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The Triumph of Hope over Experience

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Lawyers: Another Hazard of Research

Jan 8

Posted by Kevin Murphy in Science | No Comments

Here’s another entry in why I think our current judicial system sucks: Fast-multiplying lawsuits can stymie medical science. Actually, I was surprised by one reason why:

The lead author, Brad A. Racette, M.D., associate professor of neurology at Washington University School of Medicine in St. Louis, writes from personal experience: His studies tentatively linking welding to increased risk of Parkinson’s disease resulted in a torrent of subpoenas for research data. Responding to them slows or stops his follow-up research.”Participation in the legal system can be a huge burden on a researcher’s schedule,” Racette says. “There comes a point where a scientist needs the right to be able to say, testifying in court is not what I’m supposed to be doing, I’m supposed to be studying disease.”

And the authors are grown up to realize conflicts of interest cut both ways (i.e. both plaintiffs and defendants):

The authors note that the substantial financial interests at stake in lawsuits often leads to biased research by well-paid expert witnesses. They cite the example of a Texas doctor found to be overdiagnosing a disease known as silicosis. The doctor had a financial interest in the number of patients diagnosed.Peer review is of course a part of the regular scientific process, Racette notes, but a knowledgeable expert can design a study with a predetermined goal of discrediting earlier studies that linked a suspected toxin to a disease.

Industries on the defensive have also attempted to impugn the credibility of researchers. As an example, the authors cite the case of Herbert Needleman, M.D., professor of psychiatry and pediatrics at the University of Pittsburgh and the first scientist to link lead exposure to low IQ levels in children. The lead industry attacked Needleman’s integrity, alleging academic fraud and triggering investigations by the Federal Scientific Integrity Board and his university. The investigations failed to find any evidence of academic fraud, and Needleman’s results were later replicated, leading to beneficial changes such as the removal of lead from gasoline.

Slow, capricious, expensive, and fails to deliver justice is how I would describe our system, and on both the civil and criminal sides of the house. This is just one more example.

Full Disclosure: While I haven’t met them, both authors are on staff at St. Louis Children’s Hospital where my daughter has had two visits and of which I have the highest opinion.

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Stupid Headline

Jan 8

Posted by Kevin Murphy in Science | No Comments

Here’s a stupid headline:

Mental Health Risks Vary Within the U.S. Black Population

Is that a surprise? Would we ever read “Mental Health Risks Vary Within the U.S. White Population”?, or “Mental Health Risks Vary Within the U.S. Population”? Are black people some sort of homogeneous entity where no variation is expected?

This was another shocking line from the report: “He believes clinicians need to look beyond crude categories of race in order to learn more about the backgrounds of their clients in order to better treat them.” That’s your tax dollars at work, funding Captain Obvious.

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Forest Management

Dec 14

Posted by Kevin Murphy in Science | 1 Comment

My backyard would appear to have a remnant of the primeval Missouri Forest: Oak, Ash, Hickory, and Dogwood. The previous owner had marked several trees for removal by putting a big red paint blotch on them. I have removed a trio of live trees (oddly enough none had a big red splotch) and a bunch of dead trees – two white pines and the remainder dogwoods. I didn’t try to change the variety, however, but had other concerns. But in the larger forest outside my backyard, Oaks and Hickories are on the decline. Researchers at Case Western University surmise that fires caused by lightning help the Oaks compete against more shade tolerant trees:

Paul Drewa, assistant professor in Case’s biology department, and graduate student Sheryl Petersen, suspect that these kinds of fires may provide a natural mechanism to deter encroachment of shade tolerant hardwoods, especially red maples that are crowding out oaks and other plants on the ground floors of numerous forests throughout the eastern United States….

“Human alterations to the natural fire regime, especially decades of fire suppression, have changed oak-dominated ecosystems in southern Ohio and throughout the eastern US,” reported Petersen. “As a result, there is a preponderance of shade tolerant hardwoods that are preventing oaks and other native species from regenerating.”

The oak canopies of remaining forest fragments are deceptive, according to the researchers, who found that oaks are not thriving well beyond the seedling stage, with few developing into older life history stages, including juveniles, saplings, and poles.

“Eventually this means the demise of oak trees and other less shade tolerant plant species in future years,” said Drewa

This isn’t any new idea though — as a 2004 article in Missouri Conservationist Magazine makes clear:

In the fall, the hills adjacent to the Missouri and Mississippi rivers seem ablaze with brilliant orange sugar maples. Few trees are as attractive as a sugar maple in autumn, but there is something haunting in all that orange.Not long ago, these same hills contained a lot more of the reds, purples and yellows of oak and hickory. Slowly but surely, the oranges are taking over, indicating that the river hill forests are changing, and not for the better.

We have long had some sugar maple in our woods. In the last 50 years, however, the amount of sugar maple has increased dramatically. This is especially true in counties adjacent to the Missouri and Mississippi rivers, where land is especially productive because of loess, or wind blown silt. Loess is blown from the river bottoms and deposited on nearby slopes. In some areas, loess is more than 100 feet deep. In areas like these, sugar maples are overtaking most other forest vegetation.

The primary reason for the maple takeover is that over the last 50 or so years, we have stopped fires from burning our woods. Native Americans commonly used fire as a tool in Missouri. They burned the landscape to aid in hunting and fighting wars. They also used fire to improve wildlife habitat, which helped ensure an abundance of game. The first European settlers also used fire, primarily to create and improve pasture lands.

Fire played a huge role in shaping the composition of our woods. Oaks and hickories are relatively tolerant of fire. Their thick bark helps protect them from intense heat. Smaller seedlings and trees may be “top-killed,” but their deep root crown allows them to resprout quickly and vigorously.

Fighting forest fires is done with the best of intentions, but not always smartly (just like the new model, prescribed burns). The problem with the old zero tolerance policy is that it allows fuel to build up and huge conflagrations to occur. And if it weren’t for the obvious fact that the longer we fought forest fires, the worse they got, we would still have a zero tolerance policy.

The problem is how to transition back to way forests were prior to zero tolerance without burning the forests down in the process. And another thing to consider is that prior to zero tolerance, the policy was not just let natural fires burn, but set our own. For millenia, the Indians set fires across North America. So to get back to what we consider virgin forest, we have to realize that in fact there has been nothing virgin about North American forests for millenia. What we really want is to go back to actively managed forests with fire as the primary tool.

Prescribed burns seem to be the favored way for the Forest Service to manage forest fires and an immediate return to older practices, but as Mike at SOS forest points out:

So the New Plan is to destroy America’s priceless, heritage forests (whoops, we mean worthless wildlands) in catastrophic fires. The idea is to burn them down sooner so they don’t burn down later.
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Does this make sense? Burn our forests down so they don’t burn down? It makes sense to the Dale Bosworth, Chief of the FS, because he signed onto all the recommendations in the Audit.

The trouble with prescribed burns is that they are hard to control – they result in both not enough fuel removal, and far too much — causing the inferno that fire fighting was supposed to stop in the first place. The sad thing is, we already know a better way – mechanical removal of fuel. Of course, that brings up the dreaded L word – logging. But the science is clear:

Our findings indicate that fuel treatments do mitigate fire severity. Treatments provide a window of opportunity for effective fire suppression and protecting high-value areas. Although topography and weather may play a more important role than fuels in governing fire behavior (Bessie and Johnson 1995), topography and weather cannot be realistically manipulated to reduce fire severity. Fuels are the leg of the fire environment triangle (Countryman 1972) that land managers can change to achieve desired post-fire condition. However, in extreme weather conditions, such as drought and high winds, fuel treatments may do little to mitigate fire spread or severity.
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There are at least three ways to reduce tree densities and accomplish fuel treatments: wildfire, prescribed fire and mechanical thinning. The first, natural fires, are often impractical. Letting natural fires play their historical role may have unwanted effects in forests that have undergone major stand structural changes over the past years of fire exclusion. Any fire started may result in historically uncharacteristic high severity. In many ponderosa pine forests choked with dense, small-diameter trees, or encroached by shade-tolerant trees, natural fires may no longer play a strategic role.The second strategy for restoring these forests is large-scale prescribed burning. This is likely to be effective in stands that have moderate or low tree densities, little encroachment of ladder fuels, moderate to steep slopes which preclude mechanical treatment, and expertise in personnel to plan and implement such large prescribed burns. Large-scale implementation of this strategy will require funding for the planning and implementation over current expenditures and may require modifications to current air quality legislation. Future results of such expenditures may be seen down the road in lessened wildfire suppression costs, reduced fire severity, and reduced air quality impacts.

Mechanical tree removal, the third strategy, works best on forests that are too densely packed to burn, that have nearby markets for small-diameter trees, and areas where expertise and personnel are not available for prescribed burning programs. Mechanical tree removal may be accomplished by many different types of harvest, including precommercial thinning, selection or shelterwood harvest coupled with small-diameter tree removal, and thinning from below (Fiedler 1996). The goal is to manage forests for much lower tree densities leaving larger residual trees. Harvests to reduce wildfire hazard will remove small-diameter trees in contrast to traditional timber harvests. Mechanical fuel treatments can be very labor intensive, especially on steep slopes and in remote areas, and may not be commercially attractive due to the small diameter trees that need removal. To make fuel treatments more cost-effective for small-diameter trees, consistent markets are necessary (Nakamura 1996). Fiedler et al. (1997) assert that mechanized tree harvest on moderately-steep terrain coupled with removal of large amounts of biomass can generate considerable revenue. Periodic underburns and programs for restoring natural fire are critical to maintain these post-harvest stands.

In other words, go in and remove the undergrowth mechanically (i.e. logging, but not clear cutting), then use fire afterwards for maintanence. This was essentially the goal behind the Healthy Forests Initiative, but the logging (i.e. mechanical removal) aspects were controversial and unpopular with a lot of people. Another problem is that the trees and underbrush to be removed isn’t what timber companies are really after. So it looks like will be mainly using fire to fight fire for a while longer.

BTW, if you aren’t getting Missouri Conservationist Magazine, you should be if you have any interest in the Midwestern Great Outdoors.

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Computer Modeling of Cancer

Dec 6

Posted by Kevin Murphy in Science | No Comments

If we can predict the weather, can we predict the course of a tumor? Vito Quaranta, professor of cancer biology at Vanderbilt, thinks so. So he and colleagues from Vanderbilt and the University of Dundee are computer modeling cancer tumors to understand them better and eventually tailor individual treatments:

The investigators have focused on the events of invasion and metastasis (movement of a tumor to distant sites), Quaranta said, because these events mark “the critical transition of a tumor that in the end will be lethal for the patient.” A tumor that does not penetrate the surrounding tissue can often be surgically removed with curative success.”When a patient comes in with a tumor, we’d like to understand for that particular tumor, what are the chances that metastasis is going to occur,” Quaranta said. “Does that patient need to be treated very aggressively, or not so aggressively””

Today, a tumor’s size and shape are evaluated, but they can be poor indicators of invasive potential: a very small tumor can be highly invasive. Even “molecular signatures” – profiles of molecules that suggest how tumor cells will behave – are not entirely predictive, he added.

Quaranta and colleagues opted for a new approach – using the tools of mathematics to tackle the complex problem of cancer behavior.

What a great idea. Kind of makes you wonder why it hasn’t been tried before, but then that’s the way it is with lots of great ideas.

The findings suggest that current chemotherapy approaches which create a harsh microenvironment in the tumor may leave behind the most aggressive and invasive tumor cells.”In the immediate term we may be diminishing tumor burden, but the long term effect is to have a much nastier tumor than there was to begin with,” Quaranta said. There is anecdotal evidence, he added, to support the idea that changes to the microenvironment result in a tumor with more or less invasive potential. Such manipulations of the microenvironment could offer new directions for cancer treatment, he said.

Hmm, will appeasement work for cancer?

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Turns Out My Kid Can Draw Like That

Dec 6

Posted by Kevin Murphy in Science | No Comments

Physists give, and physists take away. The ability to be a master of chaotic motion that is:

In articles that appeared in scientific journals and news magazines including Nature, Physics World and Scientific American, Taylor and coworkers also claim that fractal analysis can be used to distinguish Pollock’s drip paintings from imitations.Intrigued, Jones-Smith began to examine Taylor’s articles, but quickly found that the work was seriously flawed She showed that doodles that she could make in minutes using Adobe Photoshop were as fractal as any Pollock drip painting, vividly refuting Taylor’s claim that Pollock was able to generate fractals by hand only because he had attained a mastery of chaotic motion.

Jones-Smith presented a pointed critique of Taylor’s work to Case astrophysicists and was encouraged to write up her critique for publication. But since Taylor’s original work had appeared in Nature five years earlier, she thought interest in the topic had waned.

Actually, this isn’t entirely inside baseball for a couple of reasons: the use of scientific analysis in areas they weren’t originally used is a great way to make breakthrough discoveries, and there’s a lot of money at stake in being able to determine real Pollock’s from somebody else’s work. And besides, I just don’t like people claiming more certainty than they should.

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Is Success Hereditary?

Nov 28

Posted by Kevin Murphy in Science | 1 Comment

German researchers say that success is hereditary — or at least the willingness to take risks and the willingness to trust other people runs in families. And along the way they discovered that likes, not opposites attract.

Parents shape the character of their offspring, who in turn prefer to choose a partner similar to themselves. These two effects could contribute to attitudes such as willingness to take risks and confidence in others being “inherited” across several generations. At the same time these character traits are decisive, among other factors, for economic success. “Every economic decision is risky, whether it is about buying shares, building a house or just starting to study at university,” Armin Falk emphasises. “On the other hand success in business also involves the right amount of trust.”

If you are that interested, you can read the original article here. I didn’t wade through it to see if they actually correlated economic success with the traits of risk taking and trust.

Counterintuitive: Adolescents Reason Too Much

Nov 13

Posted by Kevin Murphy in Science | No Comments

Here’s important reading for all of us with adolescents: Risk and Rationality in Adolescent Decision Making.

Is it a good idea to swim with sharks? Is it smart to drink a bottle of Drano? What about setting your hair on fire — is that a good thing to do?People of all ages are able to give the correct answer (it’s “no,” in case you were wondering) to each of these questions. But adolescents take just a little bit longer (about 170 milliseconds longer, to be exact) to arrive at the right answer than adults do. That split second may contain a world of insight into how adolescents tick — and how they tick differently from adults.
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It is often believed that adolescents think they are immortal, just plain invulnerable to life’s slings and arrows. This notion is often used to explain why young people are liable to drive fast, have unprotected sex, smoke, or take drugs — risks that adults are somewhat more likely to shy away from.

Research shows that adolescents do exhibit an optimistic bias — that is, a tendency to underestimate their own risks relative to their peers. But this bias turns out to be no more prevalent in adolescents than in grownups; adults commit the very same fallacy in their reasoning. And actually, studies on perception of risks by children, adolescents, and adults show that young people tend to overestimate their risks for a range of hazards (including car accidents and sexually transmitted diseases such as HIV/AIDS), both in absolute terms (i.e., as compared with actual risks) and relative to adults. Their estimation of vulnerability declines rather than increases with age.

So why do adolescents take risks? Decision research answers this with another counterintuitive finding: Adolescents make the risky judgments they do because they are actually, in some ways, more rational than adults. Grownups tend to quickly and intuitively grasp that certain risks (e.g., drunk driving, unprotected sex, and most anything involving sharks) are just too great to be worth thinking about, so they don’t proceed down the “slippery slope” of actually calculating the odds. Adolescents, on the other hand, actually take the time to weigh risks and benefits — possibly deciding that the latter outweigh the former.

So adolescents engage in just the sort of calculations — trading off risks against benefits — that economists wish that all people would make. But economists notwithstanding, research is showing more and more that a faster, more intuitive, less strictly “rational” form of reasoning that comes with increased experience can often be more effective. Mature or experienced decision makers (e.g., experienced vs. less experience physicians) rely more on fuzzy reasoning, processing situations and problems as “gists” rather than weighing multiple factors and evidence. This leads to better decisions, not only in everyday life but also in places like emergency rooms where the speed and quality of risky decisions are critical.

These counterintuitive conclusions about the decision-making processes of young people have major implications for how to intervene to help steer them in the right direction. For example, interventions aimed at reducing smoking or unprotected sex in young people by presenting accurate risk data on lung-cancer and HIV may actually backfire if young people overestimate their risks anyway. Instead, interventions should focus on facilitating the development of mature, gist-based thinking in which dangerous risks are categorically avoided rather than weighed in a rational, deliberative way.

Just another example of the triumph of experience over reason.

I guess you can throw those books out that tell you to calmly reason with your child to get them to see the error of their ways and go back to “Because I said so!”

It looks like McCoy wins the argument — who needs a Spock to calculate the odds of almost anything when you can imploy McCoy’s fuzzy logic so much faster to arrive at the correct answer.

Maybe its a good thing many teenagers factor in their parent’s natural overreaction when deciding whether to engage in risky behavior. So parents, let’s up the ante and overreact to just about everything. Put your thumbs firmly on the scale of right behavior.

It supports my personal study of non-adolescent reasoning, namely, that adults simply do what they think is right and engage in reason only after the fact when pressed to provide reasons for what they did.

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Ride My Bipolar SeeSaw

Nov 10

Posted by Kevin Murphy in Science | No Comments

Everything old is new again, and today’s example is the so called Bipolar Seesaw freshly discovered. The bipolar seesaw is the swing in temperatures between the two poles of earth, where if its up in one pole its down in the other. But how freshly discovered is it? Well, here’s an article from 1998 about — ta da — the bipolar seesaw, complete with polar ice cores showing temperature fluctuations.

Even more interesting is this 2001 article by Wallace S. Broecker that ties it all together:

Geologists are now investigating whether these groupings correspond to another new source of evidence of cyclic patterns in Earth’s recent history. This evidence comes from studies of sediment in the deep waters of the North Atlantic. The rock fragments in these sediments are much too large to have been transported there by ocean currents; they could have reached their present location only by having been frozen into large icebergs that floated long distances from their point of origin before melting. During the past decade, Gerard Bond, my colleague at Columbia University’s Lamont-Doherty Earth Observatory, has studied the makeup of such ice-rafted debris. Noticing that some of the sediment grains were stained with iron oxide, he reasoned that they must have come from locales where glaciers had overrun outcrops of red sandstone. Bond concluded that a detailed analysis of deep sediment cores would reveal changes in the mix of sediment sources over time. This proved to be an excellent strategy, for Bond found something so unexpected that it stunned all of us who study climate history. The proportion of these red-stained grains fluctuated back and forth over time from lows of 5 percent to highs of about 17 percent, and these fluctuations had a pattern: a nearly regular, 1,500-year cycle. Even more amazing, he found that the cycles ran virtually unchanged, in both amplitude and duration, through both ice-age and non-ice-age periods during the last 100,000 years.

Bond puzzled over what might be pacing this cycle. As a geologist, he knew that the sources of the red-stained grains were generally closer to the North Pole than were the places yielding a high proportion of “clean” grains. At certain times, apparently, more icebergs from the far north were making their way well to the south before finally melting and shedding their sediment. Bond hypothesized that the alternating cycles might be evidence of changes in ocean-water circulation.

Ocean waters are constantly on the move, and water temperature is both a cause and an effect. As water cools, it gets denser and sinks to the bottom. In one part of what I like to call the “bipolar seesaw,” the bottom layer of the world’s oceans comes from cold, dense water sinking in the far North Atlantic. This causes the warm surface waters of the Gulf Stream to be pulled northward, as they are today. Bond realized that during this part of the ocean cycle, a large proportion of the icebergs that bear red grains would melt while still fairly far north. But sometimes the ocean reorganizes itself, and the Southern Hemisphere holds sway in driving ocean circulation. At such times, surface waters in the North Atlantic would generally be colder, permitting icebergs bearing red-stained grains to travel farther south before melting and depositing their sediment.

So what we have is just more confirmation, not anything new with the latest announcement of findings. Although I can’t complain too much, because it was new to me.

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Did the Rise of Mountains Cause the Lowering of Temperatures?

Oct 25

Posted by Kevin Murphy in Science | No Comments

I’m a global warming skeptic – and by that I mean I’m skeptical that human actions are the driving factor behind current climate change. Now, that doesn’t mean we aren’t, that just means I’m not convinced that we are. So I read this article on a connection between the Appalachian Mountains and global cooling with interest — not because it supports my skepticism, but because it doesn’t.

One such debate is whether atmospheric carbon dioxide truly drives Earth’s climate. The planet has shifted between greenhouse conditions and icehouse conditions throughout its history, and research from Saltzman’s team strongly suggests that carbon dioxide levels are a key cause.”In this study, we’re seeing remarkable evidence that suggests atmospheric CO2 levels were in fact dropping at the same time that the planet was getting colder. So this significantly reinforces the idea that CO2 is a major driver of climate,” Saltzman said.

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“We observed a major shift in the geochemical record, which tells us something must have changed in the oceans,” Young said.

The timing of the strontium ratio decline matches the rise of the Appalachian Mountains . The crustal plate underneath what is now the Atlantic Ocean pushed against the eastern side of North America, lifting ancient volcanic rock up from the seafloor and onto the continent.

This kind of silicate rock weathers quickly, Young explained. It reacts with CO2 and water, and the rock disintegrates. Carbon from the CO2 is trapped in the resulting sediment.

The chemical reaction that weathered away part of the Appalachians would have consumed large amounts of CO2 from the atmosphere — right around the time that the Ordovician ice age began.

When I read the first part, I immediately thought to myself does it tell us that CO2 drives temperature, or temperature drives CO2. And that’s always the hard question – which change came first – CO2 or temperature. But part 2 contains an explanation that we would expect the CO2 to drop for a reason other than temperature, which surely strenghthens the case for CO2 to drive temperature, and not the other way around.

So we have one case, and the article goes on to say that the rise of the Himalayas may have caused our current ice age (we’re in an interglacial period at the moment). So now we have two possibles, and wikipedia claims there have been 4 major ice ages.

That leaves us with some unanswered questions, like what about the other two ice ages, and how did CO2 get back into the atomosphere to end an ice age, and what is driving our current cycle of glacials/interglacials? I’m still stuck with suggestive, but not conclusive.

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Necessity

Oct 20

Posted by Kevin Murphy in Science | 1 Comment

Congratulations to Matthew Haugland, winner of the 2006 Collegiate Inventors Competition for inventing a better way to forecast nighttime temperatures:

When Matt Haugland was a child in San Jose, California, he remembers that his parents gave him a small thermometer that he used to measure the temperature in different spots around his yard. Although the yard wasn’t large, Haugland was fascinated by the temperature differences in the different parts of his yard. As he grew older, he became fascinated by the microclimates of the San Francisco Bay region and the reasons behind them.Consequently, Haugland hoped to own land for the purpose of researching the microclimates on it. In 1999, he transferred from school in San Jose to the University of Oklahoma in search of affordable land. He bought a five-acre plot and installed several weather stations across it. Through his research, based on weather observations from these stations, Haugland developed a weather forecasting technique that accurately predicts nighttime temperatures.

As Haugland says, “I’m hoping that this model will help improve weather forecasts around the world.” The implications of his work are broad, from helping farmers protect their crops from frost and freezing, to helping predict nighttime fog formation, the biggest weather-related cause of death in transportation.

Maybe now there will be a good scientific explanation of why Beaumont Scout Reservation is always a good 10 degrees colder at night than nearby residential areas.

You should also check out the Inventor’s Hall of Fame while you’re at it.

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