Posts about scientific inquiry

Go Slow with Genetically Modified Food

My thoughts on Genetically Modified Organisms (GMO), specifically GM foods, basically boil down to:

  • messing with genes could create problems
  • we tend to (and especially those seeking to gain an advantage tend to – even if “we” overall wouldn’t the people in the position to take aggressive measures do) ignore risks until the problems are created (often huge costs at that point)
  • I think we should reduce risk and therefore make it hard to justify using GMO techniques
  • I agree occasionally we should do so, like it seems with oranges and bananas.
  • I agree the practice can be explained in a way that makes it seem like there is no (or nearly no) risk, I don’t trust we will always refrain from stepping into an area where there is a very bad result

Basically I would suggest being very cautious with GMO. I like science and technology but I think we often implement things poorly. I think we are not being cautious enough now, and should reduce the use of GMO to critical needs to society (patents on the practices need to be carefully studied and perhaps not permitted – the whole patent system is so broken now that it should be questioned at every turn).

Antibiotic misuse and massive overuse is an obvious example. We have doctors practicing completely unjustified misuse of antibiotics and harming society and we have factory farms massively overusing antibiotics causing society harm.

The way we casually use drugs is another example of our failure to sensibly manage risks, in my opinion. This of course is greatly pushed by those making money on getting us to use more drugs – drug companies and doctors paid by those companies. The right drugs are wonderful. But powerful drugs almost always have powerful side effects (at least in a significant number of people) and those risks are multiplied the more we take (due to interactions, weakness created by one being overwhelmed by the next etc.). We should be much more cautious but again we show evidence of failing to act cautiously which adds to my concern for using GMO.

I love antibiotics, but the way we are using them is endangering millions of lives (that is a bad thing). I don’t trust us to use science wisely and safely. We need to more consciously put barriers in place to prevent us creating massively problems.

Related: Research on Wheat RustThe AvocadoOverfishing, another example of us failing to effectively cope with systemic consequences

Medical Study Findings too Often Fail to Provide Us Useful Knowledge

There are big problems with medical research, as we have posted about many times in the past. A very significant part of the problem is health care research is very hard. There are all sorts of interactions that make conclusive results much more difficult than other areas.

But failures in our practices also play a big role. Just poor statistical literacy is part of the problem (especially related to things like interactions, variability, correlation that isn’t evidence of causation…). Large incentives that encourage biased research results are a huge problem.

Lies, Damned Lies, and Medical Science

He discovered that the range of errors being committed was astonishing: from what questions researchers posed, to how they set up the studies, to which patients they recruited for the studies, to which measurements they took, to how they analyzed the data, to how they presented their results, to how particular studies came to be published in medical journals. The systemic failure to do adequate long term studies once we approve drugs, practices and devices are also a big problem.

This array suggested a bigger, underlying dysfunction, and Ioannidis thought he knew what it was. “The studies were biased,” he says. “Sometimes they were overtly biased. Sometimes it was difficult to see the bias, but it was there.” Researchers headed into their studies wanting certain results””and, lo and behold, they were getting them. We think of the scientific process as being objective, rigorous, and even ruthless in separating out what is true from what we merely wish to be true, but in fact it”™s easy to manipulate results, even unintentionally or unconsciously. “At every step in the process, there is room to distort results, a way to make a stronger claim or to select what is going to be concluded,” says Ioannidis. “There is an intellectual conflict of interest that pressures researchers to find whatever it is that is most likely to get them funded.”

Another problem is that medical research often doesn’t get the normal scientific inquiry check of confirmation research by other scientists.

Most journal editors don”™t even claim to protect against the problems that plague these studies. University and government research overseers rarely step in to directly enforce research quality, and when they do, the science community goes ballistic over the outside interference. The ultimate protection against research error and bias is supposed to come from the way scientists constantly retest each other”™s results””except they don”™t. Only the most prominent findings are likely to be put to the test, because there”™s likely to be publication payoff in firming up the proof, or contradicting it.

Related: Statistical Errors in Medical StudiesMedical Study Integrity (or Lack Thereof)Contradictory Medical Studies (2007)Does Diet Soda Result in Weight Gain?

Tropical Lizards Can Solve Novel Problems and Remember the Solutions

Brainy Lizards Pass Tests for Birds

[Duke biologist Manuel Leal] tested the lizards using a wooden block with two wells, one that was empty and one that held a worm but was covered by a cap. Four lizards, two male and two female, passed the test by either biting the cap or bumping it out of the way.

The lizards solved the problem in three fewer attempts than birds need to flip the correct cap and pass the test, Leal said. Birds usually get up to six chances a day, but lizards only get one chance per day because they eat less. In other words, if a lizard makes a mistake, it has to remember how to correct it until the next day

Leal’s experiment “clearly demonstrates” that when faced with a situation the lizards had never experienced, most of them were able to devise a way to solve the problem. Their ability to “unlearn” a behavior, a skill that some mammalian species have difficulty in, is the mark of a cognitively advanced animal, said Jonathan Losos, a biologist at Harvard who was not involved in the study.

To see if the lizards could reverse this association, Leal next placed the worm under the other cap. At first, all the lizards bumped or bit the formerly lucrative blue cap. But after a few mistakes, two of the lizards figured out the trick. “We named these two Plato and Socrates,” Leal said.

It is very cool to see what scientists keep learning about animals.

Related: Insightful Problem Solving in an Asian ElephantBird Using Bread as Bait to Catch FishCrows Transferring Their Understanding to Novel ProblemDolphins Using Tools to Hunt

Scientific Inquiry Process Finds That Komodo Dragons Don’t have a Toxic Bite After All

This articles is another showing the scientific inquiry process at work. Scientists draw conclusions based on the data they have and experiments they do. Then scientists (sometimes the same people that did the original work) seek to confirm or refute the initial conclusions (based on new evidence or just repeating a similar experiment) and may seek to extend those conclusions.

Sometimes the scientists conclude the initial understanding was incorrect, such as with Komodo Dragon’s: Here Be Dragons: The Mythic Bite of the Komodo

for centuries Komodos have been feared by many, with tales of their deadly bite echoing through local cultures. It”™s even thought the monstrous lizards may have inspired the mythical beasts that share their name. Their villainous reputation only grew when these fearsome predators were discovered by Europeans in the early twentieth century. But of all the terrible tales told about these dragons, none has been so persistent and pervasive than that of their bite. The mouths of Komodos are said to be laden with deadly bacteria from the decaying corpses they feed on, microbes so disgustingly virulent that the smallest bite lethally infects prey. As the story goes, Komodos have turned oral bacteria into a venom.

It”™s a truly fascinating way for an animal to feed ”” well, truly fascinating in that it”™s not true at all.

Related: Video of Young Richard Feynman Talking About Scientific ThinkingNanoparticles With Scorpion Venom Slow Cancer SpreadBig Lizards in Johor BahruNigersaurus

Drugmakers Are Desperate to Know Why Placebos Are Getting More Effective

Fascinating article from Wired: Placebos Are Getting More Effective. Drugmakers Are Desperate to Know Why.

The fact that an increasing number of medications are unable to beat sugar pills has thrown the industry into crisis. The stakes could hardly be higher. In today’s economy, the fate of a long-established company can hang on the outcome of a handful of tests.

Potter discovered, however, that geographic location alone could determine whether a drug bested placebo or crossed the futility boundary. By the late ’90s, for example, the classic antianxiety drug diazepam (also known as Valium) was still beating placebo in France and Belgium. But when the drug was tested in the US, it was likely to fail. Conversely, Prozac performed better in America than it did in western Europe and South Africa. It was an unsettling prospect: FDA approval could hinge on where the company chose to conduct a trial.

In one study, Benedetti found that Alzheimer’s patients with impaired cognitive function get less pain relief from analgesic drugs than normal volunteers do. Using advanced methods of EEG analysis, he discovered that the connections between the patients’ prefrontal lobes and their opioid systems had been damaged. Healthy volunteers feel the benefit of medication plus a placebo boost. Patients who are unable to formulate ideas about the future because of cortical deficits, however, feel only the effect of the drug itself. The experiment suggests that because Alzheimer’s patients don’t get the benefits of anticipating the treatment, they require higher doses of painkillers to experience normal levels of relief.

Benedetti often uses the phrase “placebo response” instead of placebo effect. By definition, inert pills have no effect, but under the right conditions they can act as a catalyst for what he calls the body’s “endogenous health care system.” Like any other internal network, the placebo response has limits. It can ease the discomfort of chemotherapy, but it won’t stop the growth of tumors. It also works in reverse to produce the placebo’s evil twin, the nocebo effect. For example, men taking a commonly prescribed prostate drug who were informed that the medication may cause sexual dysfunction were twice as likely to become impotent.

Moreover, a pill’s shape, size, branding, and price all influence its effects on the body. Soothing blue capsules make more effective tranquilizers than angry red ones, except among Italian men, for whom the color blue is associated with their national soccer team””Forza Azzurri!

Medical research presents significant difficulties. The funding of the health care system also distorts behavior and pushes companies to focus on being able to justify selling drugs instead of focusing on finding effective solutions. Even without incentives distorting behavior, the challenges are difficult enough. Adding the distortions just makes it worse.

It is wonderful we have so many scientists accepting these challenges and spending their careers fighting the odds to help find us wonderful health breakthroughs.

Related: The Majority of Clinical Trials Don”™t Provide Meaningful EvidenceSystem for Approving New Medical Options Needs ImprovementMedical Study Integrity (or Lack Thereof)Discussing Medical Study Results

Loon – Balloon Enabled Internet

Project Loon, from Google:

The Internet is one of the most transformative technologies of our lifetimes. But for 2 out of every 3 people on earth, a fast, affordable Internet connection is still out of reach.

We believe that it might actually be possible to build a ring of balloons, flying around the globe on the stratospheric winds, that provides Internet access to the earth below. It”™s very early days, but we”™ve built a system that uses balloons, carried by the wind at altitudes twice as high as commercial planes, to beam Internet access to the ground at speeds similar to today”™s 3G networks or faster. As a result, we hope balloons could become an option for connecting rural, remote, and underserved areas, and for helping with communications after natural disasters.

Google testing out this system now in New Zealand. If they can get it to work they plan to use ballons to provide wireless internet access to hundreds of millions, or even billions, of people that don’t have access now. These ballons would float about 20 km above earth in the stratosphere (so well above where commercial airline traffic) and they are really working somewhat like to satellites.

Though ballons are much cheaper to put in place than satellites they also offer significant problems as they get blow around by wind (which is why they haven’t been used before and why Google is going to experiment to see if they can get it to work). The ballons will use solar power and be controlled by a mission control to move into different wind zones to position themselves.

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Introduction to Fractional Factorial Designed Experiments

Scientific inquiry is aided by sensible application of statistical tools. I grew up around the best minds in applied statistics. My father was an eminent applied statistican, and George Box (the person in the video) was often around our house (or we were at his). Together they wrote Statistics for Experimenters (along with Stu Hunter, not related to me) the bible for design of experiments (George holds up the 1st edition in the video).

The video may be a bit confusing without at least a basic idea of factorial designed experiments. These introductory videos, by Stu Hunter, on Using Design of Experiments to Improve Results may help get you up to speed.

This video looks at using fractional factorials to reduce the number of experiments needed when doing a multifactor experiment. I grew up understanding that the best way to experiment is by varying multiple factors at the same time. You learn much quicker than One Factor At a Time (OFAT), and you learn about interactions (which are mainly lost in OFAT). I am amazed to still hear scientists and engineers talk about OFAT as a sensible method or even as the required method, but I know many do think that way.

To capture the interactions a full factorial requires an ever larger number of experimental runs to be complete. Assessing 4 factors requires 16 runs, 6 would require 64 and 8 would require 256. This can be expensive and time consuming. Obviously one method is to reduce the number of factors to experiment with. That is done (by having those knowledgable about the process include only those factors worth the effort), but if you still have, for example, 8 very important factors using a fractional factorial design can be very helpful.

And as George Box says “What you will often find is that there will be redundant factors… and don’t forget about those redundant factors. Knowing that something doesn’t matter is almost as important as knowing what does.” If you learn a factor isn’t having an affect you may be able to save money. And you can eliminate varying that factor in future experiments.

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Webcast: Examining the Scientific Basis Around Exercise and Diet Claims

Tim Noakes is the Director of UCT/MRC Research Unit for Exercise Science and Sports Medicine, Department of Human Biology, Faculty of Health Science, University of Cape Town and Professor, Discovery Health Chair of Exercise and Sports Science, University of Cape Town.

Tim examines some questions on science and exercise and health in the webcast. He shows the problem with drinking too much during exercise and the correlation of hospital admissions correlated to the sport drinks marketing and changing of the official drinking guidelines. He also discusses the outdated ideas related to lactic acid and muscles.

He is currently studying the science of food and human health and is skeptical of low fat health claims: “No evidence that dietary fat is related to heath disease.” He is certainly more knowledgable than I but I would still be cautious of completely accepting that premise. It does seem to me there is lots of evidence that claims of causation between eating a high fat diet and heart disease were too strong (many other factors were critical – such as weight, exercise, genetics, unsaturated fat v. saturated fat…).

Tim Noaks: “50% of what we teach is wrong; the problem is we don’t know which 50% it is. Our job as educated people is to spend our lifetime trying to figure out which 50% is which. Until it is disproven accept that for which the evidence appears solid and logical and is free of covert or overt conflicts of interest, because unfortunately industry is driving what you believe in many many things. But don’t ever dismis lightly that for which there is credible evidence… and there is such clear evidence the diets we are eating are horrendous.”

As I have said before, scientific literacy is critical to allow us to make those judgements about what is credible evidence and what are outright lies, foolish claims or highly suspicious claims tainted by conflicts of interest.

Related: Can You Effectively Burn Calories by Drinking Cold Water?Static Stretching Decreases Muscle StrengthLack of Physical Activity Leads to 5.3 Million Early Deaths a YearScience Continues to Explore Causes of Weight GainStudy Finds Obesity as Teen as Deadly as Smoking

Europe Bans Certain Pesticides, USA Just Keeps Looking, Bees Keep Dying

For years the bee colony collapse disorder has been showing the difficulty of the scientific inquiry process. And that difficulty often becomes more difficult if interests with lots of money at stake want to block certain conclusions.

One-Third of U.S. Honeybee Colonies Died Last Winter, Threatening Food Supply

Multiple factors ”” pesticides, fungicides, parasites, viruses and malnutrition ”” are believed to cause the losses, which were officially announced today by a consortium of academic researchers, beekeepers and Department of Agriculture scientists.

“We”™re getting closer and closer to the point where we don”™t have enough bees in this country to meet pollination demands,” said entomologist Dennis vanEngelstorp of the University of Maryland, who led the survey documenting the declines.

Beekeepers lost 31 percent of their colonies in late 2012 and early 2013, roughly double what”™s considered acceptable attrition through natural causes. The losses are in keeping with rates documented since 2006, when beekeeper concerns prompted the first nationwide survey of honeybee health. Hopes raised by drop in rates of loss to 22 percent in 2011-2012 were wiped out by the new numbers.

Most losses reported in the latest survey, however, don”™t actually fit the CCD profile. And though CCD is largely undocumented in western Europe, honeybee losses there have also been dramatic. In fact, CCD seems to be declining, even as total losses mount. The honeybees are simply dying.

“Even if CCD went away, we”™d still have tremendous losses,” said entomologist Diana Cox-Foster at Pennsylvania State University. “CCD losses are like the straw that breaks the camel”™s back. The system has many other issues.”

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Homing Pigeons May Use Low Frequency Sound Maps To Locate Home

Mystery of Lost Homing Pigeons Finally Solved

Prior research had shown that birds hear incredibly low-frequency sound waves of about 0.1 Hertz, or a tenth of a cycle per second. These infrasound waves may emanate from in the ocean and create tiny disturbances in the atmosphere. Hagstrum began to think the birds used infrasound for navigation.

on the odd day when the birds reached home from Jersey Hill without problems, the infrasound traveled between the two locations. At the other locations where pigeons headed off in the wrong direction, he showed that wind currents channeled the infrasound waves in that direction.

The explanation may solve other mysteries about pigeons ”” for instance, why they circle around before heading off in one direction. Because the sound waves are so long, but the birds’ ear canals are tiny, they need to circle to reconstruct the wave and figure out which way they are oriented, he said.

More interesting scientific inquiry. It is very interesting to learn what scientists are learning about our world – even when the conclusions are still preliminary and may be adjusted or refuted.

Related: Pigeon Solves Box and Banana ProblemCool Research on CrowsBird Using Bait to FishMoth Jams Bat Sonar

How Corn Syrup Might Be Making Us Fat

How Corn Syrup Might Be Making Us Hungry”“and Fat by Katherine Harmon

…Glucose lowered the activity of the hypothalamus but fructose actually prompted a small spike to this area. As might be expected from these results, the glucose drink alone increased the feelings of fullness reported by volunteers, which indicates that they would be less likely to consume more calories after having something sweetened with glucose than something sweetened with more fructose.

Fructose and glucose look similar molecularly, but fructose is metabolized differently by the body and prompts the body to secrete less insulin than does glucose (insulin plays a role in telling the body to feel full and in dulling the reward the body gets from food). Fructose also fails to reduce the amount of circulating ghrelin (a hunger-signaling hormone) as much as glucose does. (Animal studies have shown that fructose can, indeed, cross the blood-brain barrier and be metabolized in the hypothalamus.) Previous studies have shown that this effect was pronounced in animal models…

Most of the science indicates calories consumed is by far the dominant factor in weight gain. Different foods with the same calories can affect how hungry you feel. Thus the biggest factor in reducing weight gain seems to be reducing calories and one way to help is to eat food that leaves you feeling full and avoid foods that don’t.

The science is not completely clear though on whether certain diets can have a significant affect above and beyond calorie levels. I am skeptical of such claims, however. There are concerns beyond calories for healthy eating – getting a well balanced diet is important.

Healthy physical activity is also important. Burning off calories with exercise allows more consumption without weight gain. And exercise is important for health not just to avoid gaining weight.

Related: Researchers Find High-Fructose Corn Syrup Results in More Weight GainDoes Drinking Diet Soda Result in Weight Gain?Waste from Gut Bacteria Helps Host Control WeightModeling Weight Loss Over the Long TermHow Caffeine Affects Your Body

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