Tag Archives: books

What Dogs Reveal About Evolution

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.
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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.
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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.
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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.

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.

Statistics Insights for Scientists and Engineers

My father was a engineer and statistician. Along with George Box and Stu Hunter (no relation) they wrote Statistics for Experimenters (one of the potential titles had been Statistics for Engineers). They had an interest in bringing applied statistics to the work of scientists and engineers and I have that interest also. To me the key trait for applied statistics is to help experimenters learn quickly: it is an aid in the discovery process. It should not be a passive tool for analysis (which is how people often think of statistics).

JosÃ© RamÃrez studied applied and industrial statistics at the University of Wisconsin – Madison with my father and George Box. And now has a book and blog on taking statistics to engineers and scientists

The book is primarily written for engineers and scientists who need to use statistics and JMP to make sense of data and make sound decisions based on their analyses. This includes, for example, people working in semiconductor, automotive, chemical and aerospace industries. Other professionals in these industries who will find it valuable include quality engineers, reliability engineers, Six Sigma Black Belts and statisticians.
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For those who want a reference for how to solve common problems using statistics and JMP, we walk through different case studies using a seven-step problem-solving framework, with heavy emphasis on the problem setup, interpretation, and translation of the results in the context of the problem.

For those who want to learn more about the statistical techniques and concepts, we provide a practical overview of the underpinnings and provide appropriate references. Finally, for those who want to learn how to benefit from the power of JMP, we have loaded the book with many step-by-step instructions and tips and tricks.

Stat Insights is a blog by JosÃ© and Brenda RamÃrez.

Analyzing and Interpreting Continuous Data Using JMP by JosÃ© and Brenda RamÃrez. view chapter 1 online.

[We] have focused on making statistics both accessible and effective in helping to solve common problems found in an industrial setting. Statistical techniques are introduced not as a collection of formulas to be followed, but as a catalyst to enhance and speed up the engineering and scientific problem-solving process. Each chapter uses a 7-step problem-solving framework to make sure that the right problem is being solved with an appropriate selection of tools.

William Kamkwamba on the Daily Show

Pointy haired bosses removed the video. Argh!

William Kamkwamba on the Daily show. I first posted about William’s great work in 2007 – Home Engineering: Windmill for Electricity. What a great example of what can be done by sharing scientific and engineering ideas with those who will make the effort to create workable solutions.

William has written a book on his life: The Boy Who Harnessed the Wind.

Home Engineering: Reading in Bed

Photo of Kindle, with read-in-bed holder by Randall Munroe

By Randall Munroe, author of the great XKCD comic, The Pursuit of Laziness

Since I was a kid, I’ve been looking for the perfect way to read in bed.
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I recently got a Kindle. I was intending to use it mainly as a mobile web browser, but I’ve surprised myself by using it to read an awful lot. And, with apologies to all the bibliophiles out there, I find the ergonomics better than a paperback. When snacking and reading, I can lay it flat on a table without the use of a book weight to hold it opened, and when lying in bed, I don’t have to keep moving it to read.

But it’s not perfect. There’s no way to hold it with a finger on the ‘next page’ buttons that doesn’t require a few muscles to hold it upright
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I got out of bed one night, went to the closet, and got a steel coat hanger and some pliers. After a few minutes of twisting, I created this

Continue reading →

Science and Engineering Fiction

cover of The Ice Limit

We always hear of science fiction. But what about engineering fiction? Well I finished reading a book this weekend that was at least as much engineering fiction as science fiction: The Ice Limit by Douglas Preston and Lincoln Child. It was a fun read. I enjoy the books those two collaborate on.

I also finished reading another book recently. I recommend Panic in Level 4 by Richard Preston. He wrote The Hot Zone, which is also great. He writes what “literary nonfiction” or “creative nonfiction.” The book includes 2 stories on math, about the Chudnovsky brothers, and 4 on biological science stories. I believe they were all previously stories in the New Yorker.

Douglas Preston and Richard Preston are brothers. It is just a happy co-incidence I happened to read them both recently. I just noticed the last names were the same so I looked online to see if they were related. Here is a nice bit from Douglas Preston’s web site:

As they grew up, Doug, Richard, and their little brother David roamed the quiet suburbs of Wellesley, terrorizing the natives with home-made rockets and incendiary devices mail-ordered from the backs of comic books or concocted from chemistry sets.
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After unaccountably being rejected by Stanford University (a pox on it), Preston attended Pomona College in Claremont, California, where he studied mathematics, biology, physics, anthropology, chemistry, geology, and astronomy before settling down to English literature.

Also I read Tyrannosaur Canyon by Douglas Preston a few months ago. I preferred it to Ice Limit actually (but it didn’t have the engineering fiction angle) just a fun thriller with some science fiction thrown in.

Beautiful Basics of Science

Natalie Angier’s recent book, The Canon, is a great overview of the world of science. The book gets a bit too carried away with being cute (A top-of-the-line radar can pinpoint the whereabouts of a housefly two kilometers away, although clearly this is a radar with far too much time on its hands), but overall is excellent. Such lines are find, in moderation, but this book has too many by a factor of 10 or 100. Some gems from the book:

page 19: Science is not a rigid body of facts. It is a dynamic process of discovery.

page 47: true happenstance bears a distinctive stamp, and until you are familiar with its pattern, you are likely to think it messier, more haphazard, than it is… it often makes people uncomfortable by not looking random enough.

page 92: while the different atoms are all about the same size – a tenth of a billionth of a meter across – they diverge in their mass, in the number of protons and neutrons with which their nucleus is crammed.

page 99: If you drag a comb through your dry hair, the comb will strip off millions of electrons from the outermost shells of the atoms of you coiffure.

The details are great (about a trillion electrons are involved when you get a small static electricity shock) and it is an excellent book for those interested in an overview of science that does not require in depth science education to follow. And yet with a good background in science the material presented is still plenty interesting.

The Science of Gardening

Photo of a bee by Justin Hunter

The Science of Gardening

Linda Chalker-Scott, an associate professor at Washington State University, is the author of The Informed Gardener and producer of the column “Horticultural Myths.” In The Truth About Garden Remedies: What Works, What Doesn’t, and Why, Jeff Gillman, associate professor at the University of Minnesota, is just as rational and informative
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Do go ahead and dig in soil improvements, Chalker-Scott advises, for vegetable gardens or annual flowerbeds, in which nutrients need replacing yearly. But there’s really no need to dig organic amendments—manure and peat moss, etc.—into landscapes that are permanent. Treat those plantings of trees and shrubs as if they were forest ecosystems, not agricultural fields—wood chips and decaying leaves on top, no tilling-in of fertilizer.
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It must drive both authors nuts to hear people say, “I’m an organic gardener. I never use chemicals.” Everything on earth is composed of chemicals.

The last line calls to mind the recent Royal Society of Chemistry attempt to reclaim the word chemical from the advertising and marketing industries: Â£1,000,000 for 100% chemical free material. A good example for our scientific literacy posts.

Photo by Justin Hunter.

Ender in Exile by Orson Scott Card

Ender in Exile by Orson Scott Card has just been published. It is the ninth book in the Ender Wiggen series that began with Ender’s Game (Hugo and Nebula book award winner). I love the Ender series and have a table showing the sequence of the books. The books have not been published in the order of events in the fictional world. Ender in Exile is directly follows Ender’s Game (which makes it 3rd in story order – since Ender’s Shadow took place concurrently with Ender’s Game).

You can listen to Orson Scott Card read from Ender in Exile.

I include this post because I enjoyed the book. It doesn’t really have much to do with science or engineering but here is a quote from the book (page 106): “Besides, that’s what science was – the sharing of information the pooling of knowledge. That’s my gene pool, Afriama, he thought. The meme pool, the collective knowledge of science. What I discover here, what I learn, the problems I solve – those will be my children.”

Enjoy the book, and if you have not read Ender’s Game I highly recommend it. You can read the original Ender’s Game short story online. And if you haven’t read The Investment Counselor (about Jane, Ender’s computer companion) it is excellent (included in First Meetings in Ender’s Universe)

Toward a More Open Scientific Culture

Michael Nielsen wrote a great post, The Future of Science, which is also the topic of a book he is writing. He discusses how scientific advancement has often been delayed as those making discoveries did not share them openly. And how 300 years ago scientific journals and reward systems created ways for scientists to be rewarded for publication. And he continues with the need for the process to again change and promote more open sharing of scientific knowledge, which I agree with and have written about previously: Publishers Continue to Fight Open Access to Science, Science Journal Publishers Stay Stupid, The Future of Scholarly Publication, etc..

Why were Hooke, Newton, and their contemporaries so secretive? In fact, up until this time discoveries were routinely kept secret.
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This cultural transition was just beginning in the time of Hooke and Newton, but a little over a century later the great physicist Michael Faraday could advise a younger colleague to “Work. Finish. Publish.” The culture of science had changed so that a discovery not published in a scientific journal was not truly complete. Today, when a scientist applies for a job, the most important part of the application is their published scientific papers.

This has been a great advance. Now we need to continue that advance to use the internet to make that publication open and increase the advantage of shared knowledge to society.

The adoption of the journal system was achieved by subsidizing scientists who published their discoveries in journals. This same subsidy now inhibits the adoption of more effective technologies, because it continues to incentivize scientists to share their work in conventional journals, and not in more modern media.
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This means: making many more types of content available than just scientific papers; allowing creative reuse and modification of existing work through more open licensing and community norms; making all information not just human readable but also machine readable; providing open APIs to enable the building of additional services on top of the scientific literature, and possibly even multiple layers of increasingly powerful services. Such extreme openness is the ultimate expression of the idea that others may build upon and extend the work of individual scientists in ways they themselves would never have conceived.
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To create an open scientific culture that embraces new online tools, two challenging tasks must be achieved: (1) build superb online tools; and (2) cause the cultural changes necessary for those tools to be accepted.

I agree we need to take advantage of the new possibilities to advance the practice of science. His full post is well worth reading.