Archive for the ‘Science’ Category

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Reminder: correlation is not causality

February 27, 2014

A research study by Martin Hoffman and Eswar Krishnan concludes, “Compared with the general population, ultramarathon runners appear healthier and report fewer missed work or school days due to illness or injury.”

The March 2014 issue of my local running magazine summarizes this study as follows: “Keep logging those miles, ultrarunners! Your body will thank you for it in the long run.”

See the difference?

The study itself simply notes that ultramarathoners are, by most measures, healthier than normal. The running magazine leaps (or perhaps sprints) to the conclusion that these runners’ training is what keeps them so healthy. But we can’t rule out the opposite: maybe these people’s good health is what allows them to run so much; maybe their impressive mileage tallies are an effect, rather than a cause, of their good health. Or maybe the ultrarunners surveyed differ from the general population in other ways, unrelated to running, that account for their superior health.

Numerous studies have provided strong evidence that running promotes good health, but this study isn’t one of them.

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The wisdom of crowds?

February 9, 2014

From the Seattle Times: 700,000 at Seahawks parade? Doesn’t add up, experts say.

It’s a lighthearted article, but it touches on the methodology of crowd estimation and uses some basic math to show that the number of parade attendees was less than the official estimate of 700,000.

How did readers respond to this dollop of evidence-based analysis? There were several themes, as exemplified by the following online quotes. (My interpretations are in brackets.)

(1) Semians: “Quit trying to overanalyze everything and simply live in the moment.” [We shouldn’t care about this information.]

(2) picklesp: “It sure as heck felt like 700,000 from ground level.” [This information doesn’t match my personal experience.]

(3) Peterkirk: “These guys are just trying to rain on our parade for whatever reason, and well tough, it didn’t rain on the parade on Wednesday and your diatribe (reporting?) isn’t going to make it rain today.” [This information doesn’t make me feel good, so I’ll ignore it.]

(4) Mr. Mytzlplk: “The ‘experts’ vary by 200,000 in their ‘real analysis.’ The fact that they’re so far off from each other tells me that they don’t know what they’re doing.” [Experts disagree about the details, so their analyses are worthless.]

(5) picklesp: “Experts get paid to pontificate.” [Experts have their own biases and agendas — which is true.]

(6) gloryhound: “I’m also skeptical of these two ‘experts” qualifications.” [The “experts” aren’t really experts.]

The above excerpts are from some of readers’ HIGHEST-rated comments. Here are two of the LOWEST-rated ones:

[from dawgsage:]

Actually 2.5 sq. ft /person is a square of almost 19 inches per side. Measuring the width of my body without a coat shows approximately 19 inches shoulder to shoulder, with a coat let’s add an inch making it 20 inches. A 2.5 square foot rectangle, with one side 20 inches would then require the other side to be 16.2 inches, from front to back. Conservatively, my measurement is 10 inches front to back. This means there would be 6.2 inches forward from my front to the back of the body of the person in front, and 6.2 inches in the back of me to the body of the next person, while laterally I am shoulder to shoulder to the adjacent people. So no I do not think it is not like standing in line, you really can’t get more crowded than that unless you were in an Iraqi prison under Saddam. So I believe the basis of the low estimates are credible.

[from CO Dawg:]

Rather than just say “well I don’t believe you!” to the experts, just do this simple experiment: put on a winter jacket (remember, it was cold that day) and stand against the wall with your arms against your side, then have someone mark the wall with chalk at your elbows. Measure that width. Then turn sideways and mark again the two widest points (belly and bottom for me, your points may vary). Measure that width.

Now, grab a calculator and multiply your personal width by personal depth. That is the square footage of space you occupy if you were standing in a crowd elbow to elbow belly to back and back to belly, like at a rock concert, and represents a good indication of the maximum crowd density at the parade.

When i did this with a sweatshirt on i came up with 2.1 feet wide and 1.25 feet deep, for 2.65 square feet, a little above the minimum cited. However, if i put on a winter jacket it adds an inch to all four sides so the measurements jump up to 2.25 by 1.42 feet, or 3.2 square feet. Adding just one more inch to each measurement increases my footprint to 3.8 square feet, and adding 3 inches increases it to 4.7 square feet. I wont presume anything about your personal space requirements, but when someone is 3 inches away from me, i still feel pretty crowded. I can thus conclude that the experts have presented a reasonable range for each person’s footprint

I have no means to measure the overall footprint of the crowd along the route, but had they asked me to do crowd estimates i would have employed the same methodology they use (measurements from an aerial photo), and probably would have come up with numbers similar to their’s. I would have multiplied the overall crowd foot print by an average space per person of 3.5 square feet (generally splitting the difference between my numbers), added 15% to account for people standing outside the footprint or watching from offices, and likely come up with a forecast of somewhere between 350-400k. Which is still a heck of a crowd.

And for those of you dismissing my opinion because of my location, we’re not immune to overly enthusiastic crowd estimates in Denver, too. I was at a presidential campaign speech in Civic Park that supposedly was attended by 100,000 people, and didnt even need to do the math to know that estimate was comically high.

So, to summarize: dismissal of the information for any old reason? Thumbs up! Attempts to check the math and verify its reasonableness? Thumbs down!

While no legislation hinges on this particular estimate, I’m troubled by the attitudes displayed here, i.e., limited interest in the nuances of data and relevant expertise. I submit that, in other arenas, this limited interest has led to the popularity of positions like “evolution is just a theory,” “vaccines cause autism,” “global warming is a hoax,” and “animal testing is unnecessary.”

In response, we scientists can grumpily bemoan an incurious public … or we can recognize that facts alone don’t always move the needle of public opinion, and we can get better at appealing to people’s emotions and imaginations.

comments from a data denialist

do the math!

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Calculations of bees’ impact on strawberries’ market value

January 16, 2014

In the course I’m currently teaching, we’ve been reading the paper Bee pollination improves crop quality, shelf life and commercial value by Bjorn K. Klatt et al.

As explained nicely by Erik Stokstad, the paper documents how strawberries benefit from pollination by bees, as opposed to pollination by wind or self-fertilization. It turns out that, on average, bee-pollinated strawberries are larger than others and also have fewer odd shapes, better color, and superior firmness. This detailed look at strawberry quality is a useful extension of past studies showing that insect pollination often boosts crop quantity (i.e., yield).

In making their case for the agricultural importance of bees, Klatt et al. say that bee pollination accounts for at least $1.44 billion of the value of the $2.90 billion strawberry market in the European Union (EU). While I accept the take-home message that bees add a lot of value, I sure wish the authors had explained their calculations better.

The $1.44 billion estimate is the sum of two factors: $1.12 billion in market value of the fresh berries, and another $0.32 billion corresponding to improved shelf life. Let’s consider each of these in turn.

The figure of $1.12 billion is introduced in this section of the Results:

Bee pollination resulted in strawberry fruits with the highest commercial value (figure 1a). On average, bee pollination increased the commercial value per fruit by 38.6% compared with wind pollination and by 54.3% compared with self-pollination. Fruits resulting from wind pollination had a 25.5% higher market value than self-pollinated fruits. Pollination treatments were stronger than differences between varieties and thus had a main effect across all varieties (see table 2 for AICc and likelihood values). Our results suggest that altogether, bee pollination contributed 1.12 billion US$ to a total of 2.90 billion US$ made with commercial selling of 1.5 million tonnes of strawberries in the EU in 2009 [1]—but so far without consideration of the monetary value provided by enhanced shelf life (see below).

Figure 1 indicates that the mean value of 1000 wind-pollinated berries was ~$13.80 and the mean value of 1000 bee-pollinated berries was ~$22.40. The value of the wind-pollinated berries thus represents a ~38.6% DECREASE in value relative to the bee-pollinated berries; alternatively, the value of the bee-pollinated berries is a 62.9% INCREASE over the value of the wind-pollinated ones. A 62.9% increase takes us from $1.78 billion (the hypothetical value of strawberries only pollinated by wind) up to $2.9 billion, giving us the reported $1.12 billion boost from bees. The authors’ mention of a 38.6% increase when they meant a 38.6% decrease is not exactly a big deal, but initially made their math baffling to me and my students.

Perhaps more significantly, the reported market values reflect the classification of strawberries into commercial grades by the first author. Ideally, the first author would have rated the berries while “blinded,” i.e., without knowing which ones came from which treatments (bees, wind, or self). The paper doesn’t mention blinding, so I fear that there was the potential for a pro-bee bias.

Now for the $0.32 billion due to improved shelf life:

Bee pollination strongly impacted the shelf life of strawberries by improving their firmness (figure 2a). The firmness values of each treatment and variety were related to shelf life, measured as the number of days until 50% of fruits had been lost owing to surface and fungal decay (see the electronic supplementary material, S3). Higher firmness resulting from bee pollination potentially elongated the shelf life of strawberry fruits by about 12 h compared with wind pollination, and by more than 26 h compared with self-pollination. After 4 days in storage, only 29.4% of the wind-pollinated fruits and none self-pollinated fruit were still marketable, whereas, at the same time, 40.4% of the bee-pollinated fruits remained in a marketable condition. Thus, bee pollination accounted for a decrease of at least 11.0% in fruit losses during storage. These findings suggest that the value for bee pollination calculated in section 3a(i) has to be increased to accommodate this impact on the shelf life of strawberries. Hence, pollination benefits on the shelf life of strawberries potentially added another 0.32 billion US$ to the commercial value of strawberry pollination.

Here it’s clear that the authors got $0.32 billion by multiplying 11% by $2.9 billion. What’s less clear is the meaning of “storage” (did the unspecified storage conditions simulate those typically used by strawberry farmers/distributors/vendors?) and the reason(s) why a duration of 4 days was used in this calculation (is this a typical time between harvesting and consumers’ purchases?).

Such details aside, here’s a more general question relevant to both components of the $1.44 billion estimate. To what extent are commercial strawberries pollinated by bees in the wild?

The calculations assumes that the study site — a field in Germany — is representative of most or all commercial strawberry farms in Europe. The study site was intentionally set up near well-established bee hives and nests; are most or all European strawberry farms situated similarly? Perhaps the answer is obvious to people with relevant expertise, but the paper doesn’t say. It’s worth noting that if only half of commercial strawberry fields enjoy bee pollination, the estimates of bees’ economic impact would need to be cut in half.

Considering that the paper trumpets a billion-dollar claim in its abstract, more information on the calculations underlying that claim would have been appropriate. At least that’s how I see it — comments from real ecologists (Jeremy?), as well as others, are welcome!

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Civil discourse

December 30, 2013

A recent, typically excellent post at Dynamic Ecology addressed the question of “How do you critique the published literature without looking like a jerk?”

While I like Brian and Jeremy’s suggestions, they don’t capture the extent to which perceptions of jerkiness depend on very specific choices in wording, rhetorical structure, etc. I want to emphasize here that small changes can make a big difference in how you are perceived.

Brian and Jeremy did provide the following language/writing tips (paraphrased by me):

1. Don’t make ad hominem attacks.

2. When possible, identify possible solutions to the problems you’ve identified.

3. Don’t heap too much scorn upon one individual paper or scientist if the problem is common to multiple sources.

4. Focus on facts rather than opinions.

To these, I add the following additional pointers for avoiding the label of “jerk.” (Some were taken from A guide for new referees in theoretical computer science by Ian Parberry, which I consider relevant because standards for pre- and post-publication review should be similar.)

5. Define the viewpoint from which you conducted your evaluation. What do you know about and care about? What do you NOT know about or care about? Confess possible biases.

6. Acknowledge the positive aspects of what was done.

7. Be as specific as possible in your criticisms. Statements like “the data in Figure 5 were misinterpreted” are both more justifiable and less catty than “this study adds nothing to the field.” If you are questioning one particular paper, consider your target to be the paper rather than the scientist(s) who wrote it. “What’s wrong with this paper?” is usually a reasonable question to ask, but “what’s wrong with these scientists?” often registers on the jerk-o-meter. Also be specific in providing references. Claiming support from unspecified sources is sloppy and rude, but even incomplete citations such as “Johnson 2012” may be more ambiguous than helpful.

8. Give the most space to the most important problems. Don’t dwell on minor flaws. Harping on spelling errors makes you seem like a jerk.

9. Avoid unnecessarily dramatic language. In a manuscript review, I once identified four problems as “critical flaws.” A colleague noted that my concerns would be just as clear if I used a softer phrase such as “main flaws.”

In compiling this advice, I became curious as to how well I follow it, so I rated my past critiques of Lore of Running by Timothy Noakes, Born to Run (part 1; part 2) by Christopher McDougall, “Metabolic Factors Limiting Performance in Marathon Runners” by Benjamin Rapoport, Wheat Belly by William Davis, and “Misconceptions Are So Yesterday!” by April Maskiewicz and Jennifer Lineback. Results are below.

self-critique of my critiques

By my own reckoning, I’m not a complete hypocrite, but there certainly is room for improvement.

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Dance of the Biomek FX

December 24, 2013

My lab works in part on high-throughput screening (HTS) of libraries of small molecules. Here is my low-budget tribute to the high-tech machines that facilitate this work.

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“Wheat Belly” by William Davis, MD

December 11, 2013

This post is for my dad, who bought me Wheat Belly so that I could read it and tell him what I thought of it.

WHAT’S GOOD ABOUT THIS BOOK?

1. Just as Born to Run questioned (in its entertaining but overblown way) whether we should trust shoe companies to tell us what our footwear needs are, this book advocates a healthy skepticism regarding agribusiness-influenced nutritional guidelines.

2. The book may help some people understand celiac disease and gluten-free diets. I hadn’t previously read much about gluten and was pleased to discover details about the gliadin and glutenin proteins which comprise it.

3. Likewise, I was pleased to read about wheat’s history of genetic and morphological changes, which author William Davis discusses in detail. Even if the health implications of these changes are debatable, it’s interesting to contrast the ancient einkorn wheat (14 chromosomes) and emmer wheat (28 chromosomes) with modern dwarf Triticum species (42 chromosomes).

4. There may be some truth to at least one of the author’s provocative assertions, i.e., that the breeding of wheat for more optimal baking properties may have contributed to the rise in celiac disease (van den Broeck et al. 2010).

WHAT’S BAD ABOUT THIS BOOK?

1. The central message — that wheat is evil — is irrationally and offensively simple-minded. There are a few surprising nuances in the book, such as the admission that the wheat hybridization work of Norman Borlaug helped solve the problem of world hunger. Yet Davis continually returns to his “wheat is evil” rhetoric without apparent hesitation or irony.

2. The language is often hyperdramatic at the expense of clarity and accuracy. For example, Joe Schwarcz (2013) bemoans the way wheat is blamed for osteoporosis because of its production of (tiny amounts of) sulfuric acid. “Davis panics readers with totally irrelevant statements about sulphuric acid causing burns if spilled on skin,” Schwarcz says. “Get it in your eyes and you will go blind. True, but what does that have to do with traces formed in the blood from cysteine?” Melissa McEwan (2011) accuses Davis of “anti-technology scare-mongering, preying on the agricultural ignorance of the average consumer.” She notes, “Telling me … that wheat has ‘undergone extensive agricultural genetics-engineered changes’ is hardly terrifying to me, as this describes almost all seeds on the market today.”

3. Davis writes with smug confidence about the devastating effects of wheat on human health, yet the scientific evidence for many of his claims is weak, misrepresented, or nonexistent. Pete Bronski (2012) dissects three examples of Davis’s misuse of the biomedical literature; additional examples are below.

WHAT ARE THE CENTRAL CLAIMS MADE BY THIS BOOK, AND HOW REASONABLE ARE THEY?

Wheat Belly makes numerous claims. Below are five that I personally consider important, along with some comments about their validity.

1. Wheat is unique in elevating blood sugar to unhealthy levels.

There are two issues here.

First, wheat products do not have an exceptional, uniformly high Glycemic Index (GI), the standard measure of glucose release into the blood. As McEwan writes, “If there is something special about wheat spiking blood sugar, why do some wretched coarser breads measure in the low thirties and forties (lower than many fruits and sweet potatoes), and so many gluten free breads measure so much higher? Davis mentions that the latter is often made from extremely refined processed rice, tapioca, and corn. And thus we have the answer — highly digestible carbohydrates, no matter what their provenance, are high glycemic.”

A second issue is that the GI of any carbo-rich food, including wheat, can be reduced by eating it with protein and fat. Davis describes a personal experiment in which he ingested four ounces of organic whole-wheat bread, and, sure enough, his blood glucose rose a lot. But who (other than my Uncle Scott) eats large quantities of low-fat bread, all by itself, in one sitting? It’s a pretty artificial situation, and one that is easily remedied by the addition of some peanut butter or meat or whatever.

2. Wheat is addictive.

There are multiple reasons to question this claim, which is based on the idea that wheat protein gets broken into peptides known as exorphins, which act on the brain as opioids.

First, exorphins released from wheat cannot exit the gastrointestinal tract without being further digested into non-drug-like molecules. Fred Brouns et al. (2013) explain: “Gliadorphin consists of seven amino acids (Tyr-Pro-Gln-Pro-Gln-Pro-Phe) and, as such, cannot be absorbed by the intestine. This is because the intestine peptide transporter PepT1 transports only di- and tripeptides (Gilbert et al., 2008) and transporters for larger peptides have not been identified. Gliadorphin is therefore not present in intact form in the human circulatory system and cannot reach and have an effect on the cells of the central nervous system.”

Second, as covered by Julie Jones (2012), proteins from milk and other sources yield exorphins too, so wheat is not unique in this respect (Jones 2012).

Third, Jones (2012) also points out that gluten stimulates the release of the hormones cholecystokinin and glucagon-like peptide 1, which contribute to a feeling of fullness or satiety. This is contrary to the vicious cycle proposed by Davis, in which ingesting some wheat leads to a craving for more.

3. Wheat causes obesity. Eliminating it leads to weight loss.

Michael Casper (2012) summarizes the evidence as follows: “We have to take Davis’s word that his anti-wheat diet works, because most of the cases of weight loss and recovery from illness are from his own practice.”

Jones (2012) and Brouns et al. (2013) also cite a paper from the Framingham Heart Study (E.A. Molenaar et al., Diabetes Care 2009) showing a negative correlation between whole-wheat consumption and risk of obesity. While this finding of a correlation is not a smoking gun, it is the opposite of what Davis would predict.

If wheat itself was a cause of weight gain, replacing wheat with an equivalent number of non-wheat calories would lead to weight loss. No controlled peer-reviewed study along these lines is cited by Davis; perhaps he should use some of his book royalties to finance one.

4. Wheat contributes to many other diseases besides diabetes and obesity (autism, schizophrenia, etc.).

Davis devotes full chapters to wheat’s effects on the body’s pH (Chapter 8), advanced glycation end-products (AGEs) (Chapter 9), heart disease (Chapter 10), the brain (Chapter 11), and skin (Chapter 12). There is no concise way to address all of these, but, as examples, Chris Masterjohn (2011) pokes many holes in Davis’s stories about pH and AGEs, and Jones (2012) notes a lack of strong links between wheat and autism, ADHD, or schizophrenia.

Casper (2012) adds, “Davis’s claims about wheat and schizophrenia are based on very old papers -– nothing within the past 25 years -— and this is another example of an abuse of definitions in order to further an anti-wheat agenda.”

5. Modern wheat is the product of science crossbreeding experiments. Its safety has never been tested.

Davis does not define the safety tests that he thinks are absent but needed. Apparently he considers observational studies inadequate and would prefer clinical trials (i.e., much stronger evidence than he uses to support his wheat-is-evil hypothesis). In any case, he misleads us with his implication that crossbreeding leads to radical, unpredictable, likely-to-be-dangerous changes.

For example, Davis says, “Analyses of proteins expressed by a wheat hybrid compared to its two parent strains have demonstrated that, while 95 percent of the proteins expressed in the offspring are the same, 5 percent are unique, found in neither parent.” However, his reference (Xiao Song et al., Theoretical and Applied Genetics 2009) simply reports that parents and offspring differ in the amounts of some of the proteins they produced, not changes in which proteins were present. Davis: “In one hybridization experiment, fourteen new gluten proteins were identified in the offspring.” Reality: the 14 proteins were slightly mutated versions of parental proteins, not completely new ones, and the study cited (Xin Gao et al., Planta 2010) involved somatic cell hybridization, a complicated laboratory technique not typically used by wheat breeders (NWIC 2012). Davis: “The genetic modifications created by hybridization for the wheat plants themselves were essentially fatal, since the thousands of new wheat breeds were helpless when left to grow in the wild.” Reality: yes, a plant that once grew in the wild has been adapted for domestic food production. The varieties now optimized for food production are no longer optimized for surviving in the wild, and thus do not thrive outside farms. This is neither surprising nor worrisome nor unique to wheat.

Finally, while other grains have also gone extensive optimization, Davis does not comment once upon the changes to the genomes of corn, rice, etc. In Casper’s (2012) words,

Davis argues in the second chapter of Wheat Belly that wheat has been genetically modified in the past few decades beyond all recognition, and this modification is somehow the source of the danger that wheat poses to us. It is a cunning argument, because it is certainly the case that genetic modification has taken place, and it is difficult to disprove that such changes have been harmless. But why stop at wheat? Corn, for instance, has certainly been subjected to dramatic genetic modification, as discussed in a 2003 article from the journal PLOS Biology. Why single out the genetic modifications of one crop, and not consider the implications of all the others? Or is Corn Belly intended as a sequel?

CONCLUSION

Wheat Belly offers a simple, seemingly research-based solution to a myriad of ailments. It has proven tremendously popular, especially among low-carb advocates. However, its narrative is based on “cherry-picked data, inflammatory hyperbole, misused science, irrelevant references and opinion masquerading as fact” (Schwarcz 2013). As such, it is hardly the slam-dunk case against wheat that it purports to be.

REFERENCES

Pete Bronski. Wheat Belly, busted. No Gluten, No Problem (blog), March 20, 2012.

Fred J.P.H. Brouns, Vincent J. van Buul, and Peter R. Shewry. Does wheat make us fat and sick? Journal of Cereal Science 58: 209-215, 2013.

Michael Casper. Wheat Belly, a book review. Caspersfarm’s Blog, September 13, 2012.

Julie Jones. Wheat Belly — an analysis of selected statements and basic theses from the book. Cereal Foods World 57(4): 177-189, 2012.

Chris Masterjohn. Wheat Belly — the toll of hubris on human health. The Daily Lipid (blog), October 12, 2011.

Melissa McEwan. Wheat Belly. Hunt Gather Love (blog), October 8, 2011.

National Wheat Improvement Committee (NWIC). Wheat improvement: the truth unveiled. USDA.gov (website), 2012.

Joe Schwarcz. Wheat Belly gives me a belly ache. McGill Office for Science and Society (blog), June 29, 2013.

Hetty C. van den Broeck et al. Presence of celiac disease epitopes in modern and old hexaploid wheat varieties: wheat breeding may have contributed to increased prevalence of celiac disease. Theoretical and Applied Genetics 121(8): 1527-1539, 2010.

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Making primary literature accessible to students (continued)

October 29, 2013

title slide

Here’s a semi-follow-up to the post Strategies for reading the primary literature.

Last Friday I discussed this topic with colleagues in the wonderful Biology Education Research Group (BERG), which meets weekly at the University of Washington. My starting points were the “CREATE” papers by Sally Hoskins et al. and the “Figure Facts” paper by Jennifer Round and A. Malcolm Campbell.

After briefly reviewing these papers, I asked attendees to brainstorm about how they might use primary literature in courses aimed at five distinct audiences: 10th-grade biology students, undergraduate nonmajors, undergrads in a large introductory biology course, senior biology majors, and graduate students.

The photos below (click on them for larger versions) give some record of the interesting and varied ideas that were put forth.

Thanks, BERG, for a stimulating session!

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seniors_c

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Misconceptions about misconceptions?

October 28, 2013

In checking my Google Scholar profile the other day, I was happy to find that a recent paper in CBE Life Sciences Education cited my 2012 review article on the use of music in science education. I was less happy to discover that my paper was cited as an example of bad pedagogy.

April Cordero Maskiewicz and Jennifer Evarts Lineback summarize their own paper as follows:

The goal of this paper is to inform the growing BER [Biology Education Research] community about the discussion within the learning sciences community surrounding misconceptions and to describe how the learning sciences community’s thinking about students’ conceptions has evolved over the past decade. We close by arguing that one’s views on how people learn will necessarily inform pedagogy. If we view students’ incorrect ideas as resources for refinement, rather than obstacles requiring replacement, then this model of student thinking may lead to more effective pedagogical strategies in the classroom.

I find this position interesting and sensible. I agree, of course, that how we teach should be based on research on how people learn. More specifically, I’m sympathetic to the viewpoint that (in the authors’ words) “Learning … is not the replacement of one concept or idea with another”; rather, “students learn by transforming and refining their prior knowledge into more sophisticated forms.”

The article provides two useful examples of how instructors can build upon students’ naive views of evolution, rather than simply rejecting them as wrong. So far so good.

Then comes the section “The use of the term misconceptions in current BER [Biology Education Research] Literature,” in which Maskiewicz & Lineback assert that many instructors have been slow to adopt this transform-and-refine-prior-knowledge view of learning. It’s a significant point because if everyone already holds this view and teaches according to it, there’s not much to discuss. Accordingly, Maskiewicz & Lineback searched the past three years of CBE Life Sciences Education for problematic as well as enlightened uses of the word “misconception.” Here’s what they found:

In some of these articles, the authors seemed to equate misconception with the more traditionally accepted definition of a deeply held conception that is contrary to scientific dogma (Baumler et al., 2012; Cox-Paulson et al., 2012; Crowther, 2012). Others, in contrast, seemed to use the term to reflect an ad hoc mistake or error in student understanding, one that exists prior to or emerges through instruction but, in either case, is not robust, nor does it interfere with learning (Jenkinson and McGill, 2011; Klisch et al., 2012). The authors who considered misconceptions to be “deeply rooted” spoke of instructional strategies designed to specifically elicit, confront, and replace students’ incorrect conceptions (i.e., Crowther, 2012). In contrast, authors for whom misconceptions were more tentatively held and/or emergent, suggested that students’ incorrect ideas can be amended through tailored instruction grounded in those ideas (i.e., Klisch et al., 2012). This latter perspective on learning is consistent with approaches supported by recent research in the learning sciences community (Carpenter et al., 1989; Ruiz-Primo and Furtak, 2007; Pierson, 2008).

Not only am I being dissed, but Baumler et al. (2012) and Cox-Paulson et al. (2012) are too! So, do we deserve it? Let’s look at the use of the term “misconception” in each of the articles cited.

From Baumler et al. (2012):

Questions of conservation lend themselves well to a “teachable moment” regarding the choice of nucleotide versus protein BLAST. In one group of 28 students, students were asked to provide a written response justifying their choice of using BLASTP or BLASTN. Twelve of the 14 pairs of students provided answers that were complete and exhibited clear comprehension of relevant concepts, including third position wobble. One pair gave an answer that was adequate, although not thorough, while the last pair’s response invoked introns, an informative answer, in that it revealed a misconception grounded in a basic understanding of the Central Dogma, concerning the absence of splicing in bacteria.

From Cox-Paulson et al. (2012):

Student misconceptions about DNA replication and PCR have been well documented by others (Phillips et al., 2008; Robertson and Phillips, 2008), and this exercise provided an opportunity to increase understanding of these topics.

From Crowther (2012):

My own opinion is that songs can be particularly useful for countering two types of student problems: conceptual misunderstandings and failures to grasp hierarchical layers of information. Prewritten songs may explain concepts in new ways that clash with students’ mental models and force revision of those models, or may organize information for improved clarity (e.g., general principles in the chorus, key details in the verses, other details omitted). Songwriting assignments could have similar benefits by forcing students to do the work of concisely restating concepts in their own words and organizing the information in a musical format. As an example of using music to counter misconceptions, I once team-taught a “biology for engineers” course in which my coinstructor complained that many students failed to internalize the difference between genotype and phenotype. I wrote and performed a song to drive home this distinction, the chorus being, “Genotype, ooh… It’s the genes you possess—nothing more, nothing less! Versus phenotype, ooh… Your appearance and health and reproductive success!”

Note that these were the sole instances of the word “misconception” in each article. Do they illustrate what Maskiewicz & Lineback say they illustrate? I don’t think so.

The first claim made by Maskiewicz & Lineback is that some papers (e.g., the three cited) consider misconceptions to be “deeply held” or “deeply rooted.” None of the papers cited uses either phrase, nor do I see any discussion of misconceptions’ deepness in the passages above.

The second claim is, “The authors who considered misconceptions to be ‘deeply rooted’ spoke of instructional strategies designed to specifically elicit, confront, and replace students’ incorrect conceptions (i.e., Crowther, 2012).” The “deeply rooted” business aside, is Crowther indeed advocating wholesale swapping of students’ incorrect conceptions for correct ones? No. “Prewritten songs may explain concepts in new ways that clash with students’ mental models and force revision of those models.” That is, the models should be revised — NOT discarded! As far as I can tell, this is consistent with Maskiewicz & Lineback’s recommendations up to this point. (Later in the article, they propose abandoning the term “misconceptions” altogether.)

I suspect that Maskiewicz & Lineback found the above wording (with its talk of clashing, forcing, and failures) overly adversarial, and I concede that the tone is not ideal. But the passage is basically agreeing with them!

Not being an expert on addressing misconceptions (or whatever they should be called), I was glad to get Maskiewicz & Lineback’s perspective. But if their best example of the problem is a paragraph that neglects to mention the positive aspects of one particular misconception, perhaps the problem is not as big as they are making it out to be.

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An interview with Seattle playwright Paul Mullin

October 7, 2013

The Northwest Association for Biomedical Research (NWABR.org) puts on many great events, from the Student Bio Expo to Community Conversations. In their newest program, Science On Stage, they are currently hosting staged readings of The Sequence, a play by Paul Mullin. I attended the first performance last Saturday and loved its mix of scientific and human drama. Unable to stay for the post-play discussion, I instead emailed Paul some questions. His responses are posted here with his permission.

logo for The Sequence Paul Mullin

GC: A lot of your work addresses the intersection of art and science. Have you always been interested in science? If not, when did science come alive for you, and why?

PM: I have always been interested in science. My father, who died before I was born, was working on his PhD in physics and was apparently a freak for math and the periodic table. My mom took her degree in biology and worked in a lab before getting married and working in the home full time.

I have always loved understanding how the world actually works. I love the rigors of the scientific method: the testability, the constant and never-ending process of correction and integration when new understandings are introduced to the fray. Science, at it its best, provides an invigorating model for how to proceed in all other disciplines of a free and evolving society, including the arts. I have often said that I wish we artists applied more of the rigors of science to determining which of our works succeed ultimately and which do not. It’s not a perfect 1:1 correlation between the disciplines of art and science, but there is much more room for correspondence than most artists are willing to admit.

GC: You have speculated that the late Curt Dempster of Ensemble Studio Theatre commissioned you to write The Sequence because “he recognized in Craig a kindred spirit: a kinless prickly genius who gets things done.” Can you tell me a bit more about how this play first came into existence? For example, its development was supported by a grant from the Alfred Sloan Foundation, right?

PM: So in 2001 Ensemble Studio Theatre produced the off-Broadway premiere of my play, Louis Slotin Sonata, which dramatizes the true story of a Los Alamos physicist who, while performing an unnecessary demonstration of a criticality test on a plutonium bomb core, accidentally gave himself a lethal dose of neutron radiation. He died nine days later. After the success of that production, I was invited by Curt Dempster to submit additional ideas for science plays. I wanted to work on something about human consciousness and sent in a proposal. (I would finally complete this effort a decade later, with my play Philosophical Zombie Killers. I just recently staged a public reading, info here: http://www.paulmullin.org/just-wrought/philosophical-zombie-killers/). At the time, however, Curt was more interested in a completely different subject. He had seen Craig Venter on The Charlie Rose Show and, as I have said, I imagine he recognized a kindred spirit: an arrogant, monomaniacal genius who had the raw guts to want to change the world. I knew nothing about the story, but after doing some initial research I was quickly convinced that there really was a play here. The detail that sold me for good was learning that Venter had secretly used his own “genetic material” as Celera’s sample for sequencing. The lofty fog of scientific endeavor suddenly cleared as this act of sheer human outrageousness snapped everything into crisp dramatic focus. There was a story here. Boy oh boy, was there a story! We agreed on the terms of a commission and I dug into researching and developing The Sequence.

GC: The Sequence is in some ways a small-scale production, with only three characters: genomics researchers Francis Collins and Craig Venter, and journalist Kellie Silverstein. The small cast obviously makes casting and staging easier. Were there additional reasons why you thought this story would best be told from the perspective of these three and these three alone?

PM: You’re absolutely right, of course. The primary reason I chose to make this play a three-hander with rudimentary production demands is that these days new plays are rarely considered for staging in any case, but even less so if they make vast technical demands, or have huge casts. That said, I also wanted to imbue this story with an intimacy and clarity that has been lacking in many of its presentations that I encountered while researching it. All the books, for the most part, chose to illustrate the race as this vast enterprise, as indeed it was, but my experience with audiences is that their eyes tend to glaze over when bombarded with “vastness”. They want to know how the story matters to them, and for that I chose Kellie as their proxy.

GC: My own interests include the use of music to support science education. Let’s assume for the moment that there was funding to stage a big-budget version of this play. What kind of music, if any, might be included? On the one hand, it might be entertaining, say, to represent Collins with the folk-rock music that he fancies, and Venter with some harder-driving stuff. On the other hand, the script is so packed with intense dialogue that songs with words might be a momentum-killer.

PM: I think The Sequence works well as written and wouldn’t be likely to want to alter it significantly, especially since it can be done, and has been done in its world premiere, in a much bigger way than this current reading. Check out some of the pictures from the Pasadena production at The Theatre @ Boston Court, here: http://www.bostoncourt.com/events/55/the-sequence

All that said, I love adding music to my plays, and Louis Slotin Sonata, which is by nature a much “bigger” show, actually has a huge song-and-dance number in its second act. You can hear what that sounds like here: https://soundcloud.com/paul-mullin/sodom-saki-full-length; and see what it looked like here: http://www.jenniferzeyl.com/costume.php?show_id=37 .

GC: As a scientist, I appreciated the fact that The Sequence covered substantive scientific content. For example, some good explanations and analogies were offered to contrast Venter’s shotgun sequencing with traditional sequencing. Not everyone cares about that stuff, though. Did you struggle at all with the question of how much science to include in the play?

PM: I struggle with this question with every science play I write. And once the play is written, I struggle again with artistic administrators that want to neuter the play and make it just another what I call “Einstein in Love” play, i.e. a story that has an ostensible scientist as its main character but hinges in no significant way on any actual science: a plug-in play. To me, the science is integral to the science plays I have written: just as crucial to the rising action of the story as politics is to a Shakespeare history play or as sex is to a Joe Orton farce.

Today’s theatre artistic administrator distrusts science because he doesn’t understand it. It’s a systemic distrust of objectivity and testability, because, of course, if you let those ways of measuring into the system of theatre, then you have to answer for the immense failures of American theatre over the last 50 years in a meaningful way beyond shrugging and hand-wringing. Bad artists hate science because you can’t bullshit. Of course, you can’t bullshit good art either, but you can often bullshit long enough to have a career, if not a life for your art beyond it.

GC: I have read Francis Collins’ book The Language of God and have had a couple of email exchanges with him, and I found your script generally consistent with his personality. Still, you took some liberties in turning the real-life person into a character in your play. For example, Collins the character is sometimes more condescending to the journalist than the real Collins may have been. Have you gotten any interesting reactions on how he and Venter were portrayed, either from Collins and Venter themselves or from people who know them well?

PM: By and large, the people I have encountered who know Collins or Venter or both have been very complimentary about the accuracy of my portrayals. Collins himself told me that he thought he got off easy compared to my rendering of Venter. I find this amusing, since in the theatre world at least, Venter is considered the star of the piece, the cherry role to play for actors. Of course, I think they are perfectly weighted against each other just as they were in the actual events, but then, it’s my baby and I love it.

Collins is a mensch, a truly wonderful person; but I don’t think for a second that someone who has run the Human Genome Project and then NIH after that, is not capable of the kind of condescension or deviousness that he exhibits at rare moments in The Sequence. I suspect the side of Collins you saw, was the one he allowed you to see, the same side he allowed me to see when he most graciously and generously agreed to join an impromptu post-play discussion of a reading of the play at George Mason University.

Venter, not surprisingly, has played his cards closer to his vest during the long development of this play, though I have fielded questions from his PR person, and was asked to send a copy of the play early in the process — a request that, at the time, I declined because the play wasn’t ready to share. I believe representatives of his attended the Pasadena production, and since he didn’t sue me, I have to think he wasn’t utterly outraged by his portrayal. Then again, maybe my work is just too small potatoes to worry about.

GC: The Sequence addresses a range of ethical issues relating both to tests for genetic diseases and to the funding and reporting of research. A favorable review of a 2008 Pasadena production of The Sequence commented, “[Collins and Venter] cheat, lie, manipulate the public, and generally have a good time doing so, sometimes with hilarious results.” Personally, I didn’t find your characters to be terribly unethical. To what extent are these characters intended to be morally ambiguous?

PM: I’m with you. I don’t find them all that morally malignant. These are top tier players of a hardball game. As an actual baseball player once said, “If you ain’t cheatin’, you ain’t tryin’.” I tried to illustrate what I came to believe after a long and deep period of research: that both of these men did whatever it took to best serve humanity. They simply had starkly different views how best to do that, ethically and efficaciously. They both believed that their side winning the race would be better for everyone. These divides in perspective continue to exist up to this very day in the discussion of ethics concerning genetics and genomics.

GC: One of the main concerns of The Sequence is the role of news media in presenting science to the public. In her introduction to the play, Reitha Weeks mentioned that you are not a scientist but work at Amgen. What do you do there? Are you a media relations guy?

PM: I am an administrative coordinator in the IS division at Amgen. I am neither a scientist nor a PR person. I am a glorified secretary, though I don’t know how glorified you could consider it. I book travel, meetings, and generally assist people on my team with the administrative aspects of working here. I began this job after finishing The Sequence and, even though Amgen gets mentioned in the script, it is simply a fluke that I landed here as opposed to some other company: a fluke that I am deeply grateful for every day. It’s nice to have a job, and Amgen is very kind to its employees. Life is weird sometimes, and sometimes fate seems to have a rather prosaic sense of humor.

GC: Sitting in the audience a few rows over from you, I think I heard you say that you wish there were more efforts to combine science and art. Are there particular models or examples of this that you think work especially well?

PM: Not many. We are going to have to change the minds of the people who make the decisions about what art gets advanced — what plays get staged — if we want this situation to change.

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A t-shirt’s rhetorical question is answered

August 7, 2013

Yesterday Leila and Phil and I drove from Boise to Seattle. As usual, we stopped at Sumpter Junction, a restaurant in Baker City, Oregon.

I happened to be wearing my “Got parasites?” t-shirt provided by EuPathDB.org, a wonderful database that covers the genomes of several parasites studied by me and my colleagues (e.g., Plasmodium and Cryptosporidium).

The waitress was surprised and entertained by my shirt. “Actually, yes — we DO have parasites,” she said. She was referring not to the restaurant per se but to the town of Baker City, whose water supply had recently been contaminated with Cryptosporidium. The restaurant, like most residences, was staying afloat with bottled and boiled water.

It was, at the least, an amusing coincidence.

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