Archive | April 2013

Needless Drug Shortages Threaten the Lives of TB Patients

Global_TB_incidence_2010Several 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.

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Dzhokhar Tsarnaev Exposed the Worst that America Has to Offer

George WashingtonI 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

Decibel-Jan-2013-coverI 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

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 Amazon Purchases of Decibel's Top 40

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-policy

Thanking 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:

MalariaVector

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

SCIENCEDOMAIN HQ

I’ve never heard of Valley Cottage, NY, but Google Maps will gladly tell you where SCIENCEDOMAIN international is located. From the picture, it looks like the eminent SCIENCEDOMAIN is occupying closet space in a warehouse of some kind, perhaps occupying the back of “PODS Moving and Storage” or a company that sells perfume for dogs. It looks like there might even be a meth lab across the street.

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?

Smile4You? Or SCIENCEDOMAIN?

I wondered whether clearly dubious operations like SCIENCEDOMAN aren’t preying on developing country researchers, who don’t have the budget to support publication in larger journals. It would seem an awful trade-off, convenience for quality, but a cheap way for researchers from poor countries to pad their resumes. Not only do they save money, but they aren’t subjected to rigorous review. This has awful consequences. Serious researchers get no feedback to improve their work, and poor researchers are rewarded.

The Science of Metal

Mosh Pit Simulator

Mosh Pit Simulator

Saturday, I got my metal fix by checking out High on Fire and Anthrax in Detroit. A great show, to be sure (though HoF’s Matt Pike looks a little pregnant).

I was watching the mosh pit and thinking about two things. First, that mosh pits act like particle interactions. Bodies bounce off one another, and occasionally off innocent bystanders. Second, that pits tend to tire out as the night moves on, and fade out as more as the music gets more interesting.

To my surprise, a group at Cornell already ran with the first idea (why am I always late to the game?). They took an agent based approach, and modelled the mosh pit as particles that move and bounce off one another and are constrained by non-moshers around them. They even went to the trouble of creating a simulator!

Of course, I find out now that the national news even featured their work (so I admit, my observation may have been influenced by an article I don’t consciously remember reading in the past few weeks).

I like their model and it may have agreed well with mosh pits in reality, but it fails when crowds are small. Moshers in the simulator are allowed to leave the boundaries of the floor, where in reality they are constrained to the space they occupy. The model here assumes that there are sufficient non-moshers to constrain the mosher movements. Often, this is not true. Importantly, it appears to model the particles as having random movement (though there is a limited “flock” feature), when mosh pits are anything but random. Moshers tend to be attracted to other moshers.

As for the second, point, that moshers tend to run out of steam early and take frequent breaks, I’ll leave that to debate. I would like to consider how musical complexity and “interestingness” influence mosh pits. Moshers tend to care little for whatever they mosh to (could be Justing Bieber in the end), though better music might command more attention.

For the record, I’m too old to mosh.

“Don’t Go to Graduate School”

gradschoolArrrrrrrgh….. those infuriating words….

It seems like every few months some disgruntled graduate student writes a piece on why graduate school is a terrible idea and why earning a Ph.D. is financially worthless.. In fact, one just came out the other day on Slate. A disgruntled visiting professor of Germanic Studies at Ohio State writes:

Don’t do it. Just don’t. I deeply regret going to graduate school, but not, Ron Rosenbaum, because my doctorate ruined books and made me obnoxious. (Granted, maybe it did: My dissertation involved subjecting the work of Franz Kafka to first-order logic.) No, I now realize graduate school was a terrible idea because the full-time, tenure-track literature professorship is extinct. After four years of trying, I’ve finally gotten it through my thick head that I will not get a job—and if you go to graduate school, neither will you.

To Dr. Schumann, I’m sorry that you had such an awful time in graduate school. I’m sorry that you can’t find the job you want. I’m sorry that your life is so utterly disappointing. You are right: you didn’t ever belong in graduate school. However, your empty and disappointed life has nothing to do with mine or anyone else’s.

As a guy that’s about to earn his own Ph.D., (not in literature, I learned my lesson in undergrad), these articles annoy me to no end. I regret nothing about my graduate career. In fact, it was the best thing I ever did in my otherwise miserable and pointless life (well, my life isn’t that bad, but slugging amps around the country and hounding record distributors for payment pales in comparison to studying developing world health…

and, seriously,

How fucking rad is it for a piece of trailer trash like me to be DR. LARSON??).

Probably unlike the author of this article, I worked shit minimum wage jobs. I know that most of America lives in an awful state of (institutionalized and structural) insecurity and that social mobility is but a fantasy. In 2013, one of the best ways out of the cycle of hourly slave labor is education. Sure, a lit Ph.D. is no guarantee you won’t have to work at a grocery register, but not having a degree is pretty much a guarantee (for most people) that you’ll do nothing but. No offense to the uneducated, but education allows one to surpass a lot of society’s challenges.

Having an education means that you know something about something that other people don’t. Even if you don’t apply your vast knowledge of 14th century German poetry, you know how to do important things like read and write which, in my experience, most Americans have trouble doing with any level of proficiency. You can make arguments. You can think. Importantly, though, you have a self-esteem that comes with knowledge, which is a far cry from the misery and self-loathing that comes with being on the bottom of the ladder (been there, done that).

What this writer (obviously) lacks is flexibility. She demands a tenure track academic job in an age where the entire tenure system (rightfully) is being called into question. Tenure is valuable and necessary to academics, but unfortunately, many don’t see that.

A friend in Kenya rightly pointed out “if no one will give you a job, you just have to make one.” It could be pulling fish out of the water and selling it, becoming a poorly paid journalist or creating a new start up, but, faced with the alternatives (starvation), something has to be done. Anyone with a Ph.D. has the skills to do just about anything they want.

When I first went to undergrad (after being homeless), people like the writer of this article on Slate told me not to. “It’s useless, you won’t be able to get a job anyway.”

I wanted to go to graduate school when I finished undergrad and people told me “It’s useless, you won’t be able to get a job, anyway.”

I considered going back later and was told “It’s useless, you won’t be able to get a job anyway.”

Wow. See a pattern?

Consider the source, though. I found that the people who throw out such nonsense are those who are happy to wallow in a pit of inactivity, passively waiting to be given exactly what they want. You find them in bars, working at local record stores for less than minimum wage, at music shows and anywhere else that will allow them to do absolutely nothing and let them get away with whining about it.

It’s a generalization (and a rash one), but, face it, we all know people like this. They tend to pull down everyone around them instead of encouraging their friends to do something and enjoy life and celebrating them when they do. Those, in my opinion, are the worst types of people.

For me, going to graduate school was a satisfying and enriching experience. Even if I have to do nothing but dig ditches for the rest of my days, these 7 years of doing nothing but reading books and interacting with interesting an engaged people will have been worth it.

So you know what? To hell with the haters. Spend less time on the hate, less time whining about how unfair the world is and more time figuring out what to do. Most of all, don’t discourage others from pursuing their dreams.

There are lots of things that people can’t do. You don’t know what you can’t do until you try to do it.

Climbing on Things and Other Evolutionary Pursuits

KenyaRunnerI had one of those odd old man moments today where I’m watching a squirrel run up a tree. It goes half way up the tree in a split second, stops, then decides there’s nothing to run from after all. It then spends the next 10 seconds trying to get down. In short, the squirrel can climb a tree in a tenth the time it takes to get down. I realize this is a pretty silly observation.

Humans, too, are really good at running up hills, but terrible at getting down them. I remember climbing Mt. Mulanje in Malawi once. Going up was no problem at all. Getting down was dangerous as hell.

We pull better than we push, see right in front of ourselves better than beside ourselves, and have an easier time thinking of the concerns of a few proximal people, than a vast numbers of people who live far away. The latter, obviously, has important implications for global policy.

All of these things, though, are remnants of our evolutionary past and make complete sense when put in the context of our humble, though dangerous, beginnings. Arising in the savannahs of Kenya, humans would have been easy prey for all sorts of predators. When faced with a lion or hyena, a reasonable strategy is to run up the nearest tree and wait for the threat to pass. Thus, getting up the tree is critical for survival, particularly for children. Importantly, if they are eaten before they reproduce, the survival of the species is in question. Better climbers are survivors who are able to pass their climbing abilities on to their own children.

Getting down from the tree, of course, is not critical to survival. Thus, we can take our sweet time clumsily trying to get down, live and be able to pass our clumsy genes on to our children. So threats create effective adaptations and the lack of threat creates useless ones. The same is true for eyesight. Humans, as predatory omnivores, benefit from being able to focus on their prey while hunting, especially when they have the unique ability to run long distances while they wait for their prey (which likely has a serious head start) to tire out.

The Kericho region of Kenya is famous for producing long distance runners. I wonder if they maintained a particular hunting strategy that the Europeans or Asians no longer required.

Of interest to me is why humans might be so clan centric. It has been shown that humans are able to feel empathy for individuals close to them, but have a hard time imagining the sufferings of millions of unfamiliar people. This limitation, of course, allows us to wage wars far from home, and maintain indifference toward the millions living in poverty around the world.

Again, there are evolutionary roots here. Humans, being pack animals are adapted to be concerned about their immediately family and pack members, particularly children. This is important to survival. When any member of the group is threatened, all must be ready to ward off the threat, and protect children, who pass on similar traits to their children. A group of people indifferent to those aorund them would die out quickly. We are poor fighters on our own.

We have lived only in small groups until very recently. Thus, we never formed a need to be concerned with anyone else besides those closest to us. This state of having to care about the welfare of millions (or billions) is entirely new. We haven’t yet adjusted to it, though we make noble attempts. It is possible that we may never fully develop the ability to feel the pain of billions, unless something comes along and starts wiping out those who don’t. If that happened, we’d probably all be dead, though.

I had never thought of the problems of global policy in terms of evolutionary behavior. I guess, I have the squirrel to thank.

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