‘It depends and it’s complicated’ Schaffner on the 5-second rule

Posted on October 17, 2016 by Douglas Powell

Friend of the barfblog.com shares his thoughts about the five-second rule, peer-reviewed research, and media attention. Thanks for doing this, Don.

In March 2014 I got angry. I saw an article in the popular press indicating that researchers from Aston University in the United Kingdom had “proved the five second rule was real” It was not the finding that made me angry as much as the science behind it. Or more properly the lack of science behind it.

We’ve been studying microbial cross-contamination in my lab for more than 15 years, and I have considered myself a quantitative food microbiologist for my entire career. Given those two observations, it’s only natural that I be interested in an article like this. But when I reached out to the University for more information I learned the research had not been peer-reviewed, and the best that they could offer was a PowerPoint presentation. A PowerPoint presentation is not science. Science proceeds through peer review. Like democracy it’s a terrible system, just the best one we have found so far.

After I got angry, I got busy. And like any good professor by “got busy”, I mean that a graduate student got busy doing the actual work of science. I had a brand-new MS student starting in my lab, and she had funding from another source, but needed a research project. We worked together to design an appropriate series of studies that would advance our understanding of microbial cross-contamination while at the same time could generate a press release that might get a little bit of attention. Like any good scientists we built on the work of others. We acknowledged non-peer-reviewed work from other institutions that paved the way like high school student Jillian Clarke in Hans Blaschek’s lab at the University of Illinois. We also acknowledged the first peer-reviewed research from Paul Dawson’s lab at Clemson University.

Flash forward a couple of years, we submitted our article to one of the best journals out there that publishes food microbiology research, Applied and Environmental Microbiology and after peer review and appropriate revisions our article was accepted for publication. I reached out to a colleague in the media relations department at Rutgers University, and we worked together to write a press release.

As you may have noticed, we have garnered extensive media attention with thousands of articles published around the world. The New York Times did a particularly nice piece interviewing me as well as my colleague Bill Hallman, and barfblog’s Doug Powell. It has been a fun ride, but I’m looking forward to getting back to other things. Just keeping up with the requests for interviews has been almost a full-time job, I have generally resisted the temptation to respond to commenters on the Internet, who complain about everything from the waste of grant funds (not the case, we used discretionary funds I raised myself), to suggestions that I studied the wrong thing.

But before we close the books on this one, I do want to respond to Aaron Carroll, a medical doctor who became interested in the topic when he co-authored a book on medical myths. Carroll insists that it’s not any of the factors we studied that are important, but rather how dirty the surface might be. He is certainly correct in that the level of contamination, as well as the type of contamination are important (pro tip: coliforms don’t make us sick), but the degree to which those microbes transfer is also essential in determining risk. As I’ve said in many interviews, if there are no pathogens present on the surface, the risk is zero. The immune state of the person doing the eating also makes a difference. The risk for someone who is immunocompromised is higher than the risk someone who has a healthy immune system.

So as any listener to our food safety podcast will know, it turns out “it depends” and “it’s complicated.” The level of contamination, the type of contamination, the nature of the surface, the nature of the food, as well as the immune state of the person all matter in determining risk of eating food off the floor.

Longer contact times increase cross-contamination of Enterobacter aerogenes from surfaces to food

Applied and Environmental Microbiology; Appl. Environ. Microbiol. November 2016 vol. 82 no. 21 6490-6496

Robyn C. Miranda and Donald W. Schaffner

http://aem.asm.org/content/82/21/6490.abstract?etoc

Abstract

Bacterial cross-contamination from surfaces to food can contribute to foodborne disease. The cross-contamination rate of Enterobacter aerogenes on household surfaces was evaluated by using scenarios that differed by surface type, food type, contact time (<1, 5, 30, and 300 s), and inoculum matrix (tryptic soy broth or peptone buffer). The surfaces used were stainless steel, tile, wood, and carpet. The food types were watermelon, bread, bread with butter, and gummy candy. Surfaces (25 cm²) were spot inoculated with 1 ml of inoculum and allowed to dry for 5 h, yielding an approximate concentration of 10⁷ CFU/surface. Foods (with a 16-cm²contact area) were dropped onto the surfaces from a height of 12.5 cm and left to rest as appropriate. Posttransfer, surfaces and foods were placed in sterile filter bags and homogenized or massaged, diluted, and plated on tryptic soy agar. The transfer rate was quantified as the log percent transfer from the surface to the food. Contact time, food, and surface type all had highly significant effects (P < 0.000001) on the log percent transfer of bacteria. The inoculum matrix (tryptic soy broth or peptone buffer) also had a significant effect on transfer (P = 0.013), and most interaction terms were significant. More bacteria transferred to watermelon (∼0.2 to 97%) than to any other food, while the least bacteria transferred to gummy candy (∼0.1 to 62%). Transfer of bacteria to bread (∼0.02 to 94%) was similar to transfer of bacteria to bread with butter (∼0.02 to 82%), and these transfer rates under a given set of conditions were more variable than with watermelon and gummy candy.

IMPORTANCE The popular notion of the “five-second rule” is that food dropped on the floor and left there for <5 s is “safe” because bacteria need time to transfer. The rule has been explored by a single study in the published literature and on at least two television shows. Results from two academic laboratories have been shared through press releases but remain unpublished. We explored this topic by using four different surfaces (stainless steel, ceramic tile, wood, and carpet), four different foods (watermelon, bread, bread with butter, and gummy candy), four different contact times (<1, 5, 30, and 300 s), and two bacterial preparation methods. Although we found that longer contact times result in more transfer, we also found that other factors, including the nature of the food and the surface, are of equal or greater importance. Some transfer takes place “instantaneously,” at times of <1 s, disproving the five-second rule.

How to publish a scientific paper (not)

Posted on July 30, 2015 by Douglas Powell

Apparently I’ve published another peer-reviewed paper.

In 2011.

Based on some research I did in 1986.

My undergraduate degree is in molecular biology and genetics from the University of Guelph (like Chapman), and in the summer between third and fourth year I worked in a lab and met a girl.

That girl was a veterinary student, and I wanted to hang around, so we moved in together, started a family and I started a MSc.

I spent a lot of time with tomato plants.

And our efforts at gene sequencing were slow and labor-intensive.

I eventually quit the MSc and became editor of the school paper.

And eventually I went back to Guelph and did a PhD.

My contribution was probably minimal, I’m grateful to Dr. Robb for paying me, but when I publish a paper, I make sure all authors have a chance to review it and offer their edits.

Vascular coating: a barrier to colonization by the pathogen in Verticillium wilt of tomato

Canadian Journal of Botany (Impact Factor: 1.4). 02/2011; 67(2):600-607. DOI: 10.1139/b89-082

Jane Robb, Douglas A. Powell, P. F. S. Street

http://www.researchgate.net/publication/237163772_Vascular_coating_a_barrier_to_colonization_by_the_pathogen_in_Verticillium_wilt_of_tomato

Abstract

Massive infusion of conidia of Verticillium albo-atrum.

Reinke & Berthier induced synchronous secretion of vascular coating in the petiolar xylem vessels of resistant and susceptible tomato near-isolines. More coating formed earlier in resistant than in susceptible plants. In the susceptible plants secretion was delayed in colonized trapping site vessels, but initiated in surrounding uncolonized ones. Controls were infused with water. Samples were quantified by light microscope assay techniques at 18, 48, and 120 h postinoculation for the following parameters: (i) delayed coating effect, (ii) overall coating capacity, and (iii) ability of fungus to “escape” laterally from trapping site vessels. The results showed that susceptibility to Verticillium was absolutely correlated with the presence of the delayed coating effect in the plant and increased ability of the fungus to spread laterally. Treatment of inoculated resistant plants with an inhibitor of coating secretion resulted in conversion to the susceptible phenotype. The progeny of a genetic backcross for the dominant (Ve) and recessive (ve) alleles at the Ve locus (Velve × velve) were assayed for the same parameters as well as for disease resistance based on symptom expression. The results confirmed the previous observations and suggested that in tomato the delayed phenotype is recessive. The data strongly supports two hypotheses: (i) coating forms a barrier against fungal penetration and (ii) the timing of the coating response in trapping site vessels results, directly or indirectly, from expression of the Ve gene.

Dietary pseudoscience: ‘How I fooled millions into thinking chocolate helps weight loss’

Posted on May 31, 2015 by Douglas Powell

When I first met the father of my ex-wife, I asked him if he liked hockey.

He said, nah, that’s all acting.

I watch wrestling.

Who knows what’s genuine anymore.

Science has become an adventure in chasing money rather than chasing evidence.

The following is from http://io9.com/i-fooled-millions-into-thinking-chocolate-helps-weight-1707251800 where author John Bohannon explains how he tricked the scientific process.

And it was too easy.

“Slim by Chocolate!” the headlines blared. A team of German researchers had found that people on a low-carb diet lost weight 10 percent faster if they ate a chocolate bar every day. It made the front page of Bild, Europe’s largest daily newspaper, just beneath their update about the Germanwings crash. From there, it ricocheted around the internet and beyond, making news in more than 20 countries and half a dozen languages. It was discussed on television news shows. It appeared in glossy print, most recently in the June issue of Shape magazine (“Why You Must Eat Chocolate Daily”, page 128).

Not only does chocolate accelerate weight loss, the study found, but it leads to healthier cholesterol levels and overall increased well-being. The Bild story quotes the study’s lead author, Johannes Bohannon, Ph.D., research director of the Institute of Diet and Health: “The best part is you can buy chocolate everywhere.”

I am Johannes Bohannon, Ph.D. Well, actually my name is John, and I’m a journalist. I do have a Ph.D., but it’s in the molecular biology of bacteria, not humans. The Institute of Diet and Health? That’s nothing more than a website.

Other than those fibs, the study was 100 percent authentic. My colleagues and I recruited actual human subjects in Germany. We ran an actual clinical trial, with subjects randomly assigned to different diet regimes. And the statistically significant benefits of chocolate that we reported are based on the actual data. It was, in fact, a fairly typical study for the field of diet research. Which is to say: It was terrible science. The results are meaningless, and the health claims that the media blasted out to millions of people around the world are utterly unfounded.

The story is long but thorough.

The complaints are unfounded.

PR before peer review, incomplete advice, damaging food safety reputation

Posted on July 23, 2014 by Douglas Powell

My grade 7 teacher in Canada, Mrs. Patrick, was the grammar police and instilled a strong value in getting things right (write?). My wife has now taken over that role.

I explain to students and my kids that grammar is like traffic signals: maybe it’s not efficient but it’s some rules we can agree on so that I can get to the idea of what you’re trying to express.

Science or evidence-based, has its own rules.

Whether it’s a grasp for headlines, funding or ego, press releases before publication continue, and continue to be a bad idea.

Food safety types can do better.

In Sept. 2000, I called Procter & Gamble to substantiate claims their consumer-oriented Fit Fruit and Vegetable Wash removed 99.9 per cent more residue and dirt than water alone.

The PR-thingies hooked me up with some scientists at P&G in Cincinnati, who verbally told me that sample cucumbers, tomatoes and the like were grown on the same farm in California, sprayed with chemicals that would be used in conventional production, and then harvested immediately and washed with Fit or water. The Fit removed 99.9 per cent more, or so the company claimed.

One problem. Many of the chemicals used had harvest-after dates, such as the one tomato chemical that was supposed to be applied at least 20 days before harvest.

That tidbit wasn’t revealed in the company PR accompanying Fit.

Back in 2000 I asked why the results hadn’t been published in a peer-reviewed journal, and the P&G types said it was an important advance that had to be made available to consumers as soon as possible, without the delays and messiness of peer-review.

Things haven’t changed much. What I still don’t quite comprehend is why researchers who do go to the effort of getting published in peer-reviewed journals – which isn’t easy – feel the need to share results publicly before peer review or publication. It lessens their effort.

Maybe it’s a culture thing.

Culture encompasses the shared values, morals, customary practices, inherited traditions, and prevailing habits of communities. It’s when one food service or farm or retail employee says to another, dude, wash your hands, without being told by the boss or the inspector.

Or one when PhD tells another PhD, press release before peer-review sorta sucks. And that’s the culture of science.

Or should be.

In July, 2014, the U.S. Centers for Disease Control took some bi-partisan hits for poor tracking of dangerous pathogens, to which director Tom Frieden responded the agency had corrected the specific defects cited in previous investigations, but had not realized there was a deeper problem with the culture of safety at CDC which he will now address.

For me it’s a hockey-coaching thing: try to do better than last week, have fun, and pay attention – before a 10-year-old runs over the 5-year-old. Keep your stick on the ice and don’t take wooden nickels.

And don’t produce food that makes people barf.

Press release before publication is always a bad idea – cold fusion?

Dr. Douglas Powell is a former professor of food safety who shops, cooks, ferments and coaches hockey from his home in Brisbane, Australia.

Universities blinded by rankings and scientific gobbledygook

Posted on April 23, 2014 by Douglas Powell

It’s bad enough that public institutions like Kansas State University use public funds to promote crap.

As a parent of four university daughters, I’ve seen the debt they’ve accumulated and the crap they’ve been sold.

But it’s bigger than public institutions – the foundations of science are for sale, to the highest bidder.

I tend to be the reviewer journal editors go to when they sense crap – I have a ridiculously large rejection rate because I know bullshit when I read it.

Tom Spears of the Ottawa Citizen says he’s just written the world’s worst science research paper: More than incompetent, it’s a mess of plagiarism and meaningless garble.

Now science publishers around the world are clamouring to publish it.

They will distribute it globally and pretend it is real research, for a fee.

It’s untrue? And parts are plagiarized? They’re fine with that.

Welcome to the world of science scams, a fast-growing business that sucks money out of research, undermines genuine scientific knowledge, and provides fake credentials for the desperate.

And even veteran scientists and universities are unaware of how deep the problem runs.

When scientists make discoveries, they publish their results in academic journals. The journals review the discovery with independent experts, and if everything checks out they publish the work. This boosts the reputations, and the job prospects, of the study’s authors.

Many journals now publish only online. And some of these, nicknamed predatory journals, offer fast, cut-rate service to young researchers under pressure to publish who have trouble getting accepted by the big science journals.

In academia, there’s a debate over whether the predators are of a lower-than-desired quality. But the Citizen’s experiment indicates much more: that many are pure con artists on the same level as the Nigerian banker who wants to give you $100 million.

Last year, science writer John Bohannon sent out a paper with subtle scientific errors and showed that predatory journals were often failing to catch them. The Citizen covered his sting, published in Science magazine.

Estimates of their numbers range from hundreds to thousands.

To uncover bottom-feeding publishers, the simplest way was to submit something that absolutely shouldn’t be published by anyone, anywhere.

My short research paper may look normal to outsiders: A lot of big, scientific words with some graphs. Let’s start with the title: “Acidity and aridity: Soil inorganic carbon storage exhibits complex relationship with low-pH soils and myeloablation followed by autologous PBSC infusion.”

Look more closely. The first half is about soil science. Then halfway through it switches to medical terms, myeloablation and PBSC infusion, which relate to treatment of cancer using stem cells.

The reason: I copied and pasted one phrase from a geology paper online, and the rest from a medical one, on hematology.

I wrote the whole paper that way, copying and pasting from soil, then blood, then soil again, and so on. There are a couple of graphs from a paper about Mars. They had squiggly lines and looked cool, so I threw them in.

Footnotes came largely from a paper on wine chemistry. The finished product is completely meaningless.

The university where I claim to work doesn’t exist. Nor do the Nepean Desert or my co-author. Software that catches plagiarism identified 67 per cent of my paper as stolen (and that’s missing some). And geology and blood work don’t mix, even with my invention of seismic platelets.

I submitted the faux science to 18 journals, and waited.

Predators moved in fast. Acceptances started rolling in within 24 hours of my submission, from journals wishing to publish the work of this young geologist at the University of Ottawa-Carleton.

First came the Merit Research Journal of Agricultural Science and Soil Sciences, which claims it sent me to “peer review” by an independent expert in the field who gave me a glowing review. It laid out my article and was ready to post it online 48 hours after submission — for $500.

That’s cheap. The going rate at genuine journals is $1,000 to $5,000.

I didn’t pay.

There are seven more acceptances from the International Journal of Science and Technology, Science Journal of Agricultural Research and Management, the International Journal of Current Research, Science Park, Australian Journal of Basic and Applied Research (actually based in Jordan), American Journal of Scientific Research, and International Journal of Latest Research in Engineering and Computing. Yes, “Latest.” Makes you wonder what other kind there is.

Several others are still considering and a couple are silent and appear to have shut down.

Only two turned me down, for plagiarism. And one of these will turn a blind eye and publish anyway if I just tweak it a bit.

The acceptances came embarrassingly fast. A real journal needs weeks at the very least to ask reviewers — outside experts — to check an author’s work.

I wrote back to one of these publishers explaining that my work was “bilge” and the conclusions don’t stand up.

The journal wrote right back offering to tweak a few passages and publish anyway. And by the way, it asked, where’s the $500?

At the University of Saskatchewan, medical professor Roger Pierson wonders how can scientists trust the journal system to share knowledge.

“Basically you can’t any more,” he said, except for a stable of well-known journals from identifiable professional societies, where members recognize ethical work is in all their best interests.

He had just spent time with the committee that oversees tenure and promotions at his university.

“We had three cases where people had published things in what were obviously predatory journals, and they didn’t think anything was wrong with that.

“The reality though is that these (fake journals) are used for promotion and tenure by people who really shouldn’t be there. The world is changing fast … It’s a big problem.”

And taxpayers wonder if the university system is broken.

I don’t know of a better system than vigorous and brutal peer-review, but universities are rapidly becoming redundant in their quest for meaningless metrics.

And for any university to claim they are global, geography shouldn’t be a factor.

Five-second food safety BS; PR (peer review) before PR (press release)

Posted on March 19, 2014 by Douglas Powell

Friend of the blog, Don Schaffner (left, sort of as shown), a professor of food safety at Rutgers University and co-host of Food Safety Talk writes:

I can tell when something is a big news story.

First, I read about it in my news feed from one or more sources. Second, friends and family send it to me. By these two criteria, the recent news about the five second rule qualifies as a big news story. No links to any of the news outlets blathering on about this, except for the Beacon Journal, who contacted our colleague Jeff LeJeune to comment on the story. Props to them for at least checking with a reputable expert (shurley some mistake, he’s Canadian).

barfblog.com readers are probably aware of this story. And it’s a story, or a press release, not a study.

The press release is apparently based on a PowerPoint presentation. The study has not undergone any sort of peer review, as far as I know. Science by press release is something that really bugs me. It’s damned hard to do research. It’s even harder to get that research published in the peer-reviewed literature. And when reputable news outlets publish university press releases without even editing them, that does a disservice to everyone; the readers, the news outlet, and even the university researchers.

I do have to give credit to the Ashton University press officer, who responded promptly to my request for more information when I clicked on the link on the website where the press release was posted. And it certainly is better to have a PDF of a PowerPoint presentation, instead of just a press release. But it’s still not a peer-reviewed manuscript.

A review of the slide set shows a number of problems with the study. The researchers present their data as per cent transfer. As my lab has shown repeatedly, through our own peer-reviewed research, when you study cross-contamination and present the results as percentage transfer, those data are not normally distributed. A logarithmic transformation appears to be suitable for converting percentage transfer data to a normal distribution. This is important because any statistics you do on the results generally assume the data to be normally distributed. If you don’t verify this assumption first, you may conclude things that aren’t true.

The next problem with the study is that the authors appear to have only performed three replicates for most of the conditions studied. Again, as my own peer-reviewed research has shown, the nature of cross-contamination is such that the data are highly variable. In our experience you need 20 to 30 replicates to reasonably truly characterize the variability in logarithmically transformed percent transfer data.

Our research has also shown that the most significant variable influencing cross-contamination appears to be moisture. This is not surprising. Bacteria need moisture to move from one location to another. When conditions are dry, it’s much less likely that a cell will be transferred.

Another problem that peer-reviewers generally pick up, is an awareness (or lack thereof) of knowledge of the pre-existing literature. Research on the five-second rule is not new. I’m aware of at least three groups that have worked in this area. Although it’s not peer-reviewed, the television show MythBusters has considered this issue. Paul Dawson at Clemson has also done research on the five-second rule. Dawson’s research has been peer-reviewed and was published in the Journal of Applied Microbiology. Hans Blaschek and colleagues were, as far as I know, the first lab to ever study this. Although this research was never published, it did win an Ig Noble prize.

If you don’t have any pathogens on your kitchen floor, it doesn’t matter how long food sits there. If you do have pathogens on your kitchen floor, you get more of them on wet food than dry food. But in my considered opinion, the five-second rule is nonsense. I’m a scientist, I’ll keep an open mind. I know what some people in my lab will be working on this summer. And I’ll tell you more about it… after it’s been accepted for publication in a peer-reviewed journal.

Go evidence or go home: some online journals will publish fake science, for a fee

Posted on October 4, 2013 by Douglas Powell

A long time ago in a galaxy far, far away – Canada – we ran the national food safety info line.

You can imagine rotary phones, but it was a tad more sophisticated.

The question we grappled with was, who’s evidence is right?

We came up with specific guidelines for how to answer questions based on the preponderance of scientific evidence, and were completely transparent about the limitations, using a sound risk analysis framework.

When answers in the scientific literature seemed, uh, weird or missing, we’d go do our own original research and fill in the gaps.

We questioned everything and still do. It’s good for science, but can be hard on relationships.

Any time some hack said, here’s the science to prove something, we would question it.

Apparently with good reason.

As reported by NPR, an elaborate sting carried out by Science found that many online journals are ready to publish bad research in exchange for a credit card number.

The business model of these “predatory publishers” is a scientific version of those phishes from Nigerians who want help transferring a few million dollars into your bank account.

To find out just how common predatory publishing is, Science contributor John Bohannon sent a deliberately faked research article 305 times to online journals. More than half the journals that supposedly reviewed the fake paper accepted it.
“This sting operation,” Bohannan , reveals “the contours of an emerging Wild West in academic publishing.”

Online scientific journals are springing up at a great rate. There are thousands out there. Many, such as PLOS, are totally respectable. This “open access” model is making good science more accessible than ever before, without making users pay the hefty subscription fees of traditional print journals.

(It should be noted that Science is among these legacy print journals, charging subscription fees and putting much of its online content behind a pay wall.)

But the Internet has also opened the door to clever imitators who collect fees from scientists eager to get published. “It’s the equivalent of paying someone to publish your work on their blog,” Bohannan tells Shots.

Bohannan says his experiment shows many of these online journals didn’t notice fatal flaws in a paper that should be spotted by “anyone with more than high-school knowledge of chemistry.” And in some cases, even when one of their reviewers pointed out mistakes, the journal accepted the paper anyway — and then asked for hundreds or thousands of dollars in publication fees from the author.

A journalist with an Oxford University PhD in molecular biology, Bohannan fabricated a paper purporting to discover a chemical extracted from lichen that kills cancer cells. Its authors were fake too — nonexistent researchers with African-sounding names based at the fictitious Wassee Institute of Medicine in Asmara, a city in Eritrea.

With help from collaborators at Harvard, Bohannan made the paper look as science-y as possible – but larded it with fundamental errors in method, data and conclusions.

The highest density of acceptances was from journals based in India, where academics are under intense pressure to publish in order to get promotions and bonuses.

“Peer review is in a worse state than anyone guessed,” he says.

The Internet and open access are great tools, but like any technology, hucksters will be there to exploit the tool for personal (PhD) gain.

Maybe the peer-review system needs to open up, and the Internet can help with that.

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