I Just Finished Statistics for Experimenters and I Cannot Praise it Enough

Posted on April 15, 2020  Comments (1)

Guest post by Michael Betancourt.

I just finished Box, Hunter, and Hunter (Statistics for Experimenters) and I cannot praise it enough. There were multiple passages where I literally giggled. In fact I may have been a bit too enthusiastic about tagging quotes beyond “all models are wrong but some are useful” that I can’t share them all.

photo of Statistics for Experimenters with many blue bookmarks shown

I wish someone had shared this with me when I was first learning statistics instead of the usual statistics textbooks that treat model development as an irrelevant detail. So many of the elements that make this book are extremely relevant to statistics today. Some examples:

  • The perspective of learning from data only through the lens of the statistical model. The emphasis on sequential modeling, using previous fits to direct better models, and sequential experiments, using past fits to direct better targeted experiments.
  • The fixation on checking model assumptions, especially with interpretable visual diagnostics that capture not only residuals but also meaningful scales of deviation. Proto visual predictive checks as I use them today.
  • The distinction between empirical models and mechanistic models, and the treatment of empirical linear models as Taylor expansions of mechanistic models with covariates as _deviations_ around some nominal value. Those who have taken my course know how important I think this is.
  • The emphasis that every model, even mechanistic models, are approximations and should be treated as such.
  • The reframing of frequentist statistical tests as measures of signal to noise ratios.
  • The importance of process drift and autocorrelation in data when experimental configurations are not or cannot be arbitrarily randomized.
  • The diversity of examples and exercises using real data from real applications with detailed contexts, including units everywhere.

Really the only reason why I wouldn’t recommend this as an absolute must read is that the focus on linear models and use of frequentist methods does limit the relevance of the text to contemporary Bayesian applications a bit.

Texts like these make me even more frustrated by the desire to frame movements like data science as revolutions that give people the justification to ignore the accumulated knowledge of applied statisticians.

Academic statistics has no doubt largely withdrawn into theory with increasingly smaller overlap with applications, but there is so much relevant wisdom in older applied statistics texts like these that doesn’t need to be rediscovered just reframed in a contemporary context.

Oh, I forgot perhaps the best part! BHH continuously emphasizes the importance of working with domain experts in the design and through the entire analysis with lots of anecdotal examples demonstrating how powerful that collaboration can be.

I felt so much less alone every time they talked about experimental designs not being implemented properly andthe subtle effects that can have in the data, and serious effects in the resulting inferences, if not taken into account.

Michael Betancourt, PhD, Applied Statistician – long story short, I am a once and future physicist currently masquerading as a statistician in order to expose the secrets of inference that statisticians have long kept from scientists. More seriously, my research focuses on the development of robust statistical workflows, computational tools, and pedagogical resources that bridge statistical theory and practice and enable scientists to make the most out of their data.
Twitter: @betanalpha
Website: betanalpha
Patreon: Michael Betancourt

Related: Statistics for Experimenters, Second EditionStatistics for Experimenters in SpanishStatistics for Experimenters ReviewCorrelation is Not Causation

Molecular Motor Proteins

Posted on January 27, 2020  Comments (1)

Webcast on amazing processes inside cells by Ron Vale.

Molecular motor proteins are fascinating enzymes that power much of the movement performed by living organisms. The webcast provides an overview of the motors that move along cytoskeletal tracks (kinesin and dynein which move along microtubules and myosin which moves along actin). The talk first describes the broad spectrum of biological roles that kinesin, dynein and myosin play in cells. The talk then discusses how these nanoscale proteins convert energy from ATP hydrolysis into unidirectional motion and force production, and compares common principles of kinesin and myosin. The talk concludes by discussing the role of motor proteins in disease and how drugs that modulate motor protein activity can treat human disease.

Ron Vale is a Professor of Cellular and Molecular Pharmacology at the University of California, San Francisco and an Investigator of the Howard Hughes Medical Institute. He is also the founder of the iBiology project.

Related: Animations of Motor Proteins Moving Material Inside CellsScience Explained: How Cells React to Invading VirusesLooking Inside Living Cells

Popular Posts on the Curious Cat Science and Engineering Blog in the Last Decade

Posted on January 19, 2020  Comments (1)

These were the most popular (by number of page views) posts on our blog in the last decade.

photo of John Hunter with snow covered mountain peaks in the background

John Hunter, Olympic National Park (where the mountain peaks are colder and covered in snow)

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Backyard Wildlife: Squirrel Gathering Leaves for Its Nest

Posted on May 22, 2019  Comments (5)

I saw this squirrel gathering leaves for its nest in its mouth and then climbing a tree in my backyard. It repeated this many times all morning. I saw it doing so at least 5 times and likely it did so many times when I did not see it.

See more backyard wildlife posts on the Curious Cat Science Blog

Related: Squirrel Eating Holly BerriesBackyard Wildlife: Red-tailed HawkBackyard Wildlife: Family of Raccoons

Regeneron High School Science Talent Search 2019

Posted on April 19, 2019  Comments (1)

$3.1 million in prizes was awarded through the Regeneron Science Talent Search 2019, including $2,000 to each of the top 300 scholars and their schools. The top award was for $250,000. If you want to watch the video without knowing the winner, watch it before reading the rest of this post.

Every year the accomplishments of high school students provide amazing hope for the future. I am glad for the organizations that highlight the efforts of these students and provide awards for a few of the most amazing accomplishments. The top 40 students all get at least $25,000 (with the top 10 getting more).

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Appropriate Technology: a Microscope and Centrifuge for Under $1

Posted on March 24, 2019  Comments (1)

Malaria is estimated to have killed more than half the people that have ever lived. And it continues to kill millions. One big challenge is diagnosing malaria is difficult (those infected have flu like symptoms).

The video shows two great appropriate technology solutions to help diagnose malaria and save millions of lives. Manu Prakash from Stanford talks about 2 of his labs’ inventions the Foldscope and the Paperfuge. Combined these cost only 68 cents and they can be used to diagnose Malaria. Both of these are examples not only of simple, brilliant design, but of how engineering is used to make a positive dent in the world.

Read more about the Paperfuge: an ultra-low cost, hand-powered centrifuge inspired by the mechanics of a whirligig toy (open access paper).

This solution also shows the huge benefit people everywhere have gained when immigrants can take their skills and desires to institutions like Stanford to create solutions that greatly benefit the world. This powerful force has been creating huge benefits that we all have enjoyed for decades.

Related: Appropriate Technology and Focus on Improving Lives at MIT (2014)$1 Device To Give Throat Cancer Patients Their Voice Again (2016)Video showing malaria breaking into cell (2011)Engineering: Cellphone Microscope (2009)One Scientists 20 Year Effort to Defeat Dengue Fever (2012)

Scientists Watch Single Cell Organisms Evolve Multicellular Trait in Response to Predation

Posted on February 24, 2019  Comments (2)

The scientists used the ciliate predator Paramecium tetraurelia to select for the de novo evolution of multicellularity in outcrossed populations of C. reinhardtii. They show that multicellular life cycles that evolved were passed on to future generations (the change was heritable). The evolved multicellular life cycles are stable over thousands of asexual generations in the absence of predators. Because C. reinhardtii has no multicellular ancestors, these experiments represent a novel origin of multicellularity.

De novo origins of multicellularity in response to predation

Here we show that de novo origins of simple multicellularity can evolve in response to predation. We subjected outcrossed populations of the unicellular green alga Chlamydomonas reinhardtii to selection by the filter-feeding predator Paramecium tetraurelia. Two of five experimental populations evolved multicellular structures not observed in unselected control populations within ~750 asexual generations.

The control populations remained unicellular. The populations subjected to predation evolved in different ways including one that formed stereotypic eight-celled clusters (Fig. 1A), with an apparent unicellular and tetrad life stage.

electron microscope images of multicellular colonies from evolved populations

Scanning electron micrographs of representative multicellular colonies from evolved populations. (A) Shows an amorphous cluster from population B2. Cell number varies greatly between clusters in this clone and between clones in this population. (B) Shows an eight-celled cluster from population B5. Octads were frequently observed in both populations.

an external membrane is visible around both evolved multicellular colonies, indicating that they formed clonally via repeated cell division within the cluster, rather than via aggregation.

The article also provides details on the scientific inquiry process where theory meets practical realities of observation. I think these ideas are very important and we often gloss over such details. This article was shared as an open access article and is written so that those who are interested in science but are not scientists can understand, which is a valuable. The research was funded by USA National Science Foundation, the John Templeton Foundation, the NASA Astrobiology Institute, a NASA Postdoctoral Program Fellowship and a Packard Foundation Fellowship. And the researchers work at public and private universities. Such research should all be published in an open access manner.

Related: The Amazing Reality of Genes and The History of Scientific InquiryParasite Evolved from Cnidarians (Jellyfish etc.)Why Don’t All Ant Species Replace Queens in the Colony, Since Some DoScientific Inquiry Leads to Using Fluoride for Healthy TeethMechanical Gears Found in Jumping Insects

20 Most Popular Post on the Curious Cat Science and Engineering Blog in 2018

Posted on December 30, 2018  Comments (1)

These were the most popular (by number of page views) posts on our blog in 2018.

Red-tailed hawk with squirrel

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Widespread Misuse by Those Who Use Antibiotics Infrequently Leads to Resistance

Posted on December 19, 2018  Comments (0)

Widespread, occasional use of antibiotics in USA linked with resistance

The increasing prevalence of antibiotic resistance in the U.S. appears more closely linked with their occasional use by many people than by their repeated use among smaller numbers of people, according to a large new study from Harvard T.H. Chan School of Public Health.

The study also found that antibiotic use varies across the nation, and that in areas where particular antibiotics are used more frequently, resistance to those antibiotics is higher.

“We know that efforts to reduce inappropriate use of antibiotics are critical to addressing the problem of antibiotic resistance.

“Our results show that most antibiotic use is occasional—by people taking just one antibiotic course in a year—and that this occasional use is more closely linked with antibiotic resistance than intense, repeated use.”

The problems created by misuse of antibiotics are significant and continuing. The consequences are long term and diffuse. The lack of immediate and damaging impacts makes the continued misuse seem to have little consequence. However, the consequences are dire but not immediate.

In this way it is similar to the problems caused by pumping huge amounts of green house gases into the atmosphere and causing massive climate changes (though delayed by several decades). As a society we really have to get better at changing our behavior when the long term consequences are dire and clear.

It is good to learn from these efforts to understand the most significant aspects of our continued misuse of antibiotics in order to prioritize where we focus our improvement efforts.

Related: What Happens If the Overuse of Antibiotics Leads to Them No Longer Working? (2011)Our Dangerous Antibiotic Practices Carry Great Risks (2012)80% of the Antibiotics in the USA are Used in Agriculture and AquacultureCDC Urges Increased Effort to Reduce Drug-Resistant Infections (2006)Antibiotics Breed Superbugs Faster Than Expected (2010)

Hope Exists to Reverse Bee Colonies Collapse if We Take Action

Posted on November 23, 2018  Comments (0)

photo of a bee on a flower

photo by Justin Hunter

The bee colony collapse disorder has been ongoing for more than 10 years and while some scientific understanding has been gained the complexity of the problem continues to stifle progress. The first post I wrote on this blog about colony collapse disorder was published in 2006.

As early as 2007 a virus was found to be one likely factor in bee colony collapse disorder. But progress has been slow especially since likely solutions were fought by those profiting from existing conditions (widespread use of powerful pesticides). In 2012, I wrote another post for this Curious Cat Science blog: Study of the Colony Collapse Disorder Continues as Bee Colonies Continue to Disappear.

Scientist unveils blueprint to save bees

Stefanie Christmann of the International Center for Agricultural Research in Dry Areas will present the results of a new study that shows substantial gains in income and biodiversity from devoting a quarter of cropland to flowering economic crops such as spices, oil seeds, medicinal and forage plants.

The UN conference is already debating new guidelines on pollinators that will recommend reducing and gradually phasing out the use of existing pesticides, but Christmann’s research suggests this can be done without financial pain or a loss of production.

The need for a change is increasingly evident. More than 80% of food crops require pollination but the populations of insects that do most of this work have collapsed. In Germany, this fall is by up to 75% over the past 25 years. Puerto Rico has seen an even sharper decline. Numbers are not available in most countries, but almost all report an alarming decline.

Related: Another Bee Study Finds CCD is Likely Due to Combination of Factors Including Pesticides (2013)The Study of Bee Colony Collapses Continues (2007)Europe Bans Certain Pesticides, USA Just Keeps Looking, Bees Keep Dying (2013)Apple Farmers Use Pigs Instead of Pesticides

Scientists and Engineers in Congress After the Recent Elections in the USA

Posted on November 12, 2018  Comments (0)

The recent elections in the USA added to those serving in congress with STEM (science, technology, engineering and math) backgrounds.

USA Capital Building

US Capital Building in Washington DC by John Hunter.

Here is a list of elected representatives in the USA congress with science, technology, engineering and math backgrounds (after the 2018 election).

Name State BS Notes Link
Ralph Abraham Louisiana MD bio
Ami Bera California biological sciences MD bio
Tony Cárdenas California electrical engineering bio
Sen. Bill Cassidy Louisiana biochemistry MD bio
Sean Casten Illinois molecular biology and biochemistry MS biochemical engineering and engineering management, 2018* bio
Chris Collins New York mechanical engineering bio
Joe Cunningham South Carolina ocean engineering 2018* bio
Jeff Van Drew New Jersey D.D.S. (Dentist), 2018* bio
Bill Foster Illinois physics PhD physics bio
Brett Guthrie Virginia mathematical economics bio
Sen. Martin Heinrich New Mexico mechanical engineering bio
Kevin Hern Oklahoma electro-mechanical engineering 2018* bio
Chrissy Houlahan Pennsylvania engineering MS technology and policy, 2018* bio
Joe Kennedy III Massachusetts management science and engineering bio
Ted Lieu California computer science bio
Name State BS Notes Link
Dan Lipinski Illinois mechanical engineering engineering-economic systems (MS) bio
Elaine Luria Virginia physics masters in engineering management, 2018* bio
Jerry McNerney California mathematics PhD bio
Seth Moulton Massachusetts physics bio
Pete Olson Texas computer science (BA)
Sen. Jacky Rosen Nevada psychology associat’s degree in computing and information technology
Raul Ruiz California MD, 2018* bio
Brad Schneider Illinois industrial engineering bio
Kurt Schrader Oregon Dr. of Veterinary Medicine bio
Kim Schrier Washington astrophysics MD, 2018* bio
John M. Shimkus Illinois general engineering bio
Paul Tonko New York mechanical and industrial engineering bio
Lauren Underwood Illinois nursing MS in Nursing and Master of Public Health, 2018* bio
Steve Watkins Kansas engineering 2018* bio



Those with notes including “2018*” means they were newly elected to the congress in 2018.

Please send any information on possible additions to this list (see the continually updated list).

Related: Scientific Research Spending Cuts in the USA and Increases Overseas are Tempting Scientists to Leave the USA (2013)The Science Gap and the EconomyScientists and engineers in the USA Congress in 2008 (scroll down the page to see 2008) – Diplomacy and Science ResearchUnless We Take Decisive Action, Climate Change Will Ravage Our Planet (2009)Silicon Valley Shows the Power of Global Science and Technology Workforce