Miscellaneous entries
September 2025.
Mike’s Biostatistics Book additions of late:
/MD
22 July — updated instructions — just four steps — in Mike’s Biostatistics Book for starting an R session and linking to Google Drive with Google Colaboratory (Google Colab) cloud service.
Here’s a qrcode with the url to start an R notebook.
qrcode generated with R package qrcode.
Bread making crackling sound while cooling.
King Arthur bread flour, overnight rise in the refrigerator. Almost no kneading, just a little shaping. Baked in a Dutch oven with a parchment paper sling at 475 °F. For steam, two ice cubes into the Dutch oven, outside of the sling.
Suggested light reading for undergraduate and graduate biology students
| 1491 (Second Edition): New Revelations of the Americas Before Columbus | Charles C. Mann |
| A Brief History of Everyone Who Ever Lived: The Human Story Retold Through Our Genes | Adam Rutherford |
| A Crack In Creation: Gene Editing and the Unthinkable Power to Control Evolution | Jennifer A. Doudna and Samuel H. Sternberg |
| Bad Blood: Secrets and Lies in a Silicon Valley Startup | John Carreyrou |
| Bully for Brontosaurus: Reflections in Natural History | Stephen Jay Gould |
| Empire of Pain: The Secret History of the Sackler Dynasty | Patrick Radden Keefe |
| Enlightenment Now: The Case for Reason, Science, Humanism and progress | Steven Pinker |
| Finding Darwin’s God: A Scientist’s Search for Common Ground Between God and Evolution | Kenneth R. Miller |
| Galileo’s Middle Finger: Heretics, Activists, and One Scholar’s Search for Justice | Alice Dreger |
| Herding Hemingway’s Cats: Understanding how our genes work | Kat Arney |
| Is Science Racist? (Debating Race) | Jonathan Marks |
| Life’s Greatest Secret: The Story of the Race to Crack the Genetic Code | Matthew Cobb |
| Simply Complexity: A Clear Guide to Complexity Theory | Neil Johnson |
| The Art and Politics of Science | Harold E. Varmus |
| The Emperor of All Maladies: A Biography of Cancer | Siddhartha Mukherjee |
| The Genome War: How Craig Venter Tried to Capture the Code of Life and Save the World | James Shreeve |
| The Mismeasure of Man | Stephen Jay Gould |
| The Philadelphia Chromosome: A Genetic Mystery, a Lethal Cancer, and the Improbable Invention of a Lifesaving Treatment | Jessica Wapner |
| The Selfish Gene | Richard Dawkins |
| The Society of Genes | Itai Yanai and Martin Lercher |
| What’s in your genome?: 90% of your genome is junk | Lawrence Moran |
| Weapons of Math Destruction: How Big Data Increases Inequality and Threatens Democracy | Cathy O’Neil |
| Why Big Fierce Animals Are Rare: An Ecologist’s Perspective | Paul A. Colinvaux |
| Why Evolution is True | Jerry A. Coyne |
I’ve been teaching a biostatistics class since 2003, first at UH-Hilo, and at Chaminade University since 2010. I’ve tried a number of textbooks, but in the last couple of years have elected to go with my own notes. I’m now releasing the ePub into the wild as Mike’s Biostatistics Book.
30-Sep-2020: 11 of 20 chapters posted
I’ve cobbled together a glossary page to support genetic and bioinformatics student learning. Where possible, links to original sources are provided.
GGGB: Glossary of Genetics, Genomics, & Bioinformatics
The page is a work in progress and will be completed by summer 2020.
from https://pronounsday.org/:
Referring to people by the pronouns they determine for themselves is basic to human dignity. Being referred to by the wrong pronouns particularly affects transgender and gender nonconforming people. Together, we can transform society to celebrate people’s multiple, intersecting identities.”
16 October 2019, https://pronounsday.org/
CGRC+5P Vashon, Washington
Example, use command line program get-filehash in Windows 10, or the terminal and command md5 in macOS, or call a function from the opensslR program to compare hashsum of R download file, e.g., R-3.6.1-win.exe, against fingerprint.
Open PowerShell (type “powershell” in search)
Enter on one line
get-filehash -Algorithm MD5
Navigate to folder (or note file path) which contains the file to check, highlight the file, then drag and drop to add to the command
get-filehash -Algorithm MD5C:\Users\userName\Downloads\R-3.6.1-win.exe
get-filehash uses the Sha256 algorithm by default (Microsoft).
replace userName with your user account
Open terminal (type “terminal” in Spotlight)
Enter on one line “md5” plus a space
md5
Navigate to folder (or note file path) which contains the file to check, highlight the file, then drag and drop to add to the command
md5 /Users/userName/Downloads/R-3.6.1.pkg
Alternatively, replace md5 with the better sha256
Open R, install package openssl, and follow examples provided at https://cran.r-project.org/web/packages/openssl/vignettes/crypto_hashing.html
One of the best thing going in the Division of Natural Science & Mathematics is the outreach program created and directed by Lori Shimoda. Since 2009, more than 1900 students, faculty and division staff have brought biology, chemistry, forensics, and environmental science to dozens of public schools and more than 20,000 students in Hawai’i.
From the IAS STEM website:
“I Am A Scientist STEM” is a mobile outreach program that shares our labs beyond the Chaminade University campus. Our services are FREE to Hawaii DOE schools. IAS STEM is part of a broader initiative by the Division of Natural Sciences & Mathematics at Chaminade University to encourage science awareness and education in Hawaii’s public schools.
My modest contribution to this wonderful program has been to create and manage the website, iamascientiststem.org/ .
Congratulations to Lori for ten years of success with I am a scientist STEM!