Much delayed posting of a good link or two

Here's a few articles I've put aside to post, and haven't had time for:

How to read medical papers
Applying epi to gang violence
Growing meat in vitro
The feasibility of eradicating malaria
The loss of biodiversity in developing agriculture

No promises to start posting again, just thought I'd clean up my old backlog.

Should it be law?

I'm not going to say if rBST (known most often to laymen as bovine growth hormone) is a good thing or a bad thing for the dairy industry. I'm not going to say if it is harmful to humans or not. I'm not even going to say if it is harmful to cows or not. Mind you, I have opinions on all these topics; I'm just not going to say right now.

What I am going to say is people should be able to choose to avoid it if their little hearts desire. According to this article, some people (with ties to the drug's largest producer, oddly enough), are lobbying to stop "hormone-free" labels.

I could understand, if there were local regulations banning the use of an FDA-approved drugs, lobbying to remove those regulations. Trying to create a regulation against a label that says you don't use those drugs? Unnecessary, wasteful, stupid! Allow people the choice. Maybe this means you lose your market, but that's how capitalism works (at least, in theory): informed people choose where to spend their money. If you can't afford to produce rBST-free milk at the price offered and you can't sell non-rBST-free milk, you need to get out of the dairy business.

At long last

I've been busy again, lately, and haven't really had a chance to weigh in on the humane slaughter issue. Instead of breaking news, then, here's some afterthoughts:

I was not amused by this article. This is fear-mongering, fueled by the fact that most people don't know their burgers are coming from dairy cows (I've never met a layperson who knew that; they're always a bit shocked). The understanding of epidemiology here is particularly egregious:

Dairy cows can also carry some common maladies, including mastitis, a bacterial infection of the udder; foot rot, which they can develop standing for long periods in manure, mud and damp straw; and Johne’s disease.

Scientists believe these diseases are not carried into the human food chain, with one exception: Health and animal scientists are currently debating whether the traits of Johne’s are responsible for Chron’s disease in humans. Chron’s disease is an intestinal disorder that can cause inflammation of the colon, severe abdominal pain, diarrhea and weight loss. Some argue it’s these very problems that prompt farmers to dispatch the cows to the slaughterhouse in the first place.

One: why mention all these "terrible" diseases if they aren't entering the food chain? Two: hate to say it, but milk is a bigger risk than beef for MAP transmission (MAP is the cause of Johne's disease, and is under debate as a contributing factor in Crohn's disease), so I'd rather have them at the slaughterhouse, where the risk of contamination is minimal, than in the milking parlor.

Lesson: don't get your information about your food from the editorial page!

I was very amused by this article. USDA inspectors may not have been doing their job, but that's really no excuse for the Humane Society avoiding their legal responsibility . . . and why were they contacting local DA, then releasing the video on YouTube with national promotion? Sounds like they wanted to appear to do the legal thing while making the biggest publicity. Shame on HSUS!

Humane Society grilled on not advising USDA about Hallmark

By Janie Gabbett on 2/26/2008 for Meatingplace.com

WASHINGTON — Congressmen repeatedly questioned a representative of the Humane Society of the United States on Tuesday about why the group did not immediately inform USDA of video evidence workers were abusing downed cattle at Hallmark/Westland Meat Packing Co.

At a House Energy and Commerce subcommittee hearing on food safety, Michael Greger, HSUS director of public health and animal agriculture, said the San Bernardino District Attorney's office asked the group to hold the information until it completed its own investigation. The congressmen, however, said HSUS could have discretely gone to USDA earlier than it did.

Greger hinted at more HSUS exposes, telling the committee the videographer's identity must be guarded so as not to compromise current and future investigations. The Hallmark/Westland video, which was shown at the hearing, resulted in the nation's largest beef recall. (See Hallmark/Westland recalls 143 million lbs of beef — largest in history on Meatingplace.com, Feb. 18, 2008.)

Hallmark/Westland President Steve Mendell did not attend the hearing, declining the committee's request for him to testify. Committee members said they are looking at compelling him to come before the committee sometime in the future.

Greger told the committee that Hallmark workers said in criminal testimony in California that they were pressured by supervisors to get the cows up and into slaughter. Hallmark slaughtered mostly spent dairy cattle, often fatigued after being trucked in from surrounding states.

Members of the subcommittee, which is chaired by Rep. Bart Stupak (D-Mich.), used the hearing as an opportunity to renew calls for: banning all meat from downer cattle from the food supply, mandatory traceability standards, mandatory recall authority for USDA and the Food and Drug Administration and the creation of a single food safety agency.

William Marler, a Seattle lawyer who represents victims of foodborne illnesses, however, suggested USDA might have actually gone too far with the Hallmark recall.

"Although stunned by the video …I am more stunned that the recall has ballooned to 143 million pounds of meat and is quickly encompassing products that might contain trace amounts of the meat. No people have been sickened. I wonder if resources are better spent elsewhere," he testified before the committee.

First ethanol, now methane?

Apparently the NRC guidelines for nutrients in manure are out-of-date, causing a wonderful renewable source of energy to be scrapped. I have one question, though: couldn't they just change the process to make up for the change in the manure? Oh, wait, that would probably cost more money. Sometimes I forget why corporations exist.

Smithfield says manure didn't make the grade for biofuel

By Janie Gabbett on 2/13/2008 for Meatingplace.com

Smithfield Foods said it sold its Utah biofuels plant because after three years of trying, it concluded it could not generate enough methane from the animal waste it was using to make Smithfield BioEnergy economically practical.

The company explained what went wrong a day after Beacon Energy Corp. announced it had purchased the plant. (See Smithfield biofuel affiliate sold on Meatingplace.com, February 13, 2008.)

The goal of Smithfield BioEnergy was to capture methane from manure provided by Smithfield's Circle Four Farms swine production operation near Milford, Utah, convert the methane into bio-methanol, and then convert that — along with animal and vegetable fats — into bio-diesel fuel.

"However, we determined that our bio-methanol production plant was not economically feasible — and never would be," the company said in a statement.

Why not?

The facility was designed using engineering and planning assumptions about the strength of the nutrient content of animal manure taken from government data and technical guidance manuals. Those assumptions proved to be wrong.

The nutrient content of the animal manure produced on Smithfield's farms proved to be more than 50 percent below published data estimates, which the company attributed to such factors as:

• animal genetic improvement
• improved feed conversion
• reduced water volume used in production systems
• and precisely formulated animal diets

"The fact that our Circle Four Farms operation is producing fewer nutrients than had been anticipated is a good thing from an environmental perspective, but the unintended consequence is that we don't have enough methane to make our Smithfield BioEnergy operation economically practical," the company said.

Smithfield is applying what it learned to other facilities around the country to reduce its environmental footprint. For example, projects are in place at facilities in Tar Heel, N.C., Plainwell, Mich., and Green Bay, Wis., to capture and use methane as an alternative and renewable fuel source.

I should post this on Friday . . .

. . . but at least it's still Lent. Yes, that's right, fish is not meat and poultry are not livestock! I wonder if the Pope will ratify the judge's ruling?

Judge rules poultry are not 'livestock'

By Alicia Karapetian on 3/5/2008 for Meatingplace.com

A San Francisco judge has ruled that chickens are not "livestock," and, as a result, are not subject to the Humane Methods of Slaughter Act, according to court filings. A lawsuit brought by the Humane Society of the United States against the Agriculture Department argued that USDA had misinterpreted the 50-year-old act. "The court finds the legislative history strongly demonstrates unambiguous congressional intent that livestock, as used in the HMSA, does not include poultry," U.S. District Court Judge Marilyn Hall Patel wrote in her opinion. Judge Patel granted summary judgment in USDA's favor and dismissed the lawsuit. HSUS's argument was based on a 1958 dictionary definition of livestock that said that the word encompassed "useful" animals on a farm, while USDA said that the term livestock has always internally meant to exclude poultry. "The plain language of these bills indicates that Congress intended to exclude poultry from the definition of livestock when it enacted H.R. 8308, the bill that eventually became the HMSA," Patel wrote.

You should read/listen to this

This week, NPR's series Climate Connections is focusing on the effect of global warming on disease spread. Yesterday was an interview with epidemiologists on the ground in the Amazon, today was a review of a book on yellow fever, which I reviewed here. I recommend checking out this series -- it does a spot-on job of covering some of the big issues involved, so far. We'll see what tomorrow adds.

A response to the meat industry, minus the shrillness

I've been meaning to write about this article for some time now, but I've been too busy to do it properly. Even now, it'll be brief.

The idea is that we, as Americans, eat too much meat. I would have to agree. You could say we're biased, the author and I: he wrote a vegetarian cookbook, I was a vegetarian for a few years. Still, my experience is that little or no meat in my diet makes me healthier. His research shows that Americans are eating twice as much protein (mostly animal-based) as the (high-end) recommendation. I think we have an argument.

The environmental issue is a touchy one, but he makes his point well -- we produce far too much manure in concentrated areas to spread on fields (some dairy farms are now leasing fields just to spread their manure). We use a lot of water and energy growing and transporting grain to feed livestock. It's not true that all meat production should be banned; there are places in this world, as mentioned in the article, where grass-fed livestock is the only agricultural option. I've been to a couple of those places and believe me, you wouldn't want to be a vegetarian there! We shouldn't deny people a chance to raise their own food, no matter what the moral guilt of a rich society tells us we should do.

And that's really the point -- we, as citizens of a rich country with a wide range of food options, shouldn't be eating so much meat. What should we be eating? To quote another NYT columnist, "eat food, not too much, mostly plants."

International Agents of Food Safety

This seems to be a good idea: if we're going to import food from overseas, we should put it through an equivalent inspection requirement.

I'll admit -- I like this idea, in part, because it will drive up the price for internationally sourced foods, much closer to local foods, which might give people another reason to support their local farmers!

Imagining a theory

Quick update on the cloned-animals-as-food issue: this article contains a scary quote from an FDA scientist.

It is beyond our imagination to even have a theory for why the food is unsafe.

Wow. They can't even imagine a theory. Umm, I don't want the people responsible for protecting our food supply (which mostly consists of imagining threats and counteracting them) unable to imagine a theory here. I can think of a few theories. Not good ones, of course, but he didn't say credible theory -- he said they couldn't imagine a theory.

I hope our FDA guys will start improving their imaginations, fast.

Homogenizing the world

More catch-up in spare minutes: I'm not sure this is a good idea. I've already heard from a local producer that an attempt to sell her product (goat's milk cheese) at the local Wal-Marts fell through because the contract would have required her to provide whatever amount they requested, delivered the day it was requested, to any store they chose. Small producers can't meet those standards, and they certainly can't meet these auditing requirements (or their cost).

Wal-Mart to push for uniform standards for suppliers

By Janie Gabbett on 1/25/2008 for Meatingplace.com

Wal-Mart wants to lead an effort over the next three years with other major global retailers to create common social and environmental standards for suppliers, CEO Lee Scott told employees.

"We believe that there should be one framework of social and environmental standards for all major global retailers. And there should be one third-party auditing system for everyone," he told 7,000 Wal-Mart managers at an internal leadership meeting.

Scott said Wal-Mart is working on such a system with global retail and CIES, a consumer goods network, starting with social standards then planning to expand to environmental stipulations.

Wal-Mart supplier standards

Scott also said Wal-Mart would build specific environmental, social and quality standards into its own supplier contracts. He said these standards would apply to all suppliers who work with Wal-Mart through global procurement, who are domestic importers, or who are manufacturers of Sam's Club or Wal-Mart private brands.

"We have already started doing this, and we hope to extend the requirement to all the suppliers I mentioned within the next three to five years," he said in prepared remarks. He said the company believes suppliers can reduce the amount of energy they use to make Wal-Mart products by 20 percent.

Wal-Mart will only work with suppliers who maintain these standards, will make certification and compliance part of supplier agreements and will ask suppliers to report to them regularly.

To underscore the seriousness of Wal-Mart's commitment, Scott said, "We will favor — and in some cases even pay more i for suppliers that meet our standards and share our commitment to quality and sustainability."

The pandemic that wasn't?

I have 10 minutes, so I thought I'd play a little catch-up. Basically, this article is saying that we got a combination of lucky and prepared to avoid pandemic avian flu. Good summary -- we were lucky it wouldn't (and didn't) mutate that quickly and we were prepared with large investments in vaccine and diagnostic research. The question now, of course, is how to keep those dollars coming in the face of large-scale complacency by the public. Here's hoping this doesn't turn into a "boy who cried wolf" scenario!

Epi 101: Publishing bias

Why are we now finding out that antidepressant-making drug companies only publish (the better) 2/3rds of their trials? Is it because drug companies are evil, money-grubbing, and soulless? Not exactly -- it's probably also a form of publication bias. Journals don't like to publish papers that report no differences (although this is a valid, and important, scientific finding). I've recently had that complaint from a reviewer -- we didn't find a significant difference (actually, we did, just not an easy one to distinguish, but I digress), so what's the point in publishing the results?

The point is that science consists of two types of trials:

1. trials that work, and
2. trials that don't work.

Number 1 shows us what to do next. Number 2 shows us what not to do next. Both very useful to know. Never publishing number 2 leads to repetition of useless trials. This is one of my pet peeves.

Oh, and the drug companies probably didn't want to report less than stellar findings.

Cloned meat is safe? Or offspring . . . oh, never mind

I've put off blogging for a little while (too much writing in my real job), but I do need to comment about this:

The FDA ruling does not mean you will be eating Beta. It means that people who have spent large amounts of money to clone their best cows will be able to sell you the milk and meat of their offspring. The actual cows are worth too much to butcher.

I'm not taking a stand on this issue -- I just don't want people to be more confused than the media has already made them.

Interesting thought, hard to prove

No, despite Simon's suggestion, I didn't get a special Epiphany post up. Thought about it, but it didn't happen. Oh well.

I was intrigued by this article, though. It's an interesting idea, that violent movies could reduce crime, but there's an inherent flaw: how do you prove it? I haven't read their study, but I can guess that there are a lot of potential biases. Do you control for policing or sentencing changes, which would require using data from a regional or even local scale? Then you would need to include the presence of movie theaters, the dates violent films are shown, some sort of temporal analysis relating crime to the release of a movie. If so, your power is going to rapidly decrease (the more possible biases your study considers, the lower your degrees of freedom, the harder it is to notice anything). If not, well, any or all of those things could be biasing your results. The article hints at a possible temporal relationship:

Crime is not merely delayed until after the credits run, they say. On the Monday and Tuesday after packed weekend showings of violent films, no spike in violent crime emerges to compensate for the peaceful hours at the movies. Even a few weeks later, there is no evidence of a compensating resurgence, they say.

What did they use to measure this? Survival analysis? Whatever they did, to really get these results, would be pretty tricky stats, which the article doesn't mention.

Still, interesting thought.

Epi 101: Treatment Bias

Here's another basic lesson in epi: if you give different treatments based on socioeconomic status, region, or willingness to pay, you will get different results. If you give the same treatments, but spend more money on one, you won't get different results. You will get more money.

That's the sort of bias this book seems to be addressing. There is no scientific basis for our bureaucratic nightmare of a health care system actually improving our health. All it does is improve the financial health of the people who own it.

Why typing is good, but can't do everything

One of my friends sent me a link to news about the Listeria outbreak in Massachusetts. I hadn't followed it too closely because it wasn't really a new story to me, but I have studied these things more than most normal people.

In this case, the bacteria that sickened at least 4 and killed 2 was linked to a milk processor by typing, a useful process that can tell us how related 2 cultures of bacteria are. That lets us go in, shut the plant down, find the culprit, spread the horror stories (one that I heard a few years back: cartons used to take waste milk to a swine herd were pressure-washed in the bottling room), and hopefully learn something.

What typing can't do is stop the outbreak before people get sick. For that, we need to rely on processors to follow S.O.P.'s and farmers to control disease within their herds. This is what my research group focuses on, modeling food safety at all the levels of production. No, it's not "bench" research, but it can be useful.

I'm guessing that the plant in this case will find a simple procedural change that led to a Listeria overgrowth. This is why modeling is important; we can predict what changes will do before people have a chance to get sick. No amount of fancy DNA technology will do that.

Please forgive the rant; I get peeved sometimes about the bias against modeling. We are important!