Thursday, May 31, 2007

Teaching evolution.

This is how evolution by natural selection should be taught in schools.

How do you turn this:

Shuffled Deck:
33 5 12 37 44 27 39 16 11 29 28 4 22 43 6 30 21 47 41 48 2 34 46 24 18 8 7 26 45 36 1 49 3 9 17 25 14 10 13 20 31 15 32 50 40 42 52 38 19 51 23 35

into this:

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52

using only random changes?


Dustin provides the code to be able to do this experiment yourself using MatLab. I don't know anything about coding, so I won't comment on that part, but I can say that I hope he turns this into a little Java program that anyone can run, and see in real time how we can make order out of random noise in a simple program.


Wednesday, May 30, 2007

Marketing 101 - Selling Crap to Babies

I've previously written my thoughts on Baby Einstein and other products marketed to small children. For those of you who don't pay attention to the small children market, these are products that basically promise to make your kids smarter. They're incredibly popular, and have only grown in popularity with time. today interviews Susan Gregory Thomas, the author of Buy, Baby, Buy. She sums up the value of the Baby Einstein products here:

If you look at the marketing rubric of, for example, Baby Einstein, what they talk about is enhancing a baby's natural curiosity. But what's so fascinating about it is that there is absolutely no research that undergirds those statements. There just isn't any. It's all marketing.
So these products are worthless. No evidence that they do what they're marketed to do. Well, that's not the first time (after all, when was the last time that a Coors Light actually got you lucky). But it's actually worse than that. They're marketing a product that not only doesn't help, but actually harms infants. Infants and toddlers shouldn't be placed in front of a television. She explains using a more child-friendly program, Sesame Street:
It's complicated for an infant or toddler to process television. When they are put in front of the television, the only thing they seem to be getting out of it in a verifiable way is character recognition. That's why you see babies and toddlers so thrilled when they're at the supermarket and they recognize Elmo. But still, it wears what the marketing industry calls an "educational patina."

The problem is that the great social values that Elmo and the characters on "Sesame Street" teach are lost on children under the age of 3. They get solely a flat, one-dimensional character recognition. And the only other times that children are going to encounter the character are when a company is trying to sell the kid something. You don't see Elmo running around your park. You see Elmo when he's in diapers, when he's on juice boxes, when he's on Band-Aids and when he's on toothbrushes.
So really, in addition to not learning anything from these "educational" shows, your average toddler is becoming a brand recognition machine. So what do you do about it? Keep your child away from the TV until they're old enough (4 or 5). And then, teach them what they're seeing on TV:
My daughter -- at age 3 -- came home from school talking about how certain girls at school weren't allowed to play something called the Princess Game unless they had come to school wearing a dress with the colors of a particular Disney princess. It was shocking to me that Disney had penetrated at that level. We hadn't shown her any of the Disney movies.

I said, "OK, if this is what's going on in school we'll get into it." We just did our own study of Cinderella. We went to the bookstore and the library, and it turned out that almost every culture in the world has its own Cinderella story. So we got out "Cendrillon," which was a Caribbean Cinderella story, and "Adelita," which was Mexican, and a Chinese one. Then we got the Disney Cinderella book, then we got the traditional Brothers Grimm. Then we started asking her, How come we don't see Cendrillon on Band-Aids? How come Adelita isn't on any toothbrushes? Then when we went to the grocery store, I'd ask, "Why would they put SpongeBob on that macaroni and cheese? Does SpongeBob have anything to do with that?" We began to talk about how characters are used to try to sell stuff.


Colony Collapse Disorder, an update

It's been a few weeks since I checked in on the bees. If you recall, domesticated bee populations in the U.S. and parts of Europe have been dying off at alarming rates. Bees are rather important for pollination of all kinds of crops, so this bee die-off has major implications for farmers (and for those of us who think that food is delicious). This bee die-off has been called Colony Collapse Disorder. One of the mysteries has been why they fly off from the hive and don't return (rather than dying in the hive). has an interesting round-table discussion with several experts and one beekeeping crank. The interview is actually a pretty good one, and we get some new information here that starts to make the die-off less mysterious (and less over-the-top sensational). Let's start with why the bees are "disappearing":

It's important to look at what's normal. In the summer, bees go through a six-week life cycle: three inside the hive, three outside it as foragers. Then they die of old age. When bees are coming to the end of their life for whatever reason, they just fly off and don't come back. They fly out to die because flying out and dying is what they do. The question is, Why are we seeing bees with such a shortened life cycle? Well, now we're talking about winter bees. As you move into fall, the colony is supposed to be rearing bees that have a long life expectancy -- from about October to March of the next year. The problem is the winter bees aren't making it. Everything just sort of fell apart near the end of this summer and those bees that were supposed to live up to six months didn't come close.
Ahh, so it's not the rapture, then. What about cellphones?
All the explanations that bees became disoriented by cellphone radiation, or this, that and the other thing -- there is zero evidence for any of it. All we know is we lost the worker population and they died away from the hive. What's unusual is they died over a short time period. Are they flying off to nirvana? Who knows where they are? They are just dying away from the hive, which is normal.
Not cellphones. How about genetically modified (specifically BT) corn?
When Bt crops were being used in the fields to control lepidopteron insects, or butterflies, there were a significant number of studies run to try to determine whether or not incorporating Bt into the food of the adult bees, or the larvae, would hurt the bees. And the answer was no....

....I contributed to a recent study where we directly fed the Bt toxin to whole bee colonies and could demonstrate no effects on them.
Hmmm... not BT corn. (Though the crank raises the possibility that Bt corn is responsible, both scientists point out that there is no credible evidence that suggests this is true, and plenty that suggests it's not true - well done). What's the current best hypothesis for why bees are dying?
I'm probably the strongest advocate in the United States suggesting that malnutrition was the underlying thing that set up our bees to be whacked by everything else researchers are looking at. Honeybees rely on pollen for protein, vitamins, fats and minerals. That's where their major "health food" comes from. If we are having a typical year, and the rains come, there aren't too many places in the United States where the bees cannot find their mix of pollens to meet their dietary needs and get them through a normal life cycle.

The question is, What happens when things don't go like that? Well, you get this blast of hot temperature, which is about the time the flower buds are forming and the pollen grains are beginning to form. What does that do? You get sterile pollen. A beekeeper could look into the hive and say, "I've got all kinds of pollen in there and the bees disappeared." Well, right, you've got pollen grains, but do they have any nutrition in them?

Anything that interferes with the availability of food, or the quality of the food, is going to be detrimental to the bees. They don't have much of an immune system, so the only way that they can resist being infected by a lot of things is when they have their innate resistance up, and the best resistance is when they're best fed. So my feeling is that their nutrition just wasn't what it was supposed to be, and they were susceptible when they should have been resistant. I think something happened at the end of last year in many places in the temperate climate around the world, not just here, and fouled up the bees' food supply. Unless somebody tells me differently, I'm blaming it on the weather.
Well, one major problem with his model is that this will be rather difficult to test experimentally. Was it weather related problems in their food supply? If so, one would predict that Colony Collapse Disorder won't be much of an issue this year (unless we have similar weather patterns). Though it does predict a solution. Artificial food sources in bad weather years can help keep bees healthy.

The other problem is that given that CCD may have a complex cause, it won't get reported in the news, as it doesn't fit the snug "cellphone" or "GM-corn" label. News media are pretty awful at presenting complex ideas.

In this instance, chose to have a "balanced" roundtable giving air time to a crank, they did it in a way that people with access to scientific data could correct his errors. All in all, a decent interview.


Tuesday, May 29, 2007

Irony alert!

I've previously revealed that I am an alien living in the U.S. After a particularly hairy time renewing my work visa, I've decided to finally go through with the onerous process of applying for a green card. (I've largely avoided it due to the costs and inconveniences associated with it - and due to the fact that it's not clear where in the world I'll go when I'm done being a post-doc).

That's just a long introduction to explain why I found this website while doing some searches for immigration information. I'll let them explain to you, in their own words, their mission:

Border Control is dedicated to ending illegal immigration by securing our nation's borders and reforming our immigration policies. Our organization accepts no financial support from any branch of government. All our support comes from concerned citizens who appreciate the work we are doing to seal our borders against drugs, disease, illegal migration and terrorism and wish to prserve our nation's language...
My bold. Their spelling.


Sunday, May 27, 2007

Creation "Science" Museum blog carnival

This week, Answers in Genesis opened their creation "science" museum. Many news organizations treated this uncritically on their pages, but the LA Times published the laudable editorial, Yabba Dabba Science:

THE CREATION MUSEUM, a $27-million tourist attraction promoting earth science theories that were popular when Columbus set sail, opens near Cincinnati on Memorial Day. So before the first visitor risks succumbing to the museum's animatronic balderdash — dinosaurs and humans actually coexisted! the Grand Canyon was carved by the great flood described in Genesis! — we'd like to clear up a few things: "The Flintstones" is a cartoon, not a documentary. Fred and Wilma? Those woolly mammoth vacuum cleaners? All make-believe.

Science is under assault, and that calls for bold truths. Here's another: The Earth is round.

The museum, a 60,000-square-foot menace to 21st century scientific advancement, is the handiwork of Answers in Genesis, a leader in the "young Earth" movement. Young Earthers believe the world is about 6,000 years old, as opposed to the 4.5 billion years estimated by the world's credible scientific community.
PZ Myers has organized a concerted effort to publicize the laughable ignorance on display at the museum, and writes this critique:
I wish the country's newspapers had responded that unambiguously and clearly, but the image above was modified. Journalists, you have a problem. Most of the articles written on this "museum" bend over backwards to treat questions like "Did Man walk among Dinosaurs?" as serious, requiring some kind of measured response from multiple points of view, and rarely even recognized the scientific position that the question should not only be answered with a strong negative, but that it is absurd. Let me ask any reporters out there: when you cover a story about a disaster, say the destruction of a town by a tornado, do you also feel obligated to get a few pithy quotes from a few people who want to argue that the disaster was a good thing, or that the residents deserved it?

One of the worst examples of this inane and unwarranted "fair and balanced" reporting comes from the Newspaper of Record, the hallowed New York Times. The Times published an appallingly credulous article, Adam and Eve in the Land of the Dinosaurs, that strained to give equal time to idiocy.
There are a load of blog posts there that are worth reading. Head on over and educate yourself.

UPDATE: And check out ERV's discussion of creationism, errr, I mean, intelligent design. Very entertaining.


Saturday, May 26, 2007

I am the pinnacle of evolution!

It's true. I am the pinnacle of evolution. Or rather, my son is. And so is my cat. And the rat digging in my garbage. And the slime mold growing in the drain in my tub.

Most people have this mistaken idea of evolution based off of an evolutionary tree drawn by Haeckel over a hundred years ago, that evolution is this tree of progress building from "lower" organisms like sponges, up to molluscs and then to the pinnacle: man.

That mistaken understanding of evolution makes it easy to make the mistake that we have to keep humanity "pure" of undesirable genotypes, and can be used to rationalize horrors like eugenics. But it's based on a poor understanding of evolution. It's a pity, because from conversations with other biologists, I think that it's not just a misunderstanding that lay people have, it's one that many biologists have as well.

Every organism alive today is highly evolved for its niche. Calling a dog more evolved than a bacterium is simply incorrect. As Norman Pace said* this week at the American Society for Microbiology meeting, "If you think that a dog is more highly evolved than a Prochlorococcus bacterium, do the experiment. Take them both out and drop them in the middle of the Sargasso Sea and see which one survives." The point he was trying to make was that each individual organism alive today is highly evolved, and making statements about the degree of evolution involved is incorrect. A bacterium is an incredibly evolved and efficient organism that fits very well in the niche that it lives. It has undergone many millions of years of evolution to produce a remarkable organism, just like a human (in fact, it has undergone orders of magnitude more generations, suggesting if anything, that the bacterium is more highly evolved).

PZ Myers makes a similar point at Pharyngula:

I like to compare humans with chimpanzees—are we more complex? I don't think there is any way to say that we are. We have about the same number of genes and a genome that is about the same size and that is organized in a roughly similar way. There is some speculation about the differences in our genomes that lead to the obvious differences in our morphology, but they don't postulate any increases in complexity.
Norman Pace draws evolutionary relationships between the major phylogenetic groups like this:

That every living creature alive today is at the end of those triangles, and all the "less" evolved organisms make up the lines behind them. That is, anything "less" evolved is by definition extinct. The simpler organisms have been outcompeted, and are dead. (He also suggests that part of the problem is the terminology that we use, but I'll save that discussion for another day).

I would suggest that the most useful way to visually depict evolutionary relationships would be a 3 dimensional sphere. Every living organism is on the outer edge of that sphere, and failed branches of life are in the interior of the sphere. Indeed, the last common universal ancestor would be at the center of said sphere. As such, we all represent the pinnacle of evolution, and are all well-adapted to the niche that we occupy.

*not a direct quote, but pretty close on the mark


Future shock!

Some day, my grandchildren will come home from school and tell me how they just sequenced their genome in fourth grade biology class. I will tell them that I can remember when the first bacterial genome became available in 1995, and that it was a big, fat, hairy deal. Sequencing the first genome, Haemophilus influenzae, took the efforts of 40 people nearly a year to accurately compile the 1,830,137 base pairs that comprise its genome. At the time, this was a technical tour de force, as similar projects in Escherichia coli had already been ongoing for several years with no light at the end of the tunnel.

The future is now, ladies and gentlemen.

While at the American Society for Microbiology General Meeting last week in Toronto, Canada, I visited the booth of the company 454. These folks have a fabulous new toy that you can buy for yourself for the low, low price of about $500,000. But what a toy! With this toy, you can sequence single molecules of DNA (with conventional sequencing, you need many, many pure copies of your DNA). Their machine isolates your single molecule of DNA inside of a bubble of water suspended in oil. It amplifies this single molecule of DNA, and it sequences it. Here's the cool part. There are 1.6 million wells in the machine, and they can get up to 400,000 of them operating simultaneously (about 3/4 of the 1.6 million wells get bad reads). What does this mean? Well, since you can get about 300 bp of sequence off of a single well, it means that you can sequence a ridiculous amount of DNA in an afternoon. In 8 hours, you can sequence two entire microbial genomes using the work of one person and an $8,000 chip. Two microbial genomes for a little over $8,000 of reagents and a few hours of work!

Never again will a microbiologist have to work with an isolate that hasn't been entirely sequenced. We're also getting very close to the point where having your own genome available for making choices about your own healthcare will be feasible. We're not there yet, but the time is not far away.


Friday, May 25, 2007

Friday beautiful science

This Friday's beautiful science is entirely being hosted here. While at the American Society for Microbiology meeting in Toronto, I saw a talk that discussed the amount of bacterial biomass on earth. He showed a video that animated some NASA data showing photosynthesis in the oceans. I've linked to one of them here. (It's an mpeg owned by NASA, and no one has put it up on Youtube yet, so you'll have to click through). It shows distribution of photosynthetic bacteria in the oceans, and seasonal changes. Very cool. There are more cool NASA videos here.

I'll have more posts next week when I return home and have a more reliable internet connection.


Thursday, May 24, 2007

61st Skeptics' Circle

The 61st Skeptics' Circle is up at Memoirs of a Skepchick. Go take a gander.


Tuesday, May 22, 2007


I'm currently posting from beautiful Toronto, at the annual American Society for Microbiology meeting. Last night the talks all focused on biodiversity (of microbes). The first two speakers mentioned in passing the fact that we are outnumbered in our own bodies by bacteria, about 10:1. Most of the cells in your body are bacterial cells. (Reason being is that bacterial cells are much smaller than mammalian cells).

The keynote speaker was Edward O. Wilson, biodiversity researcher extraordinaire from Harvard. After a long welcoming applause, he said, "On behalf of my mammalian self and my prokaryotic masters, I thank you."

Fifteen thousand microbiologists roared with laugher.


Friday, May 18, 2007

Who needs evidence-based medicine when you can have...


Thursday, May 17, 2007

Friday beautiful science

Today's Friday beautiful science is an animation created by the animation studio XVIVO using funding from Howard Hughes Medical Institute and Harvard University. It's a fantastic illustration of all the things that need to go inside a white blood cell during its survey of a blood vessel and subsequent invasion into infected tissue. It's reasonably accurate, right down to the structural level of the proteins that are depicted. Though the material is probably suitable for mid to upper level biology undergrads, it's still beautiful to watch.

There's a slightly lighter version put to music, if you're not all that interested in the details (or, if you're a biologist, and you recognize everything going on there without the narration).

I confess, these two are so good they give me chills...


Wednesday, May 16, 2007

A student asserts his right to stay ignorant.

What happens when a student asserts his beliefs in science class? (For the 2 of you who don't have a TV, Stephen Colbert is a satirist).

Or as Stephen Colbert says: "College students should be unformed lumps of clay fired in the kiln of unchallenged thoughts."

Video summary: Stephen Colbert lambastes a student (Barry Lucier) for saying that he was upset that his science professor was trying to get him to watch a movie he "didn't believe in". (That movie is Al Gore's An Inconvenient Truth). I'm not going to get into the merits and weaknesses of Al Gore's movie, but I would like to briefly comment on this idea of belief. One's beliefs aren't relevant in science class. Science deals with data and interpretation of said data. The interpretation can either explain the data or it can't. One's beliefs don't belong in the science classroom.

Is this just one conservative activist child? Or the start of a wave of anti-intellectuals who want scientists to accommodate their beliefs in Xenu and the Galactic Confederacy into descriptions of cosmology?

If you have the stomach, you can watch the original interview here. All kinds of stupid:

Quote of the night, "My grade was well." Ouch.

Update: Apparently Comedy Central yanks the videos after a period of time, so here's the transcript for those of you who didn't get to watch it. The parentheses refer to words appearing on the screen next to Stephen. Thanks to College Freedom:

Stephen: This savage attack on young minds brings us to tonight’s Word: Heated Debate. Folks, you know it, I know it, the left has a stranglehold on our universities. Professors are forcing our kids to submit to their pro-glacier agenda. But heroes like Barry aren’t taking it lying down.

[Video: Barry Lucier: This was forced upon me to watch something that I didn’t believe it.]

Stephen: Folks, at a “college” Barry was forced to think about something he didn’t already think. When you confront young people with information that doesn’t jibe with what they already believe they can get confused, or even worse, bitter.

{Video: Neil Cavuto: Are you bitter?
Barry Lucier: Uh, a little.]

Stephen: Of course he’s bitter! He’s enrolled in a class where the professor thinks he knows more about the subject than the students! (Boss Tweed) Last time I checked that is the definition of elitism. (Stephen has never checked) Hey, I’m no scientist but I thought there were supposed to be two sides to every story. (Mine & wrong) Sure there’s a vast consensus on global warming science, but doesn’t the opposing five percent deserve 50% of the time. (Fair & balanced) In this core science class he probably got a syllabus full of “convention wisdom.” For instance they probably also told him the Earth revolves around the sun. (Actually revolves around Stephen) This is a relatively new and untested theory that’s only been around for 500 years. (Barely longer than Law & Order) But of course the Copernicus crowd doesn’t even mention Ptolemy’s view that the Earth is the center of the universe even though that theory has been around for 1900 years. (Ptake that!) It is 1400 years truer! But these days college is all about silencing the dissenters, it’s no longer a place to raise your hand, offer your minority viewpoint and have healthy and informed debate. (That’s Hannity and Colmes) The Barry Luciers of the world are entering a minefield of knowledge. Who knows what destructive information they’ll be confronted with next. (Student loan bill) That’s why all colleges should be forced to advertise every element of their curriculum so students are guaranteed that when the leave college they’ll be exactly the same as when they went in. (Give or take $160,000) That folks, is what I believe college is for. You take these unformed lumps of clay, leave them unformed lumps, then fire them in the kiln of unchallenged thought so they become rigid and never move again. That’s how you get well educated like Barry.

[Video: Neil Cavuto: What was your grade?
Barry Lucier: My grade was well.]

Stephen: See? His grade was well. Now he make double plus think despite unwell school. Let’s just hope our future generations can do the same.

And that’s the Word.


A rushing river of stupid (Part 2): is creationism responsible for eugenics?

Creationists of late have been spending a fair amount of time writing that the theory of evolution by natural selection naturally flows into eugenics. This would only appear obvious if you have a very superficial understanding of evolution and is easily debunked. Their only smoking gun is that several prominent defenders of evolution were also proponents of forced sterilization of "mental defectives".

I'll repeat what I've written elsewhere: even if this were true, it wouldn't be a convincing argument against evolution. Relativity made the atomic bomb possible. That doesn't mean relativity is wrong.

Now, Andrea Bottaro writes in the Panda's Thumb that we can understand eugenics better as a product of its time, and that in the early and middle parts of the 20th century, prominent members of the creationism crowd also were members of the eugenics movement. This is well worth a read. Find it here.

Note that pointing out that creationists supported eugenics doesn't make creationism a natural flow into eugenics. It merely points out that eugenics was a commonly held and popular belief in the early parts of the 20th century.


Tuesday, May 15, 2007

Cost benefit analysis of a vaccine (Gardasil)

Kudos to the New York Times (again). They publish a simple, fantastic piece about the risks and benefits of the new Gardasil vaccine against HPV. The risks?

They may include pain, swelling, itching and redness at the injection site, as well as fever, nausea and dizziness.
Well, this sounds like what you might expect from any vaccine. The pain, swelling at the injection site are basically signs that your immune system is working. And the fever as well. Nausea and dizziness are pretty common side effects of any injection. And:
Another concern involves long-term safety. How do we know this vaccine will not eventually cause other problems like autoimmune or neurological disorders or lose its protective powers or foster the dominance of other HPV variants?

Actually, we don’t. But we do have at least five years of safety data that include no hints of long-term risks or waning effectiveness. But if the vaccine should begin to lose potency over time, that could easily be remedied by a booster shot.
Honest, informative. Some people may not feel comfortable with the idea that we don't know the effects of the vaccine in the long term. But any new vaccine, you won't know what the long term effects are for 20 years (until you've been using it for a long term). And so far, there are very few vaccines that have had any serious long term effects.

Hmmm... So should you have give your daughter the vaccine? What can she get from it? Well, it prevents infection with the subtypes of HPV that cause up to 70% of cervical cancer. And, in a 3 year followup, it prevents pre-cancerous lesions in nearly 100% of vaccinees who got the vaccine prior to exposure to HPV. It even provides some protection to women who have previously been exposed to the virus. Up to 17% protection from pre-cancerous lesions for women who had already been exposed.

This is why it's so important to give this vaccine to children, before they are exposed to HPV through sex. Once they're old enough to choose the vaccine for themselves, it's likely already too late to get much benefit from it.

Granted, we can't say whether or not it prevents cancer. It takes twenty to thirty years for cancer to show up in women who have been exposed to HPV, and this vaccine has only been in production for a few years. But it prevents HPV infection of the most prominent subtypes, it prevents precancerous lesions... it's not a stretch to suggest it will almost certainly prevent cancer. And that sounds pretty good to me.

There are no known risks of Gardasil (though to be fair, there is a small chance that longer term studies will find some). There are some very clear benefits to getting the vaccine. So when you're making up your mind for your child - make the calculation - prevent HPV vs. no known risks. It seems pretty clear to me.


Friday, May 11, 2007

Friday beautiful science

This week's Friday beautiful science comes from Claire Nouvian's new book The Deep. She's a journalist who collected a large number of photos from deep sea expeditions into an amazing coffee table book. I've featured a photo previously that is included in the book. PZ has also featured photos that are in this book here and here.

Get the book here:


Thursday, May 10, 2007

HPV and oral sex

Now that I have your attention...

I have a sneaking suspicion that if protecting your daughter from cervical cancer isn't sufficient reason for getting the Gardasil vaccine, then protecting your daughter (or son) from throat cancer won't change your mind:

The same virus that causes cervical cancer is the principal cause of throat cancer, according to a new study.

The research also suggests that unprotected oral sex is a major reason people are contracting throat cancer - not just smoking and excessive alcohol consumption, as previously believed.

"It's the human papillomavirus that drives the cancer," said Maura Gillison, assistant professor of oncology and epidemiology at Johns Hopkins University in Baltimore, Md., and lead author of the study.

She said the more oral-sex partners a person has, the greater the risk of contracting oral cancers (located in the tonsils, back of the tongue and throat). The good news is that the risk remains low over all.

"People should be reassured that oropharyngeal cancer is relatively uncommon, and the overwhelming majority of people with an oral HPV infection probably will not get throat cancer," Dr. Gillison said.

A new vaccine protects against infection by several strains of HPV, including the one associated with oral cancer, HPV-16. However, Dr. Gillison said it has not been specifically tested for its effectiveness against oral cancer.
As an interesting aside, I wonder why this has been picked up by 2 major Canadian news media outlets, and no major American news outlets (as of May 10 at 4:30, ET).


My woo™ is unknowable!

I've maintained in the past that science demands a "Prove it." mentality. This is in stark contrast to many practitioners of alternative medicine, who either say that their particular brand of quackery is "unknowable" in the regular sense (to which I say, "Can't I make up shit and charge for it, too, then?"). The other response is that conventional methods for evaluating success and failure don't work when applied to alternative medicine. This should set off alarm bells and get you reaching to protect your wallet. Anyone who is actually confident that their technique works won't mind subjecting it to objective testing.

Orac provides an excellent critique of one particularly revolting example of this "you just don't understand!" brand of intellectual dishonesty:

In other words, if that pesky scientific method won't show that alternative medicine has efficacy against disease or symptoms, then the answer is easy: Use a different method and "widen the definition of what works in therapy"! Ugh! I wonder who paid for this study.
While I tend to disagree with him that this might be funded by alternative medicine companies (I think the author of this study could honestly think these things - she's just wrong). Read Orac's critique, and try not to get too depressed at the example of post-modern, anti-Enlightenment thinking that he has uncovered.


60th Skeptics' Circle

The 60th Skeptics' Circle is up at Infophilia. Take a look.


Tuesday, May 8, 2007

Small molecules in the 21st century

An interesting article on the challenges and opportunities of discovering antibiotics (and other small molecules) in the 21st century. If you only have time for the summary:

My point is that bioactive small molecules are critical to life. It has been suggested that they should be ranked equal in importance with the dogmatic three: DNA, RNA and protein. There must be an enormous number of different small molecules in nature, waiting to developed and used to our advantage. We have to do a better job of finding these intriguing molecules, determining their structures, and developing ways of identifying their beneficial functions. This is an enormous task and, obviously, it cannot be left to the pharmaceutical industry alone. However the industry and government could combine to fund the innovative academic research that is required to make sure that the compounds and their uses are found.


Fearmongering at Fox News

Wow, just wow. An article on Fox News suggests that pesticides are affecting our I.Q. Yet again, a popular news article can be debunked using information only found in that article. How do they decide that pesticides are affecting our I.Q.?

Dr. Paul Winchester, a neonatologist at the Indiana University School of Medicine and director of the Neonatal Intensive Care Unit at St. Francis Hospital in Indianapolis, studied the test scores of 1,667,391 Indiana students in grades 3 through 10.

Looking at the Indiana Statewide Testing for Educational Progress (ISTEP) exam, Winchester and his researchers found scores for math and language were clearly seasonal, with the lowest scores going to children conceived in June through August.
And how much of an effect did he see?
For the females in the study the difference was a 1 to 1.5 percent drop, and the results were similar for all groups and sexes conceived in May through August.
Ok, 1-1.5%. That's a pretty small effect. But in this case, I won't even try to argue that his effect is too small to be measured. For the sake of argument, I'll agree to it and ask, "But what does this have to do with pesticides?"
"The pesticides we use to control pests in fields and our homes and the nitrates we use to fertilize crops and even our lawns are at their highest level in the summer," Winchester said in a news release.
Ahhh... Well, then. Here we are with the correlation and causation business again. His only reason for asserting this is that we use pesticides at higher rates in June, when all these stupid babies are being conceived. Why not just hypothesize that these children are dumber because of hot dogs? I'll bet there's a lot of hot dogs that get eaten in June. Or perhaps it isn't the conception date that is important, but rather the birth date? Perhaps it has more to do with being born in the depths of winter that makes these children stupid? Frost-bitten brain, perhaps? The point is that there are plenty of models one could come up with that would suggest why children conceived in June are 1-1.5% dumber.

The truth of the matter is that one can't tell why such an observation is being made, and it is rather irresponsible of Dr. Winchester to bandy such a scare-mongering hypothesis about at a news conference.

That said, I wouldn't want a pregnant mother exposed to pesticides (hell, I wouldn't let my wife operate power tools while she was pregnant - I'm all about being careful). There are already plenty of reasons to keep pesticides away from pregnant women:
According to the American Pregnancy Association, even household gardening pesticides are well-known to put pregnant women at high risk for many birth defects, including oral clefts, neural tube defects, heart defects, and limb defects.
But there's no evidence coming from Dr. Winchester that he's discovered another reason to keep pesticides away from pregnant women.


On the cause of autism.

A new Nature Medicine (subscription requried) "News & Views" article by Art Beaudet at Baylor College of Medicine summarizes some new discoveries about autism. As it turns out, somewhere between 10-30% of autism patients can be demonstrated to have de novo mutations (i.e. occurring in the sperm or egg) that cause their symptoms. This is cool work, as two different groups found copy number changes in 10-30% of autism patients that wasn't present in the parents. Why is this cool? Because it answers a longstanding question:

Autism is thought to be highly heritable, largely because of a very high concordance in monozygous (identical) twins—although the concordance in dizygous (fraternal) twins is low.
One would expect the frequency to be lower in fraternal twins, but for autistic patients, this was lower than normal. Well:
All of the genetic abnormalities discussed here would be expected to be associated with virtually 100% concordance in monozygotic twins and, for the de novo majority, very low concordance in dizygotic twins ... ... Thus, for a fraction of cases, this new understanding of the genetic etiology of autism fits perfectly with the previously puzzling data from twins.
So, if many of the changes are mutations occurring in the sperm or eggs, one would expect identical twins to have the same disease, as they would both carry the mutation. But the odds of both fraternal twins getting sperm or eggs that carry a brand new mutation are astronomical.

Beaudet hypothesizes two things:
Higher density arrays focused at the level of single exons are likely to be very productive in identifying smaller abnormalities that may be immediately traceable to specific genes.
That is, once we look more closely, it may turn out that an even higher percentage of autism patients are due to de novo mutations. And second:
Our view is that epigenetic abnormalities of chromatin that are not associated with nucleotide sequence changes might contribute to the etiology in this group; particularly given the male predominance, epigenetic abnormalities affecting the X or Y chromosome might be hypothesized. We have proposed a mixed epigenetic and genetic and mixed de novo and inherited model for autism, in which individual patients could have a genetic (mutation) or epigenetic (epimutation) etiology and these components could be inherited in some cases and de novo in others.
He suggests that epigenetic factors will prove to be important for other patients, that is that improper modification of chromosomes in the mother or father, will be the causative agent. Though to be fair, he says:
an epigenetic component, if one exists, remains elusive
Nonetheless, we are now discovering the cause of autism in some patients. Now, some important questions remain. Are the sites that are mutating de novo particularly susceptible to mutation? Or are other sites that mutate just less important? And importantly, what do these sites tell us about the pathology of autism? And can we design treatments and diagnostic tests to find and help autism patients? Can we find the cause of autism in other autistic patients?

This paper raises the possibility that we could know the causes of all autism in the near future. Very exciting, indeed!


Monday, May 7, 2007

Everything is toxic.

This weekend I received an interesting e-mail from a reader, where he asked me why I wasn't worried that BT-corn contains a toxin in it. I wrote in my response to the reader:

Everything is toxic in the wrong dose. Water. Oxygen. So the question we ask isn’t “Is BT safe?” but “Is the dose of BT that you could conceivably get safe?”.
Understanding toxicity isn't just related to BT-corn and GM-food (and I don't want this blog to become all GM all the time). This is of importance to understand everything in your life from X-rays to homeopathic medicine to the environment. So let's do a bit of a toxicology primer (I'll write about long-term health studies in the future).

So what did I mean when I said water is toxic? Was I being facetious? Water can kill you? Well, yes. Recently, a woman killed herself drinking too much water in a water-drinking competition in California. A simplified version of why drinking too much water can kill you, is that you have very specific concentrations of salts (electrolytes) in your blood (and in all the cells of your body). Your body does a pretty good job of keeping those salts at the right concentration. But if you take in a large amount of water too quickly (and we're talking about gallons, here), you essentially dilute out the salt concentration in your blood, and you die. Over longer periods, you can piss out the extra water, to keep the salt concentration within the right range, but if you drink the water too quickly, it can kill you. This is the reason that when you get an IV in the hospital, they inject a dilute salt solution, and not pure water. A pure water IV pushed at a high enough speed would kill you (and even at low speed would likely hurt like shit - any medical folks care to comment?).

Really, everything is toxic. It's much more useful to give a figure of how toxic something is. To do this, we ask the question, how much of compound X (in this case, let's go with water) would it take to kill 50% of the animals that were treated with it. We refer to this figure as the lethal dose 50, or LD50. When looking at things that are not very toxic, we may fail to calculate an LD50, in which case we use the highest dose it is possible to give to an animal, and say that the LD50 is higher than that.

For water, the oral LD50 is greater than 90 mL/kg. In this particular case, it means that they failed to reach a dose of water that killed half their rats, and are calculating based on the highest dose that they were able to give to rats. That means, that if you give a rat 90 mL of water/kg of rat into their stomach, less than 50% of them will die. If you translate this into a human (where the numbers won't be exactly the same, but will be fairly similar), you can give a little over 6L of water to a 150 lb human before 50% of them will die (6 L is about 1.5 gallons). Or around 13.5 lbs of water. That's a lot of water.

Let's compare this to pure BT. Folks who have examined the toxicity of BT have found that when administered orally, that at levels of 10,000 mg/kg, it wasn't toxic. So to compare that to water, 90g of water/kg didn't produce toxicity levels of 50%, and 10g of BT/kg, didn't produce toxicity levels of 50%. Just the fact that folks are unable to get to doses high enough to kill 50% of the animals suggests that these are both fairly safe compounds. Note, I don't say safe, I say fairly safe. There is no absolutely safe compound.

Let's look at a few other compounds that are toxic enough that we can see an LD50. Table salt has an LD50 of 3000 mg/kg (note that smaller numbers mean the compound is inherently more toxic, as it takes a lower dose to kill the animal). So table salt is more toxic than pure BT. And what about the Gabriel Garcia Marquez's favorite poison of lover's, cyanide. It has an LD50 of 5 mg/kg (or the ultratoxic-terror-weapon: botulism toxin, with the incredible LD50 of 0.0000012 mg/kg).

Now back to where I started from, that BT is a toxin. The reason that BT has been engineered into plants is that it kills some types of insects. Meaning that while it is on the same level as water or table salt for toxicity to humans, it's much more toxic to insects. While we share many of the same sensitivities to toxins with rats and mice, we share fewer sensitivities with insects.

So the next time, someone tells you, "BT-corn is toxic!", you can tell them that you know, and that you're not afraid. Everything is toxic.


Sunday, May 6, 2007

Democrats and quarks?

What are the political implications to liberals of gravity? What does the Big Bang contribute to communism? Does the libertarian party have concerns about DNA being the genetic material? Should Democrats make their social policies to suit the existence of quarks?

I'm writing these questions to point out the silliness in asking the question:

Does Darwinian theory undermine conservative notions of religion and morality or does it actually support conservative philosophy?
The New York Times asked this question in an article, published yesterday, lending a layer of credibility to the question.

Three of ten Republicans at the recent presidential debate said that they don't "believe" in evolution. (Never mind that I find believing in a theory to be silly. Belief is for churches. Science deals in evidence for and against. And in the case of evolution, the 150 years of evidence has piled up, and the results are in. Evolution is the best description of the origin of species that we have). Perhaps a followup question could have been "How many of you believe the earth is flat?". This country has the best scientific enterprise in the world, and yet presidential candidates are professing anti-scientific sentiments (in public, no less).

Let's just usher those folks off the stage, shall we? You're not qualified to be president. Buh-bye.


Friday, May 4, 2007

Gary Trudeau's take on the evolution/intelligent design "debate"

You've probably already seen this before, but I stumbled on it today, and it made me snicker.


Thursday, May 3, 2007

Friday beautiful science

Today's Friday photo is a closeup shot of a housefly. It's a bit cliché, but it's a fantastic example of the head (and eye) of an insect. This photo, taken by Charles D. Krebs, won first place in 2005 at the Nikon Small World competition. You can see last year's winners live in person at a venue near you. How's that for an original date idea? Take your date to see some cool science pics.

The 2007 awards are being judged next week, but won't be announced until the fall.


Conservapedia, an update

So, the happy little writers at Conservapedia have been busy. If you'll recall, Conservapedia is the wikipedia analogue that has a number of slightly different rules. For example:

We do not allow liberal censorship of conservative facts. Wikipedia editors who are far more liberal than the American public frequently censor factual information. Conservapedia does not censor any facts that comport with the basic rules.
Ahhh... conservative facts. Unlike, for example, communist facts. Or libertarian facts.

Conservapedia is an attempt to make a parallel universe for conservatives, where they can create their own facts. In that regard, they've been quite successful. They've filled in many details in pages that were previously barely more than a sentence or two. For example, they've fleshed out their entry on Unicorns:
The existence of unicorns is controversial. Secular opinion is that they are mythical, however some young earth believing Christian apologists have advanced various arguments that the biblical unicorn was not a fantasy animal and that the animal did not have one horn.
Wow. Unicorns are controversial? Good thing they're trying to stay "true and verifiable."

And their religious references are not that subtle. From their page on yeast:
Over 600 different species of yeast are known and God has widely distributed them in nature.
What else have they been up to? Oh, how about a conspiracy-a-palooza! (And they didn't invite me!). Here they tell us why those dirty liberals come up with god-hating ideas like evilution:
Many graduate students in anthropology and related fields need topics and funding for doctoral work, and the Theory of Evolution fills that need. If the theory were recognized to be false, then these graduate students would be left without work and jobs. The financial incentives may exceed $1 billion annually, and will cause a greater support for the theory, particularly among academics and government workers benefiting from the money, than would exist in the absence of these incentives.
Holy, moley. What a scam! The government will hand out money just because an idea exists, even if it's not true? Just 'cause? (/sarcasm) My head hurts. As it happens, according to Conservapedia the motives to spewing evilution aren't just financial, they're also political:
The more a state imposes the teaching of evolution in its schools, the more liberal that state votes on Election Day. Tennessee is an example of a state that kept evolution out of its schools for most of the 20th century, including winning the Scopes trial to ban the teaching of human evolution. It has consistently been one of the most conservative states on Election Day, and even rejected its own native son Al Gore in 2000, causing him to lose the election.
I feel faintly ill, reading this. This is a conspiracy just too grand, even for me. Fortunately for me, this little ironic gem is right at the end:
Once accepted for years, it can become difficult for some people to question that as an adult and admit that they were misled by people they trusted, or admit that they were wrong for much of their life.
Yep, at least I agree with them on that one, though perhaps not in the sense that they intend.

Go ahead. Swing on over there. And while you're there, make an account, and write something up. It seems to have fewer satirists on now, and more batshit crazy conspiracy loons.


Cynical quote

"America believes in education: the average professor earns more money in a year than a professional athlete earns in a whole week."
- Evan Esar


On pseudonyms.

I write under a pseudonym. Why?

1. Because it allows me to write personal anecdotes in a manner where I'm not sharing my laundry with people I deal with on a day-to-day basis.

2. Because it allows me to separate this part of my life from my work life. i.e. I don't have to worry about weirdos calling my boss, just because I wrote something that they disagree with.

3. Because "The Factician" amuses me. It's a combination of Factory and Tactician, which makes me laugh. Very conspiratorial. Though I've had folks on other sites claim that they think I'm spouting false facts. Not quite what I intended, and sometimes I wish I'd noticed that before I chose it...

4. It allows people to judge what I say, not who I am. I try to make arguments from a rational position, rather than a position of authority (not that anyone considers a post-doc an authority - we're just about the bottom rung of the academic science ladder).


An anecdote about anecdotes.

Shortly after my wife and I got married, we started trying to have a child. My wife is old enough that we knew it could be tricky. Womens' fertility starts declining at a fairly early age (as early as 25). My wife was 38 when we started trying to get pregnant. Shortly after she turned 39, we visited some fertility specialists. They measured her FSH levels, and discovered that she had a level of 16 mIU/mL (many organizations call >14 infertile). The first fertility person we saw said basically that there was absolutely no way we were going to have kids that were biologically ours. No chance. No hope. I'm sure you can imagine that this was rather depressing for us. It was suggested that we either use someone else's eggs, or adopt.

My wife and I are both biologists. We delved into the primary literature, and discovered for ourselves that what he had told us wasn't entirely true. We opted for a second opinion. The second fertility specialist told us what we had essentially read for ourselves. That we could *possibly* have a child. But that the odds were very, very slim. 1-5%, if we used in vitro fertilization, probably much lower if we used more conventional methods. And we were at a much increased risk for having a miscarriage. He said he generally didn't attempt fertility treatments with women in her state, as it is an expensive process, and likely wouldn't be worth it for us. When we decided to go ahead with it, he told us that it probably wouldn't work, and that we shouldn't have unrealistic hopes.

We prepared for fertility treatments over the next month. We both were tested for a variety of sexually transmitted diseases, and had our Rh factors checked. Around this time we changed the brand of toothpaste that we use, as the toothpaste that is available in CostCo changes from day to day. Four weeks before we started fertility treatments, my wife got pregnant. We knew that it was very likely that she would miscarry, so we didn't get our hopes up. She didn't. Nine months later, a healthy baby boy was born. He's now over a year old, and is healthy and cute and a damn lot of fun.

We've told this story to many of our friends and family. What have we heard from them?

"I guess you proved that doctor wrong."

"Had you changed your diet?"

"There must be something in your water."
People are really lousy at making conclusions about this. In general, people are lousy at finding causal relationships.

I assert that it was the toothpaste. I think it makes my point rather well.

There's no way to put a causal relationship on any of this. We had a baby, even though the odds were against it. But millions of women have my wife's condition. Thousands of them will become pregnant. Less than half of those thousands will carry their baby to term. My wife happens to be one of the lucky ones, and we remind ourselves that every day. That's the only viable conclusion.

I tell this story to anyone who tells me that reiki "works for them". That echinacea "cured their cold". That homeopathic belladonna "cures their son" every time. That the "president of Gambia cures AIDS". Pass it around, would you?