University of Florida eliminates Computer Science Department. At least they still have football.

Wow, no one saw this coming.  The University of Florida announced this past week that it was dropping its computer science department, which will allow it to save about $1.7 $1.4 million.  The school is eliminating all funding for teaching assistants in computer science, cutting the graduate and research programs entirely, and moving the tattered remnants into other departments.

Let's get this straight: in the midst of a technology revolution, with a shortage of engineers and computer scientists, UF decides to cut computer science completely?

Students at UF have already organized protests, and have created a website dedicated to saving the CS department.  Several distinguished computer scientists have written to the president of UF to express their concerns, in very blunt terms.  Prof. Zvi Galil, Dean of Computing at Georgia Tech, is "amazed, shocked, and angered."  Prof. S.N. Maheshwari, former Dean of Engineering at IIT Delhi, calls this move "outrageously wrong."  Computer scientist Carl de Boor, a member of the National Academy of Sciences and winner of the 2003 National Medal of Science, asked the UF president "What were you thinking?"

(Note to the students, if you need more quotes for your site: I think this move is shockingly short-sighted.  The University of Florida is moving backwards while the rest of the world moves ahead.)

Meanwhile, the athletic budget for the current year is $99 $97.7 million, an increase of more than $2 million from last year.  The increase alone would more than offset the savings supposedly gained by cutting computer science.

Now, I'm not saying that UF has chosen football over science. Actually, the real villains here are the Florida state legislators, who have cut the budget for their flagship university by 30% over the past 6 years.

Meanwhile, just two days ago, Florida governor Rick Scott approved the creation of a brand-new public university, Florida Polytechnic University, to be located near the city of Tampa.  In an unintentionally ironic statement, Gov. Scott said

"At a time when the number of graduates of Florida's universities in the STEM [science, technology, engineering, and mathematics] fields is not projected to meet workforce needs, the establishment of Florida Polytechnic University will help us move the needle in the right direction."

Heads up, Gov. Scott: no one is going to believe that you're supporting technical education when your flagship university is eliminating its Computer Science Department. Since cutting support for universities seems to be a major agenda item for you and the legislature, why stop at 30%?  With just a bit more cutting, you could get rid of those annoying universities entirely.  Let the rest of the country worry about higher education! Florida can focus on orange groves and golf courses. Oh, and football.

[Update 25 April 8:30pm: After my Forbes blog post on this topic went viral, UF President Bernie Machen announced that they are dropping their plan to eliminate Computer Science.  See my followup post here for details and a link.]

Eat more chocolate! Lose weight!

It's a holiday weekend, and many of us will be eating chocolate, especially chocolate bunnies and chocolate eggs.  (Where does that come from, anyway?  Bunnies don't lay eggs.) We don't really need an excuse to eat chocolate.  But isn't it wonderful when a scientific study tells us that we should?  Even the skeptics among us really want to believe that eating chocolate is good for you.

Last week, a new study in the Archives of Internal Medicine claimed that eating chocolate more frequently is associated with a lower body-mass index, or BMI.  The study's authors carefully stated their results as a "link," but then they went on to say that other evidence would "suggest the association could be causal."

Of course the media ate this up (pun intended), with headlines like "The Chocolate Diet?" at The New York Times.  The Times story was filled with caveats, pointing out that it was frequency of chocolate consumption (how many times per week you eat it) that was associated with lower body weight,  and that people who simply eat more chocolate tend to be, well, fatter.  Surprise!

Beatrice Golomb, the lead author of the study, explained to the Times that:

“It’s not the case that eating the largest amount of chocolate is beneficial; it’s that eating it more often was favorable.”  

Because the thinner people in the study ate less chocolate overall, they must have eaten much less at each sitting.

Alas, this is just a bad study.  The biggest problem is that it was based entirely on questionnaires, in which 1018 men and women answered questions about how often they excercise and how often they eat chocolate.  Here are some key features of these subjects:

• Their average BMI was 28.  So they are kind of fat. (A BMI of 25-30 is overweight.)
• They claim to exercise 3.6 times per week, on average.
• They report eating chocolate 2 times per week.

We all know how this works. Even though the questionnaire is anonymous, we still want to look like we're doing the right thing.  So we over-state how often we exercise (3.6 times per week? ha!) and we under-state how often you eat unhealthy foods.  The entire result can be explained by a tendency of thinner people to admit eating chocolate more often.  Observational studies like this one are notoriously unreliable.

On this note, I have to give kudos to Gary Taubes at Discover magazine, who isn't buying any of this.  Taubes explains that:

"Both of these studies were classic examples of what is known technically as observational epidemiology, a field of research I discussed at great length back in 2007 in the New York Times Magazine.  I made the argument that this particular pursuit is closer to a pseudoscience than a real science."

Taube looked at multiple observational studies done at Harvard's School of Public Health, by one of the top epidemiology groups in the country.  But when observational studies "discovered" a causal relationship, it never seemed to pan out, says Taube:

"I pointed out that every time that these Harvard researchers had claimed that an association observed in their observational trials was a causal relationship—that food or drug X caused disease or health benefit Y—and that this supposed causal relationship had then been tested in experiment, the experiment had failed to confirm the causal interpretation—i.e., the folks from Harvard got it wrong. Not most times, but every time."

A zero percent validation rate - it doesn't get any worse than that.  Taube makes a very good case that the whole "nutritional epidemiology business" is pseudoscience.  You just can't go around asking people what they eat and expect to get reliable answers.

So nope, it just isn't so, no matter how much we'd like to believe it.  Eating chocolate isn't going to lower anyone's BMI.  But the really important question is, which part of the chocolate Easter bunny do you eat first?  I go for the ears.

Got cold. Try zinc?

Having a cold is no fun.  Sore throat, runny nose, general feeling of all-around blechiness.  About the only good thing I can say about colds is that they don't last long, usually about a week.

We still don't have a cure for the common cold, but it's not for lack of trying.  For decades, Nobel laureate Linus Pauling promoted mega-doses of vitamin C as a way to prevent colds, but he turned out to be wrong on that one.  Somewhere in the neighborhood of 200 different viruses cause us to get colds, and we don't seem to be able to get rid of any of them.

In recent years, the most popular new remedy is zinc, usually in the form of a lozenge.  The evidence for zinc's effectiveness is not entirely clear, but a review published just last month, which looked at 13 different studies, concluded that zinc seems to help, just a little bit.  All 13 studies were randomized controlled trials, the gold standard of research, and collectively they included 966 people.

That sounds encouraging, but the benefit was disappointingly small: zinc seemed to shorten the duration of a cold by about one day.  So instead of being sick for 7 days, you might be sick for 6 days.

Or maybe not: Dr. Terence Davidson from UC San Diego argues that if you look at just the more rigorous studies, the effect vanishes entirely.

Chunks of elemental zinc

Then there are the worrisome reports that Zicam, a zinc-based cold remedy, causes people to lose their sense of smell.  (This may not sound so terrible, but some people reported a permanent loss.  Imagine never being able to smell fresh-baked bread again.)  In 2009, these reports led the FDA to issue a warning advising consumers to stop using three particular Zicam products.  In addition to over 130 reports directly to the FDA, Zicam's manufacturer had over 800 additional complaints about loss of sense of smell.

In an ironic twist, Zicam markets its products as homeopathic remedies, which means that the FDA cannot regulate them. It also means that they shouldn't contain any active ingredients, because homeopathic preparations are diluted until they contain nothing at all.  But Zicam does contain zinc, quite a lot of it, and the FDA's warning letter demanded that Zicam stop marketing these products because they had never demonstrated that they were safe and effective.

Zicam markets a wide range of zinc-containing products, and the FDA's warning only affected three of them.  Zicam's website today states that "there is no valid, scientific evidence showing a link between Zicam and anosmia [loss of sense of smell]."  Strictly speaking, this is correct, but there have been published reports suggesting a link, such as this one from 2006 and this one from 2009.  These studies looked at nasal sprays, not lozenges, suggesting that the risk (if any) comes from spraying the zinc product directly up your nose.

Aside: Zicam also claims that their products cure allergies too, for which there is not a shred of evidence.  Their website makes the sweeping claim that "all Zicam products are both effective and safe when taken as directed." I see no reason to trust these guys.

Conclusion: I'm not taking zinc.  The side effects might be minimal, but the benefit is very small and possibly zero.  I'll stick with hot tea, which at least makes my throat feel better.  Or chicken soup.  That can cure almost anything.

Evolution bugs me

Cover illustration for the forthcoming textbook
by Carl Zimmer and Douglas Emlen

This is a real photo.  It's the cover for a new biology textbook by Carl Zimmer and Douglas Emlen.  The photo shows three "walking leaves," or leaf insects, which have evolved to look just like the leaves around them.

These little bugs must be one of the best examples of natural selection ever.  The more closely they resemble a leaf, the more difficult it is for predators to find them.  Over the millenia, the bugs who evaded predators survived better, and eventually walking leaves looked like they do today.

In fact, these guys have been around for a long time, at least 47 million years, according to a fossil discovery published in 2006.  That paper described a fossilized leaf insect found in an ancient lake bed in Germany, which looks remarkably similar to its modern descendants.

Yes despite this amazing evidence, only 40% of Americans believe in evolution. State legislatures continue to pass bills attempting to teach children the creation myth that the world was created less than 10,000 years ago.  Just last week, a committee in Alabama's legislature proposed a new law that would give students credit for courses on creationism.  The bill's sponsor, local legislator Blaine Galliher, was very clear about his motivation:

"They teach evolution in the textbooks, but they don't teach a creation theory…. Creation has just as much right to be taught in the school system as evolution does." 

I feel sorry for the students in Alabama whose education might suffer thanks to the ignorance of their lawmakers.  But there is some hope: in the national poll showing that 40% of Americans overall accept evolution, among young adults that percentage was 49%, while among over-55 set it was just 31%, as shown in this graph:

So perhaps in another hundred years or so, Americans will start to "get" evolution.  But it might take longer: apparently 18% of Americans still believe that the sun revolves around the earth.  So it's taken us 500 years to get to 80% for that one.

Should a doctor fire an anti-vax patient?

The anti-vaccination movement continues to grow, despite the retraction and thorough discrediting of the 1998 scientific study that spurred much of its growth.  The stubborn persistence of anti-vaxxers shows how difficult it is to dispel misinformation once that information is out there, even after dozens of new studies and millions of dollars in research that demonstrate that vaccines are safe.

One of the most dangerous trends is the growing number of parents who refuse to vaccinate their kids, or who choose "alternative" vaccine schedules, such as the one promoted aggressively by Robert Sears (who goes by "Dr. Bob").  Sears appears to have simply invented this alternative schedule without bothering to conduct any scientific studies, in part to promote sales of his 2007 book, The Vaccine Book: Making the Right Decision for Your Child.  Vaccine expert Dr. Paul Offit explained, in a 2009 article in the journal Pediatrics, why Dr. Sears' schedule was a very poor choice for children and for the public health.  After thoroughly dismantling Sears' anti-science positions, Offit concludes, "Sears has a poor grasp of the scientific method."  That's an understatement.

Other doctors, perhaps jealous of all the attention that Sears has gained through his anti-vaccine writings and television appearances, have created their own alternative vaccine schedules.  One of them, Donald Miller, even goes so far as to say that vaccines cause childhood cancer, despite the complete lack of evidence for this wild claim.  Somehow Sears, Miller, and others like them have managed to convince many parents that their children don't need vaccines.

In response to parents who don't want to vaccinate, many of whom show up with Dr. Bob's schedule in hand, pediatricians have struggled to find an effective response.  Parents can be utterly convinced by the misinformation they find on the Internet, which is all too easy to find.  (For example, Googling "vaccine" brings up the National Vaccine Information Center, a hotbed of anti-vaccine propaganda and pseudoscience, on the first page of hits.)  By the time parents arrive with their babies for the first vaccine, convincing them to change their minds can be nearly impossible.

Perhaps in frustration, doctors have started to "fire" their patients if they refuse to vaccinate.  As reported by Shirley Wang in The Wall St. Journal last week, 20-30% of doctors in two different surveys, in Connecticut and the Midwest, reported having to kick patients out of their practices because of vaccine refusal.  These numbers have roughly doubled over the past ten years, according to the American Academy of Pediatrics.

Is firing a patient the right thing to do? It's a difficult question.  On the one hand, doctors should do everything they can to make sure kids are vaccinated.   If a doctor kicks a parent out, that parent may find another doctor who doesn't insist on vaccinating children, which ultimately harms the children.  Doctors have to spend more time educating parents about the tremendous benefit of vaccines, about the very strong evidence (based on tens of millions of doses) for vaccine safety, and about the frightening consequences of infection with meningitis, hepatitis, measles, polio, and other vaccine-preventable diseases.

On the other hand, unvaccinated children bring diseases into the pediatrician's office, where they can spread them to other children.  Some of these other children are too young to be vaccinated, and childhood infections can be extremely dangerous, even fatal, in the very young.  From this perspective, "firing" a patient might be the only responsible action, after first trying to convince the parents to vaccinate.  I know that I wouldn't want to bring my child to a doctor's office where unvaccinated children were in the same room.

I understand how nervous a parent can be about vaccinations.  I will never forget the day my older daughter got her first vaccine: the needle looked huge compared to her tiny leg, and she screamed when the doctor gave her the shot.  But she was fine a few minutes later, and she'll be protected against a dangerous infection for her entire life.  Vaccines have been so successful at eliminating childhood infections that parents no longer see these infections as a threat.  Ironically, the very success of vaccines has allowed the anti-vaccine movement to sway so many people.

Doctors may have to keep firing the parents of their young patients, but I hope they'll first make every effort to educate them.  They need to explain that vaccines do not cause autism, nor do the ingredients in vaccines, and that scientific studies involving hundreds of thousands of patients support these conclusions.  They should also explain that many of the anti-vaccination claims on the Internet started when Andrew Wakefield published one small study of 12 patients, now retracted, claiming a link between the MMR vaccine and autism.  Investigations later revealed that he was paid by lawyers to recruit patients for a lawsuit against vaccine makers, that he didn't reveal these payments to his co-authors or the patients, and that he manipulated the data.  Since then, the anti-vaccine movement has exploded and we've experienced multiple outbreaks of measles, mumps, and other illnesses linked directly to unvaccinated children.

Doctors interviewed by the Wall St. Journal reported that they had convinced at least some parents to follow the recommended vaccine schedule.  Perhaps that's the best we can hope for.  If we're going to avoid a return to the era when children routinely died from infections, we must keep trying.

An Alzheimer's disease breakthrough?

We all hope to get old one day.  But if we do, our chances of getting Alzheimer's disease increase dramatically as we move into our 80s.  As many as 50% of people over age 85 may be affected.  Much progress has been made in understanding the disease, which appears to be caused by "plaques" forming in the brain, but we have no treatment and no cure.

But maybe - just possibly - a dramatic new study offers the first real hope for a treatment.  In a paper published today in the journal Science, a team of researchers led by Gary Landreth at Case Western University and his graduate student Paige Cramer found that an orphan drug called bexarotene has a remarkable affect on mice afflicted with a condition similar to Alzheimer's in humans.  These mice have similar plaques in their brains, compose of beta-amyloid proteins, and they show behavioral and cognitive impairment similar to some of the problems experienced by Alzheimer's patients.

Within just hours of administering bexarotene to these mice, the plaques started to clear.  If that weren't amazing enough, within a few days the mice also recovered cognitive abilities that they had lost.  In particular, they regained the ability to make nests, a behavior that normal mice have and that the Alzheimer's mice had lost.  They also regained at least some of their sense of smell.

Bexarotene (Targretin^TM) is an orphan drug that is approved for use in humans to treat cutaneous T-cell lymphoma, a rare skin cancer.  It works by inhibiting a gene, RXR, that is involved in the production of beta-amyloid proteins.  Cramer, Landreth, and colleagues hypothesized that because bexarotene can cross the blood-brain barrier, it might just help to clear out the plaques associated with Alzheimer's.  It seems that they may be right.

A huge caveat here is that many promising drugs seem to work in mice but fail when used in humans.  This drug is different, at least in the sense that it is already approved for human use, but no one has tested it on Alzheimer's patients.  Studies are likely to begin very very soon, but it will take time - possibly years - before we know if it can slow the progress of Alzheimer's.  But for a disease that affects a huge percentage of the population, with no current treatment, this could be a huge breakthrough.

Indiana's clumsy attempt at theocracy

An edible FSM

Those state legislators are meddling with science again.  This time it's Indiana, trying to promote their religious views in public schools by dictating what science teachers will teach.  As usual when legislators try to do science, they messed up badly.

What happened?  Just a few days ago, the Indiana state Senate passed a bill, sponsored by Republican Dennis Kruse, that required the teaching of creationism.  Actually, the original bill called for schools to teach "creation science," but then the Senate amended it to make it much funnier.  Thanks Indiana!

The amended bill, which was approved 28-22, says:

"The governing body of a school corporation may offer instruction on various theories of the origin of life. The curriculum for the course must include theories from multiple religions, which may include, but is not limited to, Christianity, Judaism, Islam, Hinduism, Buddhism, and Scientology."

Holy cow!  I can't wait to see what Indiana students will be spouting when they go on to college.  Maybe they'll learn Scientology, which is one of the religions listed in the new law.  Scientologists believe that life on Earth started 75 million years ago, when an evil galactic warlord named Xenu brought 13.5 trillion of his people to Earth in a spaceship, stacked them around volcanoes, and vaporized most of them with hydrogen bombs.  (No, I'm not making this up.)

If I were teaching in Indiana schools, I'd be sure to cover the Church of the Flying Spaghetti Monster, which has a wonderful theory about the origin of life:

"We believe the Flying Spaghetti Monster created the world much as it exists today, but for reasons unknown made it appear that the universe is billions of years old (instead of thousands) and that life evolved into its current state (rather than created in its current form). Every time a researcher carries out an experiment that appears to confirm one of these “scientific theories” supporting an old earth and evolution we can be sure that the FSM is there, modifying the data with his Noodly Appendage. We don’t know why He does this but we believe He does, that is our Faith."

Now that's a theory you can sink your teeth into.

Finally, a little bit of science education for Indiana's legislators.  The next time you write a law trying to force the teaching of creationism instead of evolution, get the wording right.  You see, you wrote the bill incorrectly, because evolution is not a theory of the origin of life, as any good high school science teacher could have told you.  (Note to Indiana teachers: I've no doubt that you tried to teach these legislators back when they were in school. Apparently they're still not listening.)  Instead, evolution is a theory that explains how species arise: how a single species can evolve into many, through the process of natural selection.  You might have guessed this from the title of Darwin's book: The Origin of Species.  Scientists do have theories about the origin of life, but evolution isn't one of them.

Two years ago, South Dakota's legislature declared that astrology can explain global warming, which gave the rest of the country a bit of entertainment. Last week, it was Indiana's turn to look foolish.  After a huge flurry of embarrassing publicity, it appears that Indiana's legislature has changed its mind, and the bill will not become law.  But if they try again, I'd be happy to send them some materials on the Flying Spaghetti Monster.

[Note: I also recommend the blog posts by PZ Myers at Pharyngula and Jen McCreight at BlagHag.]