How does a scientist determine causation?

After talking it over with Mrs. Factician (who is also a molecular biologist), I realized that yesterday's post might not have made sense to everyone in the way it does to me. I would like conspiracy factory to be more than a place where scientists whine to each other that no one understands us. I'd like it to be educational to folks who don't do science every day. I'd like people like my Mom to come here and read it and find something useful for their day.

That said, I'm going to spell out the comic a little better. For those of you who are skeptics/scientists, this may seem a little like explaining a joke (if you have to explain it, it's not funny). But it should be educational, too. So go over, look at the comic, and come back if you have to. What does it have to do with autism? The joke is that scientists don't immediately assume causation if two events occur close together. The fact that the scientist gets zapped by lightning immediately after pulling the lever doesn't necessarily mean that the lever caused the lightning. (Granted, it may have caused the lightning, but until you've seen it multiple times under controlled conditions, you can't say for sure). Of course, doing an experiment that involves being shocked by lightning certainly wouldn't be performed by a scientist. It would be performed by her graduate student. ;)

What does this comic to do with autism? As it happens, the folks who claim that vaccines cause autism mostly rely on the fact that autism begins to show its ugly head around 2 years of age, right after children get a series of booster shots for their vaccines. Does this mean that vaccines cause autism? No. Especially once you realize that autistic children present with autism around 2 years of age whether they've had vaccines or not. It just happens that these things coincide in time with each other.

An experimentalist who wants to ask the question: "Do vaccines cause autism?" would examine a large group of children who get the vaccine and a large group of children who don't (who otherwise are living in similar circumstances) and see if a similar frequency of children get autism in both groups. As it happens, several groups have done this (National Academy of Sciences summarizes the studies here). And they do see similar frequencies. This pretty much kills the argument. (To further extend the analogy to the comic, this would mean that the scientist who pulls the lever a thousand more times would never get shocked again).

How science works: subtitled autism isn't caused by thimerosal

I spent a little time reading David Kirby's conspiracy mongering at the Huffington Post today. Apparently "main-stream" scientists, doctors, the CDC, philanthropists, and the pharmaceutical industry are all in on a conspiracy to make sure that children get autism. *sigh* Anyway, I was going to write a post about the difference between anecdotal and real data, but instead I give you this approximation from the nice folks at xecd.com.

Friday beautiful science

Today's image is of:

"A microplankton sample pulled from the depths of the Antarctic Sea was captured by a scanning electron micrograph."

with false color applied. This photo won an honorable mention in 2004 at the NSF's Science & Engineering Visualization Challenge. Taken by Dee Breger, you can see more images here. Happy Friday.

57th Skeptics' Circle

This week the Skeptics' Circle is up at Aardvarchaeology. Take a gander.

GM crops and bees, an addendum

At the moment, Colony Collapse Disorder (and this Spiegel article particularly) are causing a minor storm on the blogosphere. Many of the blogs are being fairly uncritical in their condemnation of GM-corn, with knee-jerk reactions predominating over reasonable analysis.

I found some interesting stuff from the Colony Collapse Disorder Working Group. This is a group of entomologists based out of Penn State that are trying to figure out why the bees in North America and Europe are dying. They're not quite as hysterical about the die-off as the conspiracy theorists at Spiegel:

During 2006, an alarming number of honey bee colonies began to die across the continental United States. Subsequent investigations suggest these outbreaks of unexplained colony collapse were experienced by beekeepers for at least the last two years. Reports of similar die offs are documented in beekeeping literature, with outbreaks possibly occurring as long ago as 1896. The current phenomenon, without a recognizable underlying cause, has been tentatively termed “Colony Collapse Disorder” (CCD), and threatens the pollination industry and production of commercial honey in the United States.

They have a number of likely suspects:

What potential causes of CCD is the Working Group investigating? The current research priorities under investigation by various members of the CCD working group, as well as other cooperators include, but is not limited to:
• Chemical residue/contamination in the wax, food stores and bees
• Known and unknown pathogens in the bees and brood
• Parasite load in the bees and brood
• Nutritional fitness of the adult bees
• Level of stress in adult bees as indicated by stress induced proteins
• Lack of genetic diversity and lineage of bees

but consider GM-corn (BT-corn) to be an unlikely suspect:

What are examples of topics that the CCD working group is not currently investigating?

GMO crops: Some GMO crops, specifically Bt Corn have been suggested as a potential cause of CCD. While this possibility has not been ruled out, CCD symptoms do not fit what would be expected in Bt affected organisms. For this reason GMO crops are not a “top” priority at the moment.

Radiation transmitted by cell towers: The distribution of both affected and non-affected CCD apiaries does not make this a likely cause. Also cell phone service is not available in some areas where affected commercial apiaries are located in the west. For this reason, it is currently not a top priority.

Now conspiracy theorists may point out that the working group hasn't completely ruled out BT-corn, but it is rather compelling that they have examined the deaths of these bees, and decided their deaths don't fit the symptoms expected by BT-poisoning. (Rather akin to finding a bullet hole in a corpse, and concluding that the person likely wasn't strangled).

Genetically modified crops are responsible for bee deaths? I don't think so...

An article from last week in Spiegel is just so breathtakingly stupid it begs to be commented on. The article: Are GM Crops Killing Bees? suggests that there is a link between the declining bee population and the introduction of GM crops, shows data that makes the answer clear (the answer is no) and continues merrily along, ending the article as if there is some doubt about what the answer is.

A bit of background is in order. Over the last decade, bee populations in the U.S. and Europe have been dropping. The last year has seen particularly large drops in commercial bee-keepers. The Spiegel article cites rates as high as 70%, though these numbers are cited for individual beekeepers. It's unclear from the article what the overall drop rate has been, and though they cite differences between the U.S. and Europe, it's hard to tell if these are meaningful because they're only citing the losses of individual beekeepers.

The bee die off is particularly important for our agriculture, as many of the flowering plants require bees to pollinate their flowers to make fruit. Loss of bees could result in major decreases in the production of flowering crops.

So what does this article say? These drops coincide with the introduction of genetically modified-insecticide producing corn, so this corn must be to blame. This is not a bad hypothesis. One could imagine that bees that find their way onto the corn might ingest some of the compound. However, let's look at the data. Germany has some pretty strict laws about introduction of genetically modified (GM) crops. GM crops made up less than one tenth of 1% of all crops grown in Germany, whereas almost all corn grown in the U.S. is genetically modified to produce the BT-insecticidal protein. So, if GM crops are to blame, one would expect bees in Germany would largely be spared the die off seen in bee colonies in the U.S. Sadly, this is not the case. German bees are dieing off at appreciable rates as well (though granted, at somewhat lower the rates than seen in the U.S. if you trust that the Spiegel numbers are representative). Game over. The fact that both countries are losing bees at high rates clearly demonstrates that GM crops are not to blame.

The National Academies of Science of the U.S. have looked into the bee die off (and have proposed spending more effort looking into it - it has serious economic consequences). Their main conclusions? Non-native mites have been responsible for a large number of deaths, as well as antibiotic-resistant bacterial pathogens (who knew? people treat their bees with antibiotics?). Their recommendations are for increased investment in bee-breeding, to allow creation of pathogen and mite-resistant bees.

Infophilia: Convenient Myths

I've been intending to write a post about global warming myths for two months already, but have found myself too busy with other things. So instead, I point you to this good post here: Infophilia: Convenient Myths.

Dr. Egnor finally gets something right

Michael Egnor is repeating his nonsense about evolution causing the eugenics movement. I'd like to point out, though, that there is one quote on that page that is accurate (though perhaps not in the way that they had intended):

The misreporting of the evolution issue is one key reason for this site.

Yes, it certainly seems that they've gotten the misreporting of the evolution issue under control...

Ricky Gervais clears up the theory of Intelligent Design

Finally we get the details of how Intelligent Design works...

EDIT: I found the video as one video, instead of split into two.

Homeopathy invades the UK

BBC News reports today that complementary and alternative medicine (CAM) has infiltrated British universities to an unprecedented level. There are more than 40 BSc Honors degrees available at British universities in the United Kingdom. It doesn't help that the heir to the throne is a quack pushing for more alternative medicine in the UK.

In the journal Nature, David Colquhoun rails against the teaching of homeopathy in British universities, but in many ways he misses the point.

His critique largely focuses on the fact that:

Some of the words are borrowed from science but they are used in a way that has no discernible scientific meaning whatsoever.

But from the public's perspective, this is irrelevant. What argument are the alternative med types going to use? Probably, oh he's an arrogant scientist. Or, he's not open-minded. Or, this is just a different modality.

The only argument that is relevant to the public is: Prove to me that it works. And on this level, the vast majority of alternative medicine treatments fail abysmally. The alties themselves say that double-blind controlled studies don't work for alternative medicine. I'm sorry folks, that means that these techniques don't work. Science is about proof. If you can't prove it, it ain't true. And if you want to hand out degrees in science, you need to be able to do science.

Friday beautiful science

Here's a solar view from a satellite orbiting the earth. The moon looks so small, due to the fact that the satellite is much further from the moon than Earth is. Read about it here.

Why do smart people say such stupid things?

How is it that such seemingly talented folks like Michael Egnor can say such blatantly ignorant and stupid things? For those who haven't been following this, Dr. Egnor is a neurosurgeon at SUNY Stonybrook. He's the chair of the neurosurgery department no less. To reach such a an esteemed position would require that he be talented and hardworking (and at least a little clever). So why is he spouting such absolute nonsense about evolution? It's not that it's just wrongheaded, it contains such obvious glaring errors regarding facts that were worked out over a hundred years ago (one of which I discuss here).

But he's not the first talented guy to fall into this trap. How about Nobel-prize winner Kary Mullis? Here's the guy who invented PCR, a technique that has revolutionized medicine, forensics, molecular biology and every element of biology. Oh, and he says that HIV doesn't cause AIDS. Huh?

And what about Michael Crichton? He's a Harvard-educated medical doctor. Award-winning author and moviemaker. Oh yeah, and he's said some pretty stupid things about global warming. How is it that these very talented, high-achieving folks can say such stupid things about issues that are way out of their field of expertise? I think it's (misplaced) confidence.

This American Life has an episode devoted to just such a thing (it's well worth listening to, skip to Act 3 if you only want to listen to the story I'll be talking about). In A Little Bit of Knowledge, we hear about an electrician who thinks he's disproven Einstein, if he could only tweak the math a bit. He's an intelligent guy who's managed to build his own business. He can take apart anything and put it back together. He's self-taught. In short, he's a success. And very confident in himself. Because of this, he feels he can understand the more difficult parts of Einstein's theories, and that any failure to understand on his part means that Einstein got it wrong. It turns out there's a lot of these type of guys out there, and that they're often e-mailing physics professors to tell them that they've proven Einstein wrong. One physicist even wrote a crackpot index to describe the phenomenon.

So does this describe our dear Michael Egnor? A smart guy, who fails to comprehend the subtleties of evolution, and blames those failings on Darwin rather than on his own education and/or intellect?

Your Monday morning funnies.

Created here.

A little levity couldn't hurt

I've had a lot of serious posts here. I thought I'd put in something topical but amusing.

Topo cloning is dead!

This post is for the molecular biologists out there (though I'll try to tone it down so anyone can appreciate the significance).

In the 1970s, the discovery of restriction enzymes made it possible to move pieces of DNA between species. This was the hallmark event that allowed modern molecular biology to flourish. The combination of restriction enzymes with ligase allows the cutting and pasting of DNA from multiple sources into a single vector. But as any graduate student or post-doc will tell you, these seemingly trivial manipulations can be a major pain in the ass. On good days, cloning (the term we use for moving bits of DNA around) is a good way to make you feel like you're being successful in the lab. On bad days, making a single construct can take weeks or months.

No more. Steve Elledge has published a new technique for cloning that allows simple movement of DNA into a new vector without the use of ligase. His method, published here in Nature Methods, allows easy manipulation of any piece of DNA into any vector. The required amounts of DNA are at least 10 fold lower than any equivalent method with ligase (he uses only 2-3 ng of DNA) but he can also assemble 10-pieces of DNA simultaneously, and get 25% of the resulting products being correct! This is a revolutionary step forward. You heard it here first: Topo cloning is dead. T4 DNA ligase sales will plummet. DNA 2.0's services will become much cheaper, or they will go out of business. And the lives of molecular biologists everywhere just became much, much easier.

I cannot emphasize enough how important this is. This is a second revolution in cloning technology.

A Gardasil limerick

A limerick posted at the Limerick Festival by the folks at Broadsheet:

Why block a vaccine? Here's our answer.
Gardasil is no values-enhancer.
To prevent HPV
Causes sex, don't you see?
And quite frankly, we prefer cancer.

Your Friday beautiful science

This is an image taken of a siphonophore taken from the Arctic in 2005. Stunning.

A rushing river of stupid. Eugenics is not evolution in action.

Okay, so I was going to let this go, since several other folks have taken it on them to give Michael Egnor a beatdown. But I've just decided that I can't. Michael Egnor is the neurosurgeon making a name for himself as an evolution denier. Others have already taken him down for spouting nonsense. I'm going to focus on the part of his post that I found offensive. That part is:

"In fact, I think it’s safe to say that the only contribution evolution has made to modern medicine is to take it down the horrific road of eugenics, which brought forced sterilization and bodily harm to many thousands of Americans in the early 1900s."

There are two major parts to his argument that are retarded.

First. Eugenics is the claim that some races are fitter than others. Does this sound a little like evolution by natural selection? It's only peripherally related. Though non-biologists like to think of humans as being the most fit species on earth, to a biologist, this statement is clearly bunk. Every living organism today is the descendant of the most fit organism in that niche. Bacteria that live in hot water vents thousands of meters below the ocean's surface are the most fit for that niche. Elephants are the most fit for the niche that they occupy. And pubic lice are the most fit for the niche that they occupy. That said, we cannot predict what exactly will be the environment that we, as human beings, occupy in the future. And even if we could, we wouldn't be able to predict who would be the most fit in that environment. Fitness is merely a measure of who survived to have the most offspring in that particular environment. It is not an absolute. It is directly related to the environment that the organism finds itself in at the time. It may turn out that in the post-apocalyptic future, that stupid people will be the most fit, and that brains will have turned out to be an evolutionary dead end, as detailed in the fictional account by Kurt Vonnegut. This is all to say, anyone who says that they know who the most fit humans are does not understand evolutionary theory, and is more than likely a garden variety bigot. Anyone who thinks that eugenics is the practice of genetics or evolutionary biology as applied to human beings doesn't understand eugenics or evolution.

Second. Let us imagine a world where evolutionary biologists were able to identify who is the most fit human for the future environment. We've decided that left-handed, red-haired, stepchildren are the most fit, and instituted a policy of executing all blondes, and artificially inseminating all other women with the fertilized eggs of people who are the most fit. Clearly this would be an inhuman and unethical state of affairs. That said, being unethical doesn't make the science behind it wrong. Creation of the atomic bomb doesn't make the physics behind it wrong. Creation of agent orange, doesn't mean the chemistry is wrong. Even if you were to use this knowledge to do terrible things, that, by itself is not evidence that the underlying science is incorrect.

Please, Dr. Egnor, please. The next time you'd like to accuse an entire field of inquiry of being responsible for the eugenics movement, please, please! speak with a historian or an evolutionary biologist. The fact that you're a neurosurgeon means that people may take you seriously. Please, please, read a little before you make more of an ass of yourself.

The 56th Skeptics' Circle is up

Check it out here.

well worth watching

A candle in the dark

Pharyngula recently provided a definition of science. While this may seem a rather boring point to pore over, I found myself spending a lot of time thinking about this over the weekend, and I found it exhilarating:

#1: Science is a changing and growing collection of knowledge, characterized by transparency (all methods are documented, and the lineage of ideas can be traced) and testability (prior work can be repeated or its results evaluated). It is an edifice of information that contains all of the details of its construction.

#2: Science is what scientists do. We have institutions that train people and employ them in the business of generating new knowledge — contributing to that edifice in definition #1 — and we have procedures like the bestowal of degrees and ranks that certify one's membership in the hallowed ranks of science.

#3: Science is a process. It is a method for exploring the natural world by making observations, drawing inferences, and testing those inferences with further experimentation and observation. It isn't so much the data generated as it is a way of thinking critically about the universe and our own interpretations of it.

I'm going to assert that he missed one very useful definition. Or at least one very important point. Science demands proof. Science requires that its practitioners provide proof for their hand-waving, otherwise you are merely spewing words. If you cannot provide an iron-clad experiment that demonstrates the point you are trying to make, then you are merely working at conjecture.

I think this is the most important point for laypeople to understand. How is someone to tell the difference between a scientist who knows what (s)he's talking about, and a pseudoscientific quack? I suspect for your average, college-educated person this isn't simple. A scientist may use technical words that are difficult to understand. A pseudoscientific quack may use technical words that are difficult to understand. A scientist may talk about the importance of molecules in their work. A pseudoscientific quack may talk about the importance of molecules in their work. But how do you tell the difference between a highly-talented medical researcher, and a pseudoscientific quack like Hulda Clark? Demand proof.

If someone tells you that worms cause all cancer? Demand the experiment that proves it.

This is the single reason why highly opinionated, egotistical scientists can emerge from a room with a consensus. Unlike in law, or philosophy, or business, or politics, scientists can change each other's minds using proof. That said, for any honest scientist, they can have their minds changed merely by providing experimental evidence that they are wrong.

This is why Carl Sagan says:

"Science is more than a body of knowledge; it is a way of thinking. I have a foreboding of an America in my children's or grandchildren's time ... when awesome technological powers are in the hands of a very few, and no one representing the public interest can even grasp the issues; when the people have lost the ability to set their own agendas or knowledgeably question those in authority; when clutching our crystals and nervously consulting our horoscopes, our critical faculties in decline, unable to distinguish between what feels good and what's true, we slide, almost without noticing, back into superstitions and darkness."

This is what gives science the power to discern truth from bullshit. This is why science is a candle in the dark. This is why scientists feel so passionately about their work. Science offers us the opportunity to say, "Prove it!" and have some possibility of doing just that.

Your Friday beautiful science

Here's an old shot (2005) from the Mars rover Spirit. It's photos like this why I got involved in science.

Anti-vaccine lunatics

I've posted earlier on anti-vaccine nuttery. The latest news on anti-vaccine lunacy was posted in Orac's blog, Respectful Insolence, today. He's got a great summary on this story of nuttery.

First off, a little background. Since the late 1990s, there have been parents groups that have been arguing that the mercury preservative thimerosal causes autism. The news media has been all too happy to promote their bunk, with articles that say things like: "Epidemiologists say there is no link between vaccines and autism, but parents disagree." It's sad that this is news, because if you substituted it with a sentence like: "Physicists say that there is no link between gravity and forest sprites, but parents disagree" there would be little discussion in the public media.

What are the data that suggest that mercury in vaccines causes autism? Well, autism usually starts to present itself around age 2. And this is an age when children get several different vaccinations. This is also an age when parents start taking toothbrushing seriously for their children. Yet no one is asserting that toothbrushes cause autism (yet). What is the evidence against mercury in vaccines causing autism? There are a number of large trials that show that children who don't receive vaccines, and children who receive vaccines that don't use the mercury preservative thimerosal, get autism at the same frequency as children who do receive mercury-containing vaccines. Case closed. That clearly demonstrates that thimerosal doesn't cause autism. Sadly, there are true believers out there, and it's hard to convince a true believer with data.

The latest in this sad story, is that there are people claiming that the symptoms of Shaken Baby Syndrome are caused by vaccines. What??? Yep, now if you want to hurt your baby and get away with it, you can just claim that those bruises and broken bones are the result of vaccines. This is made possible by the grotesque ignorance of the public at large on how science is done, and how much we know about vaccines. In some other post, I will talk about the real side-effects of vaccines (there are side-effects to most vaccines, but they are less severe than the disease that they vaccinate against). But we can clearly say, you won't break bones or get bruising on your brain from vaccines. Babies get that from abusers. Check out this example of someone who used this excuse to get away with murdering a baby.

Science is beautiful

Check out this fabulous image from the Cassini space probe, taken of Saturn in January. It's a composite of multiple over-exposed shots, to see the dark in between the rings. A glorious shot if ever there was one.

Snobbish or Exacting?

The title of this post refers to me. It's an open question.

A recent event at my institution left me wondering more about the Marcus Ross case. A struggling graduate student that I know recently passed his qualifying exam. Let’s call him Phillip. Phillip failed on his first attempt, and some year later, passed on his second. He's mostly a nice guy, but he's really not scientist material. Phillip comprehends molecular biology on the barest levels, in the naïve way that most undergrads do. He's not able to dissect an experiment to determine whether or not he agrees with the discussion of the author. His journal clubs are rote presentation of the paper. In short, Phillip is a disaster. He does not belong in graduate school.

How does this resemble the Marcus Ross case? Marcus Ross is a recently-minted PhD in geology who is a Young Earth Creationist. Many folks in the blogosphere have suggested that he shouldn't have been granted a PhD because he was dishonest, or that he couldn't possibly comprehend his material if he could maintain Young Earth beliefs in the face of all the geological evidence. Many folks have suggested that his degree-granting institution should be mocked for allowing him to use the system.

I'd say both of these cases have one thing in common: the academic system needs graduate students to keep the wheels of science moving. Most of the work in academic labs is done by graduate students and post-docs. There is very little incentive to fail a student after he has gotten into the program. In fact, there is every incentive to keep them there and working, so long as they can get something done. That’s the inherent weakness in the system. And you can’t keep a person in grad school for 7 years and then fail them (or can you?). So people like Marcus Ross and Phillip end up with PhDs.

This is a disservice to everyone but the professor who had a cheap pair of hands for a few years. Society gets another phony authority with some letters after their name. Phillip and Marcus get to work on a career they have little hope of being more than marginally successful (I would argue that Phillip would be better served to be told now he’s a lousy scientist, than to have to spend 10 years in science only to discover that he’d be better off selling jeans at The Gap). It’s the sad truth that as long as institutions aren’t held to any kind of standard, that many of the folks with PhDs after their name will end up being useless at best or quacks at worst. What’s the solution?

Skeptics' Circle

The 55th Skeptics' Circle is up. Take a gander.