Another anti-vax paper bites the dust

Anti-vaxxers learned a lesson from discredited, de-licensed former doctor Andrew Wakefield, who in 1998 published a badly flawed article in The Lancet pushing a link between vaccines and autism. Wakefield's study was eventually shown to be not only flawed but fraudulent, leading all of the co-authors except Wakefield himself to disavow it, and in 2010 the journal finally retracted it after Wakefield lost his medical license.

But it took The Lancet 12 years to retract the paper, and in that time the anti-vaccine movement flourished. Wakefield became a hero within that movement, and continues to push his anti-vaccine propaganda today, even making films presenting himself as a lone hero fighting for truth.

Other anti-vaxxers are very familiar with this saga, and they have followed Wakefield's recipe by writing scientific papers and attempting to get them published in reputable journals. Usually they fail, but now and then one slips through, which they then point to as "proof" that vaccines are harmful.

The latest example is a paper that appeared in Scientific Reports in November 2016 and that the journal just retracted last week. It has a title that sounds highly technical: "Murine hypothalamic destruction with vascular cell apoptosis subsequent to combined administration of human papilloma virus vaccine and pertussis toxin." (Wakefield's 1998 paper had a similarly obscure title.)

What that lengthy title hides is the paper's anti-vaccine message: that the HPV vaccine might cause neurological damage. The paper was quickly called out as pseudoscience by the scientific community, who reacted within days in the blogosphere and elsewhere, as described by a news article in Science that appeared just after the paper's publication.

(Aside: the HPV vaccine protects people from human papillomavirus, which causes many cases of cervical cancer as well as throat cancer. It's the first vaccine that prevents these cancers, which is an amazing breakthrough. Millions of doses have been administered with essentially zero cases of harm.)

What did the paper do? Basically, it was a setup. The authors–most of them from Tokyo Medical University–gave mice a huge dose of HPV vaccine plus (here's the kicker) a large dose of pertussis toxin. There's no valid reason to administer that toxin except to try to induce brain damage, which the authors could then blame on the HPV vaccine. The study design was clearly awful, and the paper should never have been published.

Just after the paper appeared, two groups of scientists wrote to the Nature publishing group (which publishes Scientific Reports) to protest, as reported in the Science story. One letter, from a group of HPV experts at the University of Antwerp, explained that:
"This experimental setup in no way mimics the immunization with HPV vaccines but is gross over-dosage and manipulation of membrane permeability."
This is putting it mildly. For a blunter assessment, see Orac's aptly titled "Torturing more mice in the name of antivaccine pseudoscience," which appeared in November 2016.

What was not publicly known before now was that I too wrote to the journal editors, asking them to "take action quickly, rather than waiting for over 10 years as The Lancet did." First I wrote to the immunology sub-editor, who forwarded my letter to the Editor-in-Chief, Richard White. Dr. White replied on 29 Nov 2016 that "We are looking into the specific issues raised regarding this paper."

That was the last I heard of it, until the journal announced last week that they have retracted the paper.

So in the end, the scientific record was corrected. But why did it take Scientific Reports 18 months to do it? Haven't they learned from the Wakefield debacle how much damage can be done while antivaccine articles like this one remain in the literature? The journal's editors had a responsibility to act more quickly, and they failed. The scientists who wrote those letters back in 2016 had the same complaint, as reported by Dennis Normile in Science last week. Not surprisingly, Scientific Reports refused to comment (when asked by Science) on any details of their review process.

That's not good enough. Scientific Reports is a "mega-journal," a new type of journal that publishes thousands of papers per year, with a relatively low bar for acceptance. The idea (not a bad one, in theory) is that any valid scientific study, even one that makes only a very small contribution, still merits publication somewhere.

What publishers have learned is that these mega-journals are very profitable, because they charge a publishing fee that more than covers their costs. In return for these profits, Nature Publishing has an obligation to remove harmful papers far faster than they did in this case. Otherwise, it's only a matter of time before anti-vaxxers do this again.

Finally, let me repeat something that can't be said often enough: vaccines are perhaps the single greatest medical advance in human history. They have saved millions of lives, and they continue to save lives today. Scourges such as smallpox and polio, which once swept through populations causing terrible pain, suffering, and death, have been conquered thanks to vaccines. Medical researchers continue to work on new vaccines against the infections that still plague us, and they are the real heroes.



How not to respond to the EPA's science denialism

You would think that the editors of the top science journals in the world would know how to write clearly. But if you read their joint statement in the journal Science last week, you might be forgiven for wondering what the heck they are talking about. It's not that complicated, really. Let me explain.

EPA Administrator Scott Pruitt, when he's not busy taking expensive trips, renting rooms at a deep discount from coal lobbyists, or building $48,000 soundproof booths for his office, is doing his best to make the U.S. a friendly place for fossil fuel industries. As part of his pollution-friendly mission, Pruitt denies the scientific consensus that climate change is real and is caused in part by human activities, especially by carbon dioxide emissions.

Pruitt has devised a clever new strategy to make science denialism part of official EPA policy, while pretending otherwise: he's issued a new proposed rule that requires the EPA to use only "transparent" science. (The official Federal Register entry is here.) In his press release, Pruitt stated
"The era of secret science at EPA is coming to an end. The ability to test, authenticate, and reproduce scientific findings is vital for the integrity of rulemaking process."
The press release, which is titled "EPA Administrator Pruitt Proposes Rule To Strengthen Science Used In EPA Regulations", seems to be all about science and openness. One thing I've got to give them credit for: the PR people at the EPA know how to obfuscate.

It turns out this is just a ruse. As Pruitt certainly knows, many of the EPA's rules are based on studies of human subjects, which are governed by strict privacy rules–which are necessary not only to get people to participate in the studies, but also because violating people's privacy can be highly unethical. This means that many studies showing the harms of pollution–for example, this massive study, which found that fine-scale particulate matter from coal plants increases the risk of lung and heart disease–are not "transparent" enough for the EPA, because the identities of the participants as well as all their health records are confidential.

In other words, the new EPA policy isn't about scientific transparency. It's a transparent (!) attempt to ignore the negative health effects of pollution, so that Pruitt can put in place new rules allowing polluters to dump more pollutants into our air and water. See how that works?

In response, the Editors-in-Chief of Science, Nature, the Public Library of Science, and the Proceedings of the National Academy of Sciences issued a joint statement. Alas, their statement is anything but clear. They spend about three-fourths of it explaining about how they support data sharing, and finally, in their last sentence, they write this:
"Excluding relevant studies simply because they do not meet rigid transparency standards will adversely affect decision-making processes."
That's it. Even the most sophisticated reader could be forgiven for not understanding what the issue is, not from this statement alone.

Here's what they should have said: the EPA wants to ignore the health consequences of pollution when creating policy. The EPA administrator, Scott Pruitt, has announced a new policy that pretends to be about scientific transparency, but is nothing of the sort. Instead, this policy is designed to undermine the EPA's mission, which is (and you can read this right on the EPA's website "to protect human health and the environment."

Since the EPA's creation in 1970, the U.S. has made tremendous strides in cleaning up our air and water. Let's not start backsliding just to enhance the profits of a few polluters.

[Note: I have written the EPA and asked for comment. I will update this article if they respond.]

Sniffle. It's allergy season again. Do those shots work?

Ah, spring is in the air. The flowers are blooming and the trees are bursting into leaf.

For many of us, this time of year means one thing: allergies. The price of going outside for any length of time is sneezing and itchy eyes that last for many hours, even after we return indoors. Rather than going out and enjoying the warm air and colorful vegetation, we close the doors and windows and stock up on antihistamines and eye drops. Studies show that 20–40% of people in the U.S. have allergies.

Your local pharmacy has shelf after shelf of allergy treatments, ranging from mildly effective (Zyrtec and its equivalents) to laughably ineffective (anything homeopathic). But even the best pills have side effects, and they only serve to suppress the symptoms. As one study put it:
"Patients struggle to alleviate their misery, frequently self-adjusting their treatment regimen of over-the-counter and prescription medications because of lack of efficacy, deterioration of efficacy, lack of 24-hour relief, and bothersome side effects."
Isn't there a way to tell your body to just stop it already? After all, pollen is not a pathogen. Our misery is caused by our own immune system's over-reaction: it ramps up in response to the foreign particles (pollen) in our eyes and airways and creates a histamine reaction, which is simply not necessary.

None of the over-the-counter pills prevent this reaction, but they can dampen it–hence the term "antihistamine." However, what if there were a way to tell your body to simply chill out and ignore the pollen?

Well, maybe. You can get allergy shots. This is a surprisingly simple procedure: your doctor takes a small, diluted amount of the allergen (pollen, cat dander, etc.) and injects it into your arm. Over the course of many months, your doctor will very gradually increase the amount being injected. You have to go for the shots every week, and continue them for several years.

The question is, do they work? The answer is a qualified yes.

NIH and the Agency for Healthcare Research and Quality (AHRQ) have put together a long explainer of the evidence for and against allergy shots, which you can find at PubMed Health. The NIH study looked at 74 clinical studies of allergy shots. To save you some time, I'll cut to the chase: the evidence is quite good that shots work. Or, as the AHRQ study put it,
"we found high grade evidence that subcutaneous immunotherapy reduces rhinitis/rhinoconjunctivitis symptoms."
This might seem like pseudoscience, but it's not: what's happening is that your immune system is being de-sensitized to the allergen. It doesn't work for everyone, but in many people, this gradual de-sensitization trains their immune system not to react so badly. It's not necessarily permanent, either: after stopping the shots, allergies might re-appear after a few years.

So if you're looking out your window at the beautiful spring weather with a box of tissues by your side, maybe you have a way out. Talk to your doctor or visit the AAAAI site to find an allergy specialist. Don't expect miracles or a quick fix, but allergy shots are the best we've got, for now.


Anti-vaxxers use religious exemptions as false cover for their beliefs

History of measles in the 20th century.
For several years now, anti-vaxxers have been claiming that they have religious objections to vaccines. This is nonsense.

Just last month, the New England Journal of Medicine featured an article describing how the federal Equal Employment Opportunity Commission (EEOC) has been suing hospitals that deny employee requests for religious exemptions to the hospitals' vaccination requirements. The NEJM documented 14 cases where employees sued claiming that they had religious objections to the flu vaccine. Six of the cases were settled, and in the other cases, sometimes the hospital won, sometimes the employees. It's a mess.

The NEJM article focused on the legal perspective, advising hospitals on how they might avoid lawsuits. That's understandable, but it misses the broader point: there's virtually no such thing as a religious objection to vaccines. All of the world's major religions support vaccination, and only a few tiny, extremist sects teach their followers that vaccines are contrary to their faith.

What's really going on is that anti-vaxxers are using religious exemptions as cover for non-religious (and erroneous) objections to vaccines. The anti-vaxxers have convinced people that vaccines are harmful, or scary, or both. They are wrong.

Vaccines are the probably the greatest success story in the history of medicine. They've saved millions of lives. Consider that in the decade before the measles vaccine was introduced in 1963,
"3 to 4 million people in the United States were infected each year [and] an estimated 400 to 500 people died, 48,000 were hospitalized, and 1,000 suffered encephalitis (swelling of the brain) from measles." (Source: CDC)
And that's just measles. People no longer suffer and die from smallpox and polio, which have been eradicated worldwide (except for a few countries where polio still has a foothold). Vaccines protect us from multiple other formerly common childhood infections, and they've been so effective that people are no longer afraid of these diseases. That very success is the opening that the anti-vaxxers use to spread disinformation and fear.

It's not just the EEOC that has been enabling anti-vaxxers. Many U.S. states have passed laws that allow religious exemptions to vaccination. (Note that vaccines are required before children can enroll in public school systems, an incredibly important public health requirement. The exemptions refer to this requirement.)

Here, though, there are signs of hope. After suffering from repeated outbreaks of preventable diseases like measles, many states have recently awakened to the risks caused by unvaccinated children in public schools, and they are moving to remove or tighten these exemptions.

New Jersey is the latest state to act. While the bill introduced in the New Jersey legislature last week doesn't quite eliminate religious exemptions, it makes them harder to get, requiring considerably more documentation from parents claiming a religious exemption from vaccines for their children. NJ took action after realizing that these so-called "religious" objections had risen dramatically, from 3,865 in 2009 to 10,407 in 2016. That rise was fueled, apparently, by anti-vaxxers taking advantage of the loophole in the law, not by any genuine religious objection to vaccines.

It's worth noting that all states allow medical exemptions to childhood vaccination, which are legitimate and necessary. For example, a child undergoing leukemia treatment may have a severely weakened immune system, and a vaccine would be ineffective and possibly harmful. These children are precisely the ones who can only be protected by requiring all the other children in their school to be vaccinated.

Meanwhile, the EEOC should stop suing hospitals. Hospitals are filled with very sick and vulnerable people, and employees have an obligation not to expose patients to possibly deadly infections. If a hospital employee doesn't take that obligation seriously, then s/he should find another job.

Here's $142M we'll be wasting on pseudoscience in the new US Budget

After much unnecessary drama and 6 months late, Congress finally passed a budget last week funding the government for the fiscal year that started in October 2017. While much of the news is good, or at least not too bad, the 2,232 page budget contains lots of goodies for special interests.

I downloaded the whole thing so you don't have to.

One of the worst pieces of wasteful spending is tucked away on page 934: $142,184,000 for the National Center for Complementary and Integrative Health. Incredibly, this is a 9% increase over the NCCIH's 2017 budget of $130.5 million. Is this because they've discovered new and effective treatments? Alas, no.

NIH has been spending money on so-called alternative medicine since 1992. Over the years, the budget has increased from just $2 million to the very hefty $142 million this year. NIH has now spent a total of $2.366 billion dollars on its alternative medicine center.

The NCCIH started as an "office," funded by a $2 million earmark by former Senator Tom Harkin, who later elevated it to a National Center called NCCAM. On Harkin's retirement in 2015, his buddies renamed it as NCCIH, adopting the buzzword "integrative" as a jazzier word than "alternative." It's a classic (and sad) example of how once something gets started by Congress, it grows relentlessly, creating its own constituency of people and industries who consume the funding and clamor incessantly for more.

What have we learned for our $2.4 billion? Have new cures been developed, new medicines been discovered? Has NIH provided good scientific evidence that any of the "alternative" methods–which include acupuncture, homeopathy, naturopathy, Ayurveda, therapeutic touch, reiki, aromatherapy, and others–actually work? The answer to all these questions is no.

On the other hand, the real work of biomedical research, funded by the rest of NIH, has yielded tremendous progress on a wide range of diseases. These include cures that we could only have dreamed about 10 or 20 years ago, such as this amazing stem cell cure of a 7-year-old boy with a devastating skin disorder, or this leukemia treatment reported in 2013.

After 26 years and $2.3 billion spent trying–and failing–to prove that alternative medicine works, it's long past time to end this nonsense and shut down NCCIH, as I and many other scientists have been saying for years. That $142 million could be used far more effectively studying real treatments for real diseases, rather than imaginary treatments that have failed, time and again, to prove their merits.

$142 million. To those who argue that it's only a small percentage of the NIH budget, I would point out that a typical NIH research grant is under $500K. This means we could fund at least 300 additional biomedical research projects every year if we got rid of this giant special-interest earmark that has utterly failed to produce anything useful.

Instead, someone in Congress managed to sneak in the largest budget increase that NCCIH has seen in 15 years. What a waste.

Starving science: a petty, shortsighted national "strategy"

This image taken approximately 438 miles above the earth's
surface provides a spectacular view of the Lena Delta in
Russia. Image courtesy of the U.S. Geological Survey, whose
 images are all in the public domain.
150 years ago, passenger pigeons were so numerous that they could black out the sky when their flocks passed overhead. The last passenger pigeon, a female named Martha, died in the Cinncinnati Zoo in 1914. All we have left of this species are specimens held in museum collections.

One of the most extensive collections of animal specimens in the world is managed by a tiny unit of the U.S. Geological Survey, called the Biological Survey Unit. A small group of curators maintains a collection of more than one million animals collected over the past 130 years by scientists and ordinary citizens across the U.S.

Now, for reasons that are at best mysterious, the USGS is planning to eliminate the Biological Survey Unit. The BSU has a very small budget, a mere $1.6 million out of the USGS's budget of $1.1 billion, and an even tinier fraction of the country's $4.4 trillion budget.

What the heck are they thinking? Shutting down the Biological Survey Unit won't save enough money in the vast government budget to even be noticed, but the loss of its precious collections will reverberate through the decades. Does someone in the USGS or the Department of the Interior have a grudge against the BSU? Or are they just petty?

The BSU's collection resides in the Smithsonian Museum of Natural History, one of the great museums of its type in the world. The collection contains some 370,000 birds, 300,000 mammals, and 390,000 amphibians and reptiles, many of them dating back to the late 19th century. These specimens represent a unique view back in time, illustrating the natural history of our continent and the animals that have lived on it over the years.

It's only through collections like this that scientists can understand how human activities have affected our natural world. For example, historical collections of eggs from wild birds allowed scientists to document the thinning of eggshells caused by the pesticide DDT, which was made famous by Rachel Carson's book Silent Spring.

Just a few weeks ago, the presidents of three of the leading animal science societies in the U.S. wrote a letter to Science magazine pleading for the USGS to continue funding its Biological Survey Unit. So far, the USGS has not responded to them.

Museum collections may not be as flashy as some areas science (perhaps we need a new Indiana Jones movie to raise their profile), but that doesn't mean they are not critically important to our understanding of the natural world. Once the BSU disappears, it's not coming back: the curators will retire or find other jobs, and the collection will become inaccessible, even if it still exists somewhere in the bowels of the Smithsonian.

The plan to shutdown the Biological Survey Unit seems indicative of a larger trend of neglecting investment in our future. It may reflect a particular form of neglect by the USGS, as pointed out by Cynthia Ramotnik in a 2015 article. It also reflects the severe cut to the USGS budget proposed by Donald Trump last month: he requested a total budget of $860 million, which represents a 20% cut from the current year's budget of $1.08 billion. But in the case of the BSU, the budget impact is so small that it seems worse than neglectful to cut it: it is shortsighted and petty.

When asked by the Washington Post, former House speaker (and current Trump enthusiast) Newt Gingrich admitted that the cutting the BSU's $1.6 million budget wouldn't matter to the larger budget, but he then went on to comment, “if this collection is that valuable, there are probably 20 billionaires that could endow it.”

Great: let's hand over our national resources to billionaires, and if they're not interested, well, it must be that the resources weren't that valuable in the first place. Not.

This is ridiculous. We're still a rich country, and we shouldn't be eliminating projects like the Biological Survey Unit just to give a massive tax cut to rich people, or just to make a point about budget cutting, or whatever the reason that the USGS and the Department of the Interior might offer. (The USGS hasn't responded to my inquiries.) Maintaining our museum collections not only shows respect for the thousands of people who built them over the years, but it benefits the countless scientists, educators, school children, and others who will learn from these collections in the future.

Coffee causes cancer. Coffee prevents cancer. Who to believe?

California might soon start requiring Starbucks to warn its customers that coffee causes cancer. Has  California gone nuts, or is there something to this?

A lawsuit filed in 2010 by a group called the Council for Education and Research on Toxics is in its final stages, and the judge might rule soon unless the plaintiffs settle the case. Several of the plaintiffs, including 7-Eleven, have already settled and agreed to post warnings in their stores.

The basis for the lawsuit is that brewing hot coffee produces acrylamide, which is on a list of substances that California claims cause cancer or reproductive toxicity. (It's a very long list.) Even though acrylamide has been on the list since 1990, it wasn't until 2002 that Swedish scientists discovered that acrylamide is present in many foods.

As the American Cancer Society explains,
"Acrylamide is found mainly in plant foods, such as potato products, grain products, or coffee. Foods such as French fries and potato chips seem to have the highest levels of acrylamide."
Uh oh. Coffee, french fries, and potato chips. Where's the joy in life without these?

But wait a second: how come people aren't keeling over with cancer left and right, especially in our coffee-loving, french-fry-loving society? (And what about the French?)

It turns out the evidence against acrylamide is pretty sketchy. If you give it to mice in the lab, at doses 1000 times greater than the amounts found in food, it does seem to increase their risk of cancer. But mice are not people, and 1000 times is a whole lot of acrylamide. The ACS concludes that
"it’s not yet clear if acrylamide affects cancer risk in people."
It's just as easy to find claims that coffee prevents cancer. A 2017 review found that one cup of coffee a day is associated with a slight reduction in the risk of liver cancer and endometrial cancer. A 2010 review of over 500 studies found the same reductions, but a slight increase in the risk of bladder cancer among heavy coffee drinkers. Another large review in 2017, by Robin Poole and colleagues in the UK, found not only a reduced risk of cancer, but a reduction in heart disease and overall mortality.

The Poole study concluded:
"Coffee consumption seems generally safe within usual levels of intake, with [the] largest risk reduction for various health outcomes at three to four cups a day, and more likely to benefit health than harm."
Coffee lovers, rejoice! But let's not kid ourselves: no one is drinking coffee for its health benefits, are they? The stuff just tastes good.

Finally, in answer to my own question at the top of this article: yes, California has gone a bit nuts. Or, as the nonprofit American Council on Science and Health put it:
"If coffee is deemed carcinogenic, then the State of California will be required to give up all pretense at common sense and sanity."
An afterthought: the lawsuit may be just about money. As Bloomberg News explained last October, in a story about the California coffee case: "Unfortunately, it is very easy for ‘bounty hunters’ to file Prop. 65 lawsuits against even small businesses and the cost of settlement and defense often exceeds other types of abusive litigation." The American Council on Science and Health was even more blunt, calling it an attempt to grab "a giant bag of money."

Let's hope the judge in the California case pays attention to the science. Meanwhile, the rest of us can focus on more important questions, such as: dark roast or light? French press or drip?