Posts about books

We are Not Us Without The Microbes Within Us

I Contain Multitudes is a wonderful book by Ed Young on the microbes within us.

Time and again, bacteria and other microbes have allowed animals to transcend their basic animalness and wheedle their way into ecological nooks and crannies that would be otherwise inaccessible; to settle into lifestyles that would be otherwise intolerable; to eat what they could not otherwise stomach; to succeed against their fundamental nature. And the most extreme examples of this mutual assured success can be found in the deep oceans, where some microbes supplement their hosts to such a degree that the animals can eat the most impoverished diets of all – nothing.

This is another book exploring the wonders of biology and the complexity of the interaction between animals and microbes.

For hundreds of years, doctors have used dioxin to treat people whose hearts are failing. The drug – a modified version of a chemical from foxglove plants – makes the heart beat more strongly, slowly, and regularly. Or, at least, that’s what it usually does. In one patient out of every ten, digoxin doesnt’ work. Its downfall is a gut bacterium called Eggerthella lenta, which converts the drug to an inactive and medically useless form. Only some strains of E. lenta do this.

The complex interactions within us are constantly at work helping us and occasionally causing problems. This obviously creates enormous challenges in health care and research on human health. See related posts: Introduction to Fractional Factorial Designed Experiments, “Grapefruit Juice Bugs” – A New Term for a Surprisingly Common Type of Surprising Bugs and 200,000 People Die Every Year in Europe from Adverse Drug Effects – How Can We Improve?.

Every person aerosolized around 37 million bacteria per hour. This means that our microbiome isn’t confined to our bodies. It perpetually reaches out into our environment.

Avoiding bacteria is not feasible. Our bodies have evolved with this constant interaction with bacteria for millions of years. When we are healthy bacteria have footholds that make it difficult for other bacteria to gain a foothold (as does our immune system fighting off those bacteria it doesn’t recognize or that it recognized as something to fight).

A few pages later he discusses the problem of hospital rooms that were constantly cleaned to kill bacteria and largely sealed to reduce airflow. What happened is those bacteria the sick people had in them were the bacteria that were flourishing (the number of other bacteria to compete for space was small). Opening the windows to welcome the outside air resulted in better results.

Outdoors, the air was full of harmless microbes from plants and soils. Indoors, it contained a disproportionate number of potential pathogens, which are normally rare or absent in the outside world

Human health is a fascinating topic. It is true antibiotics have provided us great tools in the service of human health. But we have resorted to that “hammer” far too often. And the consequences of doing so is not understood. We need those scientists exploring the complex interactions we contain to continue there great work.

Related: People are Superorganisms With Microbiomes of Thousands of Species (2013)Bacteria are Always Living in Our Bodies (2014)Gut Bacteria Explored as Medical Treatment – even for Cancer

The Amazing Reality of Genes and The History of Scientific Inquiry

cover of The Gene

The Gene by Siddhartha Mukherjee is a wonderful book. He does a great job of explaining the history of scientists learning about genes as well as providing understandable explanations for the current scientific understanding of genes and how they impact our lives.

As I have mentioned before, I find biology fascinating even though I found biology classes utterly boring and painful. I wish everyone could learn about biology with the insight people like Siddhartha Mukherjee provide. I realize not everyone is going to find the history and understanding of genes to be fascinating but for those who might this book is a great read. And don’t rule the idea out just because you found biology classes painful.

Life may be chemistry, but it’s a special circumstance of chemistry. Organisms exist not because of reactions that are possible, but because of reactions that are barely possible. Too much reactivity and we would spontaneously combust. Too little, and we would turn cold and die. Proteins enable these barely possible reactions, allowing us to live on the edges of chemical entropy – skating perilously, but never falling in.
– page 134

Whether it is the physics of our solar system or our biology there is a precarious band that allowed beings such as ourselves to evolve.

most genes, as Richard Dawkins describes them, are not “blueprints” but “recipes.” They do not specify parts, but processes; they are formulas, not forms. If you change a blueprint, the final product is change in a perfectly predictable manner: eliminate a widget specified in the plan, and you get a machine with a missing widget. But alteration of a recipe or formula doesn’t not change the product in a predictable manner: if you quadruple the amount of butter in a cake, the eventual effect is more complicated than just a quadruply buttered cake (try it; the whole thing collapses in an oily mess).
– page 454

The is a powerful idea. And when combined with turning genes on and off it is understandable how complex determining genetic impacts on biology and disease are. A few diseases or results (e.g. blue eyes) are nearly as simple as 1 or a few genes being altered in a specific way but most are not nearly so easy. And it isn’t like even that is so easy but with the amazing efforts scientists have made and the advanced tools those scientists created it can now seem simple to identify some such diseases.

The genetic code is universal. A gene from a blue whale can be inserted into a microscopic bacterium and it will be deciphered accurately and with near perfect fidelity. A corollary: there is nothing particularly special about human genes.
– page 480

This is something I have known and understood but it is still amazing. Genes and proteins and how they act to create the incredible diversity of life is something that is awe inspiring.

This book is a wonderful adventure for those interested in life and scientific inquiry.

Related: Epigenetics, Scientific Inquiry and UncertaintyHuman Gene Origins: 37% Bacterial, 35% Animal, 28% EukaryoticUnexpected Risks Found In Editing Genes To Prevent Inherited DisordersEpigenetic Effects on DNA from Living Conditions in Childhood Persist Well Into Middle AgeWhy Don’t All Ant Species Replace Queens in the Colony, Since Some Do

Mountain Lion Roams from South Dakota all the way to 30 Miles from Manhattan

book cover with image of a mountain lion

A Cougar’s Thousand-Mile Quest to Find a Mate

In the late summer of 2009, a young male cougar set off from the Black Hills of South Dakota to look for a mate. And kept going—east across the Great Plains to the Upper Peninsula of Michigan and on to New England, through backyards and parking lots, across highways and railroad tracks, driven by the most powerful force on earth.

Over time he showed up in the Twin Cities of Minnesota and in Wisconsin. He disappeared for a couple months, then shows up almost two years later, 30 miles from Manhattan, in Greenwich, Connecticut. In all he probably traveled 2,000 to 5,000 miles, enough to cross the country twice. He forded all the major rivers of the East, navigated highways and an international boundary. It was one of the most spectacular journeys by an animal ever recorded.

image of map showing the cougar's path across usa

In Heart of a Lion: A Lone Cat’s Walk Across America William Stolzenburg provides an exciting tale of the cat’s journey.

Related: Backyard Wildlife: Mountain Lion (2012)Mountain Lions Returning to the Midwest USA for the First Time in a Century (2012)Big Cats in America (2004)USA Designates Large Areas of New Mexico and Arizona as Critical Habitat for Jaguars (2014)

George Box 1919 to 2013 – A Great Friend, Scientist and Statistician

Reposted from my management blog.

I would most likely not exist if it were not for George Box. My father took a course from George while my father was a student at Princeton. George agreed to start the Statistics Department at the University of Wisconsin – Madison, and my father followed him to Madison, to be the first PhD student. Dad graduated, and the next year was a professor there, where he and George remained for the rest of their careers.

George died today, he was born in 1919. He recently completed An Accidental Statistician: The Life and Memories of George E. P. Box which is an excellent book that captures his great ability to tell stories. It is a wonderful read for anyone interested in statistics and management improvement or just great stories of an interesting life.

photo of George EP Box

George Box by Brent Nicastro.

George Box was a fantastic statistician. I am not the person to judge, but from what I have read one of the handful of most important applied statisticians of the last 100 years. His contributions are enormous. Several well know statistical methods are known by his name, including:

George was elected a member of the American Academy of Arts and Sciences in 1974 and a Fellow of the Royal Society in 1979. He also served as president of the American Statistics Association in 1978. George is also an honorary member of ASQ.

George was a very kind, caring and fun person. He was a gifted storyteller and writer. He had the ability to present ideas so they were easy to comprehend and appreciate. While his writing was great, seeing him in person added so much more. Growing up I was able to enjoy his stories often, at our house or his. The last time I was in Madison, my brother and I visited with him and again listened to his marvelous stories about Carl Pearson, Ronald Fisher and so much more. He was one those special people that made you very happy whenever you were near him.

George Box, Stuart Hunter and Bill Hunter (my father) wrote what has become a classic text for experimenters in scientific and business circles, Statistics for Experimenters. I am biased but I think this is acknowledged as one of (if not the) most important books on design of experiments.

George also wrote other classic books: Time series analysis: Forecasting and control (1979, with Gwilym Jenkins) and Bayesian inference in statistical analysis. (1973, with George C. Tiao).

George Box and Bill Hunter co-founded the Center for Quality and Productivity Improvement at the University of Wisconsin-Madison in 1984. The Center develops, advances and communicates quality improvement methods and ideas.

The Box Medal for Outstanding Contributions to Industrial Statistics recognizes development and the application of statistical methods in European business and industry in his honor.

All models are wrong but some are useful” is likely his most famous quote. More quotes By George Box

A few selected articles and reports by George Box

Related: It is not about proving a theorem it is about being curious about thingsBox on QualitySoren BisgaardLearning Design of Experiments with Paper HelicoptersPeter Scholtes

Book Explores Adventures in Making

image of the cover of Made by Hand

Made by Hand by Mark Frauenfelder, the editor-in-chief of Make magazine. explores his adventures in the world of do-it-yourself.

Frauenfelder spent a year trying a variety of offbeat projects such as keeping chickens and bees, tricking out his espresso machine, whittling wooden spoons, making guitars out of cigar boxes, and doing citizen science with his daughters in the garage. His whole family found that DIY helped them take control of their lives, offering deeply satisfying alternatives for spending time together. Working with their hands and minds helped them feel more engaged with the world around them.

Frauenfelder also profiles fascinating “alpha makers” leading various DIY movements and grills them for their best tips and insights. He offers a unique perspective on how earning a few calluses can be far more rewarding than another trip to the mall.

Related: Science Toys You Can Make With Your KidsGifts for the Maker in Your Lifescience booksTeaching Through Tinkering

The Information: A History, a Theory, a Flood by James Gleick

book cover image of The Information

James Gleick is a great science writer. I remember first reading his book, Chaos, which I loved. He continues to write engaging and entertaining books on science. His 2011 release The Information: A History, a Theory, a Flood, is now available in paperback.

From the invention of scripts and alphabets to the long-misunderstood talking drums of Africa, Gleick tells the story of information technologies that changed the very nature of human consciousness. Gleick provides portraits of the key figures contributing to the inexorable development of our modern understanding of information: Charles Babbage, the idiosyncratic inventor of the first great mechanical computer; Ada Byron, the brilliant and doomed daughter of the poet, who became the first true programmer; pivotal figures like Samuel Morse and Alan Turing; and Claude Shannon, the creator of information theory itself.

And now the information age arrives. The Information is the story of how we got here and where we are heading.

Related: science booksWhat Dogs Reveal About EvolutionMicrocosm by Carl ZimmerThe Last Lecture Book

Wesley the Owl: Love Story of an Owl and His Girl

This story begins on Valentine’s Day in 1985 when biologist Stacey O’Brien meets a four-day-old baby barn owl in a fateful encounter that would turn into an astonishing 19-year saga. With nerve damage in one wing, the owlet’s ability to fly was forever compromised and he had no hope of surviving on his own in the wild. A young assistant in the owl laboratory at Caltech, O’Brien promised to care for the helpless owlet and give him a permanent home. O’Brien’s heartfelt memoir of life with this wild bird, Wesley the Owl: The Remarkable Love Story of an Owl and His Girl recounts their dramatic, and often humorous, life together.

For almost two decades, O’Brien studied Wesley and his strange habits intensively and providing a mice-only diet. With a heart-shaped face and outsized personality that belied his 18-inch stature, the gorgeous white-and-gold Wesley fascinated everyone he met, and touched many lives. Stacey and Wesley’s bond was especially deep; O’Brien discovered that owls are highly sentient beings with individual personalities, subtle emotions, and a playful nature that can also turn fiercely loyal and protective.

Cool fact: “While we hear in two dimensions, owls hear in three.” Owls can detect a mouse heartbeat under three feet of snow.
Related: Friday Fun: Cat and Owl PlayingBird Brain (smart crows)Using Barn Owls for Bilogical Pest Control in Israel
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Teaching Through Tinkering

I wrote about the Tinkering School, Engineering camp previously. I am a strong believer in the value of helping kids (even adult kids – the few that haven’t resigned themselves to limited capacity to wonder since they now are grown up and not suppose to waste their time dreaming) explore their ideas and assisting them in making those ideas into reality. I think this is the best way to learn, not learning to pass a test, but learning to gain knowledge and accomplish things. Here is a nice 15 minute talk by the founder of the Tinkering School, Gever Tulley: “Turning Curriculum Design On Its Head: Engage First Then Look for Learning Within”

The format of the tinkering school is week long sessions where the kids stay overnight.

Some quotes: “we would use real tools and real materials and we would build real things, not model building, [but instead] actual building.” “create a meaningful experience and learning will follow”

Gever Tulley recently published: Fifty Dangerous Things (You Should Let Your Children Do).

Related: Home Engineering: Building a HovercraftKids Need Adventurous PlayAutomatic Cat FeederScience Toys You Can Make With Your KidsWhat Kids can Learn

Electric Wind

photo of William Kamkwamba on his windmillphoto of William Kamkwamba on his windmill from his blog.

I have written about William Kamkwamba before: Inspirational EngineerHome Engineering: Windmill for Electricity. And along with the post, Make the World Better, donated to his cause. His new book, The Boy Who Harnessed the Wind, is quite enjoyable and provides an interesting view of how he persevered. His talk of the famine, not being able to afford school and putting together a windmill using scrape parts and a few books from the library (donated by the American government – much better foreign aid than all the military weapons that are often counted as aid) is inspirational. And should help many sitting in luxury understand the privileged lives they lead.

“I’d become very interested in how things worked, yet never thought of this as science. In addition to radios, I’d also become fascinated by how cards worked, especially how petrol operated an engine. How does this happen? I thought? Well, that’s easy to find out – just ask someone with a car… But no one could tell me… Really how can you drive a truck and not know how it works?” (page 66)

“Using Energy, and this book has since changed my life… All I needed was a windmill, and then I could have lights. No more kerosene lamps that burned out eyes… I could stay awake at night reading instead of going to bed at seven with the rest of Malawi. But most important, a windmill could also rotate a pump for water and irrigation.” (page 158)

William set out to demonstrate his windmill for the first time to a skeptical crowd saying (page 193)

“Let’s see how crazy this boy really is.”… “Look,” someone said. “He’s made light!”… “Electric wind!” I shouted. “I told you I wasn’t mad!”

I like how the story shows how long, hard work, reading, experimenting and learning is what allowed William to success (page 194-5)

For the next month, about thirty people showed up each day to stare at the light. “How did you manage such a thing?” They asked. “Hard work and lots of research,” I’d say, trying not to sound too smug…
[to William’s father] “What an intelligent boy. Where did he get such ideas?”
“He’s been reading lots of books. Maybe from there?”
“They teach this in school?”
“He was forced to drop. He did this on his own.”
The diagram demonstrated twenty-four volts being transformed to two hundred forty. I knew voltage increased with each turn of wire. The diagram showed the primary coil to have two hundred turns, while the secondary had two thousand. A bunch of mathematical equations were below the diagram – I assumed they explained how I could make my own conversions – but instead I just wrapped like mad and hoped it would work. (page 200)
Soon I was attacking every idea with its own experiment. Over the next year, there was hardly a moment when I wasn’t planning or devising some new scheme. And though the windmill and radio transmitter had both been successes, I couldn’t say the same for a few other experiments. (page 215)

William is now attending the African Leadership Academy in South Africa, with an amazing group of classmates. See how you can support the Moving Windmills Projects.

Related: Teen’s DIY Energy Hacking Gives African Village New HopeMake the World BetterWilliam Kamkwamba on the Daily ShowWhat Kids can Learnappropriate technology

What Dogs Reveal About Evolution

cover of the Greatest Show on Earth by Richard Dawkins

From, The Greatest Show on Earth: The Evidence for Evolution by Richard Dawkins

All breeds of dogs are domesticated wolves: not jackals, not coyotes and not foxes.

Coppinger points out that when domestic animals break free and go feral for many generations, they usually revert to something close to their wild ancestor. We might expect feral dogs, therefore, to become rather wolf-like. But this doesn’t happen. Instead, dogs left to go feral seem to become the ubiquitous “village dogs” – “pye-dogs” – that hang around human settlements all over the Third World. This encourages Coppinger’s belief that the dogs on which human breeders finally went to work were wolves no longer. They had already changed themselves into dogs: village dogs, pye-dogs, perhaps dingos.

Real wolves are pack hunters. Village dogs are scavengers that frequent middens and rubbish dumps.

Belyaev and his colleagues (and successors, for the experimental programme continued after his death) subjected fox cubs to standardised tests in which an experimenter would offer a cub food by hand, while trying to stroke or fondle it. The cubs were classified into three classes. Class III cubs were those that fled from or bit the person. Class II cubs would allow themselves to be handled, but showed no positive responsiveness to the experimenters. Class I cubs, the tamest of all, positively approached the handlers, wagging their tails and whining. When the cubs grew up, the experimenters systematically bred only from this tamest class.

After a mere six generations of this selective breeding for tameness, the foxes had changed so much that the experimenters felt obliged to name a new category, the “domesticated elite” class, which were “eager to establish human contact, whimpering to attract attention and sniffing and licking experimenters like dogs.” At the beginning of the experiment, none of the foxes were in the elite class. After ten generations of breeding for tameness, 18 per cent were “elite”; after 20 generations, 35 per cent; and after 30 to 35 generations, “domesticated elite” individuals constituted between 70 and 80 per cent of the experimental population.

The tame foxes not only behaved like domestic dogs, they looked like them. They lost their foxy pelage and became piebald black and white, like Welsh collies. Their foxy prick ears were replaced by doggy floppy ears. Their tails turned up at the end like a dog’s, rather than down like a fox’s brush. The females came on heat every six months like a bitch, instead of every year like a vixen. According to Belyaev, they even sounded like dogs.

These dog-like features were side- effects. Belyaev and his team did not deliberately breed for them, only for tameness.

The famous domesticated silver fox experiment offers interesting insight into animal traits and evolution.

Related: The Selfish Gene by Richard Dawkins – The Evolution of House CatsDarwin’s Beetles Still Producing SurprisesBackyard Wildlife: Fox

Microcosm by Carl Zimmer

cover of Microcosm by Carl Zimmer

Microcosm: E. Coli and the New Science of Life by Carl Zimmer is an excellent book. It is full of fascinating information and as usual Carl Zimmer’s writing is engaging and makes complex topics clear.

E-coli keep the level of oxygen low in the gut making the resident microbes comfortable. At any time a person will have as many as 30 strains of E. coli in their gut and it is very rare for someone ever to be free of E. coli. [page 53]

In 1943, Luria and Delbruck published the results that won them the 1969 Nobel Prize in Physiology or Medicine in which they showed that bacteria and viruses pass down their traits using genes (though it took quite some time for the scientific community at large to accept this). [page 70]

during a crisis E coli’s mutation rates could soar a hundred – or even a thousandfold… Normally, natural selection favors low mutation rates, since most mutations are harmful. But in times of stress extra mutations may raise the odds that organisms will hit on a way out of their crisis… [alternatively, perhaps] In times of stress, E coli. may not be able to afford the luxury of accurate DNA repair. Instead, it turns to the cheaper lo-fi polymerases. While they may do a sloppier job, E coli. comes out ahead [page 106]
Hybridization is not the only way foreign DNA got into our cells. Some 3 billion years ago our single-celled ancestors engulfed oxygen-breathing bacteria, which became the mitochondria on which we depend. And, like E. coli, our genomes have taken in virus upon virus. Scientists have identified more than 98,000 viruses in the human genome, along with our mutant vestiges of 150,00 others… If we were to strip out all our transgenic DNA, we would become extinct.

I highly recommend Microcosm, just as I highly recommend Parasite Rex, by Carl Zimmer.

Related: Bacteriophages: The Most Common Life-Like Form on EarthForeign Cells Outnumber Human Cells in Our BodiesAmazing Designs of LifeAmazing Science: RetrovirusesOne Species’ Genome Discovered Inside Another’s

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