Book Reviews, Engineering

Book Review: “What is a p-value anyway? 34 Stories to Help You Actually Understand Statistics” by Andrew J. Vickers

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Review on Video:

When I was studying engineering, Statistics was not a required subject. It wasn’t until I started working that I appreciated the power of statistics. In this imprecise world, many things can be explained only in statistic terms like confidence level, insufficient sample size and etc. I got a full lesson of statistics as part of the my MBA degree curriculum. Ever after taking many more statistics-related class and going through a full Six Sigma Green Belt training, there are a few things about statistics that are still hard to grasp. It’s not just p-value that confused people, there are simply too many pitfalls when novices or even experts apply statistics to real life problems.

The author organizes 34 stories across 34 chapters. Since the author works in the medical field, he mentioned quite a few tidbits about how drugs were clinical tried. It’s a good book for beginners as well as people who used statistics regularly to watch out for its pitfalls. You might get a different perspective about statistics. I did.

My key takeaways – some refresher and something new:
1. Many things in life doesn’t follow normal distribution, especially the ones involve physical ability (pregnancy duration, body BMI). Sometimes log scale fits better.
2. Two sorts of variation: observable natural variations (reproducibility), variation of study results (repeatibility).
3. Statistical ties, e.g. in election poll, means that the confidence interval includes/overlaps with no difference.(Chap. 12)
4. P-values test hypotheses. (Chap. 13)
5. Statistics are mainly used for inference (test hypotheses) or prediction (extrapolation, interpolation).
6. Null hypotheses is a statement suggesting that nothing interesting is going on (status quo) that there is no difference between that observed data and what was expected or no difference between two groups. The P-value is the probability that the data would be at least was extreme as those observed if the null hypotheses were true.
6. T-test vs. Wilcoxon test (new to me). If the data is very skewed, use Wilcoxon test whose data must be converted to ranks first. (Chap. 16)
7. Precision (width of confidence interval) = variation/ sqrt(sample size). To reduce the confidence interval (enhance precision) by half, you’d need 4 times of the sample size – very expensive. To get the sample size for a specific test = (noise or variation / signal or confidence interval )^2.
8. “Adjust the results” can be applied to multi-variable regression to help with confounding (confusing). (Chap. 19).
9. Sensitivity is the probability of a positive diagnostic test given that you have the disease (true positive). Specificity is the probability that a negative diagnostic test given that you don’t have the disease (true negative). The most worrisome situations are when the test comes back positive if they indeed have the disease (positive predictive value) or when the test comes back negative and the patient is truly free of disease is the negative predictive value. (Chap. 20)
10. Don’t accept the null hypothesis. Instead say “we could not show a difference.” Don’t use a p-value of 0, say “P < 0.001" instead. 11. Some test methods, e.g. chi-squired and ANOVA, only provides P-value - no estimates. Correlation provides estimates but no inferences. 12. One common error is to calculate the probability of something that has already happened. Then come into conclusions about what caused it based on whether that probability is how or low. E.g. calculation of the odd OJ killed his wife. Instead, the question to ask is "if a woman has been murdered and has been previous beaten by her husband, what is the chance of he was the murderer." 13. Conditional probability depends on both the probability before the information was obtained (prior probability of a heart disease) and the value of he information (such the accuracy of the heart test). 14. The more statistical tests you conduct, the greater the chance that one will come up statistically significant, even if the null hypothesis is true. 15. A smaller study has a good chance of failing to reject the null hypothesis, even if it's false. Subgroup analysis increases both the rise of falsely rejecting the null hypothesis when it's true and falsely failing to reject the null hypothesis when it's false. 16. P-values measure strength of evidence, not size of an effect.
17. Don’t compare p-values.
18. Many statistical errors occur because of starting the clock at the wrong time.
19. Lead time bias. If you find a way to find the problem earlier, then the time between the problem and the end result will be longer.
20. Statistics is used to help scientists analyze data, but is itself a science.
21. Statistics should be about linking math to science: a. think through the science and develop statistical hypotheses in the light of specific question. b. interpret the results of the analysis in terms of their implications for those questions.
22. Statistics is about people even if you can’t see the tears.

Book Reviews, Gardening

Book Review: “Teaming with Microbes – A Gardener’s Guide to the Soil Food Web” by Jeff Lowenfels & Wayne Lewis

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My first time with the book review on video: It’s a lot of work but worth a try.

Learned a lot of bacteria and fungi and how they affect the plants – the symbiotic relationship among them. Very interesting. This is a must read for any one aspiring to be have a green thumb – gardener.

The book starts out with the basic science of the food web – how the roots secretes exudates to feed the microbes which in turn feed the the root. The nutrients come from the microbes in the organic world instead of the N-P-K petroleum-based fertilizers.

The food web from USDA.
USDA Food Web

Chapter 2 goes into the soil science – informative but not very interesting.

Chapter 3 covers the bacteria. Now that’s the half of the magic. The two groups: aerobic and anaerobic bacteria. The good soil smell comes from the volatile chemicals given out by the actinomycetes – particularly adept at decaying cellulose (long chain of carbon-based glucose that gives plants structure) and chitin. The Nitrogen cycle is introduced here.

Chapter 4 covers the fungi. The job of fungi is still mysterious to many scientists and it’s a huge topic by itself. I think this chapter added more confusion than clarification. I’ll find other sources to dig deeper.

Chapter 5, 6, 7, 8, 9, 10, 11 cover the Algae and Slim Molds. (Not much there). Protozoa (single-cell organism that eats bacteria), Nematodes (nonsegmented, blind roundworms), antropods (flies, beetles, and spiders), earthworms, and gastropods (snails), reptiles, mammals, and birds.

Part 2: is about applying soil food web science to yard and garden care.

I got the most out of the compost tea making. But for the most parts the following 19 rules are the key points:

1) Some plants prefer soils dominated by fungi; others prefer soils dominated by bacteria.
2) Most vegetables, annuals, and grasses prefer their nitrogen in nitrate form and do best in bacterially dominated soils.
3) Most trees, shrubs, and perennials prefer their nitrogen in ammonium form and do best in fungal dominated soils.
4) Compost can be used to inoculate beneficial microbes and life into soils around your yard and introduce, maintain, or alter the soil food web in a particular area.
5) Adding compost/ compost teas and its soil food web to the surface of soil will inoculate the soil with the same soil food web.
6) Aged, brown organic materials support fungi; fresh, green organic materials support bacteria.
7) Mulch laid on the surface tends to support fungi; mulch worked into the soil tends to support bacteria.
8) If you wet and grind mulch thoroughly, it speeds up bacterial colonization.
9) Coarse, dryer mulches support fungal activity.
10) Sugars help bacteria multiply and grow; kelp, humic and fulvic acids, and phosphate rock dusts help fungi grow.
11) By choosing the compost you begin with and what nutrients you add to it, you make teas that are heavily fungal, bacterially dominated, or balanced.
12) Compost teas are very sensitive to chlorine and preservatives in the brewing water and ingredients.
13) Applications of synthetic fertilizers kill off most or all of the soil food web microbes.
14) Stay away from additives that have high NPK numbers.
15) Follow any chemical spraying or soil drenching with an application of compost tea.
16) Most conifers and hardwood trees (birch, oak, beech, and hickory) form mycorrhizae with ectomycorrhizal fungi.
17) Most vegetables, annuals, grasses, shrubs, softwood trees, and perennials form mycorrhizae with endomycorrhizal fungi.
18) Rototilling and excessive soil disturbance destroy or severely damage the soil food web.
19) Always mix endomycorrhizal fungi with the seeds of annuals and vegetables at planting time or apply them to roots at transplanting time.

Gardening

The Making of Bokashi Soil Maker

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In this video, I’d like to show I turn the Bokashi-pickled kitchen waste into fertilized soil. This is the second step of the whole process:

1. Pickle Kitchen Waste with Bokashi bran for 2 weeks,
2. Bury into or pile on to the native soil for 4 to 6 weeks
3. Fertilized soil or compost. Apply it to plants or plant on top of it.

Hope you enjoy the video!

Gardening

Bokashi Soil Maker Harvest – A Big Surprise!

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Bokashi compost consists of two steps: 1. Pickling the kitchen wastes with Bokashi bran, 2. Mix or bury them into native soil to complete the composting process. For the second step, instead of digging a hole and burying them into the hole, I used a hollowed up bucket to build up the compost so I can use them directly to fertilize plants. This was called the “Soil Maker” technique by some experts. Well, I got a big surprise when I open up the Soil Maker bucket at the end of the 2nd stage. Check out the video: Be forewarned that you probably don’t want to watch this while eating.

It was all crawling with some kind of worms, maggots, or larvaes. They are called Black Soldier Fly larvaes, I later found out that they’re beneficial bugs, believe it or not. People actually harvest them to feed the chickens, ducks and birds. Very interesting and gross. I never intended to grow them but they showed up and ate up half of the pickled Bokashi kitchen waste.

I learned that things don’t always turn out to be what you expected. If that happened, you may learn something from it.

Tips for computer

Cygwin Installation Problem – “Unable to get setup.ini”

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For those people who work between Windows and Unix environments (like Solaris, Linux and etc.), Cygwin and Cygwin-X is like a godsend. Cygwin-X allows the PC to work in the X-windows environment with ease. Most of the Unix X-windows applications can be “hosted” under Cygwin-X running on MS Windows, making it a seamless extension of the Unix OS.

During one of the Windows 7 update, my Cygwin app environment got wiped out, probably because I installed the 32-bit version of the Cygwin-X, while my Windows 7 is 64-bit. So I had to re-install it from Cygwin.

I downloaded the “setup.exe” from the website and kept encountering the “Unable to get setup.ini” error message (see below) after switching to many other mirror download sites.

Cygwin_setup_init

To spare you of the pain I went through, I downloaded and ran the setup-x86_64.exe from Cygwin.com directly. Voila, the problem was fixed. I was able to install all of the Cygwin apps without any issue.

Gardening

Why and How I do Bokashi Compost

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As I mentioned before, I practice Bokashi composting at home. The key benefits of Bokashi composting:
1. It doesn’t stink: The traditional compost can easily go stinky and attract gnats and flies if not properly aerated or turned.
2. Almost all kitchen wastes can be composted: Yes, add your fish, meats and other protein-rich materials, which traditional compost won’t do without being taken over by an army of critters.
3. The compost process is relatively fast: takes 2 weeks to “pickle” or for the Kokashi bacterial to propagate and another month for the 2nd phase of breakdown in the soil – about a 1 1/2 month effort. The traditional composting could take as long as a year.
4. You can compost kitchen wastes incrementally in small batches like in a typical urban home. The traditional compost requires a big batch of 3’x3’x3′ critical mass to be effective.
5. It can be used to feed your vermicompost (worm compost). Worms devour them. But it needs to fed in small amount and allows it to sit in the corner of the worm bin for the acidity level to go down a bit before worms would work on them.

Nothing is more exciting for me to see a big chunk of our family garbage not go into the landfill but turn into some kind of vibrant, rich fertilizer for my garden which in turn feed my family. All is done with a little help from the microbes in the Bokashi bran! It’ a win-win for everyone. I encourage you all to give it a try.

Now you’re all pumped up and ready to take some actions! The next question:
How do you do Bokashi compost? Here’s a video how I do it:

To give the proper credit, I learned a lot from other websites and Youtube videos as follows:
1. Prokashi.com and his video channel.
2. Bokashi Videos – no new updates.

Where to buy your Prokashi bran?
1. Amazon.com
2. Prokashi.com.
3. Do It Yourself. See my video.

Learn by Blogging (and Sharing) – Derek Tsai's Personal Blog