Trump to appoint non-scientist as chief scientist of USDA

Scientists work here now, but Trump's new overseer
will 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 incompetence enables and even encourages corruption, because the appointees don't understand or respect the mission of their own agencies. Instead, they follow their own agendas, whatever those might be.

The 2008 Farm Bill stipulated (section 7511) that the Under Secretary for REE must be chosen from
"distinguished scientists with specialized or significant experience in agricultural research, education, and economics."
Sam Clovis is not such a person, but Donald Trump just doesn't seem to care.

Trump's Energy Department just killed jobs in 19 states

ARPA-e's announcement sounded good. But now it turns out
to 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

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

Graphic depiction of risk without or with PSA tests, from
the 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 diagnosis of prostate cancer in their lifetimes, although only 2.9% will die of it, most of them older than 75. Nonetheless, PSA screening does not help: it carries a significant risk of harm. In this week's NEJM article, Pinsky et al. conclude:
"Under the `first do no harm principle,' it seems reasonable to forgo mass screening as a public health policy at this point."
Someday we may have a better test for prostate cancer, but for now, we don't. If your doctor offers you a PSA test, your best response is probably to tell him no thanks.

[Aside: the article in the New England Journal of Medicine was written by scientists from the National Cancer Institute at NIH, yet it's behind a paywall that prevents anyone from reading it without paying a costly fee or an even more expensive subscription to the journal. Why do we have to pay a fee to read work that the taxpayers already paid for?]

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

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. Let's hope that Congress will ignore this shortsighted, cruel, and pointless proposal to cut medical research to the bone, and instead will continue to invest in what is, for now, the strongest biomedical research community in the world.

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

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 activities are the primary driver of climate change. They've also explained (hello, Scott Pruitt?) that carbon dioxide is the most important human-driven cause of global warming, and that it has increased 80% since 1970.

Because Scott Pruitt is a denialist–not a skeptic–he will simply deny these facts.

The New York Times and other media need to stop calling Pruitt a skeptic. Skepticism can be healthy; all good scientists are skeptics. Denialism, on the other hand, can lead to great harm. Cigarette companies were not being skeptical when they denied, for decades, that cigarette smoking causes cancer. They too called for more research. They were protecting their profits, and millions of people died while the companies denied and delayed.

Oil and coal companies are now playing exactly the same game, sowing doubt in order to preserve their profits. Scott Pruitt demonstrated this when he claimed, on CNN, that "there's tremendous disagreement about the degree of impact [of human CO2 emissions]." No, there isn't. Quite the opposite is true: there's remarkable agreement among climate scientists that humans are causing global warming. The only source of disagreement is the profit-driven fossil fuel industry, which cares far more about its short-term profits than about the world that future generations will inherit.

So let's not be surprised when Trump and his minions deny climate change, or deny that human activities are causing it. Perhaps it would be better to consider what the harms will be, and whether we can prevent them. Just don't expect any help from the government.

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

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:

  1. 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."
  2. 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.)
  3. 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." 
  4. 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."
  5. Acupuncture for lower urinary tract symptoms in men. This too doesn't work. I wonder where they stick the needles?
  6. 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, frankly, primitive and terribly cruel. The study concluded starkly that "there is no evidence to support the use of acupuncture to treat hyperbilirubinaemia–NICE recommends that this treatment not be used in this population." (NICE is the Australian National Institute for Health and Clinical Excellence.)
  7. Laser acupuncture for carpal tunnel syndrome. Multiple studies found that acupuncture doesn't work for this either. One study concluded that "more rigorous studies are needed." Why waste more time on this hopeless pursuit?
  8. Acupuncture for depression. Lots of studies, most with a "high risk of bias," and all of them finding that acupuncture doesn't work for depression. This is depressing.
  9. Acupuncture for osteoarthritis. Not surprising, acupuncture for arthritis is no better than placebo.
  10. Acupuncture for Bell's palsy. Eight trials, none of them showing any reliable benefits. Subject patients to more of these trials would be cruel and unethical.

So there you have it: 10 out of the 156 bad medical practices involved acupuncture. If you want to see the rest of the list, check out the full study. As for acupuncture, this is by no means a complete list of the claims that acupuncturists make. Indeed, just last week a new study claimed that acupuncture helps treat migraines, prompting a rebuttal from UC San Francisco's Amy Gelfand, in the same journal, saying no, it doesn't. (Dr. Gelfand explained a lot more than that, but I'm summarizing.) The pro-acupuncture study was done in China, where virtually all acupuncture studies report positive results, and the lead author works at the Acupuncture and Tuina School, Chengdu University of Traditional Chinese Medicine.

We should all thank Drs. Elshaug, Watt, Mundy, and Willis for their tireless effort in reviewing thousands of studies, so that the rest of us don't have to. Acupuncture studies will keep appearing, but there's no reason to believe anything new will emerge. It's time for people to stop fooling themselves about this particular brand of pre-scientific pseudoscience.