Archive for the 'General Science' Category

Feb 24 2014

What’s in a Name?

Published by under General Science

Classification systems are important in science. They often reflect our fundamental understanding of nature, and are also important for efficient and unambiguous communication among scientists. But there is also an emotional aspect to the labels we attach to things.

Perhaps the most famous example of this from recent history is the “demoting” of Pluto from planet to dwarf planet in 2006. There was a great deal of hand wringing about this decision, which ultimate was based on a practical operational definition – a planet needs to be in orbit around the sun, be large enough to pull itself into a spherical shape, and have cleared out its orbital neighborhood. Pluto failed the third criterion, and so was reclassified a “dwarf planet.”

It is very telling that most news reports discussing the category change characterized it as “downgrading” or “demoting” Pluto. Clearly people felt that being a planet was more special or prestigious than being a dwarf planet. This is not unreasonable – planets are generally larger and have a more dominant presence in the solar system. There are currently 8 planets, and that number is now very unlikely to change. There are only 5 named dwarf planets, but that number can climb very high as new Kuiper belt objects are discovered and named.

Still, it is interesting that what should be a technical issue appealing to those who love the Dewey Decimal System became such an emotional controversy for the general public.

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Feb 18 2014

GM Potatoes and Disease Resistance

Published by under General Science

The issue of genetically modified food is an excellent one for skeptics – it is a complex question that mostly revolves around scientific data, popular beliefs are rife with myths, misconceptions, and ideology, there are active and well-funded campaigns of misinformation regarding GM, and it is a hugely important topic for society. The topic is too big to cover in one blog post, which is why I have been writing about it sporadically to cover different angles of this issue (see here, here, here, and here). I also was recently interviewed for Mother Jones, with the result in both article and podcast form. The comments after the article are especially revealing.

Much of the discussion around GMO involves the two most common GM traits, pesticide(Bt) production and herbicide resistance. While these traits can be very useful when used intelligently, the potential for GM technology is perhaps much greater in other realms, including disease resistance. Late blight alone, a disease that affects potatoes and tomatoes, is estimated to cost 3-5 billion dollars per year in the US, Europe, and developing countries, through the cost of fungicide use and crop loss.

A three year trial of a new GM potato variety has just concluded, demonstrating impressive resistance to late blight. The researchers took a gene (Rpi-vnt1.1) isolated from a wild relative of potato, Solanum venturii, and placed in into the potato variety known as Desiree. The results:

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Feb 13 2014

P-Hacking and Other Statistical Sins

Published by under General Science

I love learning new terms that precisely capture important concepts. A recent article in Nature magazine by Regina Nuzzo reviews all the current woes with statistical analysis in scientific papers. I have covered most of the topics here over the years, but the Nature article in an excellent review. It also taught be a new term – P-hacking, which is essentially working the data until you reach the goal of a P-value of 0.05. .

The Problem

In a word, the big problem with the way statistical analysis is often done today is the dreaded P-value. The P-value is just one way to look at scientific data. It first assumes a specific null-hypothesis (such as, there is no correlation between these two variables) and then asks, what is the probability that the data would be at least as extreme as it is if the null-hypothesis were true? A P-value of 0.05 (a typical threshold for being considered “significant”) indicates a 5% probability that the data is due to chance, rather than a real effect.

Except – that’s not actually true. That is how most people interpret the P-value, but that is not what it says. The reason is that P-values do not consider many other important variables, like prior probability, effect size, confidence intervals, and alternative hypotheses. For example, if we ask – what is the probability of a new fresh set of data replicating the results of a study with a P-value of 0.05, we get a very different answer. Nuzzo reports:
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Feb 04 2014

The GMO Controversy

Published by under General Science

The controversy surrounding genetically modified organisms (GMO) has intrigued me for some time, and recently I have been reading everything I can on the topic. It is an excellent topic for skeptics – it is mainstream (not a fringe topic), it has real importance for society, there are complex scientific and logical issues to sort through, and the topic is rife with misinformation and motivated reasoning.

I wrote recently about the fact that beliefs concerning GMO tend to be dominated by two opposing narratives: GMO critics despise corporate control and greed, and fear the unnatural, while GMO advocates see this technology as an example of the triumph of human ingenuity and science. I admit that with regard to this issue my bias is toward the latter narrative, however, I can understand caution regarding huge corporations (the tobacco industry comes to mind).

But, as a skeptic I have really tried to follow a critical thinking process and pull back from my initial gut reactions. Here, then, is my overview of the issues regarding GMO.

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Jan 30 2014

Nutritional Content of Produce

Published by under General Science

This is a frequent question I receive that I have yet to address – is the nutritional content of our produce diminishing over time? The claim that our produce is less nutritious is often used as a reason to justify routine vitamin supplementation, and various other dubious health claims, or recommendations to eat locally or eat organic.

The answer is a clear, “it depends” followed by, “it’s complicated.”

There are three levels to this question I want to address: is the nutritional content of produce decreasing over time; if so, what’s the cause; and what should we do about it?

The most often study I see cited is this 2004 study by Davis et al – they examined the nutrient content of 43 crops from 1950 to 1999. They found:

As a group, the 43 foods show apparent, statistically reliable declines (R < 1) for 6 nutrients (protein, Ca, P, Fe, riboflavin and ascorbic acid), but no statistically reliable changes for 7 other nutrients. Declines in the medians range from 6% for protein to 38% for riboflavin. When evaluated for individual foods and nutrients, R-values are usually not distinguishable from 1 with current data. Depending on whether we use low or high estimates of the 1950 SEs, respectively 33% or 20% of the apparent R-values differ reliably from 1. Significantly, about 28% of these R-values exceed 1.

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Dec 10 2013

Do Seed Companies Restrict Research?

Published by under General Science

Well, yes and no. Such questions are often complex. With some exceptions, we generally do not live in a world with cartoon heroes and villains. Rather we live with people who have conflicting perspectives and priorities. Yet we have a universal human desire for simplicity and the sense of control, so we often reduce the horrific complexity of the world to white hats and black hats.

This tendency makes my job difficult, although also useful – specifically whenever I attempt to wrap my head around a controversial issue, such as GMO crops and agritech, I have to wade through tons of ideological propaganda in order to dig down to some clear information.

In the world of GMO, anti-GMO activists have generally made Monsanto (and big agritech generally) into the cartoon villain. Many of the claims made by critics against Monsanto, however, turn out to be gross distortions. They don’t sue companies for accidental contamination, only deliberate piracy, for example. Pointing this out does not make one a Monsanto shill.

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Dec 03 2013

Seralini GMO Study Retracted

Published by under General Science

Elsevier has announced that they are retracting the infamous Seralini study which claimed to show that GMO corn causes cancer in laboratory rats. This is to the anti-GMO world what the retraction of the infamous Wakefield Lancet paper was to the anti-vaccine world. At least this retraction only took one year.

The Seralini paper was published in November 2012 in Food and Chemical Toxicology. It was immediately embraced by anti-GMO activists, and continues to be often cited as evidence that GMO foods are unhealthy. It was also immediately skewered by skeptics and more objective scientists as a fatally flawed study.

The study looked at male and female rats of the Sprague-Dawley strain of rat – a strain with a known high baseline incidence of tumors. These rats were fed regular corn mixed with various percentages of GMO corn: 0 (the control groups), 11, 22, and 33%. Another group was fed GMO corn plus fed roundup in their water, and a third was given just roundup. The authors concluded:

The results of the study presented here clearly demonstrate that lower levels of complete agricultural glyphosate herbicide formulations, at concentrations well below officially set safety limits, induce severe hormone-dependent mammary, hepatic and kidney disturbances. Similarly, disruption of biosynthetic pathways that may result from overexpression of the EPSPS transgene in the GM NK603 maize can give rise to comparable pathologies that may be linked to abnormal or unbalanced phenolic acids metabolites, or related compounds. Other mutagenic and metabolic effects of the edible GMO cannot be excluded.

Sounds pretty scary. Now let’s look at the multiple criticisms:

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Nov 05 2013

Is Science Broken?

Skeptics are often in a tricky position. We simultaneously are cheerleaders for science, promoting science education, scientific literacy, and the power of science as the best method for understanding the universe.

At the same time the skeptical approach requires that we explore and discuss all the various flaws, errors, and weaknesses in the institutions and process of science. Science in theory is fantastic, but it is practiced by flawed people with all their cognitive biases and perverse incentives (much like democracy or capitalism).

I think the best approach to this apparent contradiction is transparency, honesty, to be as constructive as possible, and avoid sliding into nihilism. It’s easy to focus on all the negatives about any institution, and conclude that it’s hopelessly broken. Some institutions are broken and unfixable, so it’s not an inherently unreasonable position. We should strive for a balanced and fair assessment (just like Fox news).

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Oct 24 2013

Golden Rice – A Touchstone

Published by under General Science

Psychologists have documented a human tendency to pick a belief and then defend it at all costs. We all do this to varying degrees, and the more emotionally invested we are in a belief, the more extreme we are in our defense.

In fact, a skeptical world-view is largely about avoiding this mental trap by tentatively accepting or rejecting claims based upon available evidence, and modifying our beliefs as new arguments and evidence come to light. Skepticism values the process over any individual belief.

Since reality is complicated, if one follows an objective process it will often be true that any controversial issue will have valid points on both or all sides. This is not always true (creationists are completely wrong in their denial of evolution, making this a false controversy), but it often is. For this reason, one of my skeptical “red flags” to alert me to the probability that someone is an ideologue rather than an honest broker of information and analysis is whether or not their opinions point entirely in one direction on a genuinely controversial topic.

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Oct 22 2013

Free Energy and the Casimir Effect

Free energy is to physics what creationism is to evolutionary biology. Both offer a teaching moment when you try to explain why proponents are so horribly wrong.

Free energy proponents have been abusing the laws of thermodynamics (come to think of it, so have creationists), and more recently quantum effects a la zero-point-energy. Now they are distorting a new principle of physics to justify their claims – the Casimir effect. Apparently this was a hot topic at the Breakthrough Energy Conference earlier this month.

Before I get into the specifics, I do want to address the general conspiratorial tones of the free-energy movement. I wonder if anyone influential in the free-energy subculture realizes that their conspiracy-mongering over free energy is perhaps the greatest barrier to their being taken seriously. There is also the fact that they get the science wrong, but if they think they are doing cutting edge science (rather than crank science), then convince us with science and ditch the conspiracy nonsense.

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