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?

The federal government is wasting over half a billion dollars a year on chiropractic and osteopathic manipulation

A book on the abuses of chiropractic,
written by a former chiropractor
Here's a quick way for the U.S. government to save over half a billion dollars. Stop paying for coverage of medical procedures that have little or no evidence to support them.

The Centers for Medicare and Medicaid Services (CMS) now releases annual reports of how much it spends, broken down according to the procedures. Their latest data, for the year 2015, reveals that Medicare spent $564,165,721 on pseudoscientific medical practices.

I'm talking about chiropractic and osteopathic manipulation. These are similar but distinct belief systems, both involving bones, and both with little high-quality evidence to back them up. Most people think that chiropractors' spinal "adjustments" can relieve pain from injured or aching backs. It turns out that it's just an elaborate placebo: a back rub at home is likely to work just as well. And that home treatment is probably safer–I'll get to that below.

Osteopathic manipulative therapy (OMT) was invented out of whole cloth in the mid-19th century by Andrew Still. Still believed that every part of the body was linked by a mysterious "myofascial continuity" and that manipulating it could treat a vast range of aches, pains, and other ailments. Most of this is not true. (There is some evidence that OMT can be beneficial in carefully selected cases of lower back pain, but the evidence is quite thin (see this review), and the CMS codes don't distinguish different uses of OMT.)

Osteopathic manipulation is what Larry Nassar, the now-convicted sexual predator, claimed he was doing to the hundreds of young girls whom he molested over the years when he was a sports doctor at Michigan State University and a doctor for the U.S. Olympic gymnastics team. (Osteopathic physicians, which is what Nassar was, generally practice real medicine, and I don't mean to suggest that any of them endorse Nassar's awful abuses. However, OMT is a relic of their pseudoscientific past, and Medicare should not be covering it.)

Chiropractic is no better than OMT. It was invented by D.D. Palmer in the 1890s, around the same time that Andrew Still was concocting OMT.  Palmer mistakenly believed that misalignments of the spine, which he called subluxations, caused a vast range of health problems, even infectious diseases. As retired chiropractor Samuel Homola has written,
there is "no evidence at all to support chiropractic subluxation theory," 
but thanks to clever marketing, chiropractors have convinced millions of people to see them on a regular basis. (See for much, much more.)

Even more alarming is that chiropractic adjustments carry a small but frightening risk of causing a stroke, as a result of tearing the vertebral artery, as I've written about before. In fact, the American Heart Association issued a warning in 2014 that "neck manipulation may be associated with stroke". Not surprisingly, the chiropractors association strenuously denied this, but the evidence speaks otherwise. Indeed, a 2015 study that I described when it appeared showed that Medicare patients–the same cohort whom we are paying half a billion dollars a year to provide chiropractic treatments–suffered a significantly higher risk of stroke after seeing a chiropractor than those who instead saw a real doctor.

And a 2003 study in the journal Neurology show an equally alarming increased risk of stroke due to tears in the vertebral artery after chiropractic in younger patients. The lead author of that study, Dr. Wade Smith, warned that
"physicians and patients should be aware of spinal manipulation therapy as a rare but potentially causal factor in stroke."
[Update: note that a 2016 study, in the journal Cureus, found that the link between chiropractic neck manipulation and arterial dissection was not causal; i.e., that chiropractic did not appear to cause arterial tears. However, concerns remain, as demonstrated in this 2017 case report of cerebral hemorrhage following chiropractic activator treatment.]

The 2015 numbers from the Centers for Medicare and Medicaid Services show that the vast majority of the wasted funds, $545 million, went to chiropractic treatments, with another $19 million going to osteopathic manipulation. Neither amount is justified by scientific evidence.

Let's stop wasting our money on procedures that don't help, and may harm, Medicare patients. If we want to help patients, let's insist that Medicare spend our money on real medicine.

The flu is getting worse, just as the government shuts down.

Uh oh, this is not good.

The flu season is looking particularly bad this year. We already had signs of trouble back in November and December, when it emerged that the flu vaccine was not very effective against the dominant strain that is circulating this year, which is called H3N2.

Until this past Friday, it seemed that the peak of the flu season might have occurred just around the new year, as shown in this chart from the CDC:
The chart shows a peak in the very last week of 2017, and then the number of reported cases seemed to decline. But then on Friday the CDC reported this alarming trend:
That red line spiking upward in the middle of the chart shows the number of flu-like cases reported by the CDC's national network this year. Rather than going down, the trend shows a sharp rise over the past two weeks. We don't know exactly what it is (these are not laboratory-confirmed flu cases), but more people are getting sick.

Even more alarming are the reports of young, healthy people dying of the flu. This past week the Washington Post reported on a healthy 10-year-old boy who caught the flu and died within just a few days. Just before Christmas, a healthy 21-year old young man in Pennsylvania came down with the flu, and went rapidly downhill until he was rushed to the emergency room on Dec. 27. The hospital was unable to save him, and he died the next day. These cases are truly alarming, and even though the CDC hasn't seen a statistically significant increase in deaths among young people (not yet, at least), everyone needs to take the flu very seriously this year.

With the government shut down, a difficult situation becomes worse. Most of the CDC staff will be forced to sit on their hands when they could be working–and many of them want to work, but they won't be allowed to. What's especially frustrating (and wasteful) is that the U.S. will almost certainly pay all federal employees for this forced time off, as it did in previous shutdowns.

We also need a better way to make the flu vaccine. The U.S. still relies on vaccines that are produced by growing the virus in chicken eggs, a decades-old method. This sometimes requires us to use a strain that doesn't match the circulating virus, because some strains just won't grow in eggs. So instead we manufacture a mediocre vaccine, rather than investing in new, modern technology that wouldn't need eggs and could produce more effective vaccines at lower cost. (Why are we stuck with old technology? It's a long story, but essentially it boils down to the fact that we rely completely on private companies to make the flu vaccine. The government doesn't make vaccines and has no plans to do so.)

With the right technology, we should be able to produce a universal flu vaccine, one that we can take once and never need again, like most other vaccines. Scientists are getting closer to that, with much help from the (currently shut down) NIH.

Meanwhile, we are looking at a particularly dangerous flu season, with few weapons to guard against it other than the not-very-good vaccine. (Aside: ineffective doesn't mean useless. Even if the vaccine is only 30% effective, as some estimates have it for this year, it's still a good idea. Everyone in my family got it.)

Oh, and one more thing: the flu shot cannot give you the flu. I only mention this because anti-vaxxers continue to promote this particular myth. 80% of people who have come down with the flu this year did not get vaccinated.

The #1 bogus argument that quacks and the government use to promote pseudoscience

This does not reduce pain.
Chairman Mao would be delighted, if he were alive to see it. He now has the U.S. government buying into arguments that he used to hoodwink his own people, decades ago. Never mind that the arguments are all bogus.

This morning, the front page of The Baltimore Sun describes how the U.S. Veterans Administration is using acupuncture to treat chronic pain in veterans. The VA especially likes something called "ear acupuncture," the creation (out of thin air) of a VA doctor who claims that a few needles inserted in your ear will cure pain anywhere in your body. The VA also calls this "battlefield acupuncture," and it is not only fake but also dangerous, so much so that in 2011 I labelled it the worst quackery of the year.

And yet it hasn't gone away, as the Baltimore Sun reports. The VA uses acupuncture "across the country," offering it to veterans who have little choice about their health care provider. A few years ago, the VA argued this could help veterans manage chronic pain from war injuries. Now they're claiming that acupuncture will help solve the opioid epidemic. Whether it works or not seems beside the point: a VA doctor quoted in the story argues that "if patients believe that it’s helping their pain, then it is." Unfortunately for her patients, she seems unaware that science has shown that acupuncture does not work–for anything (as Yale neurologist Steven Novella succinctly put it).

Why is the VA offering quack treatments to veterans? One reason is that these treatments are popular. The same argument appears in countless forms, but it boils down to: "the people want this, so we should give it to them."

I get it: popularity is good news if you're an actor, or a writer, or a singer, or an athlete, or especially a politician. But it means nothing when we're trying to decide if a medical practice is effective. Doctors in medieval Europe used to bleed their patients, often killing them, in the belief that sickness was caused by "ill humors" in the blood. Bleeding was popular, but it was a very bad idea.

It's not just the VA. This past fall, two Colorado Congressmen, Jared Polis (D) and Mike Coffman, (R) announced the creation of a bipartisan Integrative Health and Wellness Caucus, explaining that:
"While at least a third of Americans use complementary or alternative medicines, access is often inconsistent."
It's not surprising that Polis and Coffman believe that we should give people whatever treatments they ask for. Neither of them is a scientist, so they live in a world (politics) where popularity counts for a lot. How ironic that, in the hyper-partisan U.S. political scene today, the parties have come together to support something that is flat-out wrong.

Just stop it already. Stop arguing that just because something is popular, it must be true, or at least worth investigating (at taxpayer expense). For centuries, most humans believed the Earth was flat, but that didn't turn out to be true, though it was popular. We figured it out and moved on.

Today's versions of medieval bleeding include acupuncture, homeopathy, naturopathy, chiropractic, reiki, Ayurveda, healing touch, various "detox" treatments, and more. Science has figured out that all of these are nonsense, and moved on. (And by calling them "nonsense," I am being generous. Some of them are dangerous.) But people who make money off these practices have been waging a decades-long campaign to keep them going.

Acupuncture is a scam foisted on the Chinese people by Mao Tse-Tung, whose country was too poor to provide real medicine to its population. Instead, Chairman Mao launched a marketing campaign to convince them that the old, traditional medicine was just as good. Kimball Atwood wrote a 4-part history of these events; in part 3 he reveals this gem, from Mao's personal physician:
"Publicly, the Chairman was the leading advocate of traditional medicine, but he refused to use it himself."
And now the U.S. government has fallen for the same scam.

Universities are prey to this as well. This fall, we saw the University of California at Irvine announce a $200 million gift to create a new medical center dedicated to integrative medicine, a disturbing intrusion of junk science into the academic mission of the university. One of the donors, Susan Samueli, argued that "The public is not only interested [in integrative medicine], but they are clamoring for it.”

There it is again–the argument from popularity. And even though this might be privately funded, it is based at a public, state-funded university.

One might hope that the NIH would help set things straight. Think again. Here's an example from NIH's National Center for Complementary and Integrative Health (NCCIH:
"Many Americans—more than 30 percent of adults and about 12 percent of children—use health care approaches developed outside of mainstream Western, or conventional, medicine."
NCCIH's website is careful not to state explicitly that popularity is equivalent to evidence. But then what are they saying? That NIH thinks that 30% of Americans are wrong? (By the way, that 30% number is highly dubious. It includes a wide array of practices, some reasonable and others wacky.)

Why do we even have an NIH center devoted to integrative medicine? It's not because there's any science behind it. On the contrary, NCCIH is a monument to a deep misunderstanding on the part of former Senator Tom Harkin, who created it back in 1991. For an excellent summary of NCCIH's history, see this short video from Reason TV:

or my own talk from a 2015 conference, here. Harkin earmarked a few million dollars to create a small Office of Alternative Medicine in 1991, and with his help it grew over the years into a large, money-wasting administrative behemoth.

NCCIH's website is replete with misleading statements. After pointing out that "millions of Americans use complementary health approaches" (there's that popularity argument again), they offer this sage advice:
"Choose a complementary health practitioner, such as an acupuncturist, as carefully as you would choose a conventional health care provider."
Face, meet palm. No one shouldn't be choosing a "complementary" health provider in the first place, and NIH shouldn't be telling people to do it carefully, whatever the heck that means.

Yes, this stuff is popular. And its popularity has enriched the numerous practitioners of bad medicine, many (most?) of whom may genuinely believe that their snake oil works. But popularity doesn't make something true. Or maybe it does–I hear that the tooth fairy is very popular.

NIH opens the floodgates to creating super-viruses

Some scientists really want to earn their "mad scientist" label. Ever since Mary Shelley's Frankenstein, novelists and screenwriters have shown us the dangers of letting mad scientists pursue their dreams without any controls. Of course, those stories are fiction.

In the microbial world, though, technology has caught up with fiction. Scientists today can create viruses from scratch, as they've already done with the polio virus, back in 2002. Using the tools of modern genomics, virologists and microbiologists can make pathogens much, much more deadly. But would anyone really want to do this? The answer, it turns out, is yes.

A few years ago, some virologists had the clever idea of modifying the bird flu virus to make it more deadly to humans. What would it take, they wondered, to turn the bird flu into a human flu? They decided to give it a try, and they announced their plans to the world. Then, just a few months later, they published results showing that they had succeeded, at least partially, using a bird flu called H7N9.

That wasn't even their first try. Only a year earlier, they did the same thing using a different flu virus (H5N1). Both of these bird flu strains have killed people, but the wild-type version of the virus rarely infects humans. The scientists running these experiments aimed to create a strain that could get into humans much more easily.

Many scientists were mortified. 18 leading microbiologists and infectious disease experts, including Nobel laureate Sir Richard Roberts, formed the Cambridge Working Group to oppose efforts to create super-viruses in the lab. Hundreds of other scientists, including 3 more Nobel laureates, joined the group as charter members.

In response to the concerns raised by scientists and other public health experts, NIH announced a moratorium on these so-called "gain of function" (GOF) experiments, at least in the U.S. (The scientists leading the charge for GOF experiments were based primarily in The Netherlands, although they did get some funding from NIH.) The NIH convened an expert panel, the NSABB, who commissioned a 1,000-page report and then issued their own report, which was released in May of 2016.

The NSABB panel avoids taking very strong positions, but they do raise some alarms. Here's their definition of "research of concern," for example:
"...research that could generate a pathogen that is: 1) highly transmissible and likely capable of wide and uncontrollable spread in human populations; and 2) highly virulent and likely to cause significant morbidity and/or mortality in humans." 
This does not sound like a good idea! So what does the NSABB recommend? Well, this:
"Research proposals involving GOF research of concern ... should receive an additional, multidisciplinary review, prior to determining whether they are acceptable for funding."
I can't argue that research like this doesn't need "additional" review–but the wording here suggests that at least some experiments like this might be worth funding. Mad scientists must be rubbing their hands together in glee.

And finally, just last week NIH announced it will end the moratorium on gain-of-function research. (They made this announcement just a week before Christmas, when many people are probably not paying attention. Coincidence? Perhaps.) In his statement announcing the end of the moratorium, NIH Director Francis Collins wrote:
"I am confident that the thoughtful review process ... will help to facilitate the safe, secure, and responsible conduct of this type of research in a manner that maximizes the benefits to public health."
I am not so confident. Harvard's Marc Lipsitch, one of the leaders of the Cambridge Working Group, commented that "we don't need to do these dangerous experiments. Indeed there are many ways that can (and have) been used to answer the public health question with greater generality, little to no safety risk, and much lower cost."

But just in case there is some question, let's weigh the pluses and minuses, shall we?
  • Creating novel pathogens might lead to insights in the basic biology of viruses and bacteria.
  • Creating hard-to-kill pathogens might help us develop better anti-virals and anti-bacterials, although more effective strategies already exist.
  • The viruses could accidentally escape, and millions of people could die.
  • The viruses could get into the wrong hands, and millions of people could die.
I don't know about you, Dr. Collins, but I'm leaning towards banning such research permanently.

No, Google didn't just create AI that could "build your genome"

Most scientists don't have their own PR machine to hype their work. After reading the announcement last week from Google's genomics group, I realized that's probably a good thing.

Wired article last Friday reported that "Google is giving away AI that can build your genome sequence." Sounds impressive–two high-tech innovations (AI and genomes) in the same title! Unfortunately, the truth is somewhat different. It turns out that Google's new "AI" software is little more than an incremental improvement over existing software, and it might be even less than that.

I'm going to have to get into the (technical) weeds a bit to explain this, but it's the only way to set the record straight. The Wired piece opens with this intriguing challenge:
"Today, a teaspoon of spit and a hundred bucks is all you need to get a snapshot of your DNA. But getting the full picture—all 3 billion base pairs of your genome—requires a much more laborious process."
Interesting, I thought. The writer (Megan Molteni) seems to be talking about genome assembly–the process of taking billions of tiny pieces of DNA sequence and putting them together to reconstruct whole chromosomes. This is something I've been working on for nearly 20 years, and it's a fascinating but very complex problem. (See our recent paper on the wheat genome, as one of dozens of examples I could cite.)

So does Google have a new genome assembly program, and is it based on some gee-whiz AI algorithm?

No. Not even close. Let's look at some of the ways that the Google announcement and the Wired article are misleading, over-hyped, or both.

1. The Google program doesn't assemble genomes. That's right: even though the Wired piece opens with the promise of "getting the full picture" of your genome, the new Google program, DeepVariant, doesn't do anything of the sort. DeepVariant is a program for identifying small mutations, mostly changes of a single letter (called SNPs). (It can find slightly larger changes too.) This is known as variant calling, or SNP calling, and it's been around for more than a decade. Lots of programs can do this, and most of them do it very well, with accuracy exceeding 99.9%.

How could Wired get this so wrong? Well, the Wired piece is based on a Google news release from a few days earlier, called "DeepVariant: Highly Accurate Genomes With Deep Neural Networks," written by the authors of the software itself. Those authors, who obviously know what their own software does, make the misleading statement that DeepVariant is
"a deep learning technology to reconstruct the true genome sequence from HTS sequencer data with significantly greater accuracy than previous classical methods."
If you read on, though, you quickly learn that DeepVariant is just a variant caller (as the name implies). This software does not "reconstruct the true genome sequence." That's just wrong. To reconstruct the sequence, you would need to use a program called a genome assembler, a far more complex algorithm. (I should add that many genome assemblers have been developed, and it's an active and thriving area of research. But I digress.)

The Wired article also points out that
"the data produced by today’s [sequencing] machines still only produce incomplete, patchy, and glitch-riddled genomes."
Yes, that's true. Again, though, DeepVariant does nothing to fix this problem. It can't assemble a genome, and it can't improve the assembly of an "incomplete, patchy" genome.

2. Wild hyperbole: the caption on the lead image in the Wired piece says "Deep Variant is more accurate than all the existing methods out there."  The Google press release, presumably the source for that caption, claims that DeepVariant has "significantly greater accuracy than previous classical methods."

No, it does not. This is the kind of claim you'd never get away with in a scientific paper, not unless you rigorously demonstrated your method was truly better than everything else. The Google team hasn't done that.

How good is it? First, let me remind you that variant calling programs have been around a long time, and they work very well. An incremental improvements would be nice, but not "transformative" or a "breakthrough"–words that the Google team didn't hesitate to use in their press release. They also used the word "significant," which they'd never get away with in a scientific paper, not without statistics to back it up. Press releases can throw around dramatic claims like these without anyone to check them. That's not a good thing.

About a year ago, the Google team released a preprint on bioRxiv that shows that their method is more accurate (on a limited data set) than an earlier method called GATK, which was developed by the same author, Mark DePristo, in his former job at MIT, which he left to join Google. GATK is quite good, and is very widely used, but other, newer methods are much faster and (at least sometimes) more accurate. The Google team basically ignored all of the other variant calling programs, so we just don't know if DeepVariant is better or worse than all of them. If they want to get this preprint published in a peer-reviewed journal, they're going to have to make a much better case.

(As an aside: a much-less hyped method called 16GT, published earlier this year by a former member of my lab, Ruibang Luo, is far faster than DeepVariant, just as accurate, and runs on commodity hardware, unlike DeepVariant which requires special resources only available in the Google Cloud. And it does all this with math and statistics–no AI required. But I digress.)

(Another aside: if we really wanted to get into the weeds, I would explain here that the "AI" solution in DeepVariant is transformation of the variant calling problem into an image recognition problem. The program then uses a method called deep neural networks to solve it. I have serious reservations about this approach, but suffice it to say that there's no particular reason why treating the problem as an image recognition task would provide a large boost over existing methods.)

3. More wild hyperbole. The Google news release opens with a sentence containing this:
"in the field of genomics, major breakthroughs have often resulted from new technologies."
It then goes on to describe several true breakthroughs in DNA sequencing technology, such as Sanger sequencing and microarrays, none of which had any contribution from the Google team. Then–pause for a deep breath and a paragraph break–we learn that "today, we announce the open source release of DeepVariant." Ta-da!

I can only shake my head in wonder. Does the Google team truly believe that DeepVariant is a breakthrough on a par with Sanger sequencing, which won Fred Sanger the 1980 Nobel Prize in Chemistry? This is breathtakingly arrogant.

4. DeepVariant is computationally inefficient. Even if it is better than earlier programs (and I'm not convinced of that), DeepVariant is far slower. While other programs run on commodity hardware, it appears that Google's DeepVariant requires a large, dedicated grid of computers working in parallel. The Wired article explains that two companies (DNAnexus and DNAStack) had to invest in new GPU-based computer hardware in order to run DeepVariant. An independent evaluation found that DeepVariant was 10 to 15 times slower than the competition. Coincidentally, perhaps, Google's press release also announces the availability of the Google Cloud Platform for those who want to run DeepVariant.

No thanks. My lab will continue to use 16GT, or Samtools, or other variant callers that do the job much faster, and just as well, without the need for the Google Cloud. As a colleague remarked on Twitter, the "magic pixie dust of 'deep learning' and 'google'" doesn't necessarily make something better.

Genomics is indeed making great progress, and although I applaud Google for dedicating some of its own scientific efforts to genomics, it's not helpful to exaggerate what they've done so far, especially when they take it to this level. Both the Google news release and the Wired article contain the sort of over-statements that make the public distrust science reporting. We don't need to do that to get people excited about science.