Kenya (Again)
I’m not completely over my jetlag from Japan and now I’m fighting it in Kenya…. so I thought I’d finally post again for the first time in nearly a month (!). This will be a short one, but…
What I’ve seen today:
1) Iron Man 3 is playing in IMAX in Nairobi. The best that a lot of African countries have for cinema choices are small (but excellent) one room DVD/TV theaters which run gore and action movies all day long. At one time, cinemas were present all over Africa. DVDs and problems with security led to their decline. Nairobi, the oasis of development it is, offers current IMAX movies. A little disorienting.
2) People are so excited that the election went smoothly and with little violence, despite the sensationalist pessimistic predictions of the western media. What happens to those who were to stand trial at the ICC, but are now (and again) elected members of the Kenyan government, remains to be seen. I’m pretty sure that Kenyans are far more familiar with the International Criminal Court that just about any other group of people on the planet.
3) A wave of hysteria (a diagnosible and treatable medical condition in Kenya) has attacked students in a nearby town. A teacher was accused of bewitching the students. 2,000 locals attacked the school and attempted to beat the teacher, though she escaped.
4) It is an offense to talk on the cel phone while driving in Kenya. Offenders must appear in court and pay a $75 fine. It is rare to see people talking on the phone and driving in Nairobi.
That’s all I have today. Gotta take this return to blogging thing in baby steps….
Economics, Austerity and the Selective Use of Data
Reinhart and Rogoff
Policy makers in the US and Europe seized on the paper as proof that cutting stimulus and social programs was a good idea, and proceeded to do so with abandon. Of course, right wingers wanted to cut money to social programs anyway, and would have done so regardless, but the paper was held out as scientific proof that it was a solid plan of action.
I won’t comment on how strange it was that Republicans were interested in science at all, given recent efforts to politicize the NSF and micromanage the grant decision process.
The trouble was that the results presented in RR were shown to be based on the selective use of data. Thomas Herndon, a 28-year-old graduate student, obtained the dataset from RR themselves and couldn’t reproduce the results.
In fact, he found that the only way to accurately reproduce the results in RR’s paper that showed that high debt restrained economic growth was to exclude important cases. When including the missing data, high debt was associated with consistently positive growth, though modestly slowed.
Originally, I took the view that this was a case of sloppy science. RR had a dataset, got some results which fit the narrative they were pushing and didn’t pursue the matter any further. Reading Herndon’s paper, however, I changed my mind.
Economic growth vs. debt to GDP Ratio (1946-2010). Loess curve included to illustrate trend.
To me, this is a pretty fuzzy result. Though the loess curve (an interpolation method to illustrate trend) suggest that there is *some* decline in growth overall, I’d still ding any intro stats student for trying to suggest that there’s any relationship at all. There is no way that RR, both trained PhD’s and likely having the help of a paid research assistant, didn’t produce such a plot.
Noting that the loess curve drops past approximately 120%, I calculated the median growth for each country represented. Only 7 countries have had debt to GDP ratios greater than 120% in the past 60+ years: Australia, Belgium, Canada, Japan, New Zealand, the UK and the United States. Out of these only two had (median) negative growth: Belgium (-.69%, effectively zero) and the United States (-10.94%), which has only had a debt to GDP greater than 120% one time. All other countries has positive growth under high debt, even beleaguered Japan. New Zealand can even claim a strong 9.8% growth under high debt. The US, then, is a major outlier, possibly bringing the entire curve down.
As this doesn’t fit their story, RR’s solution was to categorize debt to GDP ratios into five rough classifications, and calculate the mean growth within each group. This is a common trick to extract results from bad data. It’s highly tempting for researchers (and epidemiologists do it far too often), but a bad idea to present it without all the caveats and warnings that should go with it.
I’m not surprised that ideologues such as RR would be so keen to produce the result they did. After all, they published the popular economics work “This Time Is Different: Eight Centuries of Financial Folly” where they try to suggest that budget policy of the US in 2013 should somehow be informed by the economy of 14th century Spain.
I am, however, surprised that reviewers let this pass. If I would have been a reviewer, I would have:
1) pointed out the problems of categorization, where data doesn’t require it
2) noted that categorizing the data (or even plotting it) tears out temporal correlation. For example, one data point from 2008 (stimulus) may be put in the high debt category, but another from 2007 (crash) in the low debt category. While budgets of one year may have little to do with the budget of another, the economy of one year is likely related to the economy of the previous year.
3) questioned the causal mechanisms behind debt and growth. This is obviously a deep question for economists (and not epidemiologists), but of particular import. When does the economy start to react to debt? I’m pretty sure that there is a lag effect as spending bills tend to space disbursements over the course of the fiscal year.
The RR debacle should be a lesson, not only to economists, but to all scientists. While we may always be under pressure to produce results and hope that those results fit and support whatever position we take, shoddy methods don’t get us off the hook. In RR’s case, I would call this fabrication. A good many studies are merely guilty of wishful thinking, but the chance always exists that someone will come out of the woodwork and expose our flaws. After all, that’s what science is all about.
Jeff Hanneman, RIP
There’s not much I can say about Slayer that hasn’t been said already. I’m truly saddened.
Needless Drug Shortages Threaten the Lives of TB Patients
Several drugs to treat Tuberculosis have made it to the FDA’s drug shortage list. (I recommend a quick glance at the list. Big government (thankfully) at work!)
A friend/acquaintance of mine posted that the following medications are presently in short supply, or unavailable: Isoniazid, Rifampin, Ethambutol, Amikacin, Streptomycin, Tubersol and Aplisol.
Now, I’m not going to pretend to be an expert on TB, though I do know enough about the condition to know that TB is most common among the poorest and most marginalized members of society. In Malawi, I’ve seen active and advanced cases of TB. It’s an awful sight.
People who live in substandard housing in urban areas, prisoners, alcoholics and homeless people are at particular risk for infection. It’s particularly common in Africa, and a problem that seem to be getting worse, rather than better. Coinfections with HIV are common.
Japan, specifically the Airin area of Osaka, where homeless men and day laborers congregate in substandard and densely occupied housing units, is well known to have one of the highest incidence rates of TB in the developed world. Russian prisons are also famous for TB transmission, as the work of Paul Farmer has shown.
According to the FDA list, many of the drugs are in short supply due to “Demand increase for the drug.” I find the claim to be somewhat dubious. Drug companies have long been known to be sleeping at the wheel when it comes to development of new drugs for TB. Most of the drugs that are currently used were developed in the early the mid 20th century, with one very recent exception (Bedaquiline).
I find it highly unlikely that demand for the drugs went by unnoticed to drug companies. I suspect that there simply isn’t enough profit in the drugs to warrant ramping up manufacturing.
The implications are, of course, immense. If drugs to treat TB are unavailable, opportunities to transmit TB will persist. Given the nature of the populations which are at risk for the disease, we can expect a resurgence in cases. Worse yet, the longer a patient has the disease, the more likely it is that the infection will become resistant to all medications, making treatment nearly impossible.
Dzhokhar Tsarnaev Exposed the Worst that America Has to Offer
I was going to write a thoughtful post on Dzhokhar Tsarnaev and why it’s important to 1) not torture him, 2) give him a fair trial and 3) not kill him, but I lost my way. In lieu of my now aborted (though thoughtful) piece, I leave you the following piece of history.
While the Revolutionary War raged, a certain General George Washington left these very unambiguous instructions regarding the treatment of British prisoners of war:
“Treat them with humanity, and let them have no reason to complain of our copying the brutal example of the British Army in their treatment of our unfortunate brethren who have fallen into their hands,’ he wrote. In all respects the prisoners were to be treated no worse than American soldiers; and in some respects, better. Through this approach, Washington sought to shame his British adversaries, and to demonstrate the moral superiority of the American cause.”
Yet, Americans in 2013 don’t seem to share this sentiment. In fact, even our highest elected officials are calling to 1) torture him, 2) NOT give him a fair trial by denying him protections afforded under the Constitution, and 3) seek the death penalty.
Not to be insulting to insects, but it’s like turning over a rock and exposing the unpleasant for the world to see. Dzhokhar Tsarnaev and his brother may have killed several and injured many, but within a week they have exposed the awful underbelly of the United States and given it power.
Washington knew how the mistreatment of prisoners by the British galvanized the hatred of the colonies. In this respect, I’m sure that Washington was speaking practically. I suspect, however, that the General (who eventually freed his slaves even), considered human dignity to be essential to a free state. In fact, he had this to say about slavery:
Not only do I pray for it, on the score of human dignity, but I can clearly forsee that nothing but the rooting out of slavery can perpetuate the existence of our union, by consolidating it in a common bond of principle.
How unfortunate that Americans 200 plus years later may have forgotten this important lesson, preferring mob violence to order and vengeance to the preservation of human rights.
Metal Networks: Analysis of Decibel Magazine Top 40 2012
I had some free time today so I decided to apply some network analytic techniques to one of my favorite subjects: metal records.
A couple of weeks ago, I attended a lecture on network analysis where the investigators analyzed popular political books on Amazon.com.
Amazon lists not only information on the book but also the titles, in order of purchasing frequency, of other books that customers may have purchased. The researchers here were able to identify left leaning and right leaning books by examining the purchasing habits of Amazon customers.
Decibel “is America’s only monthly extreme music magazine” and has been in publication since 2004. Every year, they publish the titles of the 40 best metal records of the year, according to their review staff.
Here is 2012′s list:
40 Gojira – L’Enfant Sauvage
39 Meshuggah – Koloss
38 Agalloch – Faustian Echoes EP
37 The Shrine – Primitive Blast
36 Incantation – Vanquish In Vengeance
35 Samothrace – Reverence To Stone
34 Devin Townsend Project – Epicloud
33 Panopticon – Kentucky
32 Saint Vitus – LILLIE: F-65
31 Mutilation Rites – Empyrean
30 Author & Punisher – Urus Americanus
29 A Life Once Lost – Ecstatic Trance
28 Asphyx – Deathhammer
27 Farsot – Insects
26 Gaza – No Absolute For Human Suffering
25 Inverloch – Dark/Subside
24 Swans – The Seer
23 Horrendous – The Chills
22 Killing Joke – MMXII
21 Early Graves – Red Horse
20 Liberteer – Better To Die On Your Feet Than Live On Your Knees
19 High On Fire – De Vermis Mysteriis
18 Napalm Death – Utiltarian
17 Torche – Harmonicraft
16 Grave – Endless Procession Of Souls
15 Satan’s Wrath – Galloping Blasphemy
14 Testament – Dark Roots Of Earth
13 Cattle Decapitation – Monolith Of Inhumanity
12 Blut Aus Nord – 777: Cosmosophy
11 Municipal Waste – The Fatal Feast
10 Pig Destroyer – Book Burner
09 Paradise Lost – Tragic Idol
08 Royal Thunder – CVI
07 Enslaved – Riitiir
06 Neurosis – Honor Found In Decay
05 Pallbearer – Sorrow and Extinction
04 Witchcraft – Legend
03 Evoken – Atra Mors
02 Baroness – Yellow & Green
01 Converge – All We Love We Leave Behind
I looked all of these records on Amazon. For each of them, I noted which of the others were in the first 12 titles that were purchased with it, creating a 40 by 40 adjacency matrix where rows (i) and columns (j) represented records. For each entry, a zero was noted where the customer which purchased the i-th record did not purchase the j-th record, and a one where they did.
I found that many of the records on the list were purchased with one another. The most common record purchased in combination with another on the list was Neurosis‘ “Honor Found in Decay.” Fifteen of the other records on this Top 40 were purchased with “Honor Found in Decay.”
In network terms, the Degree of this record would be 15. Pallbearer’s “Sorrow and Extinction” had a degree of 11, Royal Thunder’s “CVI” and Blut Aus Nord’s “777: Cosmosophy” both had a degree of 9.
The network of Decibel’s Top 40 looks like this:
Network of Amazon Purchases of Decibel Magazine’s Top 40
You can see that some records get purchased with other records more than others. The size of the dots represent the degree of the record.
Now, I did some cluster analysis on the data, looking for related groups of records within the network. Using R, I produced the following dendrogram:
Dendrogram of Decibel’s Top 40
There are two major clusters, each with its own subcluster (dendrograms are hierarchical). One includes Converge, Neurosis, Pallbearer Royal Thunder, Evoken and Inverloch with a subcluster including only the first four. These are all bands that might be expected to be purchased with one another. The other big one includes all the rest. Main clusters are designated by color.
I found one containing the three entries for Baroness, Municipal Waste and Napalm Death, very different bands. I’m truly not sure why those three would be in a cluster together (is the cluster is based on lonliness in the network?).
Anyway, I’m done, but glad I got any results at all. I’ll let readers (especially metal fans!) interpret the results.
Scientific Publication Scams or Tooth Whitening??
Science requires publication. Unfortunately, publication requires money. Researchers have to put up hefty publication fees to appear in prestigious journals, though much of the prestige comes from the quality of it’s (unpaid) review staff. In the past, journals could rely on library subscriptions to subsidize the costs of publication. As paper copies diminish and the demand for open access increase, however, journals have had to rely on researchers for revenue.
The NYT ran an article the other day on shady publishing houses which offer to publish anything for a fee. You can imagine what these journals are like. Peer reviews are non-existent or light and content questionable.
I get emails from these companies regularly. One that stuck out to me was from the “European Journal of Medicinal Plants” from the publishing house SCIENCEDOMAIN [sic]:
Dear Colleague,
I am approaching you with the peer-review request of the below mentioned manuscript submitted in European Journal of Medicinal Plants
Title : Mosquito larvicidal activity of Urtica dioica of urticaceae against Malaria Vector.
I would be grateful if you would kindly find some time to review the above mentioned manuscript and send your valuable comments within 15 calendar days. Manuscript and the “Review comments Form” have been attached herewith.
I know that your time is valuable and therefore, as a token of our appreciation you will be awarded a complimentary ‘RERP coupon’ of 50 US$ for each manuscript, if quality review is completed within the stipulated period of time. Please be informed that the RERP coupon can be redeemed against only the publication fee of your accepted manuscripts as mentioned in SCIENCEDOMAIN international website (http://www.sciencedomain.org/page.php?id=reviewers-editors).
Please inform as early as possible if you agree to accept my invitation to review. Would you not be able to find time to act as a reviewer this time, please let me know through an email and in that case you may also suggest someone of your colleague to review the manuscript.
I understand that our proficient reviewers highly contribute to maintain the high standards of the Journal, and I express my gratitude to you for your present and/or future contribution.
Journal scope link: http://www.sciencedomain.org/about-journal.php?id=13
General Editorial Policy link: http://www.sciencedomain.org/page.php?id=sdi-general-editorial-policyThanking you
—————–
P. Mondal
Editorial Office
SCIENCEDOMAIN international
http://www.sciencedomain.org
The email sounded like something out of North Korea.
The paper was attached. Here is the header:
The text was approximately 1,000 words, and they listed six references. No authors were listed. Now, besides the sub-standard level of English and the glaring spelling errors (“alkoloids”), you will notice that the mosquito species in question is Culex quinquefasciatus. I don’t know anything about plants and mosquitoes, but I do know, that despite the title “Mosquito larvicidal activity of Urtica dioica of urticaceae against Malaria Vector,” NO mosquito in the genus Culex transmits malaria.
Some addresses were included in the email:
UK: SCIENCEDOMAIN international, Third Floor, 207 Regent Street, London, W1B 3HH, Fax: +44 20-3004-1542
USA: SCIENCEDOMAIN international, 616 Corporate Way, Suite 2 #4000, Valley Cottage, NY 10989, Fax: +1 845-231-6220
India: SCIENCEDOMAIN international, U GF, DLF City Phase-III, Gurgaon, 122001, Delhi NCR, Fax: +91 11-66173993
SCIENCEDOMAIN HQ
I did some more digging on the address listed for SCIENCEDOMAIN. It appears that have the exact same mailing address as Smile4You USA, a company that sells dubious teeth whitening formulas. In fact, both SCIENCEDOMAIN and Smile4You have offices in the US and the UK. I couldn’t verify that the addresses were the same in the UK. I also checked the WHOIS info on both Smile4You (which is registered in Delaware) and SCIENCEDOMAIN (which is registered in Sunnydale, CA) and wasn’t able to confirm a link.
I perused science domains research offerings. It would appear that most of the authors come from developing countries. I also noticed that the publication charges are far less than that of established journals.
Smile4You? Or SCIENCEDOMAIN?
