Showing posts with label USDA. Show all posts
Showing posts with label USDA. Show all posts

Climate change is making us sneeze

Allergy sufferers are having a rough time of it this spring. If you're among them, and if you think it's getting worse, you're right–and climate change is at least partly to blame.

Admittedly, warming climate has far more severe consequences, such as the eventual flooding of entire coastal cities. On a personal level, though, pollen allergies make people pretty miserable. (I write this as a lifelong sufferer myself.) When springtime comes and trees burst into buds, some of us shut all the windows and huddle inside.

I hadn't thought that climate change would affect the pollen season until I read a newly published study in a journal called The Lancet Planetary Health. (Aside: yes, there really is a journal with that name, a specialty journal created two years ago by the venerable publishers of The Lancet.)

The new study, by USDA scientist Lewis Ziska and colleagues from 15 other countries, looked at airborne pollen data from 17 locations, spanning the entire globe, and stretching back an average of 26 years. The news isn't good for allergy sufferers:
"Overall, the long-term data indicate significant increases in both pollen loads and pollen season duration over time."
In other words, it's a double whammy: we getting more pollen than ever before, and the allergy season last longer. Okay, not that much longer, only an average of one day. But if you have hay fever, every day is one too many.

To be fair, not every location experienced a significant increase in pollen. Here are the 12 (of 17) that did:
  • Amiens, France
  • Brussels, Belgium
  • Geneva, Switzerland
  • Kevo, Finland
  • Krakow, Poland
  • Minneapolis, USA
  • Moscow, Russia
  • Papillion, USA
  • Reykjavik, Iceland
  • Thessaloniki, Greece
  • Turku, Finland
  • Winnipeg, Canada
Perhaps not coincidentally, the pollen season this spring is making headlines in the U.S. As the NY Times reported this week, "extreme" pollen has blanketed the middle of North Carolina this week. It's so bad that the air has taken on a yellowish tinge, as shown in this unaltered photo, one of several taken by photographer Jeremy Gilchrist and shared last week on social media.
A yellow haze caused by pollen over Durham, North Carolina
in April 2019. Photo credit: Jeremy Gilchrist via Facebook.

According to Ziska et al.'s study, more pollen-filled springs are the new normal. Their projections indicate that pollen seasons will continue to get longer in the future, and that the amount of pollen in the air will also increase during the spring and again in the fall, when ragweed pollen is at its peak.

What can you do about spring allergies? I wrote about this last year: for some people, over-the-counter antihistamines help, although they only treat the symptoms. Allergy shots can provide long-term relief, if you have the time to go through the months-long regimen. Other than these options, the best you can do is stay inside and wait for pollen season to end. You can always catch up on your reading of The Lancet Planetary Health.

Clever food hacks from Cornell Food Lab might all be fake

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 Singal, who called Wansink's work "really shoddy research," concluded that
"Until Wansink can explain exactly what happened, no one should trust anything that comes out of his lab."
In response to these and other stories, Cornell University issued a statement in April about Wansink's work, saying they had investigated and concluded this was "not scientific misconduct," but that Cornell had "established a process in which Professor Wansink would engage external statistical experts" to review many of the papers that appeared to have flaws.

And there's more. Retraction Watch lists 14 papers of Wansink's that were either retracted or had other notices of concern. Most scientists spend their entire careers without a single retraction. One retraction can be explained, and maybe two or even three, but 14? That's a huge credibility problem: I wouldn't trust any paper coming out of a lab with a record like that.

But how about those clever-seeming food ideas I listed at the top of this article? They all sound plausible–and they might all be true. The problem is that the science supporting them is deeply flawed, so we just don't know.

Finally, an important note: Brian Wansink is a Professor of Marketing (not science) in Cornell's College of Business. He is not associated with Cornell's outstanding Food Science Department, and I don't think his sloppy methods should reflect upon their work. I can only imagine what the faculty in that department think about all this.

Reject this incompetent Trump appointee

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-working real scientists at the USDA, and to millions more who depend on, and benefit from, the USDA's research programs. Senators: do the right thing and tell Trump to appoint a real scientist to this job.

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.

The perfect hamburger, spoiled


20 years ago, we cooked hamburgers the way we liked them.  If you wanted your burger medium rare, well, good for you.  A thick, juicy burger, seared on the outside and just a bit pink on the inside, was the centerpiece of any good summer cookout. That was a more innocent time.

In 1993, a deadly outbreak of E. coli infections hit the northwestern U.S., sickening hundreds of people and killing four children.  The outbreak was traced to undercooked ground beef from a hamburger chain called Jack in the Box.

Fortunately, we live in a highly educated, advanced society, where the citizenry understands that its health depends on having bacteria-free food.  The unsanitary conditions that allowed E. coli to enter the food supply, including assembly-line slaughterhouse practices, were quickly halted.  New government regulations assured that any factory that shipped contaminated beef would be shut down.  Inexpensive, accurate DNA testing now detects almost all bacteria at a neglible cost.  Food-borne outbreaks of bacterial infections have been rare ever since.

Ha ha ha ha ha!  Just kidding!  Of course we can't have government regulators getting in the way of efficient food manufacturing!  Consumers ought to know that it's their fault if they get sick.  We must cook our burgers until they're as sterile as a Martian landscape.  That's simply the trade-off we must make to have such cheap food these days.

It's not that we don't check for any bacteria at all.  In fact, the U.S. Department of Agriculture recently announced that it would begin testing beef for six different deadly strains of E. coli.  Until now, it has only tested for the O157:H7 strain, which was behind the 1993 outbreak.  I guess this is progress.  However, the USDA will not be testing for salmonella bacteria or for any other nasty microbes.

The beef industry is opposed to any efforts by the government to test its products for bacteria.  For many years now, it has been remarkably successful, through lobbying efforts in Congress and through lawsuits, at rendering the USDA powerless.  As one example: twelve years ago the USDA tried to shut down a beef plant in Texas that failed its salmonella tests.  The beef industry challenged the USDA in court and won, and the USDA still doesn't have the power to shut down a plant for salmonella contamination.

We have the technology to detect all the bacteria that keep turning up in beef and chicken.  DNA testing technology has gotten much faster, cheaper, and more accurate in the 20 years since the Jack-in-the-Box outbreak, but we still don't use it on our food.  The meat industry won't say why it opposes DNA tests for contamination, but no one knows how consumers might react if they knew how much bacteria was really in their meat.

The USDA does test for E. coli O157:H7.  In the first half of this year, it tested 6,427 beef samples.  Out of those, 470 (7%) tested positive, which is pretty startling, considering that this is just one strain out of six known to be deadly to humans, and considering that we've known about this one since 1993.

(Chicken, by the way, has similar problems, with most raw chicken (organic or not) being contaminated by salmonella or campylobacter bacteria.  It helps that no one likes chicken cooked rare.)

Where does all this bacteria comes from, anyway? You may already know the answer: poo.  Beef and chicken production facilities aren't very good at keeping the (ahem) waste material separated from the meat.  Changing the way our beef is produced would cost more, undoubtedly. But is it unreasonable to ask a food producer to deliver safe food?

Luckily, if you cook meat long enough, it can't hurt you.  It might not taste as good, but hey, we all make compromises.  So broil those burgers through and through, and if they're a bit dry, well, that's what ketchup is for.