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Redesigning Scientific Literature

Scientific literature has a traditional style and format, which evolved over many years and likely has its merits, but this no longer reflects how people read these papers:

“I start by reading the abstract. Then, I skim the introduction and flip through the article to look at the figures. I try to identify the most prominent one or two figures, and I really make sure I understand what’s going on in them. Then, I read the conclusion/summary. Only when I have done that will I go back into the technical details to clarify any questions I might have.”

– Jesse Shanahan, master’s candidate in astronomy at Wesleyan University in Middletown, Connecticut

Shanahan’s habit reflects nicely the theme from most of the people quoted in the story linked above. As it turns out, few people—especially the target audience of professional researchers—read a study the way it’s presented, which means the presentation is wrong. Scientists, researchers, academics and intellectuals now have to deal with a flood of papers as human knowledge expands. The outline of these papers should reflect this reality.

Here is how a standard paper is organized:

Abstract
Introduction
Materials and Methods
Results
Discussion
References
Acknowledgments

It should be an easy task to rearrange the sections of a scientific paper in such a way as to match the needs of the primary readership. The first change that’s required is very easy: Don’t bury the lede, the conclusions of the paper should not be buried somewhere in the middle of the latter third of a paper. Abstracts normally state the conclusions of the study, and I believe the abstract as it exists is pretty much perfect. A well-written abstract is one of the most wonderful experiences in a world of technical literature that is generally dreadful as the phrase “technical literature” implies. Therefore, the abstract remains at the top.

Next would be a “select” graphic, preferably just one graphic but two or three would be fine. A graphic is perhaps the most important element of a study, as it turns data into something visual, which is easier to grasp. If warranted, a select graphic should appear just below the abstract. Properly captioned, this should assist the readers in understanding the magnitude and importance of the results of a paper. Some papers won’t have graphics, and in its place we could perhaps find a table or equation.

The results of the paper, written in clear language, is perhaps the most important part of the paper. It is very important to not overstate the conclusions, and to make any issues of context clear and explicit. It should be the first thing people read, after the abstract. In all likelihood, the conclusions section will end up being the only section of the main body of the text to be read.

Following this should be the discussion section, including clear references to previous research in the topic (I would even bold those references to make them easier to find). These references are important—several researchers mentioned it—because it allows them to immediately see the study in relation to previous literature and they can even see any bias (such as avoiding an important previous study). The introduction section is eliminated, any concepts that have to be introduced to understand the problem or study can be mentioned in the discussion.

The actual methodology of the study is only useful to those trying to replicate the study or specialists in the field and we therefore put it at the end. It will contain all the nitty gritty details of how everything in the study was done, with all the excruciating minutiae and jargon and acronyms a subfield specialist would demand. Personally, I would still attempt to make everything in the paper accessible to non-specialists. Ideally, even the methodology section should be written in clear enough language that someone outside the field can understand how the research was done. However, as long as the conclusions and discussions are clear, the methodology section can be as incomprehensible as the authors feel is necessary to communicate their own expertise.

Finally, all the tables and graphics should come at the end, including a reproduction of anything used at the top of the paper.  A standard reference section should follow, with any acknowledgments coming at the very end. Here is the final outline:

Abstract
Select Graphics or Tables
Results or Conclusions
Discussion (with any introductory material and a select summary of previous research)
Methodology
All graphics and tables
References
Acknowledgements

A physicist friend of mine from college (we shared an addiction to handball) told me “If it’s not in the first or last sentence of the abstract, it didn’t happen.” So maybe this was all for naught.

Interesting Abstract

Aspartame consumption is implicated in the development of obesity and metabolic disease despite the intention of limiting caloric intake. The mechanisms responsible for this association remain unclear, but may involve circulating metabolites and the gut microbiota. Aims were to examine the impact of chronic low-dose aspartame consumption on anthropometric, metabolic and microbial parameters in a diet-induced obese model. Male Sprague-Dawley rats were randomized into a standard chow diet (CH, 12% kcal fat) or high fat (HF, 60% kcal fat) and further into ad libitum water control (W) or low-dose aspartame (A, 5-7 mg/kg/d in drinking water) treatments for 8 week (n = 10-12 animals/treatment). Animals on aspartame consumed fewer calories, gained less weight and had a more favorable body composition when challenged with HF compared to animals consuming water. Despite this, aspartame elevated fasting glucose levels and an insulin tolerance test showed aspartame to impair insulin-stimulated glucose disposal in both CH and HF, independently of body composition. Fecal analysis of gut bacterial composition showed aspartame to increase total bacteria, the abundance of Enterobacteriaceae and Clostridium leptum. An interaction between HF and aspartame was also observed for Roseburia ssp wherein HF-A was higher than HF-W (P<0.05). Within HF, aspartame attenuated the typical HF-induced increase in the Firmicutes:Bacteroidetes ratio. Serum metabolomics analysis revealed aspartame to be rapidly metabolized and to be associated with elevations in the short chain fatty acid propionate, a bacterial end product and highly gluconeogenic substrate, potentially explaining its negative affects on insulin tolerance. How aspartame influences gut microbial composition and the implications of these changes on the development of metabolic disease require further investigation.

Low-dose aspartame consumption differentially affects gut microbiota-host metabolic interactions in the diet-induced obese rat.

Random Link

http://www.feynmanlectures.caltech.edu/I_toc.html

Random Link

http://skywarn.org/

Random Link

http://smp.uq.edu.au/content/pitch-drop-experiment

Random Link o’ the Day:

http://www.aircaraccess.com

Random Link o’ the Day:

http://mythbusters-wiki.discovery.com/

Gun Powder Engine

Sometimes the people on the Mythbusters, one of my all time favorite shows, gets things really wrong. A recent rerun of the “Gunpowder Engine” episode brought about a google search which came up with this YouTube video of a mechanical engineer pwn3ing the Mythbusters. His deal? Using an old external combustion design combined with a homemade slow-burning gunpowder he gets 600rpm on his prototype design.

(YouTube videos aren’t embedding properly on WordPress right now, don’t know why, so I’ll be linking to them until things get fixed up)


Climate Change

On Jupiter?

For about 300 years Jupiter’s banded atmosphere has shown a remarkable feature to telescopic viewers, a large swirling storm system known as The Great Red Spot. In 2006, another red storm system appeared, actually seen to form as smaller whitish oval-shaped storms merged and then developed the curious reddish hue. Now, Jupiter has a third red spot, again produced from a smaller whitish storm. All three are seen in this image made from data recorded on May 9 and 10 with the Hubble Space Telescope’s Wide Field and Planetary Camera 2. The spots extend above the surrounding clouds and their red color may be due to deeper material dredged up by the storms and exposed to ultraviolet light, but the exact chemical process is still unknown. For scale, the Great Red Spot has almost twice the diameter of planet Earth, making both new spots less than one Earth-diameter across. The newest red spot is on the far left (west), along the same band of clouds as the Great Red Spot and is drifting toward it. If the motion continues, the new spot will encounter the much larger storm system in August. Jupiter’s recent outbreak of red spots is likely related to large scale climate change as the gas giant planet is getting warmer near the equator*

I’m sure it’s just a product of an irregular orbit and not anything that has anything to do with the sun or it’s effect on climate. Just ignore the 300 years of observation versus a 12 year orbit. Ignore any effect on Mars too.

We simply can’t let anything get in the way of the government forcing us to change our lightbulbs.

This article goes into more detail and suggests the climate change on Jupiter is just a natural cycle. Clearly, there are no natural cycles on Earth. Bring on the mercury bulbs.

*From NASA’s website: Each day a different image or photograph of our fascinating universe is featured, along with a brief explanation written by a professional astronomer.

Random Link o’ the Day:

The Museum of Unworkable Devices