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Genomics, Medicine, and Pseudoscience



This is Steven Salzberg's blog on genomics, pseudoscience, medical breakthroughs, higher education, and other topics, including skepticism about unscientific medical practices. Here's where I can say what I really think about abuses and distortions of sci



Last Build Date: Fri, 15 Dec 2017 19:07:56 +0000

 



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

Mon, 11 Dec 2017 12:30:00 +0000

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.A 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 hav[...]



Soon your Internet will look just like cable

Sun, 26 Nov 2017 13:00:00 +0000

The new FCC chairman, Ajit Pai, formerly worked as a lawyer for Verizon. His plan to eliminate net neutrality is a bigger gift to Verizon than anything he's ever done before.In just a few weeks, the FCC will vote to eliminate net neutrality. The vote isn't in doubt: with Pai in charge, the anti-neutrality votes have a 3-2 edge. Without net neutrality, Internet service providers will be able to charge web companies for "fast lanes," which they can't do now. Smaller companies and individual's websites may be slowed down so much as to render them unusable. The biggest service providers (Netflix, Google, Amazon, and others) will have to cough up extra money, but the consumers won't see any of that–all the benefits will go to the ISPs. Consumers will see their rates go up.Higher fees for lousier service. Does this sound familiar? That's how cable companies have operated for years.Not surprisingly, virtually everyone hates this idea except the cable companies themselves. The telecommunications industry, though, is very excited about the prospect of all the money they're going to make. When previous FCC commissioner Tom Wheeler proposed to weaken net neutrality just a couple of years ago, the ensuing public outcry convinced him to reverse himself, resulting in a strong ruling in 2015 preserving neutrality. This week, Wheeler blasted Pai's new rules, saying that "this proposal raises hypocrisy to new heights."But don't take my word for it. Check out this terrific and entertaining explainer from John Oliver, earlier this year: allowfullscreen="" class="YOUTUBE-iframe-video" data-thumbnail-src="https://i.ytimg.com/vi/92vuuZt7wak/0.jpg" frameborder="0" height="266" src="https://www.youtube.com/embed/92vuuZt7wak?feature=player_embedded" width="320">If Ajit Pai and his telecom buddies get their way, here's what your Internet service might look like next year–I altered the first line, just to convey the idea; the rest is from a list of Comcast's current cable TV services:That's right: your Internet service provider (ISP) will be allowed to bundle websites just like they bundle television channels. Of course, ISPs claim they will do no such thing, but why should we trust them?If net neutrality goes away, no longer will anyone be able to set up a website and turn it into a thriving business by offering popular content. They'll first need to raise money to pay the ISPs, or else face being throttled back before their business even has a chance..No one wants this change except a few large telecom companies. Interviewed by The Nation, former FCC Commissioner Michael Copps said"There can be no truly open internet without net neutrality. To believe otherwise is to be captive to special interest power brokers or to an old and discredited ideology that thinks monopoly and not government oversight best serves the nation."Ajit Pai, our new FCC chairman, clearly belongs to the former. Verizon is now in charge of the FCC.[...]



Transgenic stem cells lead to a miraculous cure

Mon, 13 Nov 2017 12:30:00 +0000

Sometimes I read a science paper and I just say "Holy cow, this is amazing." I don't have that reaction very often, but I did last week.Amidst all the hype, the hope, and the controversy about gene therapy and stem cell research, some very real progress is being made. Scientists can create working versions of human genes, package them into a virus, and then use the virus to deliver the genes to a real person. This approach creates "transgenic" cells that have bits of virus DNA within them, but the virus can be engineered to be harmless.Last week, scientists reported in the journal Nature how they saved the life of a 7-year-old boy using transgenic stem cells. Twenty years ago, this would have been science fiction. Even today it is nothing short of astonishing.Here's the story, summarized from the paper by Tobias Hirsch, Michele de Luca, and their colleagues. In June 2015, a 7-year-old boy was admitted to the Burn Unit of Children’s Hospital of Ruhr University, in Bochum, Germany, where Hirsch and his colleagues (Tobias Rothoeft, Norbert Teig, and others) work. The child wasn't suffering from burns: he had a devastating genetic disease, junctional epidermolysis bullosa (JEB), that had caused him to lose 80% of his skin.Figure 1b from Hirsch et al. Schematicrepresentation of the clinical picture. The denuded skin is indicated in red; blistering areas are indicated in green. Flesh-colored areas indicate currently non- blistering skin. Transgenic graftswere applied on both red and green areas.Children with JEB suffer from constant blistering, wounds, and scarring. The disease is uncurable and children often die before reaching their teens. The 7-year-old boy was near death when he was admitted to the hospital–his weight had dropped to 17 kilograms (38 pounds) and he had severe skin infections from streptococcus and pseudomonas bacteria.Dr. Hirsch and his team were struggling to keep the boy alive, and they had no treatments to offer. In desperation, they searched the scientific literature and found a possible treatment using gene therapy, developed by Michele De Luca, of the Center for Regenerative Medicine at the University of Modena and Reggio Emilia in Italy. Dr. De Luca had only tried this treatment twice before, and even then only on tiny patches of skin. He had never tried it on such a severe case.The boy and his parents had no other options to save his life. They agreed to let Dr. De Luca try.In September of 2015, De Luca took a small patch of undamaged skin (4 square centimeters) back to his lab in Italy. There, he used a retrovirus containing a functioning copy of the LAMB3 gene–the gene that was mutated in the boy–to infect the skin cells. The retrovirus integrated itself into the genome of many of the skin cells, giving them the ability to function normally. Then De Luca grew the repaired cells into new skin grafts, enough to cover 80% of the child's body.In a series of surgeries starting in October 2015, Hirsch and his colleagues applied the skin grafts to the young boy. The results were amazing.As reported in the paper itself:"Virtually complete epidermal regeneration was observed after 1 month.... Over the following weeks, the regenerated epidermis surrounding the open lesions and the epidermal islands spread and covered most of the denuded areas."In other words, it worked. The new skin completely replaced the missing or damaged skin on 80% of the boy's body. What's even more remarkable is that two years later, his skin remains normal. The new skin is functioning perfectly and the young boy has returned to school.The science behind this treatment represents the culmination of decades of research into gene therapy, stem cells, retroviruses, and genomics. To make it all work, we had to know: the identity of the gene that caused the disease (LAMB3); the DNA sequence of a normal LAMB3 gene; how to insert the human gene into a retrovirus; how to create a modified retrovirus that wouldn't harm humans; and much more.The success of the therapy also rev[...]



The new Star Trek series gets biology terribly, terribly wrong.

Mon, 30 Oct 2017 12:00:00 +0000

The new Star Trek: Discovery series is based on a massive scientific error. Can it survive?It didn't have to be this way. Those of us who have followed Star Trek through its many TV series and movies, including the excellent trio of recent moves (2016's Star Trek Beyond is the latest) were eager to jump on board the newest show, Star Trek: Discovery.Despite some rather uneven acting in the pilot, I was willing to give it a chance. So were millions of other Star Trek fans.But alas, the writers have stumbled into a scientific error so egregious, and so entangled in the entire plot line, that I fear the new Star Trek cannot recover. (Note: a few mild spoilers ahead.)Episodes 4 and 5, released on October 8 and 15, revealed that the USS Discovery, the ship that the series revolves around, has an advanced form of transport that allows it to travel anywhere in the universe instantaneously. Unlike all previous Star Trek transport tech, this one uses a biological mechanism, based on mushrooms.Yes, you read that right. The DASH (Displacement Activated Spore Hub) drive uses mushroom spores as its power source. They've discovered a special fungus whose root system extends "throughout subspace" all over the galaxy. Using spores from this fungus, the ship can jump into subspace (or something like that) and jump out somewhere else in real space, light years away, in a matter of seconds. As bizarre and this sounds, the worst is yet to come.To power its DASH drive, the Discovery maintains a large greenhouse full of spore-producing mushrooms. (Mycologists might love this, but how big a fan base can they be?) The problem for the Discovery, in the first few episodes, is that the experimental drive will only let them jump short distances.Then they discover the tardigrade. Tardigrades are a real thing: they are microscopic animals, only 0.5 millimeters long, that live all over the planet. Here's a picture of one:Electron microscope image of Milnesium tardigradum, from E. Schokraie et al., PLoS ONE 7(9): e45682.They are also surprisingly cute for a microscopic animal, and they are colloquially known as water bears, moss piglets, or space bears. "Space bears" comes from their ability to survive in extreme environments, possibly including interplanetary space.Star Trek Discovery's tardigrade is, shall we say, rather different. It looks a bit like the picture shown here, but it's the size of a large grizzly bear, incredibly strong, and extremely fierce. On the show they call it a "giant space tardigrade."But that's not all. Thanks to a unique biological property that the show's writers apparently misunderstood, the space tardigrade can access the mushroom network to travel throughout the universe, wherever and whenever it chooses.Here's how the space tardigrade accomplishes this remarkable feat of interstellar travel, as explained by Michael Burnham, the show's central character (in Episode 5, "Choose your pain"):"Like its microscopic cousins on Earth, the tardigrade is able to incorporate foreign DNA into its own genome via horizontal gene transfer. When Ripper [the space tardigrade] borrows DNA from the mycelium [the mushroom], he's granted an all-access travel pass."And just like that, not only the tardigrade but the entire spaceship jump across the galaxy. Is this sounding a bit crazy? It should.Horizontal gene transfer (HGT) is a real thing. It's a process through which bacteria sometimes take up DNA from the environment and integrate it into their own genomes. Animals can't do HGT, but rather infamously, a paper was published in December 2015 that made the bold claim that tardigrades had a unique ability to absorb all kinds of DNA. That paper was instantly controversial in the scientific community, and not surprisingly its findings were being disputed in the Twittersphere within days of its appearance. Surprisingly, the same journal (PNAS) that published the bogus HGT claim published a second paper just a few months later showing that tardigrades do not a[...]



Should we all be on statins? (reprise)

Thu, 19 Oct 2017 11:30:00 +0000

Should you be on statins? New guidelines and an online calculator may allow you to answer this question yourself.Back in 2011, I asked whether we should all be on statins. At the time, it was clear that statins offered benefits for people who had already suffered heart attacks or other serious cardiovascular problems. But for the rest of us, it wasn't clear at all. A number of studies had been published suggesting that millions more people (in the U.S. alone) might benefit from statin therapy, but most of those studies were published by drug companies that made statins. As I wrote at the time, "we need more data from completely unbiased studies."So has anything changed? Actually, it has. Last year, the U.S. Preventative Services Task Force (USPSTF) reviewed all of the evidence and updated its former (from 2008) recommendations. The evidence now suggests that some people–even those who have never suffered a heart attack–would benefit from statins.Here's what the current USPSTF recommendations suggest. If you've never had a heart attack and have no history of heart disease, you still might benefit from statins if:you're 40-75 years old,you have one or more "risk factors" for cardiovascular disease (more about this below), ANDyou have a 10-year risk of cardiovascular disease (CVD) of 7.5%-10%, using a "risk calculator" that I'll link to below.Now let's look at those risk factors for CVD. There are four of these, and any one of them puts you in the category of people who might benefit from statins: diabetes, high blood pressure (hypertension), smoking, or dyslipidemia.Most people already know their status for the first 3, but "dyslipidemia" needs a bit more explanation. This is simply an unhealthy level of blood cholesterol, defined by USPSTF as either "an LDL-C level greater than 130 mg/dL or a high-density lipoprotein cholesterol (HDL-C) level less than 40 mg/dL." You can ask your doctor about these numbers, or just look at your cholesterol tests yourself, where they should be clearly marked.For that last item, how do you calculate you 10-year risk of CVD? Most people should ask their doctor, but if you want to see how it's done, the calculator is at the American College of Cardiology site here. It's quite simple and you can fill it in yourself to see your risk.A big caveat here, as the USPSTF explains, is that the "risk calculator has been the source of some controversy, as several investigators not involved with its development have found that it overestimates risk when applied to more contemporary US cohorts."Another problem that I noticed with the risk calculator is that using it for the statin recommendation involves some serious double counting. That's because the risk calculator relies in part on your cholesterol levels and blood pressure, but those same measurements are considered to be separate risk factors for CVD. This puts a lot of weight on cholesterol levels–but on the other hand, statins' biggest effect is to reduce those levels.The USPSTF is a much more honest broker of statin recommendations than industry-funded drug studies, so we can probably trust these new guidelines. Note that if the risk calculator puts you in the 7.5%-10% range, you will only get a very small benefit from statins–as the USPSTF puts it, "Fewer persons in this population will benefit from the intervention."Don't rush to go on statins without giving it some serious thought. As Dr. Malcolm Kendrik put it last year (quoted by Dr. Luisa Dillner in The Guardian),“If I was taking a tablet every day for the rest of my life, I would want to know how long I would have extra to live. If you take statins for five years and you are at higher risk, then you reduce the risk of a heart attack by 36%. But if you rephrase the data, this means on average you will have an extra 4.1 days of life.” So no, we shouldn't all be on statins. But until something better comes along (and I hope it will), they are worth consideri[...]



Clever food hacks from Cornell Food Lab might all be fake

Mon, 02 Oct 2017 11:30:00 +0000

Have you heard that serving your food on smaller plates will make you eat less? I know I have. I even bought smaller plates for our kitchen when I first heard about that study, which was published in 2011.And did you know that men eat more when other people are watching? Women, though, behave exactly the opposite: they eat about 1/3 less when spectators are present. Perhaps guys should eat alone if they're trying to lose weight.Or how about this nifty idea: kids will eat more fruits and vegetables at school if the cafeteria labels them with cool-sounding names, like "x-ray vision carrots." Sounds like a great way to get kids to eat healthier foods.Or this: you'll eat less if you serve food on plates that are different colors from the food. If the plate is the same color, the food blends in and it looks like you've got less on your plate.And be sure to keep a bowl of fruit on your counter, because people who do that have lower BMIs.Hang on a minute. All of the tips I just described might be wrong. The studies that support these clever-sounding food hacks all come from Cornell scientist Brian Wansink, whose research has come under withering criticism over the past year.Wansink is a professor at Cornell University's College of Business, where he runs the Food and Brand Lab. Wansink has become famous for his "kitchen hacks" and healthy-eating tips, which have been featured on numerous media outlets, including the Rachel Ray show, Buzzfeed, USA Today, Mother Jones, and more.Last week, Stephanie Lee at Buzzfeed wrote a lengthy exposé of Wansink's work, based on published critiques as well as internal emails that Buzzfeed obtained through a FOIA request. She called his work "bogus food science" and pointed out that"a $22 million federally funded program that pushes healthy-eating strategies in almost 30,000 schools, is partly based on studies that contained flawed — or even missing — data."Let's look at some of the clever food hacks I described at the top of this article. That study about labeling food with attractive names like "x-ray vision carrots"? Just last week, it was retracted and replaced by JAMA Pediatrics because of multiple serious problems with the data reporting and the statistical analysis.The replacement supposedly fixes the problems. But wait a second: just a few days after that appeared, scientist Nick Brown went through it and found even more problems, including data that doesn't match what the (revised) methods describe and duplicated data.How about the studies that showed people eat more food when others are watching? One of them, which found that men ate more pizza when women were watching, came under scrutiny after Wansink himself wrote a blog post describing his methods. Basically, when the data didn't support his initial hypothesis, he told his student to go back and try another idea, and then another, and another–until something comes up positive.This is a classic example of p-hacking, or HARKing (hypothesizing after results are known), and it's a big no-no. Statistician Andrew Gelman took notice of this, and after looking at four of Wansink's papers, concluded:"Brian Wansink refuses to let failure be an option. If he has cool data, he keeps going at it until he finds something, then he publishes, publishes, publishes."Ouch. That is not a compliment.Soon after Gelman's piece, scientists Jordan Anaya, Tim van der Zee, and Nick Brown examined four of the Wansink's papers and found 150 inconsistencies, which they published in July, in a paper titled "Statistical Heartburn: An attempt to digest four pizza publications from the Cornell Food and Brand Lab." Anaya subsequently found errors in 6 more of Wansink's papers.It doesn't stop there. In a new preprint called "Statistical infarction," Anaya, van der Zee and Brown say they've now found problems with 45 papers from Wansink's lab. Their preprint gives all the details.New York Magazine's Jesse S[...]



How much brain damage is too much? NFL players head for the exits.

Mon, 18 Sep 2017 11:30:00 +0000

The smartest player in the NFL just quit.Not because he was unable to play, and certainly not because of his age–he's only 26. No, Baltimore Ravens' player John Urschel decided to quit because the risk of permanent, irreversible brain damage is just not worth it.Urschel is a very smart guy. He's currently pursuing a Ph.D. in mathematics at MIT, one of the best and most demanding science universities in the world. Until this summer, he was (impressively) balancing his studies with being a full-time NFL player.But when Dr. Ann McKee and colleagues published a new study showing that 110 out of 111 former NFL players had suffered serious brain damage, Urschel could no longer pretend he wasn't putting his future at grave risk. McKee's study, the largest study yet of chronic traumatic encephalopathy (CTE), showed alarmingly high rates of CTE in college and high school players as well (91% of former college players).Let's get one point out of the way: everyone involved with the study, including Dr. McKee, knows that it was biased. The scientists examined brains of deceased players that had been donated to the study because family members–or the players themselves, before they died–suspected something was wrong. So perhaps the true risk of brain damage is lower than 99%. Maybe it's only 50%, or 20%. Do young men playing football want to take that risk?John Urschel isn't the first player to quit because of the growing realization that football may cause irreversible brain damage. In 2015, San Francisco 49ers player Chris Borland retired at the age of 24, and in 2016 Kansas City Chiefs player Hussain Abdullah retired at 30, both over concerns about concussions and brain damage.The NFL has been denying or downplaying the risk for years. A few years ago, after the suicide of former player Junior Seau, they announced a $30 million partnership with the NIH to study the risks of football on the brain. As results started coming in, showing that the risk was far more serious than most people knew, the NFL backed out of the deal with $16 million still unspent.Meanwhile, the chorus of warnings has been growing steadily louder from the medical community. Last year, a former team doctor and a former football player and coach wrote in JAMA that"unless there is a way to reduce the number of TBIs [traumatic brain injuries] caused by the sport, football will remain a threat to the brains and health futures of the players, including impaired cognitive function and reasoning, memory loss, emotional depression, and other sequelae that profoundly erode quality of life."Earlier this year, a study out of the CDC reported that "3 high school or college football players die each year from traumatic brain and spinal cord injuries that occur on the field," most them as a result of being tackled during games.Over the years, football players have grown ever larger (the average NFL lineman today weighs over 300 pounds) and the intensity of the violence on the field has grown with them. It's not just in the NFL, either: last year, three high school teams in the state of Washington forfeited their games against a local team out of a legitimate fear that players would be badly injured by the opposing team's 300-plus pound linemen. Their fears were justified: the human head simply wasn't built to withstand the repeated blows that players endure.All players might do themselves a favor by listening to John Urschel. He explained his decision–and his abiding love for the game of football–in a lengthy interview on the Freakonomics podcast a couple of weeks ago. That interview should be required listening for young players, and even more so for parents who might be dreaming that their sons have a future career in football.[...]



Houston, we have a problem. It's called global warming, whether you admit it or not.

Tue, 05 Sep 2017 11:30:00 +0000

Hurricane Harvey poured more rain on Texas and Louisiana last week than this country has ever seen from a single storm. The city of Houston is now suffering from historic flooding, with many calling this a "1000-year flood." Congress is likely to pass a huge bailout bill in the coming days, starting with a $14.5 billion "down payment," suggesting much more is to come.The storm's eventual costs could rise even higher than the costs of 2005's Hurricane Katrina, which cost $160 billion according to NOAA.Let's not dance around the issue: Hurricane Harvey was a direct consequence of global warming, which in turn is a direct consequence of human activities.It's ironic that Texas (and Houston in particular) has an economy that is dominated by on oil and fossil fuels. Burning these fuels is what got us in this mess.It's also ironic that Texas Senator Ted Cruz, who is now at the front of the line asking for a federal government rescue package, is a scientifically illiterate climate change denier. As I wrote shortly after he announced his candidacy for President in 2015, Cruz not only denied that global warming was happening, but he then went on to compare himself to Galileo, as if he were taking a brave and bold scientific position. Right.A few facts: the Gulf of Mexico is 4 degrees warmer than normal this year, and it has been getting worse. Back in March of this year, the Washington Post's Jason Samenow reported that the Gulf was "freakishly warm, which could mean explosive springtime storms." Warm water feeds hurricanes, and Harvey feasted on it, sucking up energy and using it to dump ridiculous amounts of water onto south Texas.Noted climate scientist Michael Mann, writing in The Guardian, took the slightly more nuanced position that "climate change made Hurricane Harvey more deadly." True enough: if you want to be strictly accurate, we can't prove that warming temperatures are the sole cause of Harvey. Maybe with cooler temperatures, we'd have had a hurricane anyway–but it would have been a far smaller one, and the damage would have been far less severe.Mann also pointed out that global warming has already caused sea levels to rise over half a foot, which made the flooding in Houston significantly worse than it would have been otherwise.Now it's time to rebuild, which raises a dilemma. The U.S. can't just abandon Houston, one of our country's largest cities, even if most of its residents deny the reality of global warming (and perhaps they don't). But given that global warming is well under way, with rising sea levels and warming oceans, more catastrophic flooding events like Harvey are highly likely. Should we pay to rebuild the city exactly as it was, basically ignoring the problems of floodwater management as Houston has done until now? Or should we use the government bailout funds to reduce the risk from future flooding?Actually, it might do even more good to impose a simple requirement, before Texas gets any of our bailout funds. Let's require U.S. senators Ted Cruz and John Cornyn, and Texas governor Greg Abbot, to state publicly that global warming is real, that humans are making it worse, and that they will work in the future to mitigate the risks posed by continued climate change. Wouldn't that be something? A simple statement, nothing more, to unlock billions of dollars in aid.If we just rebuild everything like before, then Houston will continue to have a problem.(*Note about the title of this article. The original quote was "Houston, we've had a problem," famously utterly by Apollo 13 astronaut Jim Lovell. In the movie Apollo 13, actor Tom Hanks (playing Lovell) instead said, "Houston, we have a problem.")[...]



NIH institute purges climate change references, but not very well

Mon, 28 Aug 2017 11:30:00 +0000

Last week, one of NIH's institutes, the National Institute for Environmental and Health Sciences (NIEHS), did something rather mysterious. The institute purged references to climate change on its website by replacing the phrase "climate change" with "climate."For example, a page formerly titled "Health Impacts of Climate Change" is now titled "Health Impacts of Climate," a title that obscures the main point of the page's content, which is all about climate change. Another page formerly called "Climate Change and Human Health" is now called "Climate and Human Health." Ironically, the web addresses of both these pages still contains the term 'climatechange':  https://www.niehs.nih.gov/research/programs/geh/climatechange/health_impacts/  https://www.niehs.nih.gov/research/programs/geh/climatechange/which is something of a smoking gun showing the after-the-fact alterations. The attempted purge was first revealed by the nonprofit group EDGI, a group dedicated to addressing "potential threats to federal environmental and energy policy." The Washington Post revealed that these changes were made by Christine Flowers, the NIEHS Director of Communications. As quoted in the Post, Flowers explained that:"It’s a minor change to a title page, but the information we provide remains the same. In fact, it’s been expanded."True, the contents of these pages seem to be unchanged. But in that case, why change the titles and headings? Clearly something more is afoot. Is NIEHS trying to pretend that climate change isn't real, or that it has no effect on human health? If so, this would undermine the very mission of the institute. Are the NIEHS staff fearful that one of Trump's minions will attack them for describing objective scientific facts? If so, perhaps they should get another job.NIEHS's attempt to re-write its own history has been woefully ineffective. It's easy to find other NIEHS webpages devoted to climate change, such as:https://www.niehs.nih.gov/health/topics/agents/climate-changewhich has the title "Climate Change" right at the top, and which links to a major report called "The Impacts of Climate Change on Human Health in the United States: A Scientific Assessment." There's also the NIEHS Climate Change and Environmental Exposures Challenge, a competition sponsored by NIEHS to create graphical visualizations showing the effect of climate change on health.The WashPost story did not mention whether the NIEHS director, Dr. Linda Birnbaum or her boss, NIH Director Dr. Francis Collins, had plans to restore the original language to the website. I've written to them both to ask, and I'll post an update here if they do.[...]



Reject this incompetent Trump appointee

Tue, 15 Aug 2017 12:00:00 +0000

Sam Clovis standing next to Trump during the campaign.Trump has nominated a non-scientist to be chief scientist at the U.S. Department of Agriculture. This is an outrageous slap in the face to science. It's also a slap in the face to Congress.As I predicted back in May, Trump has nominated Sam Clovis, a former right-wing radio talk show host and failed Senate candidate from Iowa, to be the chief scientist of the USDA. ProPublica was the first to break this story, and they also pointed out that Clovis was a vocal climate change denialist. Clovis has an undergraduate degree in politics and graduate training in business, but he has no formal training in science at all.Clovis does have one qualification, though. As ProPublica pointed out, he has been a "fiery pro-Trump advocate on television." Sounds like a good candidate for a chief scientist job to me.Fortunately (perhaps), the Senate has to approve this appointment. The Senate itself stipulated, in a bill that Congress passed in 2008, that the USDA's chief scientist (the Under Secretary for Research, Education, and Economics) must be appointed from"distinguished scientists with specialized or significant experience in agricultural research, education, and economics."The law also says, just to make it crystal clear, that the Under Secretary "shall hold the title of Chief Scientist of the Department."Why is this appointment so wrong? I'll repeat what I wrote back in May:Overseeing the USDA's research programs requires strong expertise in biological science. A non-scientist has no basis for deciding which research is going well, or what questions need further study, or which questions present the most promising avenues for research. A non-scientist is simply incompetent to choose among them–and I mean this in the literal sense of the word; i.e., not having the knowledge or training to do the job. This does not mean that I think Sam Clovis is incompetent at other things; I don't know him and he might be very capable in other areas. Among other problems, a non-scientist leader of a scientific agency will be incapable of using scientific expertise to set priorities, and instead can make up his own priorities.If the Senate has any backbone at all–if Republicans are willing to show that they are capable of doing something other than rubber-stamping every action, no matter how damaging, of our self-absorbed, ignorant President–then they will turn down this nomination. Sam Clovis is so obviously unqualified that this should be easy to do.Actually, if Mr. Clovis cared about the USDA's mission, he would recognize that he's the wrong man for the job and refuse the nomination. Even Dan Glickman, the former Secretary of Agriculture, said "I wouldn't be qualified for that job" (about himself–he's a lawyer) in a recent interview about Clovis' appointment. The current and previous Chief Scientists at the USDA have Ph.D.s and extensive scientific publication records. Mr. Clovis does not. (Note that when I wrote to Mr. Clovis in May to ask about his pending appointment, he declined to respond on the record.)The Senate's Republicans have confirmed all of Trump's nominees so far, and I fear they will rubber-stamp this one as well. Let's hope that a few of them (and only 3 have to object, assuming all 48 Democrats vote no) realize that appointing a non-scientist to be Chief Scientist of the USDA is a slap in the face not only to science, but to Congress itself, because the appointment scoffs at Congress's own law, passed during the George W. Bush administration.Trump can find another political appointment for Sam Clovis, as he has for other Trump loyalists. But appointing a former talk radio host, a non-scientist who has never published a single scientific paper, as the Chief Scientist of the USDA is a gross insult to the thousands of hard-[...]



Will this be the end of college football? The risk of brain damage is startlingly high.

Wed, 09 Aug 2017 11:30:00 +0000

Parents send their kids off to college with high hopes and great expectations. Universities, in turn, have a responsibility to provide an education in an environment that supports and also challenges the students.Universities are not supposed to encourage activities that may result in permanent brain damage.And yet, they do. As revealed in a new report by Jesse Mez and colleagues from Boston University, just published in the Journal of the American Medical Association, a shockingly high number of former football players, from both college and professional teams, suffered chronic traumatic encephalopathy (CTE) later in life, likely as a result of their years playing football.The study authors looked at 202 deceased former football players whose brains had been donated for research, and found that 87% of them had some degree of CTE. The highest rates of CTE were among former NFL players, which affected 110 out of 111 players. CTE was nearly as bad in college football players, though, with 91% of them (48 out of 53) suffering from CTE.Over half of the high school players (27) had "severe pathology." The authors noted that in deceased players with severe CTE, the most common cause of death was neurodegenerative disease. As they also explain:"There is substantial evidence that CTE is a progressive, neurodegenerative disease."In other words, CTE is a death sentence.The authors of the study stated their conclusions carefully, noting that the study was not randomized, and that players and their families may have been motivated to participate because they were concerned about a possible link between football and CTE. Nonetheless, even if the risk of CTE is much lower than found in this study, universities should be taking a very hard look at the risks that they are exposing their students to.Or to put it another way, is it okay to ask young men to play football if the risk of permanent brain damage is only 50%? What if it's just 10 or 20%? Is that okay? Is football that important?Readers of this column know my answer: no. College is not about football, and if it disappears completely, universities will be just fine. The University of Chicago eliminated its football program in 1939, and brought it back in decades later as much-reduced program, now in NCAA Division III. The university itself has remained a powerhouse, routinely ranked in the top universities in the country academically.As I've written before, football is corrupting our universities, blinding them to their true mission (education and research) in the pursuit of a profitable entertainment business. University presidents seem helpless to stop or even slow down the enormous machine that is big-time college football. For example, in 2015 the University of Maryland (where I used to be a professor) paid millions of dollars to buy out the football coach, so that he could quit a year early and the university could pay millions more to a new coach. Ironically, Maryland had done exactly the same thing in 2011 to buy out the previous coach, at a time when the entire state had hiring and salary freezes in place. None of these actions benefitted the university or its students.All the while, universities pretend that they are educating the players. Here's a quote from Bleacher Report's interview with star UCLA quarterback Josh Rosen:"Look, football and school don't go together. They just don't.... No one in their right mind should have a football player's schedule, and go to school."This from one of the top college football players in the country. (On this topic, Taylor Branch's 2011 exposé in The Atlantic is particularly worth reading. Or this article by a disillusioned former Michigan fan.)Universities now face an ethical dilemma far more serious than merely taking advantage of athletes' [...]



ClinicalTrials.gov, a great resource for patients, is being abused to market bad medicine

Mon, 24 Jul 2017 12:00:00 +0000

This wasn't supposed to happen.Since 1997, the National Institutes of Health has maintained a database of clinical trials, ClinicalTrials.gov, that lists trials under way in the U.S. and throughout the world. It's an invaluable resource, providing a single source for patients trying to find where to get the newest experimental treatments, and for doctors and scientists looking to enroll patients in their trials.In recent years, companies offering questionable stem cell therapies got the bright idea that they could describe their treatments as clinical trials, register them on ClinicalTrials.gov, and thereby get some free advertising. Most stem cell treatments are not FDA-approved, and many have little or no data supporting their effectiveness, but clinics can still register their "trials" on the NIH site, making it appear that they are supported and endorsed by the government. A new study by Leigh Turner, published this week in Regenerative Medicine, reveals the growing extent of this problem.What's especially worrisome is that some stem-cell treatment clinics charge patients very high fees to participate in their "trials." Some patients (perhaps most) don't know that legitimate clinical trials virtually never charge fees.Consider this example, reported last July by Emily Bazar at Kaiser Health News: California resident Linda Smith has knee osteoarthritis, and was looking for treatments that could restore her knees to health without surgery. She found a stem cell trial at ClinicalTrials.gov that was run by StemGenex, a clinic in La Jolla. The clinic promised it could inject stem cells into her knees to replace lost cartilage. When she inquired about signing onto the trial, Smith was shocked to learn that StemGenex wanted a $14,000 fee for her to participate.StemGenex claimed that “The actual treatment is not part of the study protocol”: you pay for the treatment, they explained, and the study is merely a followup to see how you did afterwards.What nonsense. I checked the StemGenex site today (a year after the quotes above), and they proudly boast that they are registered on ClinicalTrials.gov, and that"Stem cell therapy for Osteoarthritis is being studied for efficacy in improving the complications in patients through the use of their own stem cells."Hmm. This sure sounds like the study is about the treatment. StemGenex's site strongly suggests that their therapy works wonders:"The goal of each stem cell treatment is to inject the stem cells into the joint to create cartilage (chondryte cells)."Sounds good, right? If only it were true.I've got bad knees myself, so I've been following the research on stem cell treatments for cartilage replacement for years. I would love to be able to get a simple injection that could repair my damaged cartilage. Alas, though, no one has yet developed an effective stem cell treatment for bad knees, although it is plausible, and legitimate trials are under way right now (here's one).Unfortunately, the lack of evidence hasn't stopped clinics from offering stem cell injections right now, accompanied by all sorts of promises that are not backed by science. It's not just knee injections, either: this past March, Sharon Begley at STAT reported on three women who were blinded by stem cell therapy injected into their eyes.Most patients think, mistakenly, that if a clinic offers stem cell therapy, it must have been approved by the FDA. That's not true–clinics offering these therapies don't have FDA approval, and they argue that they don't need it (which might be correct, but that's a topic for another day).Patients also assume that trials listed on ClincialTrials.gov must have been approved by some government agency, but that's not true either. The site is a clearinghouse that uses the h[...]



CRISPR gene editing controversy - does it cause unexpected mutations?

Mon, 10 Jul 2017 11:30:00 +0000

Just over a month ago, a short paper appeared in Nature Methods saying that the gene editing technique known as CRISPR-Cas9 has a big problem: it creates unexpected mutations all over the genome. This was startling news for a technique that has been hailed worldwide as a dramatic breakthrough, not only because it is the easiest gene-editing method yet invented, but also because it is (supposedly) very precise.This new paper, by Kellie Schaefer and colleagues, found hundreds of mutations (in experimental mice) that weren't supposed to be there. The results contradicted earlier studies that showed CRISPR caused very few of these "off-target" mutations. One of the authors, Stephen Tsang, commented that"We feel it's critical that the scientific community consider the potential hazards of all off-target mutations caused by CRISPR."Not surprising, the resulting news headlines were gloomy. The stock in three companies trying to commercialize gene editing–Editas Medicine, Intellia Therapeutics, and CRISPR Therapeutics–all fell sharply.  (Interestingly, the stocks started falling on May 24, and bottomed out on May 31. The paper appeared online on May 30.) Scientists involved with these companies quickly responded, arguing that the study was flawed, but of course those scientists have a lot of money at stake.Who was right? Well, a new paper by Caleb Lareau and colleagues, just released in the bioRxiv preprint repository, re-examines the same data and concludes that CRISPR is just fine. I've read both papers so you don't have to. Here's what seems to be going on.The study by Schaefer et al. used CRISPR-Cas9 to create mutations in two mice (called F03 and F05), and then sequenced their genomes. They also sequenced the genome of a third mouse, called FVB. All three mice were supposed to be genetically identical.Then they compared all three genomes to a "reference" mouse to find mutations. (Aside: this is something my own lab does all the time, so I know the techniques well.) They found over 1,500 mutations in each mouse (which wasn't surprising, because the reference mouse differs from their 3 lab animals), but they found hundreds more mutations in the two CRISPR-edited mice. That was the main surprise from Schaefer's paper, and it's the basis for their claim that CRISPR causes numerous off-target mutations.I had a big problem with this claim even before reading Lareau's paper. Just TWO mice? That's a ridiculously tiny sample. But I digress.Lareau et al. pointed out, correctly, that Schaefer's conclusion depends on the mice being genetically identical. But what if the two CRISPR mice (F03 and F05) were closer to each other than to the third mouse, FVB? (It's analogous to comparing two siblings with a first cousin, although these mice are much more inbred than any humans.) In that case, the result falls apart.Fortunately, Schaefer et al. made all their data available (props to them for doing that), so Lareau could answer this question quite precisely.It turns out that F03 and F05 are much closer to each other than either one is to FVB.  Lareau discovered that the two CRISPR mice share thousands of mutations that FVB doesn't have.What does this mean? Lareau and colleagues conclude that the "unexpected" mutations in the CRISPR-edited mice were already there before the experiment began, and were not caused by gene editing. As they put it,"the CRISPR-treated embryos most likely already harbored these private SNPs and indels prior to nuclease treatment whereas the control mouse did not."In other words, it seems highly unlikely that CRISPR gene editing caused hundreds of unexpected mutations in these mice.Even though CRISPR is being over-hyped right now, it is nonetheless genuinely exciting[...]



Gwyneth! How did you learn so much about health?

Mon, 26 Jun 2017 11:30:00 +0000

Gwyneth Paltrow has invented stickers that promote healing. Yes, stickers. Little circular stick-on thingies that you might give to your 1st-grader as a reward for doing her homework.Gwyneth, though, has discovered something much deeper about stickers. If you make them with just the right materials, and then stick them on your body in the right places, they "rebalance the energy frequency in our bodies."(A quick warning: if you follow the links in this article, put down your coffee first. You might laugh so hard that you'll spill it all over yourself.)Until a day or two ago, Gwyneth Paltrow's Goop website–a "lifestyle" business that sells all things Gwyneth–advertised these stickers as using "NASA space suit material," which presumably was the source of their magic healing properties. Then Gizmodo called someone at NASA to check out this claim, and got a very clear answer.Nope. Goop's stickers are not made of space suit material. (Not that space suit material has healing properties in the first place–it doesn't.) Gizmodo's quote from a former NASA scientist, Mark Shelhamer, sums it up nicely:“Wow,” Shelhamer told Gizmodo. “What a load of BS this is.”   Goop quickly updated their site, and now they don't claim anything about NASA space suits in their stickers. But they didn't dial back any of their magical healing claims. Here's what Goop says now, in an article called "Wearable Stickers that Promote Healing (Really!)":"Human bodies operate at an ideal energetic frequency, but everyday stresses and anxiety can throw off our internal balance, depleting our energy reserves and weakening our immune systems. Body Vibes stickers come pre-programmed to an ideal frequency, allowing them to target imbalances."Wow. What gobbledygook. I see what that NASA scientist meant. But wait, there's more! Goop tells us:"Studies have shown that when your frequency slips, your immune system is compromised, which opens the door to getting sick."Studies? No such studies exist. People don't have a "frequency," and there's nothing to "slip." I think it's fair to say that the Goop claims about these stickers are so ridiculous that they're not even wrong.These stickers are powerful, though, so you must be careful. Goop warns that"We recommend starting with 1 or 2 for sensitive people. Wearing more than 4 may cause some dilution of the individual frequencies."Oh boy.Paltrow sells these magic stickers (and all of her products) using pictures of beautiful models doing healthy activities while wearing stickers. This is part of Goop's appeal: Paltrow is suggesting, in essence, "I'm beautiful and healthy and I'm in my forties, so I know the medical secrets that will keep you beautiful too."Of course, the special Goop stickers aren't cheap: they cost $60 for a 10-pack.Not surprisingly, Goop sells lots of overpriced dietary supplements too, such as a bottle of multivitamins with fish oil for $90, which comes with claims about keeping the immune system strong. Almost no one needs these supplements, and they don't do anything for your immune system, as I've explained before.It took me just a few seconds to find that you can get a sheet with about 50 "dreams come true" stickers at stickersgalore.com for less than $2. These don't come with any wild health claims, but they do make kids happy. I recommend trying these before you get the Goop stickers.Goop's (and Gwyneth's) claims about their stickers are so ridiculous, so laughably nutty, that I can't really feel sorry for the people who fall for them. Anyone who can afford to waste $60 for a pack of stickers probably has too much money and not enough sense. It's just too bad that they're giving their money to a wealthy actres[...]



Apple's next iPhone iOS will save lives

Mon, 12 Jun 2017 11:30:00 +0000

There's no way that we can convince people to stop texting while driving. It's incredibly dangerous, selfish, and reckless. According to the National Highway Traffic Safety Administration, distracted driving killed at least 3,477 people in 2015 alone. Many states have outlawed texting while driving, including my own state of Maryland, but every day I pass people on busy roads who are looking at their phones.

The only solution is technological. The phone itself needs to stop distracting you while you're driving. People aren't going to put their phones down voluntarily.

Apple's iOS 11, coming this fall, finally offers a solution. It may not solve the problem entirely, but it will likely save lives.
(image)
Apple's IOS 11, coming in the fall of 2017,
will offer Do Not Disturb while driving
The solution is very simple, technically speaking. Your phone already knows when it's on a roadway, and it knows that it's moving. So the phone's software–iOS, if it's an Apple phone–can simply disable any apps that might cause distractions.

Apple's preview of iOS11 says it will do more than that. It will not only silence all incoming calls, text messages, and other notifications, but it will text people back automatically and tell them that you're driving.

You'll still be able to use maps and GPS for directions, which is an extremely useful feature that many people just can't do without (and that doesn't cause traffic accidents).

This is a great idea that is long overdue. Apparently, Apple couldn't resist allowing passengers in the car to override the do-not-disturb mode, which I think is a pretty terrible idea. I doubt that the phone will recognize when a passenger just hands it to the driver, but I'll have to wait and see how Apple implemented this override feature. I hope it's really hard to do.

iOS 11 is coming in the fall. Google hasn't yet said anything about whether Android phones will have a similar feature, but I hope they will. This is desperately needed, and it will save lives.

Google, the ball is in your court.



Germany takes action to stem measles outbreak. Anti-vaxxers to blame–again.

Mon, 29 May 2017 12:00:00 +0000

Measles is on the rise in Europe, driven by "vaccine gaps" which in turn are due to misinformation about the benefits of vaccines. Vaccines are possibly the single greatest contribution to human health in the past century. Literally millions of people are alive today who would not be, thanks to vaccines.And yet: vaccine rates have dropped in recent years in multiple countries. In March, the BBC reported that measles had become endemic (meaning that it is self-sustaining, continuing to spread within the country) in France, Germany, Italy, Poland, Romania, Switzerland and Ukraine. The worst measles outbreak is in Romania, which reported over 3,400 cases and 17 deaths in just the first 3 months of this year.Now measles is spreading in Germany, which is scrambling to contain it. Germany had 504 cases through mid-April, versus just 33 cases for the same period last year. At least one person, a young mother of three children, has died. The primary reason for the spread of the disease, as reported by the German news outlet RT, is unvaccinated individuals, and the reason their numbers are growing is simple: the anti-vaccine movement.In the U.S., the anti-vaccine movement caused the worst measles outbreak in 20 years in 2015. The outbreak in Germany appears even worse, despite the fact that parents can be fined as much as €2500 ($2800) for failing to vaccinate their children. In a remarkable effort to try to get this outbreak under control, the German parliament has decided to require kindergartens to report parents who don't vaccinate their kids. Let's hope this works.Vaccination is safe and remarkably effective, but the anti-vax movement is furiously trying to convince parents not to vaccinate. Their latest gambit is "Vaxxed," a conspiracy-mongering anti-vaccine screen produced by Andrew Wakefield, the notorious ex-doctor who published a fraudulent (and later retracted) study claiming that MMR vaccines caused autism. Nearly 20 years later, despite Wakefield losing his medical license because of his "elaborate fraud," he continues to push his debunked claims.Fortunately, many people are now pushing back. Just last week, noted New Zealand physician Dr. Lance O'Sullivan jumped up on stage at a screening of "Vaxxed" to warn people in the audience that they were being defrauded. O'Sullivan was named New Zealander of the Year in 2014 for his efforts to bring health care to disadvantaged people in rural areas. I will close with his words from a Radio New Zealand story describing the dangers of vaccine refusal:"We are trying to save a child's life, we put it on a helicopter, it flies to Starship Hospital. The kidneys are failing, its heart's failing, its lungs are failing. All because we didn't put a bloody $7.50 meningococcal vaccine into that child's thigh."[...]



Trump to appoint non-scientist as chief scientist of USDA

Sun, 14 May 2017 12:00:00 +0000

Scientists work here now, but Trump's new overseerwill probably make them all want to flee.This is how corruption starts.Donald Trump's expected appointment for under-secretary for research at the USDA will be a right-wing talk radio host with no scientific credentials, according to a new report from ProPublica. The expected appointee, Sam Clovis, worked as a political aide to Trump on his transition team, and was installed at the USDA in a temporary role soon after Trump took office, to be Trump's "eyes and ears" until a permanent USDA director was approved.Clovis has no scientific background or credentials. As ProPublica explained, he was a talk radio host in Iowa who ran unsuccessfully for the Senate in 2014. He majored in political science in college and studied business administration in graduate school, and has never published a scientific paper.Now Trump is appointing Clovis to be Under Secretary for Research, Education, and Economics (REE) at the Department of Agriculture. This administrator is responsible for a large portfolio of research, both internal and external, conducted by and supported by the USDA, including NIFA, the National Institute for Food and Agriculture.I've had several research grants supported by USDA's NIFA, through which my colleagues and I sequenced the genomes of many agriculturally important animals and plants. I've also collaborated with internal USDA scientists who work for the Agricultural Research Service, another branch of the USDA that will soon report to Sam Clovis. I've met many outstanding scientists, both inside and outside the USDA, through these projects.Overseeing the USDA's research programs requires strong expertise in biological science. A non-scientist has no basis for deciding which research is going well, or what questions need further study, or which questions present the most promising avenues for research. A non-scientist is simply incompetent to choose among them–and I mean this in the literal sense of the word; i.e., not having the knowledge or training to do the job. (This does not mean that I think Sam Clovis is incompetent at other things; I don't know him and he might be very capable in other areas.) Among other problems, an non-scientist leader of a scientific agency will be incapable of using scientific expertise to set priorities, and instead can make up his own priorities. In the case of Sam Clovis, his history leads me to believe that his priorities will be based on his conservative political agenda.The previous under secretary, Catherine Woteki, has a Ph.D. in human nutrition and was previously the dean of the school of agriculture at Iowa State University. The current Acting Under Secretary, Ann Bartuska, has a Ph.D. in ecology and has worked in many scientific positions, including high-level positions at the U.S. Forest Service and the Nature Conservancy.Both Dr. Woteki and Dr. Bartuska could run circles around Sam Clovis on any of the scientific issues under the purview of the USDA's Under Secretary for Research. Nonetheless, Clovis will soon oversee thousands of scientists currently working at the USDA, despite the fact that he has no idea what they do. It is still possible that Trump will appoint someone else, or that the Senate will decline to confirm Clovis, but these possibilities seem unlikely.When leaders are incompetent, they appoint people under them who are also incompetent. Trump's intention to appoint Sam Clovis as the chief scientist of the USDA isn't the first demonstration of his incompetence, and I don't expect it to be the last. What's most dangerous about this appointment (and others like it) is that inco[...]



Trump's Energy Department just killed jobs in 19 states

Sun, 30 Apr 2017 11:30:00 +0000

ARPA-e's announcement sounded good. But now it turns outto be just a tease.It's a lot easier to kill jobs than to create them. It is much easier to kill innovation than to create it. Trump's Department of Energy, led by former Texas governor Rick Perry, seems to be taking the easy route.As reported in the journal Science this week (and first reported by Politico Pro), DOE has halted its process to award $70 million in new grants that its research agency, ARPA-E, had announced this past December. ARPA-E is the Energy Department's Advanced Research Projects Agency, created to fund high-risk, high-reward new ideas about energy.Even more alarming is that DOE has imposed a gag order on the program managers, so that scientists have no idea why their funding is being delayed, or it if will ever arrive. According to the Science story,"The resulting uncertainty is having a devastating impact on research teams, scientists say, and even threatens the viability of small companies for whom these major awards are so important."The move, which came with no warning, leaves many scientists, including young Ph.D.s just starting new jobs, suddenly without jobs. Bloomberg BNA was able to extract this tiny bit of explanation from an Energy Department spokesman:"As with any transition from administration to administration, we have undertaken a full review of all department programs, policies and taxpayer-funded grants."I'm sure that makes the unemployed scientists and struggling energy technology companies feel much better.Cutting funding that has already been awarded–and which used money that was already appropriated by Congress–is especially disruptive. How can anyone hire new scientific staff when the federal agency might yank away a grant that it had already announced? The Science story described a young Ph.D. plant biologist from Penn State, Molly Hanlon, who was due to start work next week on one of the new ARPA-e projects, but now she might not have any job at all.The 26 projects, all of them now on hold, were originally announced by DOE in December. Here are the states that are homes to the threatened projects:California, Connecticut, Colorado, Delaware, Florida, Illinois, Iowa, Kansas, Massachusetts, Minnesota, New Mexico, New York, North Carolina, Pennsylvania, South Carolina, Texas, Utah, Washington, West Virginia 15 of the 26 projects are led by companies, most of them small companies trying to creative innovative new technologies. The other 11 are housed at universities, including Energy Sec. Rick Perry's alma mater, Texas A&M (so at least we can't blame Perry for bias). And 9 of these 19 states voted for Trump last November.This isn't even the whole story. Eight more projects under a different ARPA-E program, ENLITENED, were told in mid-March that they would be funded, Science reports. Just a week later, though, the press conference to announce the awards was cancelled, and the program now appears to be in danger of cancellation.I'm sure that all of these project teams invested many months in preparing their winning proposals. Leaders of the projects announced back in December were poised to begin their research until the sudden announcement this week, with no explanation, that everything was on hold.All that Mr. Trump has to do to save these valuable, high-tech jobs is nothing; just let the DOE's ARPA-E program do its work. Unfortunately, this seems to be too much to ask.[...]



An aspirin a day keeps the grim reaper away

Sun, 16 Apr 2017 11:30:00 +0000

Low-dose aspirin is good for you. Any brand of aspirin will do, Bayer or otherwise.Should you take an aspirin every day to prevent some types of cancer? The evidence is growing, and it all points to the same answer: yes.In 2016, the US Preventive Services Task Force, a science-guided panel that reviews the evidence for a wide range of treatments, recommended regular low-dose aspirin use for people between the ages of 50 and 69 as a way to prevent heart attacks, strokes, and some types of cancer. For people younger than 50 or older than 69, the USPSTF said that the evidence was inconclusive.The 2016 recommendations came with a caveat: long-term aspirin use carries a slightly increased risk of bleeding in the stomach and intestinal tract, and a small increase in the risk of a hemorrhagic stroke–although it reduces the risk of ischemic strokes. (Ischemic strokes are caused by blood clots in the brain, while hemorrhagic strokes are caused by bleeding. Aspirins reduces the blood's ability to clot, so this tradeoff makes sense physiologically.)Later in 2016, a study by Yin Cao and colleagues at Harvard found that aspirin use reduced the risk of cancers, especially colon cancer. To be specific, they found a benefit from taking 0.5 to 1.5 aspirin tablets per week for at least 6 years (a standard tablet is 325 mg). For people who followed this regimen, the risk of colon cancer was about 19% lower.Now, a new study also led by Yin Cao and others at Harvard, just reported in the annual meeting of the American Association for Cancer Research, shows even clearer benefit. They looked at long-term results in a group of 130,000 women (mostly nurses) and men (doctors and other health professionals) who have been followed since the 1980s. Overall, woman had a 7% reduction in the relative risk of dying from any cause and men had a 11% reduction.Most of the reduction in mortality was due to the reduced risk in dying from colon cancer, breast cancer, and prostate cancer. Just as with the previous study, the benefit appeared in people who took 0.5 to 1.5 aspirin tablets per week for at least six years.A decrease in the risk of dying by 7-11% seems like a mighty nice benefit from such a simple treatment. For those (like me) whose stomach is upset by aspirin, a low-dose aspirin tablet taken with food may be easier to tolerate. The low-dose pill contains 81mg, one-fourth of a standard tablet, so 2-6 of these per week is equivalent to the 0.5-1.5 tablets that provided a benefit in the latest study.It's very encouraging when the evidence for a simple, low-cost treatment consistently shows the same benefit. An important caveat is that that if you have any bleeding problems, you should consult your doctor before taking aspirin.As for me, I've already stocked up on low-dose aspirin. I'm trying the chewable ones first.[...]



Guys: you don't need a PSA test for prostate cancer

Mon, 03 Apr 2017 11:30:00 +0000

Graphic depiction of risk without or with PSA tests, fromthe Harding Center for Risk Literacy.I learned a new word this week: pseudoepidemic. That's what happens when people start looking really hard for a disease that didn't get much attention earlier, and then–not surprisingly–the disease suddenly becomes much more prevalent.This is precisely what happened with prostate cancer in the early 1990s, just after screening tests for prostate-specific antigen (PSA) became widely available. As explained by NIH's Paul Pinsky and colleagues in an article in the New England Journal of Medicine this week, prostate cancer rates rose from 135 (cases per year, per 100,000 men) in 1988 to 220 in 1992, a 63% increase in just four years. Rates slowly dropped after that, but they remained above 150 through 2009.No one believes that this increase represented an actual increase in the rate of prostate cancer. Instead, it was an increase in the rate of diagnosis, made possible by the PSA test. After this simple blood test became available, millions of men started getting routine PSA testing. The idea was that, because prostate cancer increases the levels of PSA in the blood, this test could detect cancer early, which in turn would save lives.It hasn't worked out that way. The problem is that, as a large body of evidence has now shown, most prostate cancers are slow-growing, "indolent" tumors that don't kill you, at least not before something else does.What's worse is that the treatments for prostate cancer have very serious, life-altering side effects. 20-30% of men treated with surgery and radiation suffer from long-term incontinence, erectile dysfunction, or both.This is especially problematic given that the false-positive rate of PSA testing is as high as 80%. In other words, if your doctor tells you that your test was positive, there's an 80% chance that you don't have cancer. Many men, though, elect for further, much more invasive testing after a positive result, because who can sleep at night without knowing for certain?But how about the benefits of early detection? Alas, they did not materialize. Very large trials (including the PLCO study, with over 75,000 participants) showed that routine PSA screening did not prevent any deaths. The only study to show any benefit, ERSPC, had serious flaws, as explained by Ian Haines and George Miklos in the Journal of the National Cancer Institute.Putting all these facts together, the US Preventative Services Task Force concluded that the harms of PSA testing substantially outweigh the benefits, and it recommends, bluntly:"Do not use prostate-specific antigen (PSA)-based screening for prostate cancer."The American Academy of Family Physicians agrees, stating:"There is convincing evidence that PSA-based screening leads to substantial over-diagnosis of prostate tumors. Many tumors will not harm patients, while the risks of treatment are significant. Physicians should not offer or order PSA screening unless they are prepared to engage in shared decision making that enables an informed choice by patients."Even the American Urological Association, which strongly opposed the USPSTF recommendation when it first appeared, now recommends against PSA screening except in one age group, men 55-69 years old. The AUA, though, is highly biased in favor of testing, because its members make significant income from PSA tests and the subsequent follow-ups.Prostate cancer is a very serious disease among older men. According to the American College of Physicians, 1 out of 16 men will receive a diagno[...]



Trump's budget proposal eviscerates biomedical research, for no good reason

Mon, 20 Mar 2017 12:00:00 +0000

Donald Trump proposed a budget this week that will cut funding to NIH by nearly $6 billion, or 20% of its $31 billion budget. A cut of this magnitude would be devastating for biomedical research, and for the health of the nation.This is colossally short-sighted, stupid, and even cruel. The U.S. budget this year is $4.0 trillion, which means that the entire NIH budget is only 0.75% of the budget. A 20% cut to NIH, while incredibly damaging to medical research, would only reduce expenditures by 0.15%.Besides being shortsighted, this proposed cut is heartlessly cruel. What diseases, Mr. Trump, do you want people to die of? Should we halt research on aging? (Not a good idea for 70-year-olds like you.) How about cancer, or diabetes, or infections, or schizophrenia, or heart disease, or lung disease? Or maybe Trump wants to eliminate the NIH Children's Inn, where desperately ill children stay while receiving treatments. The list is very long; NIH supports work on 265 diseases and health conditions.Everyone who is reading this either already benefits from medical research, or will some day.  Even if you are in perfect health, someone close to you probably uses a treatment that was supported by NIH. Virtually every major medical center in the United States depends on this funding. There are few investments with broader impact, and broader public support, than biomedical research.For those who want to look at this from an economic perspective (as I explained in 2013), NIH funding is a terrific investment. A nonpartisan study in 2000 concluded that:"Publicly funded research generates high rates of return to the economy, averaging 25 to 40 percent a year."That's an amazingly good investment. The same report provided detailed examples showing how NIH-funded work saves billions of dollars per year in health care costs. But keep in mind that most of these benefits don't appear for many years. The private sector simply won't make such long-term investments.On a more mundane level, NIH generates thousands of jobs in states all across the nation. If you want to see how it affects your state, check out this graphic from United for Medical Research. Do you live in Ohio? NIH directly supports over 11,000 jobs and $670M in funding, affecting 2,500 businesses in your state. Florida? Another 11,000 jobs, $520M in funding, and over 5,000 businesses. Texas? 21,000 jobs and over $1B in funding. And so on.Does Congress want to kill NIH? I seriously doubt it. Does Donald Trump? I'm just speculating, but I think the ansswer is no. I think Trump doesn't understand what NIH does, but that someone in his inner circle–someone with a wildly distorted worldview–has inserted his own warped ideology into the President's budget proposal.Finally, what's the motivation for these cuts? The U.S. economy is doing quite well, far better than it was in 2008 when Obama came into office. The economy then was in a devastating recession, but we didn't implement drastic cuts then, and we climbed out of it. We've had low unemployment and steady growth for years. It's not clear we need to cut the budget at all, much less make draconian cuts that would eviscerate and eliminate enormously beneficial programs. And if Trump wants to reduce spending, it makes no sense to cut programs that collectively only represent a tiny part of the total. One can only conclude that Trump's proposed budget cuts are entirely ideological, not financial.Fortunately, budget making authority in the U.S. rests with Congress, not with the President[...]



The new EPA Chief is a climate denier: why are you surprised?

Mon, 13 Mar 2017 11:30:00 +0000

On Thursday, newly appointed EPA chief Scott Pruitt said he doesn't think human-driven carbon dioxide emissions cause global warming. The internet exploded with outrage.Why so surprised? We already knew that Scott Pruitt was a climate change denialist.Donald Trump is also a climate change denialist. Why is anyone surprised that Trump is appointing other denialists to top posts in his administration?During his campaign, Trump claimed that climate change was a "hoax" perpetrated by the Chinese. Mr. Trump just made that up: it's complete nonsense, and he would be laughed out of the room in a serious discussion of climate science. Unfortunately, he now has too much power for us to ignore him.The Secretary of Energy, former Texas governor Rick Perry, has also been a climate change denier, although he "softened" his position during his confirmation hearings. At those hearings, Perry said"I believe the climate is changing. I believe some of it is naturally occurring, but some of it is also caused by man-made activity." [Secr. of Energy Rick Perry]How refreshing! What really matters, though, is whether Perry's newfound awareness will be reflected in actual policy or it will turn out to be just a pose he adopted for the hearings.Scott Pruitt, though, is unreprentant. Pruitt has spent much of his recent career suing the EPA on behalf of oil companies (despite the fact that he worked for the state of Oklahoma, not for those companies). Oil companies, coal companies, and others who make their money from fossil fuels–notably the Koch brothers and their fake-science-pushing Heartland Institute–have devoted millions of dollars and years of effort to climate change denialism. We already knew Scott Pruitt was one of them.On CNN, Hawaii's Senator Brian Schatz commented:"If there was ever any doubt that Scott Pruitt is a climate denier, this settles it."Sen. Schatz is correct, of course–but there wasn't any doubt in the first place.The New York Times couldn't have been surprised. Just two days before Pruitt's on-air denial, they ran a story headlined "E.P.A. Head Stacks Agency With Climate Change Skeptics." The Times pointed out that Pruitt's chief of staff and top deputies are former staffers of Senator James Inhofe, one of the Senate's leading climate change deniers.I do have a major disagreement with The Times, though: stop calling these people "skeptics." They are not skeptics. A skeptic is someone who insists on solid evidence before accepting claims about science, medicine, or other fact-based issues. Once evidence is produced, a good skeptic acknowledges the evidence and changes his/her views, if necessary.Denialists, in contrast, stick to the same rigid narrative regardless of the facts. When evidence contradicts their views, they have no choice but to deny, deny, deny. When pushed, they obfuscate and delay, often arguing that the evidence is not yet clear and more studies are needed. This is precisely what EPA head Scott Pruitt and his boss, Donald Trump, have been doing with climate change. Pruitt argued on Thursday that "we need to continue the debate and continue the review and the analysis." No, we don't. The evidence is overwhelming that the planet is warming, that rising CO2 emissions are a major contributor to that warming, and that human activities are causing much of it.The Intergovernmental Panel on Climate Change (IPCC), summarizing the work of thousands of scientists from around the globe, has concluded with very high confidence that human activ[...]



Don't do this: 150 medical practices that all fail, especially acupuncture

Mon, 27 Feb 2017 13:22:00 +0000

This is ineffective - and cruel.Why do people keep doing things to their bodies that don't work, and that even hurt them? This seemingly self-destructive behavior is what allows bad medicine to thrive. One problem is that people are easily fooled by self-interested con artists selling snake oil: homeopathy and acupuncture fall into this category. Another problem is that even doctors can be fooled, especially when a practice seems to make sense.One great example of this is stenting: the use of a small, flexible tube to re-open and hold open clogged arteries. This seems like such a reasonable idea–if a pipe is clogged, unclog it and put something in there to keep it clear. And it does work, sometimes, but the evidence shows that for people with minor blockage, it usually does more harm than good. A new article in The Atlantic, "When Evidence Says No, but Doctors Say Yes", explains that in a recent 5-year period in the U.S., "about half of all stent placements in stable patients were either definitely or possibly inappropriate," as shown in a new study. The authors also point out that stenting remains the go-to procedure for any patient with clogged arteries, even among physicians who have read the studies. The problem here is that stenting just seems so darned logical.At least stents work some of the time. What about procedures and medications that don't work at all, and that sometimes cause harm? Five years ago, a team of scientists in Australia conducted a massive review of evidence for thousands of medical practices, and found 156 that either don't work or actually cause harm. Their list of ineffective and harmful procedures should be required reading for anyone who is considering a medical procedure.I can't go through all 156 bad practices, but one group of procedures stands out as particularly ridiculous (by which I mean the original sense of the word, "deserving of ridicule"). These are the various uses of acupuncture, all of them ineffective, none of them with even the slightest plausibility, but all of them promoted by quacks acupuncturists. Here they are–and remember, each of these has been tested scientifically and shown to be either useless or, even worse, harmful:Acupuncture for women in labor. From the study: "In the absence of sufficient evidence that proves either effectiveness or harm, acupuncture as a method of induction is not recommended."Acupuncture for uterine fibroids. "There is no reliable proof of effectiveness of acupuncture for uterine fibroids." (Aside: if a woman has fibroids, multiple options are available, many quite effective. The claim that acupuncture might treat them is patently ridiculous.)Acupuncture for irritable bowel syndrome. Studies have found "no significant effect of acupuncture on IBS global symptoms, pain, and quality of life compared with placebo." Acupuncture for otitis media with effusion (fluid in the middle ear). This condition is common in children, and acupuncturists are only too happy to plunge their needles into unsuspecting kids. The study found no evidence that this works, and concluded that "acupuncture should not be used for the management of patients with OME."Acupuncture for lower urinary tract symptoms in men. This too doesn't work. I wonder where they stick the needles?Acupuncture to treat hyperbilirubinaemia. This condition, commonly known as jaundice, is often seen in very young infants. The suggest that we treating babies with acupuncture is, fra[...]



World's cutest mammal critically endangered because of Traditional Chinese Medicine

Mon, 13 Feb 2017 12:30:00 +0000

A pangolin. Photo (c) Christian Boix.Pangolins, timid little anteaters that are covered with scales, are being hunted to extinction. Why? Because some humans think their scales can be used as medicine. Pangolin scales are made of keratin, the same stuff that makes fingernails and claws, and they have no more medicinal value than any other fingernails–which is to say, none at all.Pangolins are gentle, toothless mammals that eat ants with their long, sticky tongues. They are covered with scales (sort of like a walking artichoke) which protect them from predators but not from humans, who simply pick them up to harvest them. Baby pangolins ride, adorably on their mothers' tails or backs, as shown in the picture here.Photo by Firdia Lisnawati.How could someone look at these creatures and want to kill them? And yet pangolins are being slaughtered in large numbers because some practitioners of traditional Chinese medicine (TCM) think (wrongly!) that pangolin scales can treat nervousness or palsy. They are also being killed for meat: regrettably, pangolin meat and fetuses are considered a delicacy by some people in China.Just a few months ago, the CITES organization (Convention on International Trade in Endangered Species) banned trade in all eight species of pangolins. We can only hope that this blanket ban is not too late. Previously CITES had declared that Asian pangolins were endangered, but had allowed trade in African pangolins, but because the meat is indistinguishable, the limited ban did little to stop the widespread killing of Asian pangolins. Just before the CITES meeting, Annamiticus (@annamiticus) reported that in the first nine months of 2016, 18,670 tons of pangolin scales from 19 countries had been seized from smugglers, mostly in Hong Kong. And that's just the amount that was stopped; many more tons doubtless slipped through.Despite the new CITES restrictions, trade in pangolins continues. In December, customs officials in Shanghai arrested 3 people who were attempting to smuggle over 3 tons of pangolin scales into China. That shipment alone represents 5,000 to 7,500 pangolins that were killed for their scales.Next Saturday (18 February) is World Pangolin Day. Let's hope that the new CITES restrictions, and greater public awareness of the endangered pangolin, can save these gentle animals from extinction.*note: perhaps it's not the "world's cutest mammal," but the pangolin is still worth saving.[...]



Government scientists go rogue. What a great idea!

Mon, 30 Jan 2017 13:00:00 +0000

Government scientists are very worried, apparently with good reason, that their new boss wants to muzzle them. They've just come up with a brilliant strategy to circumvent this attempt at censorship.Donald Trump and his minions have already made moves to suppress science within the government, with word going out that government employees cannot say anything to the public without the prior approval of political appointees. This has the marks of Stalinist (or should I say Putinist?) repression of free speech, not the sort of thing any of us ever expected to see in the United States. However, after running a campaign marked by outrageous anti-science claims on climate change and vaccine safety, Trump appears on track to use the enormous power of the federal government to suppress basic scientific facts.Vladimir Putin has done the same thing. Most Russians think that Malaysia Airlines Flight 17, which was shot down in Ukraine in 2014, killing all 298 passengers, was shot down by Ukraine–despite the overwhelming evidence that the plane was shot down by a Russian missile provided to Russian-backed separatists by Russia. Putin had a record of suppressing, threatening, and even murdering those who speak out against him. Yet Donald Trump seems to find him the most admirable of all world leaders. And one of his closest advisors, Newt Gingrich, has said that he wants to fire all federal workers who didn't vote for Trump.In just the past few days, though, government scientists have come up with a devilishly clever–and entirely legal–strategy to oppose the Trump administration's efforts to suppress their speech. Using Twitter, the same vehicle that Trump himself used so effectively throughout his campaign, they have created a set of "rogue" and "alt" accounts that have already started tweeting the real news about science, medicine, and the environment.All of these accounts are run by non-government employees with no government sponsorship, but government scientists, in their off-hours time, can't be prevented from sending them information. In just a few days, these accounts have over 3.3 million followers, a number that is rising fast. Here's are some of the account with their total followers as of January 29:@NotAltWorld 1.3 million followers@RogueNASA  734K followers@altUSEPA  226K followers@ActualEPAFacts (a second alt-EPA) 176K followers@BadHombreNPS (National Park Service) 158K followers@alt_fda 144K followers@altusda 145K followers@altHHS 121K followers@alt_CDC 106K followers@alt_NIH 104K followers@AlternativeNWS 93K followers (deactivated on 29 Jan - no idea why)@ungaggedEPA 79K followers@altNOAA 69K followers@NatParkUndrgrnd 52K followersHere are just a few of the tweets from these accounts so far:As one tweet already pointed out, quoting the ACLU, "the First Amendment still protects workers' ability to speak in their own private capacities, on their own time, about matters that concern the public."We might not be able to trust any official statements from the government for the next few years, but perhaps we'll still be able to find accurate science through the alt-gov Twitter accounts. So when you hear the Secretary of Health and Human Services (far right Congressman Tom Price, if he's confirmed) making claims about health care, check out @AltHHS to find out the real story. And when you hear Secretary of Big Oil Energy Rick Perry claim that glo[...]