Saturday, May 25, 2013

Gun Deaths vs. Gun Ownership


http://mark.reid.name/blog/gun-deaths-vs-gun-ownership.html

Gun Deaths vs. Gun Ownership

In the wake of the tragic shooting at Sandy Hook Elementary School there was a flurry of discussion about gun control in my Twitter and Facebook feeds. One statistic from an April 2012 New Yorker article caught my attention:
The United States is the country with the highest rate of civilian gun ownership in the world. (The second highest is Yemen, where the rate is nevertheless only half that of the U.S.) No civilian population is more powerfully armed.
I posted this quote on Facebook and was asked whether there was any correlation between rates of gun ownership and gun-related deaths. After 20 minutes of grabbing some data on worldwide gun ownership and gun deaths from Wikipedia and running it through R I produced the following graph.
Gun deaths vs. Gun Ownership for OECD countries
Gun-related deaths per capita vs. gun ownership per capita in OECD countries.
Update - 19 Dec. 2012: The above graph was correct for the data I obtained for Wikipedia on the 17th. It has since been updated. See the update at the end of this post for details.
I posted this graph on Twitter late on Sunday night and woke up this morning to find it had been retweeted over 200 times. In addition, there were a large number of questions and requests for different graphs.
So that others can analyse the data I used themselves, I thought I would write up how I created the graph.

The Data

The first step was finding data on gun ownership and gun-related deaths and getting it into R.
A quick search revealed Wikipedia articles on countries by firearm-related death rate andNumber of guns per capita by country. I cut and pasted the tables in these articles into atext editor and saved them as CSV files. I also grabbed a list of OECD countries from Wikipedia and converted it. You can grab the resulting files here:
Update - 19 Dec. 2012: The above data was what was available on Wikipedia when I wrote this post. It has since been changed. See the discussion at the end of this post for details.

The Code

The R code I used to create the plot is given below. It simply reads in the data from the guns and deaths CSV files, merges them, adds a column denoting whether a country is in the OECD, and then plots the results.
guns <- read.table("data/guns.csv", sep="\t", header=TRUE)
deaths <- read.table("data/deaths.csv", sep="\t", header=TRUE)
oecd <- read.table("data/oecd.csv", sep="\t", header=TRUE)

data <- merge(guns, deaths, by="Country")
data$OECD <- data$Country %in% oecd$Country

with(subset(data, data$OECD == TRUE), {
 plot(Deaths ~ Guns,
  main="Gun Deaths vs Gun Ownership",
  xlab="Guns per 100 people",
  ylab="Gun deaths per 100k people",
  xlim=c(0,100)
 );
 text(Guns, Deaths, Country, pos=1)
})
You can get all the code I used to generate the figures in this post here:

Other Graphs

I was asked a number of good questions about the graph I posted on Twitter. In particular, several people were surprised at the number of gun-related deaths for Switzerland. As the following graph of gun homicides vs. gun ownership shows, most of those deaths are actually suicides.
Gun homicides vs. Gun Ownership for OECD countries
Gun homicides per capita vs. gun ownership per capita in OECD countries.
Gun homicides vs. Gun Ownership for OECD countries (Detail)
Detail of gun homicides per capita vs. gun ownership per capita in OECD countries.
Finally, here is a plot of homicide vs. ownership across all countries — not just those in the OECD. The mass of countries in the lower left corner is unreadble but you can see those countries with either high homicide rates or high gun ownership clearly.
Gun homicides vs. Gun Ownership for all countries
Gun homicides per capita vs. gun ownership per capita in all countries.
Just to be clear, I am not making any claims about the effect of gun ownership on shootings. I just wanted to show how easy it is to use freely available data to help answer reasonable questions about heated political issues like gun control.
I’ll leave you to draw your own conclusions.

Update (19th Dec. 2012)

The response and attention to these plots — both positive and negative — on Twitter, in the comments below, and via email has been a little overwhelming. So much so that my site went down yesterday due to me hitting the (usually sufficient) bandwidth cap my host provides.

Data Updates

Several people noted that the data I plotted for Switzerland was inconsistent with what was on Wikipedia. If you look at the edit history for the firearm-related death rate page on Wikipedia you will see that someone updated the Switzerland data late on the 16th of December. Taking into account that Canberra, Australia is GMT+11 this update occurred after I scraped the page for the data I used here.
I have redone the OECD plots with data scraped from the same pages as of 3:30pm on the 19th. You can see the results and get the new data below.
Gun Deaths vs. Gun Ownership for OECD countries Gun homicides vs. Gun Ownership for OECD countries
Gun deaths (left) and homicides (right) per capita vs. gun ownership per capita in OECD countries (click to view larger images).
The new data is here:

Other Analyses

A number of people pointed me to analyses they had done of similar data, criticisms of this post, and alternative sources of data. Here is a summary of some of those other contributions:

Disclaimer

Finally, in light of some of the more vocal criticism I’ve received, I feel I should reiterate a few points:
  • At no point have I ever claimed that this is even close to a rigorous analysis. In my original tweet and here I have made it clear that I have used data from Wikipedia. Since I thought it was common knowledge that Wikipedia should never be used as a primary source for any kind of real research, I didn’t expect people to confuse this post with a serious study.
  • I have not attempted to use these plots to draw any kind of conclusion about the relationship between gun ownership and gun deaths. Indeed, I do not think there exists a simple explanation. All I intended to do was attempt to shed some light on a question I was asked about a possible correlation.
  • I will not run any kind of statistical test on the above data (e.g., rank correlation coefficients). For any such quantity to be meaningful I would need to assume that the data I collected was much more carefully controlled for. Since I just grabbed it from Wikipedia, this is clearly not a valid assumption.
  • I do not intend to create more graphs showing other data or other statistics. Other people (see the links above) have already done so for a variety of alternative data. Also, I realise their are better sources of data out there than Wikipedia. However, as I’ve said before, my intention was not to do a definitive study but rather show how a readily accessible source (i.e., Wikipedia) can be used to quickly get an overview of a topic.
I will probably not the last person to use Wikipedia for this sort of amateur analysis. Therefore, if you believe the data I have used is incorrect or out of date, I suggest you solve the problem at the source and update (with references) the relevant entries on Wikipedia.
If you have a question about other possible correlations or relationships, feel free to apply the code above to what ever sources of data you think might help answer it. I’d appreciate it if you link to what you find in the comments below.
Mark ReidDecember 17, 2012Canberra, Australia
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Friday, May 24, 2013

Cooked Meat, Carcinogens, and Other Diet Issues



20130513 Diet Notes for fb version 2.3
Friends have been asking me to explain why I am so convinced a plant-based diet leads to better health. Here is an overview. These are short, two to four minute videos by Dr. Greger. They are based on articles from peer-reviewed medical journals yet they are very easy to understand. On http://nutritionfacts.org/ you can find citations for the original papers. You can follow links to the original papers. If you start reading the references to the original papers, you will soon discover there are thousands of studies behind the research in these videos.


If you have any questions on integrative health I have an online subscription to Natural Standard and can provide a quick answer to many questions.



"Natural Standard was founded by healthcare providers and researchers to provide high-quality, evidence-based information about complementary and alternative medicine including dietary supplements and integrative therapies. Grades reflect the level of available scientific data for or against the use of each therapy for a specific medical condition."

And, if you want to see the original research papers, I also have access to PubMed.


"PubMed comprises more than 22 million citations for biomedical literature from MEDLINE, life science journals, and online books."

Dr. Greger can, at times, be overly enthusiastic. And, at other times, he can be too simplistic. If you have any doubts at all, I strongly recommend you both read the original papers and consult Natural Standard.



My interest first started when I discovered T. Colin Campbell and The China Study

About the same time I discovered the work of Caldwell Esselstyn, MD.

I was so taken by the Campbell and Esselstyn videos that I began to read and read and read. I have stayed away from the popular press and especially discussions on fad diets. I want evidence so I look to large scale epidemiological studies, in vitro studies, and in vivo studies. I want to see causal explanations based in biochemistry. And, I want to see multiple, independent studies where the preponderance of evidence converges.

In my reading, I was often inspired to follow new paths by Dr. Greger’s DVDs ( http://www.drgreger.org/ and http://www.drgreger.org/DVDs/ ). In 2011, he made all the DVD segments available on-line at http://nutritionfacts.org/. What follows are the videos that most influenced me.

The Tomato Effect

“Why does the medical establishment sometimes ignore highly efficacious therapies such as plant-based diets for heart disease prevention and treatment?” 20111014

My Personal Favorites

“How to essentially eliminate the great scourge of the Western world.” 20110217

“Dr. Dean Ornish proved decades ago that heart disease could be reversed solely with diet and lifestyle changes.” 20111011

“Dr. Dean Ornish turns from reversing heart disease to trying to reverse prostate cancer.” 20110218

“Profile of an editorial published by Dr. Dean Ornish in the American Journal of Cardiology describing the optimal diet and how simple choices can be as powerful as drugs and surgery.” 20110611

For many more videos and papers on cancer and diet see http://nutritionfacts.org/topics/cancer/. Especially interesting are

“Researchers discovered a dietary intervention that may slow the progression of cancer.” 20100818

“Two weeks on a plant-based diet appears to significantly enhance cancer defenses against breast cancer and colon cancer cells. The blood of those eating a vegan diet for a year suppresses cancer cell growth nearly eight times better.” 20120918

“Breast cancer can take decades to develop, so early detection via mammogram may be too late.” 20110919

Stem Cells

“A new theory of cancer biology—cancer stem cells—and the role played by sulforaphane, a phytonutrient produced by cruciferous vegetables.” 20120312

“In a test tube, the broccoli phytonutrient sulforaphane appears to target breast cancer stem cells, but how do we know it’s even absorbed into the body? Have women undergoing breast reduction surgery eat some an hour before their operation and directly measure the level in their tissues.” 20120313

See more at

IGF-1

“Insulin-like growth factor (IGF-1) is a natural human growth hormone instrumental in normal growth during childhood, but in adulthood can promote abnormal growth—the proliferation, spread (metastasis), and invasion of cancer.” 20120925

“Lower cancer rates among those eating a plant-based diet may be a result of reduced blood levels of IGF-1 and enhanced production of IGF-1 binding protein.” 20120927

“Those eating vegan had significantly lower IGF-1 levels and higher IGF binding proteins than those just eating vegetarian, suggesting that the more plant-based one's diet becomes, the lower one's risk of fueling growth hormone dependent cancer growth.” 20120928

“Animal protein consumption triggers the release of the cancer-promoting growth hormone IGF-1.” 20121001

“The reason animal proteins trigger the release of the cancer-promoting growth hormone IGF-1 more than plant proteins may be because the relative ratios of amino acids in animal proteins more closely resembles our own.” 20121002

“While animal proteins increase levels of the cancer-promoting growth hormone IGF-1, and most plant proteins bring levels down, “high quality” plant proteins such as soy may not significantly affect levels in either direction. This, however, may depend on the quantity consumed.” 20121003

Inflammation

“A single meal of meats, eggs, and dairy can cause a spike of inflammation within hours that can stiffen one's arteries. Originally this was thought to be the result of saturated animal fat causing our gut lining to leak bacterial toxins into our blood stream leading to endotoxemia.” 20120704

“The endotoxemia (bacterial toxins in the bloodstream) that follows a meal of animal products and results in inflammation and stiffened arteries may come from the food itself rather than from one's own gut bacteria.” 20120705

“The high bacteria load in raw or cooked animal foods and fermented foods may trigger an endotoxemic surge of inflammation that may be exacerbated by the presence of saturated animal fat.” 20120706

Protein and Heart Disease

“Why is the intake of animal protein associated with heart disease–even independent of saturated fat—and the intake of plant protein protective?” 20121109


“Because certain tumors such as breast cancers thrive in settings of low-grade inflammation, our immune response can sometimes facilitate tumor growth.” 20121210

“Because certain tumors such as breast cancers thrive in settings of low-grade inflammation, our immune response can sometimes facilitate tumor growth.” 20121210
“This is the first of a seven video series that takes a deep dive into the human immune system to bring you Neu5Gc, a molecule in meat that human tumors may use to facilitate growth. It's one of the most fascinating topics in modern day nutrition—stay tuned! I've done similar in-depth series on reversing cancer cell growth, why animal products cause inflammation, changing vitamin D recommendations, arugula athleticism, why nuts don't appear to cause expected weight gain, as well as the latest dietary guidelines.” 20121210

“We may have a billion different types of antibody-releasing cells in our immune system, such that each recognizes a different molecular signature.” 20121211
“Isn't our immune system spectacular?! In Wednesday's video of the dayClonal Deletion Theory of Immunity we'll explore the flipside—how our immune system avoids attacking us. See yesterday’s NutritionFacts.org video-of-the-day Cancer as an Autoimmune Disease for an explanation of the autoimmune theory of cancer. Why all this background? This is all a set up so everyone can understand the dietary implications of Thursday's video The Inflammatory Meat Molecule Neu5Gc.” 20121211

“Plant-based diets may be protective against multiple sclerosis because IGF-1 can prevent our immune system from eliminating autoimmune cells.” 20121212
“This is the third video in a series on understanding the autoimmune theory of cancer outlined in Monday's video Cancer as an Autoimmune Disease, followed up with Tuesday's video-of-the-day Clonal Selection Theory of Immunity. For the story of how dietary manipulation of IGF-1 may affect cancer risk, see The Answer to the Pritikin Puzzle and How Plant-Based to Lower IGF-1? IGF-1 also appears to affect prostate gland growth. See Some Prostates Are Larger than Others, Prostate Versus Plants, and Prostate Versus a Plant-Based Diet. Tomorrow we'll finally get around to the star of this video series, The Inflammatory Meat Molecule Neu5Gc.” 20121212

“Plant-based diets may help rheumatoid arthritis by decreasing exposure to an inflammatory compound found in animal products.”20121213
“Bacterial endotoxins are another reason animal products may trigger an inflammatory immune reaction. See The Leaky Gut Theory of Why Animal Products Cause Inflammation, The Exogenous Endotoxin Theory, and Dead Meat Bacteria Endotoxemia. For more on arthritic joint disorders, see Diet & Rheumatoid Arthritis and Preventing Arthritis. For the role saturated animal fat may play in heart disease and cancer see Blocking the First Step of Heart Disease, Breast Cancer Survival, Butterfat, and Chicken, and Trans Fat, Saturated Fat and Cholesterol: Tolerable Upper Intake of Zero. What does this video have to do with the previous few about Cancer as an Autoimmune Disease? You'll see in tomorrow's video of the day How Tumors Use Meat to Grow: Xeno-Autoantibodies.” 20121213

“Cancer may use a molecule found in animal products to trick our immune system into feeding it with inflammation.” 20121214
“Make sure you see the "prequels" to this video Cancer as an Autoimmune Disease and yesterday’s NutritionFacts.org video-of-the-day The Inflammatory Meat Molecule Neu5Gc. Why else might those eating plant-based diets have lower risk of all cancers combined? It could be the lack of IGF-1, heme iron, inflammation, viruses, antibiotics, saturated fat,nitrosamines, and arachidonic acid associated with animal product consumption. Or it could be the DNA repair, cellular stress defenses, anti-inflammatory properties, soy, lignans, phytonutrients, and fiber associated with healthy plant food consumption.” 20121214

“The foreign meat molecule Neu5Gc builds up in human tumors and atherosclerotic plaques and may play an inflammatory role in the progression of both diseases.” 20121217

“See The Inflammatory Meat Molecule Neu5Gc for background and Friday's video-of-the-day How Tumors Use Meat to Grow: Xeno-Autoantibodies for the role it might play in cancer growth. Inflammation (also caused by exogenous endotoxins) is one of the three steps en route to fatal heart disease. See Arterial Acne, Blocking the First Step of Heart Disease, and Making Our Arteries Less Sticky. Antioxidants found predominantly in plants may also decrease inflammation within the body. Nuts may be particularly useful in this regard. Tomorrow we'll close out the Neu5Gc story with Meat May Exceed Daily Allowance of Irony.” 20121217

“The foreign meat molecule Neu5Gc may not only contribute to the progression of cancer and heart disease by supplying inflammation, but also set children up for life-threatening reactions to E. coli toxins originating in the same animal products.” 20121218

See a summary at

PhIPs

“DNA-damaging chemicals formed when meat is cooked stimulate breast cancer cells almost as much as pure estrogen and can infiltrate the ducts where most breast cancers arise.” 20120116

“The cooked meat carcinogen PhIP found in fried bacon, fish, and chicken may not only trigger cancer and promote tumor growth, but also increase its metastatic potential by increasing its invasiveness.” 20120118

“Those who eat meat risk food poisoning from undercooked meat, but also exposure to cooked meat carcinogens in well-cooked meat. By boiling meat, non-vegetarians can mediate their risk of both.” 20130121

“Even vegetarians could potentially be exposed to the carcinogens typically formed by cooking meat though eggs, cheese, creatine sports supplements, and cigarette smoke.” 20120121

“Using the cooked meat carcinogen PhIP to turn normal breast cells cancerous, researchers explore the use of green tea to interrupt this malignant transformation.” 20130125

“Garlic and flavonoid phytonutrients found in fruits, vegetables, greens, and grains appear to protect against DNA damage induced by mutagenic chemicals found in cooked meat.” 20130128

“The boost in detoxifying enzymes triggered by cruciferous vegetable consumption may last for weeks!” 20130130

“The polycyclic aromatic hydrocarbons in the vapors released from cooking meat may be hazardous for fetal development and increase the risk of cancer.” 20130201

A popular press summary article. 20120201


Real Anti-Aging

“The first dietary intervention shown to boost telomerase activity.” 20110222
Uprooting the Leading Causes of Death 

“Death in America is largely a foodborne illness. Focusing on studies published just over the last year in peer-reviewed scientific medical journals, Dr. Greger offers practical advice on how best to feed ourselves and our families to prevent, treat, and even reverse many of the top 15 killers in the United States.” 20120726




More Than an Apple a Day: Combating Common Diseases

Dr. Greger has scoured the world’s scholarly literature on clinical nutrition and developed this brand-new live presentation on the latest in cutting-edge research on how a healthy diet can affect some of our most common medical conditions." 20130715



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