I'd like to introduce you one of the faces of the project: Alex, the genomics rat idol.
Arguably, Alex is the most popular rat on the internet. For the justification of this strong statement, read on.
Alex was born in May 2000. It's well known that a rat's cuteness reaches maximum at about 3-4 weeks. After this critical time, a pet store rat is less likely to be purchased and may be asked to act as snake food. In Alex's case, she was perilously close to her deadline. Luckily for her, we paid a ransom of $6.99 to the Noah's Ark pet shop in Vancouver. She was on her last cute leg.
From May 2000 Alex spent most of her time hoarding food pellets and riding on shoulders.
Alex liked to bite. And rats only bite hard — they don't nibble. Her contention for this unattractive behaviour was the uncanny similarity between a finger and a pellet of food.
Other than unpredictable bouts of biting (by far the most exciting aspect of her personality), Alex lacked other distinguishing characteristics.
Alex died of a seizure in late 2002. She was buried outside of the Museum of Anthropology. A ratty pair of underwear served as a burial shroud.
And I hope you got that last pun.
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Despite my best efforts at meaningful work, this web page continues to be the most popular of all my online offerings, making for a somewhat embarrassing achievement.
Alex's images consistently show up first in Google's web search for 'rat', 'rat image' and image search for 'rat'.
Finally, Alex appears as the first entry in Google images for 'rat'.
Alex's Public Appearances
More recently, she's appeared on the cover of Ethnologie Francaise (Jan-Mar 2009 issue).
The topic of the issue was the relationship between animals and humans. It is fitting therefore to recount here the relationship I shared with Alex during her sojourn with us.
I have selected several figures from our past columns and show how they evolved from their draft to published versions.
Clarity, concision and space constraints—we have only 3.4" of horizontal space— all have to be balanced for a figure to be effective.
It's nearly impossible to find case studies of scientific articles (or figures) through the editing and review process. Nobody wants to show their drafts. With this writeup I hope to add to this space and encourage others to reveal their process. Students love this. See whether you agree with my decisions!
The goal of these designs is to observe a reproducible effect that can be due only to the treatment, avoiding confounding and bias. Simultaneously, to sample enough variability to estimate how much we expect the effect to differ if the measurements are repeated with similar but not identical samples (replicates).
We need to distinguish between sources of variation that are nuisance factors in our goal to measure mean biological effects from those that are required to assess how much effects vary in the population.
Altman, N. & Krzywinski, M. (2014) Points of Significance: Two Factor Designs Nature Methods 11:5-6.
1. Krzywinski, M. & Altman, N. (2014) Points of Significance: Designing Comparative Experiments Nature Methods 11:597-598.
2. Krzywinski, M. & Altman, N. (2014) Points of Significance: Analysis of variance (ANOVA) and blocking Nature Methods 11:699-700.
3. Blainey, P., Krzywinski, M. & Altman, N. (2014) Points of Significance: Replication Nature Methods 11:879-880.
We've previously written about how to analyze the impact of one variable in our ANOVA column. Complex biological systems are rarely so obliging—multiple experimental factors interact and producing effects.
ANOVA is a natural way to analyze multiple factors. It can incorporate the possibility that the factors interact—the effect of one factor depends on the level of another factor. For example, the potency of a drug may depend on the subject's diet.
We can increase the power of the analysis by allowing for interaction, as well as by blocking.
Krzywinski, M., Altman, (2014) Points of Significance: Two Factor Designs Nature Methods 11:1187-1188.
Blainey, P., Krzywinski, M. & Altman, N. (2014) Points of Significance: Replication Nature Methods 11:879-880.
Krzywinski, M. & Altman, N. (2014) Points of Significance: Analysis of variance (ANOVA) and blocking Nature Methods 11:699-700.
Krzywinski, M. & Altman, N. (2014) Points of Significance: Designing Comparative Experiments Nature Methods 11:597-598.