## Math, Engineers, Bridges, and Hand Waving

31 05 2012

By Steve Tung

After seeing the alarming video of the Minnesota I-35 bridge collapse in class today, I’m reminded from my recent reporting on the flattening of the Golden Gate Bridge 25 years ago on how flexible numbers can be. Searching for a simple detail revealed how much hand waving goes on that I hope is reserved for the press and not actual analysis.

In 1987, hundreds of thousands of people crammed onto the iconic Golden Gate Bridge. Image from wikimedia commons, taken by Cary Bass.

To quickly summarize: hundreds of thousands of people crossed the Golden Gate Bridge on foot to celebrate its 50th anniversary. The weight, more than two times of cars in bumper to bumper traffic, was enough to make the middle sag 7 feet, flattening the suspension bridge’s slight curve.

The number I was looking for was pretty simple: just the amount of weight the bridge was designed to support. The original design load of 4,000 pounds per foot of bridge is pretty well documented, but renovations during the mid-80s removed a dense concrete layer and replaced it with lighter and stronger steel frameworks. Those renovations should have boosted the design capacity of weight, and I just wanted to know what it was. But no one I talked to (including officials and engineers that oversee the bridge) could tell me what that new number was. More surprisingly, three of the four engineers I talked to for the story gave me starkly different ideas about the bridge’s strength and how to think of it that day, none of which particularly agreed with the chief engineer’s numbers as reported by the Merc at the time. (The other engineer I talked to recused himself from analysis because he wasn’t familiar with the Golden Gate’s particulars).

Off the bat, all the experts agreed that it would be practically impossible for the Golden Gate to break and drop people to their deaths from simply cramming more and more weight onto it. But they disagreed at the point where

the bridge would start getting damaged– at what load metal might start to permanently bend (like a bent paper clip), rivets might break, joints get overstressed, all which would require maintenance.

According to the Merc’s story in that era, the day after the bridge flattened, the bridge’s chief engineer said that the bridge was no where close to being damaged. He said that the bridge was designed to hold 5,700 pounds per foot of bridge, while the crowd weighed about 5,400 pounds, using rather generous estimates. But even then there’s a buffer where the bridge can gain even more weight without any deleterious effects. Some engineers call it the factor of safety. “There’s no way we could have gotten enough people on the bridge to cause any problem,” the chief engineer said at the time.

But now, one engineer insisted that the bridge was close to being damaged. Partly because the bridge flattened, which should never happen, he said, and also because he estimated that the weight on the bridge was substantially higher than the standards set by AASHTO (the wordy American Association for State Highway and Transportation Officials), which he didn’t think the Golden Gate far exceeded. He said that the load already significantly intruded upon the factor of safety, and was close to completely exhausting it. But he also said that because the bridge went back to its original shape, that was a sign that it wasn’t permanently damaged.

Another engineer, who analyzed the bridge in the years after the bridgewalk, remembered that the load on the bridge was about the same as the design load. But his concept of factor of safety was a little bit different. Dipping into the factor of safety meant that the bridge would start getting damaged, but not completely fall apart. In a way, this idea is similar to the previous idea that the bridge was being close to damage, but the difference of such a simple, standard idea, was a little odd.

The current chief engineer gave me a far different answer, saying that the bridge is and was capable of being completely filled with 36 ton, 28 foot long trucks, which would be far heavier than the 1987 crowd of people. Rough calculations would put that capacity at more than 15,000 pounds per foot of bridge, more than 2.5 times the 1987 estimate. On top of that there’s an additional safety factor which would put that capacity through the roof, before the bridge would begin to get damaged. In short, the engineer said, there was no practical way to put enough weight on the bridge to get it to crack.

Now all of these experts are pretty well established– they’re either professionals who design or analyze bridges for a living, or professors at prestigious universities. What are we to do if they can’t agree on what seems to be a pretty straightforward concept?

## A Field Guide for SciCom

15 05 2012

By Meghan Rosen

Two quarters ago, David Cohn—the web whiz and crowd-funded journalism advocate who invented Spot.us—left the SciCom class of 2012 with a note-worthy nugget of internet advice.

“It’s cheaper and easier to try something,” he said, “than to debate about whether or not to try it.”

Instead of carefully considering the pros and cons of making a webpage, starting an internet-based project, or creating a social media network, his thinking goes—just do it. Instead of trying to iron out all the possible kinks before launching a new idea, figure them out on the fly. Or, in Cohn’s words, “Fail early and fail often.”

In essence, the best way to carry a new idea forward on the web is to dive in and get started. Cohn calls it “agile and iterative” development. This learn-and-go method helped him pick up new tools, develop partnerships, and nail down the ideas that eventually built the backbone of Spot.us. It even helped him generate a little pre-project buzz.

In this spirit of experimentation, I decided to do something a little different for this blog post. I decided to create another blog. A field guide, of sorts, for SciCom.

As we wrap up nine months of science-writing boot camp, I’ve been thinking about how much our class has learned over the past three quarters. We haven’t just learned how to write and report, we’ve learned how to navigate the program too.

So I wanted to create a place where future classes could come for advice: tips and tricks from the class of 2012 (and past classes too, if they want to contribute.) The platform is simple: a tumblr blog that’s open to posts from former SciCom class members (or people who know the password: scicom).

Because I want visitors to quickly find the advice they’re looking for (without scrolling through pages of past entries) I’ve included a list of tags to help group advice into categories (such as fall, winter, and spring quarters, multimedia, investigative report, etc.).  But I’m open to adding more tags, if anyone has suggestions.

I’ve also set up a questions page for new students to ask about anything that pops up during their classes and coursework. The page will forward questions to me, but I’m thinking of sending them to our class Google groups email address. This way, anyone who has the time, interest, and expertise can take a crack at answering (while letting the rest of us know who’s fielding what).

As of this posting, the SciCom Field Guide has advice from four members of this year’s class. Initially I envisioned practical tips and technical advice, but I was surprised (and a little warmed) to see that many of my classmates offered support and perspective instead of tricks of time management. So I added tags for ‘encouragement’ and ‘life.’ “Agile and iterative” in action, I suppose.

I don’t know how inspired my class will be to post to the Field Guide, but for it to work well, it will have to be a community effort (otherwise, I might overrun the blog with advice that’s specific to me—like how to pump between classes.) I also don’t know if next year’s class will look to us for help. (I, for one, would have loved to learn the clever tip about carrying business cards in your nametag at meetings. I had been stuffing my (slightly rumpled) set into a purse pocket.)

But I do know that the collective knowledge of SciCom class 2012 could potentially help students struggling with internships, class assignments, and work/life balance.

This might not but be the best way to gather and group our thoughts, but I thought I’d give it a shot. After all, it was cheap and easy.

## SOD Blitz: Volunteers take on Sudden Oak Death

10 05 2012

UC Berkeley students survey trees for sudden oak death. Photo: E. Loury

Erin Loury

by Erin Loury

Ah, the signs of spring. The sun is out, the rain has stopped (for now)—and sudden oak death is on the move. This invasive, fungus-like tree killer, which is related to the Irish potato blight, moves in fits and spurts with bouts of warm spring rains. Every spring for the past four years, scientists from UC Berkeley have mobilized hundreds of volunteers to track the disease’s whereabouts in the Bay Area.

A bay leaf showing classic signs of sudden oak death. Photo: E. Loury

This massive citizen scientist effort is called a SOD Blitz (“SOD” for sudden oak death). “It started mostly as a way to engage people,” says organizer Matteo Garbelotto, a researcher at UC Berkeley who helped identify the disease-causing water mold, Phytophthora ramorum, in 2001. Because SOD outbreaks have a cyclical nature, they fall out of the news spotlight fairly quickly.  Garbelotto wanted to keep up public interest and awareness in the disease.  “When you actually do something, you look at it differently than just sitting in the chair and listening to even the brightest researchers in the world talking about it,” he says.

I recently attended the SOD Blitz at UC Berkeley, where Garbelotto briefed about 70 volunteers in how to spot the signs of the disease and collect data. The blitzes focus on bay laurel trees, which spread the disease to oaks without succumbing themselves, the way mosquitoes transfer malaria to people. Oaks can’t pass the disease to each other, so surveying bay trees provides the clearest picture of infection risks. The symptoms are also easy to spot on bay leaves. Garbelotto instructed the participants to look for brown leaf tips, where water droplets (and the water-borne disease) would accumulate. Other classic signs include a black line and yellow halo above the tip lesion, and little black specks throughout the leaf from disease carrying water droplets.

UC Berkeley student Heather Leslie collects leaves from a bay tree that shows symptoms of sudden oak death. Photo: E. Loury

I joined a pair of UC Berkeley students surveying the bay trees on a fire road behind the campus. The girls carried a collection packet of materials in a big manila envelope. When they spotted an infected bay tree, they jotted down its GPS coordinates (with the help of an iPhone ap), collected a handful of symptomatic leaves in a small envelope, and marked the tree with flagging tape.  They also made a note of any nearby oak trees that showed symptoms of the disease – which in oaks include bleeding bar and black opportunistic fungi.

Garbelotto’s lab will test all the collected leaves for the disease agent, and create a map of infected trees.  The maps can help homeowners decide whether their oaks might be at risk, and whether they ought to take steps to treat them. “When you combine all these maps, you have a really great distribution,” Garbelotto says. “There’s no way we can do it without the volunteers.”

If you care about oak trees in Santa Cruz, there’s a SOD Blitz coming up on Saturday, May 19 at10:30am. The location is the Cal-Fire Training Room on Gushee Street (behind the forestry office at 6059 Highway 9) in Felton. For more information, contact Nadia Hamey, nadiah@big-creek.com.  And you can find out about other SOD Blitzes throughout the Bay Area.  It’s a great way to spend a few hours outdoors and do something good for science!

Look for my feature in the upcoming edition of Science Notes this summer to get the full story on sudden oak death!

Citizen scientists collect data that will help researchers track the spread of sudden oak death. Photo: E. Loury

## The Lyme Twilight Zone

8 05 2012

Beth Marie Mole

by Beth Marie Mole

When my mom said she was headed to the doctor for a sore knee last month, I didn’t think much of it. I figured she probably just twisted it doing yard work or something. But, when she called back to say her swollen knee was Lyme arthritis, she had my attention. And I braced myself for the dizzying world we were about to walk into.

Lyme is one of those diseases you almost can’t mention in mixed company – unless you want to pick a fight. It exists in a world where patient advocate groups distrust the medical community; where advocate-backed legislation rather than clinical evidence defines treatment options; where seemingly ordinary doctors practice “alternative” medicine; and where a long standing disease has no settled diagnostics, treatment, or even definition.

Since scientists identified it in Lyme, Connecticut in 1975, it has become the most common tick-born disease in North America. Lyme disease is endemic to the Northeast and the Pacific coast, and it’s spreading. Disease ecologists consider it a high priority emerging infectious diseases.

Yet, nearly everything else about it is hotly contested.

An adult black leg tick (deer tick)
Public domain image

Last fall, in the medical journal The Lancet, a group of doctors equated people who believe in “chronic Lyme disease” to people who deny the existence of AIDS (1). On the other side, patient advocate groups, such as the Lyme Disease Association, disagree with standard medical guidance set by the Infectious Disease Society of America (IDSA), and endorsed by the Centers for Disease Control and Prevention. Many have pushed (successfully) for laws that protect patients and doctors who believe in chronic illness and don’t follow standard treatments.

To say the least, the divide is unfortunate, says Dr. Robert Lane, a leading tick-born disease expert and epidemiologist at UC Berkeley. “I think that both sides want to get to the truth,” he says.

Part of the controversy stems from Lyme disease’s vague start. Nymph ticks the size of poppy seeds or slightly larger adults can deliver the spiral bacteria, Borrelia burgdorferi, to skin, where they mount their attack. The result might be the famous bulls-eye rash. But, advocate groups claim that as little as 30 percent of infected people will have/see this rash. While doctors who side with CDC guidelines say as much as 80 percent will have/see it. My mom didn’t even notice a tick.

After that, things get fuzzier. Early Lyme disease symptoms include fatigue, headache, fever, and depression. If you miss those super obvious signs, the bacteria invade the body, and launch late stage disease. This can fire up months to years later as fatigue, joint pain (Lyme arthritis), mental fogginess, and sometimes even heart and liver problems. For some patients, it can be a slow road to a proper diagnosis, where relationships with doctors erode along the way.

It doesn’t help that many advocate groups believe that standard tests for Lyme—ELISAs and Western blots—are wildly inaccurate. An ELISA measures the bacteria’s presence indirectly, by detecting antibodies—your immune system’s response to the infection. Advocate groups claim that immune responses fluctuate, and are unreliable. Western blots, which also detect antibodies, may miss dormant infections, they also claim. Ultimately, advocacy groups—one of the most vocal is the California based LymeDisease.org—feel that Lyme disease is under-diagnosed. Some patients with similarly vague symptoms believe they have the disease without positive diagnostics.

Members of the IDSA, which is comprised of over 9000 physicians, scientists and health care professionals, acknowledge that no test is perfect and that the ELISA test may not be accurate in the first few weeks of infection (before your immune system mounts a response). But they point to clinical data validating its use for diagnosis (2, 3). ELISAs are also a common diagnostic tool for many other infections, including West Nile virus and HIV.

However it happens, once someone is diagnosed with Lyme, the IDSA recommends (4) two weeks of an oral antibiotic, such as doxycycline or ceftriaxone, for early disease. It’s a four-week course for late stage. When my mom got her diagnosis, she immediately went on a 28-day course of doxycycline and started feeling better. But a week after she finished, she felt run down and her headaches returned.

This is where things get crazy. The IDSA would say she may just have residual symptoms, and, at most, should try another four weeks of antibiotics. Patient advocate groups say she may need antibiotics for *six months to multiple years* and that her disease could be chronic.

In multiple double blind, randomized clinical trials, long-term antibiotic therapies did not improve symptoms or the rate of recovery (5,6,7).

A deer tick on a fingernail

When I contacted the California Department of Public Health for their opinion on chronic Lyme disease, they said they had no comment.

Some doctors who believe in chronic infection support unsafe “alternative” treatments such as injections of toxic dinitrophenol, which is banned in the U.S. Such doctors call themselves Lyme Literate MDs. LLMDs are difficult to separate from infectious disease specialists who treat Lyme disease within standard protocols. In fact, to identify a LLMD, you usually have to go through patient advocate group that will give you a referral after you sign up on their website. Moreover, many LLMDs have conflicts of interest with laboratories that produce alternative tests, or have sanctions by medical licensing boards, or been in trouble with federal agencies (8,9,10). In 2008, a Kansas state court found an LLMD guilty of killing a Lyme patient with bismuth injections (11).

“[The LLMDs] are very clandestine— for good reason,” says Dr. Paul Auwaerter, a Lyme disease specialist at Johns Hopkins and the lead author on The Lancet opinion piece. At his clinic, most of the patients that come in with a chronic Lyme disease diagnoses never even had Lyme disease. Rather, they were suffering from something else, he says.

In the Northeast, where over 90 percent of Lyme disease cases are diagnosed, less than 3 percent of doctors used chronic Lyme disease as a diagnosis.

Right now, my mom is waiting for her next appointment with an infectious disease doctor (not a LLMD, I checked). She may be in the 5 percent pool of patients that need another round of antibiotics, or may just get something to treat her symptoms. Either way, she’ll get some bug spray—from me—for the next time she does yard work.

## Drink at your own perceived risk

2 05 2012

by Helen Shen

How dangerous is unpasteurized milk? Many health-conscious consumers want to know. The answer depends on how you look at the numbers.

In March, CDC scientists published a study in the journal Emerging Infectious Diseases that tried to quantify this risk by analyzing milk-related disease outbreaks from 1993 to 2006.

The research was widely covered in the mainstream news media, including in a story I wrote for the San Jose Mercury News. The study also attracted a fair amount of online outrage from many raw milk enthusiasts, who treated it as a piece of biased government propaganda.

The CDC media press release, several news stories, and the research paper itself highlighted two main points: first, that 75 percent of raw milk outbreaks occurred in states where raw milk was legal at the time (in an interview with me, first author Adam Langer called this “the most important result of the study”); and second, that raw milk is 150 times more dangerous than pasteurized milk.

Plenty of aspects of the raw milk debate are unscientific. Food choices are personal, cultural, and political. Twelve states allow retail sales of raw milk. Twenty states ban raw milk sales outright. The remaining states allow only limited raw milk sales, such as on-farm transactions.

Unfortunately, emphasizing those particular research findings may have hindered a truly scientific discussion about raw milk risks.

Photo credit: cyclonebill, Wikimedia Commons

Proving the obvious

Let’s think about the first conclusion. Between 1993 and 2006, raw milk caused more outbreaks in states where the unpasteurized product was legal. Is that like saying car accidents happen more often on roads that permit cars?

Langer told me, “It is not necessarily surprising. We do occasionally have to do scientific studies in order to prove what one would think would be obvious. But it is important evidence to show that laws that restrict the sale of unpasteurized dairy products are very important public health tools to reduce the number of outbreaks that are caused by these products.”

Basically, the study suggests that in states that ban raw milk sales, few people consume and get sick from black market raw milk, says Michele Jay-Russell, a food safety expert at UC Davis and a former scientist with the California Department of Public Health.

Hm. That’s probably good news, but it doesn’t offer any real information about how risky raw milk actually might be. That’s where the second point could help.

Outbreaks versus individuals

The authors concluded that raw milk carries 150 times greater risk than pasteurized milk of causing disease outbreaks. (A disease outbreak is a cluster of illnesses thought to originate from the same source. It could involve 2, 200, or 2,000 people.)

Here’s some of the math: Only about 1 percent of the population is thought to consume raw milk. Assuming they consume milk in roughly the same quantities as other milk drinkers, and assuming the two types of milk were equally safe, you’d expect about 1 percent of outbreaks to be related to raw milk. Instead, the CDC found 60 percent of outbreaks—150 times more than expected—were linked to raw milk.But what happens if, instead of using outbreaks, you look at those individuals involved in milk-related outbreaks? Those numbers tell a slightly different story.

In total, raw milk outbreaks sickened 1571 people. Pasteurized milk sickened 2842. So, while raw milk was implicated in 60 percent of outbreaks, it accounted for only 35 percent of all outbreak-sickened individuals. Thirty-five percent is still 55 times more than you’d expect to see from the small fraction of milk drinkers who consume unpasteurized dairy. That’s cause for concern, but it’s a much smaller effect than if you measure risk by outbreaks.

The average reader doesn’t think in terms of disease clusters, but is interested in individual risk. Health agencies, on the other hand, get concerned and become involved when outbreaks occur, says Jay-Russell.

“If you’re part of an outbreak, or if you’re the only one that got sick, it’s all the same ‘badness’ for you personally. From a public health resource standpoint, having these dozens of outbreaks, every one of those requires stopping work on other public health issues,” she said.

Milking a goat
Photo credit: Teunie from nl, Wikimedia Commons

The authors didn’t communicate the reasons for their choice—non-intuitive for the general public—for calculating outbreak statistics in their paper. Nor did they include the relative risk statistics for individuals. Doing so could have helped their case.

But because the omitted statistics would have produced a weaker result, the authors invited criticisms of manipulating the numbers to their advantage.

In a press release entitled “CDC Cherry Picks Data to Make Case Against Raw Milk,” the pro-milk non-profit Weston A. Price Foundation said, “Perhaps most troubling is the authors’ decision to focus on outbreaks rather than illnesses… In addressing the risk posed for individuals who consume a food, the logical data to examine is the number of illnesses, not the number of outbreaks.”

Distracting from the data

Jay-Russell says she’s more concerned that young people and children are disproportionately sickened by raw milk—a finding that received relatively less attention. The CDC study found that 60 percent of individuals sickened by raw milk outbreaks were younger than 20. That number contrasts with 23 percent for pasteurized milk outbreaks.

Even though a small fraction of the population drinks raw milk, the majority of those sickened in raw milk outbreaks are young. This effect is partly explained by the fact that raw milk is touted by its fans as a health food—not just acceptable for children, but especially beneficial to their growth and well-being.

In my next blog post, I’ll examine some of these health claims.