resources
visualizations
presentations
lunch break
Distractions and amusements, with a sandwich and coffee.
Alex — Internet's Most Popular Rat
Poster Rat for Rat Genome Sequencing
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The rat genome sequencing project at the Baylor College of Medicine Human Genome Sequencing Centre is complete. The genome has been analyzed and published. 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, the rat. Rattus norvegicus on an ABI 3700 genome sequencer.
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▲ Alex, the rat. Rattus norvegicus on an ABI 3700 genome sequencer.
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Alex's BiographyAlex 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. 
▲ Portrait of Alex, the genome rat (Rattus norvegicus). Here, she is seen in a forced portrait position
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From May 2000 Alex spent most of her time hoarding food pellets and riding on shoulders. 
▲ Portrait of Alex, the genome rat (Rattus norvegicus). Riding on shoulder.
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. |
DOWNLOAD ALL PHOTOS.
Photos are for public use. Use, modification and distribution of these photos is unrestricted. Alex's PopularityDespite 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'. 
▲ Alex image is the first for Google's 'rat' search query (retrieved 16 Mar 2013).
(rat Google search)
▲ Alex image is the first for Google's 'rat image' search query (retrieved 16 Mar 2013).
(rat Google search)
Finally, Alex appears as the first entry in Google images for 'rat'. 
▲ Alex image is the first for Google's 'rat image' search query (retrieved 16 Mar 2013).
(rat Google search)
Alex's Public AppearancesAlex is neither without modesty nor public fame. Her first cover-ratgirl appearance was on the April 2004 issue of Genome Research. 
▲ Alex the rat appeared on the cover of Genome Research (April 2004).
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More recently, she's appeared on the cover of Ethnologie Francaise (Jan-Mar 2009 issue). 
▲ Alex the rat appeared on the cover of Ethnologie Francaise (1/2009).
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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. |
news + thoughts
Optimal experimental design
Customize the experiment for the setting instead of adjusting the setting to fit a classical design.The presence of constraints in experiments, such as sample size restrictions, awkward blocking or disallowed treatment combinations may make using classical designs very difficult or impossible.
Optimal design is a powerful, general purpose alternative for high quality, statistically grounded designs under nonstandard conditions.
We discuss two types of optimal designs (D-optimal and I-optimal) and show how it can be applied to a scenario with sample size and blocking constraints.
Smucker, B., Krzywinski, M. & Altman, N. (2018) Points of significance: Optimal experimental design Nature Methods 15:599–600.
Background reading
Krzywinski, M., Altman, N. (2014) Points of significance: Two factor designs. Nature Methods 11:1187–1188.
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.
The Whole Earth Cataloguer
All the living things.An illustration of the Tree of Life, showing some of the key branches.
The tree is drawn as a DNA double helix, with bases colored to encode ribosomal RNA genes from various organisms on the tree.
All living things on earth descended from a single organism called LUCA (last universal common ancestor) and inherited LUCA’s genetic code for basic biological functions, such as translating DNA and creating proteins. Constant genetic mutations shuffled and altered this inheritance and added new genetic material—a process that created the diversity of life we see today. The “tree of life” organizes all organisms based on the extent of shuffling and alteration between them. The full tree has millions of branches and every living organism has its own place at one of the leaves in the tree. The simplified tree shown here depicts all three kingdoms of life: bacteria, archaebacteria and eukaryota. For some organisms a grey bar shows when they first appeared in the tree in millions of years (Ma). The double helix winding around the tree encodes highly conserved ribosomal RNA genes from various organisms.
Johnson, H.L. (2018) The Whole Earth Cataloguer, Sactown, Jun/Jul, p. 89
Why we can't give up this odd way of typing
All fingers report to home row.An article about keyboard layouts and the history and persistence of QWERTY.
My Carpalx keyboard optimization software is mentioned along with my World's Most Difficult Layout: TNWMLC. True typing hell.
McDonald, T. (2018) Why we can't give up this odd way of typing, BBC, 25 May 2018.