Short and sweet: the strawberry genome

Happy holidays to everyone, and here's a very short seasonal post: the strawberry genome is here! Kevin Folta from the University of Florida led the effort to put the paper together for the journal Nature Genetics, and he has a nice behind-the-scenes summary on his blog here. One tasty tidbit is that the initial proposal for funding failed because the peach and apple genomes had stronger support - but strawberry beat them both (neither of those genomes is yet complete). It's the first plant to be assembled entirely from next-generation sequences, thanks in large part to the efforts of assembly guru Art Delcher.

And the genome really is "short and sweet", weighing in at just 240 million bases of DNA. (See the paper here.) That's pretty small, for a plant. The apple tree genome is over ten times larger, and the pine tree is 100 times larger. But strawberries are sweeter.

Non-GMO foods: nonsense

I was at a local organic food market recently buying lunch, and I noticed that my avocado-and-hummus sandwich proclaimed that it contained "non-GMO" ingredients (GMO = "genetically modified organism).

Now, I happen to like organic groceries. The ones near me tend to have better produce and fish, two of the main ingredients in my diet. But organic markets are a hotbed of bogus, even laughable health claims, and I often have to suppress my urge to complain to the store's management. (I once wrote to Whole Foods, but they never responded.)

Here in the U.S., most of our food supply is filled with so-called GMO foods, but in Europe the situation is dramatically different. For some reasons, our otherwise well-educated European friends are terrified of GMO foods. They don't seem to realize that we've been modifying the genes in our foods for centuries, and it's generally been a good thing. The latest biotechnology merely allows us to modify plants (and animals too, though none are yet on the market) much more quickly, and more intelligently. Today we can alter just a few genes to produce a more-desirable plant, rather than doing it by trial-and-error over many generations.

In fact, the "GMO" foods of the past likely had hundreds of unknown gene modifications.Farmers selected plants for seed because they looked and tasted good, without having any idea of what was really different about them.

Let's take a look at corn. The corn we eat today, organic or not, looks nothing like the "real" corn (or maize) from centuries ago. The earliest corn cobs discovered by archaeologists were tiny, with only a few kernels. This picture shows a primitive form of corn, called teosinte, compared to modern corn:

The history of corn is a history of genetic modifications made by earlier humans who didn't even know what a gene was. Today's GMO food is simply a continuation of that history.

That hasn't stopped opponents of GMO foods from sounding the alarm. Even the World Health Organization makes some errors on its website, where it discusses three main "issues of concern for human health":

1. Allergenicity. Not a problem. The WHO says "No allergic effects have been found relative to GM foods currently on the market."
2. Gene transfer. The WHO gets this one wrong. They write that "gene transfer from GM foods to cells of the body or to bacteria in the gastrointestinal tract would cause concern if the transferred genetic material adversely affects human health." Gene transfer is a topic that I've studied in some detail, and published papers on. The WHO says that the likelihood of a gene transfer event is "low," but in fact it is vanishingly small - so small, in fact, that not a single gene transfer event has ever happened. In the history of our species, and of all mammals, going back tens of millions of years, not a single gene from something we've eaten has been transferred into the human genome or, as far as we can tell, into bacteria within our guts.
3. Outcrossing. This is "the movement of genes from GM plants into conventional crops," and this really can happen - they're the same species, so they can interbreed. But it's only a concern if GM plants are harmful, which they're not.

The bottom line is, you're far more likely to be harmed by being hit on the head by a corn cob than by some kind of deviant GMO corn gene.

The WHO concludes that GM foods "are not likely to present risks for human health." Of course, not all GMO foods are good. I'm not a fan of engineering crops to be more tolerant of pesticides, for example: this type of GMO food benefits big agricultural firms rather than the consumer. And it is theoretically possible to insert harmful genes into plants, but agricultural firms wouldn't have any reason to do that.

So the next time you see the non-GMO claim in your grocery, ask yourself whether the ingredients could really be completely unmodified from their "natural" state. I doubt it.

My sandwich was really good, by the way.

At the movies: popcorn and anti-vaccine fearmongering

The anti-vaccinationists have launched a new campaign this holiday season to spread cheer – oops, I mean fear – to moviegoers everywhere. Yes, the folks at SafeMinds and Age of Autism have produced an advertisement that they are trying to place in AMC theaters across the country. In fact, they almost succeeded, but quick action by skeptical science bloggers at SkepChick, Respectful Insolence, and their readerships convinced AMC to cancel the ad – for now.

The ad that SafeMinds is trying to run is intended to scare people away from getting their flu vaccine, just as flu season is beginning. The vaccine this year will protect you against both the new “swine” flu, called H1N1, and the previous flu strain, H3N2. Early data from the CDC makes it clear that both strains are still around, with H3N2 showing up somewhat more frequently so far this fall. The vaccine not only protects you, but also your family, your colleagues, and the many other people you might come into contact with each day while at work, shopping, or elsewhere.

Why try to scare people? Well, the people behind SafeMinds and Age of Autism believe that the preservative thimerosal, which is used in some but not all flu vaccines, causes autism. This theory has been thoroughly investigated over the past 10 years, and just as thoroughly discredited. In fact, it never had any positive evidence to support it in the first place, but it has been promoted aggressively by a journalist, David Kirby, who made his fortune off a book based on the thimerosal-autism hypothesis. (I’m not providing a link – Kirby has already made far too much money off this bogus claim, and I don’t want to give him the web traffic.)

Thimerosal was introduced into vaccines in the 1930s, and it is a very effective means to prevent the growth of bacteria without affecting the potency of the vaccine itself. In over 60 years and hundreds of millions of doses, it has proven to be quite benign. Nonetheless, it contains a form of mercury called ethylmercury, which anti-vaccinationists claim causes autism and other neurological disorders.

The claim that thimerosal causes autism was the central question of a large, multi-year Autism Omnibus trial, which ruled definitively last year that thimerosal does not cause autism. I wrote about that ruling at some length back in March, and I won’t repeat it here, except to quote again from the Special Master’s decision:

“The numerous medical studies concerning the issue of whether thimerosal causes autism, performed by medical scientists worldwide, have come down strongly against the petitioners’ contentions. Considering all of the evidence, I find that the petitioners have failed to demonstrate that thimerosal-containing vaccines can contribute to the causation of autism.”

The anti-vax crowd will not give up, unfortunately. Rather than spending their time and effort trying to find the true causes of autism, they continue to repeat claims that have already been shown false. For example, the SafeMinds website lists 5 “key points” that are just flat-out wrong. Here are the first two:

1. “The autism epidemic that began in the late 1980’s is likely due primarily to toxins adversely affecting fetus and infants during development.” Wrong, in at least two ways. First, there is no autism “epidemic.” The best evidence today indicates that the rising rates of autism are due to a combination of factors, primarily (a) rising rates of diagnosis due to increased awareness among physicians and patients and (b) a dramatically broader medical definition of autism that was introduced in the early 1990s.
2. “Mercury is likely a major contributor to this toxin-induced autism, whether the source of the mercury is from vaccines or environmental mercury exposure.” Wrong again. This is the claim that was so thoroughly refuted in the lengthy Autism Omnibus trial, with hundreds of pages of testimony from dozens of experts, and epidemiological data from literally hundreds of thousands of people.

But data doesn’t seem to have any effect on the anti-vax zealots at Age of Autism and SafeMinds.

Because AMC refused to run their ad, Age of Autism is telling its readers to stay away from AMC theaters this holiday season. I hope they do! Why? Because these unvaccinated individuals are a genuine threat to public health. Movie theaters, and the malls in which they are located, are an ideal place for infectious diseases to spread. Without vaccines, countless thousands of people would fall ill every holiday season after mingling with other shoppers, and some would likely die. My message to the unvaccinated crowd at SafeMinds is: stay away from the rest of us.

And I encourage everyone else to get your flu shot, get your kids vaccinated, and then go see a movie at an AMC theater. Meanwhile, you can also tell them at this link that you appreciate their taking a stand against misinformation and for the benefit of public health.

Oscillo – what? Homeopathic flu “cures” and dead ducks

Oscillococcinum sounds like medicine. And if you saw this package in a store next to all the other cold and flu remedies, you might be tempted to give it a try. It looks just like a box of anthistamines or other real medicines. With flu season coming soon, you might want to look at this box more closely before you buy it.

You can buy oscillococinum at Walgreen’s, Target, Amazon.com, and many other places. At Walgreen’s, one of the largest pharmacy chains in the U.S., it’s listed under “Cough and Cold” where it sells for $9.99 (a savings of $4.50!) for 6 doses.

It sounds like medicine, but it’s not. The front of the box says (in small print) that it’s “homeopathic medicine,” which isn’t medicine at all. In fact, it’s nothing more than a sugar pill, which is why the product can advertise that it has “no side effects” and “no drug interactions.”

But in much larger print, the package says “Flu-like Symptoms”, followed by a list of symptoms: “Feeling run-down, hadaches, body aches, chills, fever.” Anyone might be fooled into thinking this product is supposed to treat these conditions. If you go to the manufacturer’s (Boiron) website, they make the explicit claim that it “Temporarily relieves flu-like symptoms such as feeling run down, headache, body aches, chills and fever.” The Walgreen’s website says the same thing.

What’s in Oscillococcinum, and how can its producer get away with these claims?

Oscillo contains “Anas barbariae hepatis et cordis extractum 200CK.” Don’t be fooled by the Latin – it just means extract from the heart and liver of a duck. Yes, they kill ducks to make this stuff. The manufacturer then dilutes it to 200C, which in homeopath-speak means that 1 gram of extract is diluted to one part in 10⁴⁰⁰. Yes, that’s 10 raised to the power 400. Wow! The entire known universe has far fewer than 10⁴⁰⁰ molecules. If you filled the entire solar system with water, and mixed in one molecule of duck liver, it would be much more concentrated than this stuff. Oscillo is so diluted that there is essentially zero chance that even a single molecule of the original extract is in the product. The package does say that sugar is added to the pills, and that’s all they are: sugar pills.

The idea that infinitely diluted substances can cure disease is a type of magical thinking, and it’s at the heart of homeopathy, whose proponents believe that the more dilute something is, the more powerful its effects. This bit of nonsense goes against basic principles of chemistry and physics, but no matter: homeopaths continue to insist on it.

And I shouldn’t forget to mention that there’s not a whit of evidence that extracts made from the heart and liver of a duck can cure the flu. Nope, not a chance.

The French-based manufacturer, Boiron, and the U.S. stores selling Oscillo can get away with this because it’s not a drug at all – it’s a supplement. Supplements are basically unregulated in the U.S., thanks to laws passed decades ago, some of them specifically designed to protect homeopaths. As long as you don’t claim that your product can treat a specific illness, you can sell it.

The box itself doesn’t say that Oscillococcinum cures the flu, but the product’s manufacturers have been making this claim on their website. Some of them have stepped over the line: the FDA sent a warning letter to one homeopathic marketer this past summer telling them that Oscillo “has not been approved or otherwise authorized by FDA for use in the diagnosis, mitigation, prevention, treatment , or cure of the H1N1 Flu Virus” and requesting that they “immediately cease marketing unapproved or unauthorized products for the diagnosis, mitigation, prevention, treatment, or cure of the H1N1 Flu Virus.”

Unfortunately, the FDA only steps in when the claims get particularly outrageous, or when (as here) they involve a high-profile disease such as avian flu. The purveyors of Oscillo can simply modify their packaging (and websites) slightly and go right ahead misleading the public.

So if you want to waste $10 on 6 sugar pills, go ahead. But at least try find a product that doesn’t require dead ducks.

Further reading: see Orac’s recent post on this same topic here.

U.S. comes down against gene patents

In a surprising move, the U.S. Justice Department filed a brief last Friday that declared, for the first time, that the U.S. government does not support the patenting of naturally occurring human genes. This new position is contained in a document filed as part of the ongoing legal challenge to the gene patents on the human breast cancer genes, BRCA1 and BRCA2.

As background: a company called Myriad Genetics has held the patents on these two genes since the late 1990s. They sell diagnostic tests that cost nearly $4,000, and if a woman wants to test her own DNA for any mutations in the BRCA genes, they are required to pay for this very expensive test. The gene patents prevent any competitors from offering the same test without paying Myriad a license fee. Earlier this year, the ACLU challenged these patents in federal court, and the initial court ruling, which came as a surprise to many, invalidated the patents. Myriad appealed, and it seems likely this will end up in the Supreme Court before it is finally settled.

I have a scientific interest in this case, having just published a paper that directly challenges gene patents by providing free software that allows anyone to test their own DNA for mutations in the BRCA genes. Our software requires that you first have your genome sequenced, which (of course) is not feasible for most people today, but which I think will be routine in the not-too-distant future.

It seems absurd that, having your own DNA in hand (on a flash drive, perhaps), you wouldn’t be allowed to check your own genes for mutations without first paying a license fee to a company. Actually, under current law you might have to pay hundreds of license fees, because thousands of human genes have already been patented.

The same government that issued these patents has finally woken up to this absurdity. In their amicus brief, the Justice Department wrote:

“the unique chain of chemical base pairs that induces a human cell to express a BRCA protein is not a ‘human-made invention.’ Nor is the fact that particular natural mutations in that unique chain increase a woman’s chance of contracting breast or ovarian cancer. Indeed, the relationship between a naturally occurring nucleotide sequence and the molecule it expresses in a human cell – that is, the relationship between genotype and phenotype – is simply a law of nature. The chemical structure of native human genes is a product of nature, and it is no less a product of nature when that structure is ‘isolated’ from its natural environment than are cotton fibers that have been separated from cotton seeds.”

Rarely have I seen such sensible scientific reasoning from lawyers, and I must say it is very refreshing. Just in case the text quoted above is isn’t clear enough, the brief goes on to point out that “the patent laws do not, however, embrace the products and processes of nature itself.” The reason for the bit about “isolated” DNA is that Myriad’s patents cover DNA that has been “isolated” from the cell, and the Justice Department wanted to make it clear that this distinction should not somehow make the DNA patentable.

The legal implications of my own challenge to the BRCA gene patents were discussed at length at Genomics Law Report, and by Forbes blogger Robert Langreth. It will be interesting to see how this latest filing by the Justice Department changes the picture. The implications go far beyond the BRCA gene patents: if the initial court ruling and the Justice Department’s position hold up, then virtually all gene patents, on human genes and on many other species’ genes, will become invalid.

It’s about time. New genes have been the basis of many exciting discoveries, but they are not inventions. No one should have exclusive rights to a gene that occurs naturally in a human, another animal, a plant, or any other living species.

Osteopathic medicine redux

Some of you may have noticed that I removed my blog post on osteopathic medicine. Over at Forbes there is a fierce debate in the comments section, and I've put up a new post there, at this link, correcting what may have been a too-harsh commentary, if anyone wants to follow this discussion further.

Whooping cough in California: deaths caused by the anti-vaccination movement

California is suffering the worst epidemic of pertussis, or whooping cough, in 60 years, with over 5,200 cases already, the most since 1950. Nine babies have died, all of them too young to receive the vaccine. Michigan is also reporting a serious outbreak, with over 600 cases so far this year. The deaths of the infants in California are tragic, and what’s more tragic is that some of them almost certainly could have been prevented if more people had been vaccinated.

The pertussis vaccine, called DTaP (diphtheria, tetanus, and pertussis) has been responsible for a dramatic drop in whooping cough in recent decades. It isn't 100% effective, but its effectiveness relies in part on “herd immunity”: if enough people are immune to the bacteria, then even if someone gets sick, the disease cannot easily spread through the community. This is especially true for very young infants, who are too young to be vaccinated and whose immune systems are not yet strong enough to defeat the bacteria on their own.

Unfortunately, it’s not a coincidence that California is the center of the new pertussis epidemic. Vaccination rates among adults in California have been dropping in recent years, largely due to the influence of anti-vaccination zealots such as Jenny McCarthy and groups such as Age of Autism. Anti-vaccination sentiments seem to strike a chord with relatively well-educated segments of the population – the same people who favor organic food and want to use “natural” products as much as possible. Anti-vaxers appeal to this group by arguing that vaccines are unnatural, and that the body’s own immune system can be “boosted” by various natural treatments. Appealing though this may sound, it has no basis in science. California makes it easy for parents to claim exemptions from the required vaccinations for their children, and exemptions have more than doubled since 1997, according to the L.A. Times.

Among the anti-vaccinationists who deserve blame for the current pertussis outbreak is “Dr. Bob” Sears, a kindler, gentler anti-vaxer who claims (like many of them) to be in favor of vaccines, but only under his own, unscientific terms. He stated flatly in the Huffington Post (a hotbed of medical misinformation) recently that pregnant women should not get the DTaP vaccine. But as Dr. Paul Offit tells us in a tragic story, refusing the vaccine can lead directly to the death of an infant. Dr. Bob is just wrong. I should add that Sears has written two books on vaccines and autism, promoting his misguided “alternative” vaccine schedule (see this article in Pediatrics about that) and his rather naive theories about the rise in autism diagnoses.

Everyone should have their children vaccinated. On top of that, in order to maintain herd immunity, most of us should get the pertussis booster shot if we haven’t had one in the last ten years. That’s what vaccine expert Paul Offit recommends, and I’m planning to follow his advice myself. It won’t take long, and it might save a life.