongest when people can see all sides of the data. So where do the speakers place themselves?

They could stand away from the data, letting the audience surround the sphere but remaining separate themselves. This focuses attention on the sphere, not the presenter. This would seem to totally separate the speaker from the data being shown. In fact, a disembodied narration would work similarly.

The other approach is to mingle in the audience around the data, sort of acting simply as an interlocutor of the science. It would provide a much more personal collaboration between the audience and the speaker. It would be more like an educated member of the audience is presenting rather than an occupant of some white castle

Both of these approaches completely changes the relationship of the speaker with the audience. I think explaining science to an audience as a member of the community makes for better understanding. It permits the data to speak for itself and to convince people, rather than the authority of a particular speaker.

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Revenge?

Bad sex from food poisoning:
[Via Effect Measure]

I have a particular interest in food poisoning. I admit there is something unhealthy about my fascination but there it is. One of the more interesting ones is ciguatera fish poisoning, and CDC has just reported an unusual cluster from North Carolina. Ciguatera fish poisoning (CFP) happens when a carnivorous fish higher in the food chain (e.g., barracuda, amberjack, red snapper, grouper) eats a smaller plant eating species that itself has dined on a large dinoflagellate called Gambierdiscus, commonly found around coral reefs in the Caribbean and in the Pacific. These little guys have a toxin that is converted to another toxin that interferes with the transport of sodium through cell membranes. In fact the toxin, called ciguatoxin, is the most potent sodium channel toxin known. It’s not related to spoilage of the fish and isn’t destroyed by cooking. The only way to prevent it is not to eat fish from Gambierdiscus infested reefs. If you do eat ciguatera toxin containing fish, attack rates can be as high as 80% or 90%. One of the unusual and characteristic features of ciguatera poisoning is the reversal of the sensations of heat and cold. In this case, there was an additional unusual feature. Bad sex:

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Perhaps the world is out to get us. Luckily we seem to be killing the reefs that house the dinoflagellate. This nice toxin needs to show up on House.

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Why the History Channel is a farce

alien by kevindooley
How easy is it to fool UFO believers? Easy, if you have a flare for it:
[Via Bad Astronomy]

[Update (April 3, 2009): The two men who perpetrated this hoax have been charged by a local prosecutor as "disorderly persons", evidently a minor offense. Not surprising, and I'm sure it won't be a big deal. Still, don't try this at home, folks. Thanks to Kevin Conod for the tip.]

This …

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You know, something called the History Channel should be concerned with known facts. That is what history is.

But they now have a show called UFO Hunters that looks like it was fooled by this ‘experiment.’ It reminds me a lot like what happened when crop circles were revealed to be manmade.

At least the prosecutor was skeptical early on. He asked whoever was doing this to stop because he was worried about aircraft traffic. He was not fooled.

The UFO Hunters were but then their game is to play to the credulous. They do not seem to bring a skeptical eye, at least not in this instance.

The article written by the young men is pretty interesting, more so than anything I have seen on the History Channel recently.

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Posted in General. 1 Comment »

Skeptical, not contrary

plumeria by eye of einstein
Are skeptics of climate consensus anti-science?:
[Via CEJournal]

Some climate activists think so, but skepticism is what gives science its power
I found myself agreeing with much of the criticism directed at Nicholas Dawidoff’s profile of theoretical physicist Freeman Dyson in the New York Times Magazine last Sunday. Although he wrote an engaging and fascinating story, Dawidoff was out of his league when it came to

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An interesting discussion. The comments are also very educational and ably describe the difference between a useful skeptic and a simple contrarian. The former helps move science forward, while the latter often only acts to mess up the works.

People often mistake the place of a skeptical scientist with that of a contrarian. Simply saying ‘You are wrong’ adds little to our knowledge. One has to add something else. Something like ‘…because you left out this’ or ‘since this explains the data much better’ or ‘ because you made an inaccurate assumption.’

These add to our knowledge of the world around us. Refusing to accept data without reason or not trying to find an alternate explanation for the facts are sure signs of being contrary simply for the sake of it.

Some people get more recognition for knocking over the house of cards than trying to build a better foundation.

Science often works by removing the things that are incorrect in a model, discarding the things that it can not be.

Anyone who has watched House knows what a differential diagnosis is. A scientist often works similarly. When given a set of data, a scientist works through models, discarding ones that do not fit the data.

At the end, there may be a couple of hypotheses left, maybe even one that is the researcher’s favorite. After all, we are human and have our bias.

But a good researcher recognizes they have bias, and also recognizes that other hypotheses may be the favorites of other scientists. So they work very hard to design experiments to discern between the choices that are left.

In fact, researchers gain stature by designing experiments that can discern between hypotheses, that can tell which model comes closer to describing the natural world more accurately.

If done well, this ‘competition’ , whether done by the original scientist who wants to make sure their hypothesis is correct or by others doing their own work, eventually arrives at a semblance of the real solution. In some cases, the results are so close to reality that no meaningful difference can be revealed.

Now, some hypotheses may not initially be totally correct because the useful data are not as accurate as needed. This often drives the search for new and better data. This new data moves a particular description of the natural world further towards reality. Or new data demonstrates that the model is actually not correct at all and a new model must be developed. But the new model also needs to explain all the data, both old and new.

So, a good scientific skeptic might look at a hypothesis and try to figure out what alternative models have not been examined or might also explain the data. In an episode of House, they often try to figure out what illnesses were not on the list at the beginning and never considered.

Useful skeptics look for the holes in logic, faulty assumptions or things unexplained by the models. Then they suggest research to discern why and how a new model may be developed. They help get us move closer to what is really going on, either by strengthening the model or finding ways to create a new one.

Every skeptic of relativity who suggested experiments to find out whether it was correct helped us gain a better understanding of the world around us.

A contrarian, on the other hand, just likes to say ‘wrong’, usually as an attempt to gain attention. They are not interested in really doing any work to correct the current model, to suggest how another model would explain things better, or what work could really be done to help us understand.

They do not engage in any of the competition of ideas that foster good science. They do not want to really do any work. They deprecate the research of others, who are spending years of their own lives on exploring a problem, but seldom devote much energy themselves to the problem. They simply sit back and say ‘wrong.’

It used to be much more the case that these sorts of contrarians were usually the old men of science, the ones who had done great things when young. But, having achieved greatness, they no longer had the time to spend on new data that might invalidate their old models.

As Max Planck said:

A scientific truth does not triumph by convincing its opponents and making them see the light, but rather because its opponents eventually die and a new generation grows up that is familiar with it.

This describes not the skeptics but the contrarians who seldom add to human knowledge when they spend so much time saying ‘No.’

The media, unfortunately, does a poor job discerning the difference between a skeptic and a contrarian. But most people who work to find better ways to describe the world around us – let’s call the ‘scientists’ – can see the difference.

The skeptic makes many of us want to start a set of experiments to demonstrate who is right. The contrarian simply makes most of us heave a big sigh, shake our heads and get back to work.

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Will it be accepted by the ADA?

toothpaste by digicla
Targeting specific disease-causing bacteria in the mouth:
[Via EurekAlert! - Infectious and Emerging Diseases]

(Society for General Microbiology) Research to develop a narrow-spectrum antibiotic that can target a particular species of bacteria without harming the other “good” bacteria present was described at the Society for General Microbiology meeting at Harrogate Thursday, April 2.

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This is a nice example of using our knowledge of biology to engineer new antibiotics. In this case, the researchers wanted to kill a specific type of bacteria but leave the others alone.

A broad spectrum antibiotic kills almost everything. But finding an antibiotic that is specific for just one type of bacteria is difficult if not impossible in some cases.

However, every bacteria has something that makes it unique. That is what makes it different from other types. In this case, there was a surface receptor. So the researchers took a broad spectrum antibiotic and attached it to the end of the protein that binds to the receptor.

Only the bacteria with the receptor will take up this engineered molecule. Only these bacteria will then die, leaving the other types around.

Nice way to make a magic bullet with antibiotics. Now, these sorts of approaches have been used before (i.e. attaching a toxic moiety to a specific antibody). However, this requires fairly straightforward approaches. Maybe it will even make it into toothpaste.

Maybe.

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They are over 1775 days past warranty

rocks by jfaherty17
Spirit sees phenomenal Martian vista:
[Via Bad Astronomy]

I’ve been so taken with HiRISE lately that I haven’t written much about the Mars rovers Spirit and Opportunity. They’ve been traversing Mars for almost six years now, taking tons of images and great in situ data. And now I feel remiss, because Spirit has stumbled on something very cool.

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The Mars rovers are still producing amazing pictures. These are some of the most unusual and important yet. If we could only visit.

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