Unsightly Mental Blemishes

Peter Abrams discusses the Hydra Effect in NewScientist (30 May 2015, paywall):

A decade ago, my collaborator Hiroyuki Matsuda and I coined the term hydra effect to describe all situations where a higher death rate in a particular species ultimately increases the size of its population. We named this phenomenon after the multi-headed serpent of Greek myth that grew two heads for each one that Hercules cut off. The hydra effect is just one example of a more general phenomenon where adverse changes in the environment that reduce the growth rate of a population may ultimately lead to greater numbers.

What could cause populations of animals or plants to bounce back so strongly in spite of a continued higher death rate? When a population experiences increased mortality – due to, say, harvesting – the initial effect is almost always diminishing abundance. However, after this initial decline, other organisms they interact with are likely to change. In most cases the organisms they eat go up in abundance. Diseases and predators that depend on the harvested population decline. Also, a higher risk of death often causes individuals to reduce their activity levels and to spend more time hiding, allowing their over-exploited food species to recover. Tadpoles in ponds with more predatory dragonfly larvae have been shown to end up getting more algae to eat, despite spending less time feeding. In a large food web many other complicated positive feedbacks exist.

The mathematics of populations must be fascinating, mostly in the modeling, so as to best characterize the relationships and how a change at one point in the web of life ripples through the rest of it.

But what about the political dangers of recognizing the hydra effect?

“I don’t know if it’s true, but I hope it isn’t.” This was the response of a fisheries biologist after I gave a talk about the hydra effect a decade ago. He was right to be concerned. If it were widely known that harvesting can potentially increase the size of fish stocks,fisheries quotas might have been raised too rapidly. Fishers may welcome the counter-intuitive idea that catching fish may bump up the population, but hydra effects are not yet predictable. And modelling shows that the harvest rate which maximises a fish population is surprisingly often only slightly smaller than that which results in a dramatic collapse or extinction.

Which leaves me wondering how many Fishing Ministers ponder how to determine that sweet spot, without ever considering how much illegal fishing actually goes on….

Continuing my faintly ridiculous hobby, I thought I’d add a note on XML validity constraints and how they interact with the EBNF of XML: which is to say, they don’t.

Which is reasonable, of course: the point of the EBNF is to specify the syntax, not the semantics.  But this does make validity checking a little more difficult.  Here’s the first example of a constraint:

Validity constraint: Root Element Type

The Name in the document type declaration MUST match the element type of the root element.

And an illustration:

<?xml version="1.0"?>
<!DOCTYPE greeting SYSTEM "hello.dtd">
<greeting>Hello, world!</greeting> 

Note the word “greeting” in the !DOCTYPE and in the XML element.   So what does Production 1 look like?

document ::= prolog element Misc*

element is the important piece here:

element ::= EmptyElemTag | STag content ETag

Both EmptyElemTag and STag reference Production 5:

Name ::= NameStartChar (NameChar)*

And it’s this Name which we’ll match against the DTD’s name.  But, of course, Name is used in many other places, which I’ll omit listing here, so clearly we cannot modify the processing at Name to validate against the DTD; or, more accurately, a hacker might find some way to get there, but that’s not really good enough.

More importantly, the element Production is also referenced from another location, namely Production 43, and again it would be inappropriate to modify the element Production to validate a special case.  So, how to handle this, and potentially other special cases, and properly highlight the purpose of the modification to the EBNF?

I hit upon using the previously described debug mechanism.  First, I defined the notion of a Production Post Processor:

Post_Production_Processor = Handlers -> List(XML_OnePass) -> Dtd -> Int -> Int -> (Handlers, Dtd);

In English, a production post processor accepts all the SAX handlers provided by the user, the current state of processing, the DTD, and (for convenience) the current line and column numbers; it returns potentially new versions of the handlers and the DTD.  (Yes, I’m wondering if returning a new DTD is pointless.)

I added an integer (name of Production) map to Post_Production_Processor map to the internal state of the SAX parser.  This is updated by a new function, validity_constraint, which functions as a parser, accepting a production Name and Post_Production_Processor and modifying the previously mentioned map with the information before executing the success function.

As you might have guessed, then, I’ve modified the p_out function for a match between its name argument and anything in the map from name to Post_Production_Processor.  If one is found, the entry is deleted, and the post processor is executed.  The success function is then invoked, but using the results of the post processor rather than those passed in.

Usage?

vc = validity_constraint;    # purely for readability

…

xml_doc = p_in 1 & start_doc & prolog & vc 5 validate_dtd_name & element & <misc> & one_p & p_out 1;

validate_dtd_name is invoked when Production 5 terminates, and I’ve determined that the next Production 5 will ALWAYS be the outermost element’s name.

For comparison, here’s the original EBNF of Production 1:

document ::= prolog element Misc*

The added implementation elements are p_in, start_doc, vc, one_p, and p_out.  The transformation is rather large, but still straightforward:

p_in is the debug (and now validity constraint) mechanism;

start_doc implements the content handler’s start_document functionality;

vc, as discussed;

one_p, the processor specific to Production 1 – not all Productions have processors, but this one does (it returns the handlers to the caller);

p_out, as discussed.

Most productions only have p_in and p_out additions.  A few have processors.  So far, only Production 1 has a post processor, for which I should probably come up with a better name: validity processor, perhaps.  Let me know if you have a better name.

I should change xml_doc to document, just for consistency.  (Consistency is rarely of interest to me, sadly.)

Testing of this mechanism has yielded positive results, in that I can see the processor invoked.  I have to modify one of my tests to have a DTD in order to really test it, and I haven’t gotten that far; if a DTD is not defined, the requirement is ignored.

I look forward to trying to implement other validity constraints with this mechanism.

A hidden component of the recent agreement between Egypt and Ethiopia in regards to the Nile waters has recently been revealed, reports NewScientist (30 May 2015, paywall):

The solution involves reducing the losses to evaporation from Lake Nasser, the reservoir behind Egypt’s Aswan High Dam in the Nubian desert. Up to 16 cubic kilometres of water evaporate annually from its surface – a quarter of the Nile’s average flow and up to 40 per cent in a dry year.

Storing more of that water in the reservoir behind Ethiopia’s dam could cut those losses, as it is deeper, has a surface area less than a third as great and sits in the cool and wet highlands. But it would also cut Egypt’s electricity generation, so Ethiopia would need to share electricity from its new dam, says Kenneth Strzepek at the Massachusetts Institute of Technology.

Sudan, too, could benefit from the dam and a more even water flow, reducing the risk of flooding and increasing the potential for irrigation. “The government of Sudan is already selling land leases for new farmland by the river,” says Alex de Waal of the World Peace Foundation at Tufts University in Boston.

Sometimes the most important news starts out as a couple of short paragraphs; for me, that’s how the Deepwater Horizon disaster began.  I recall reading those two paragraphs, wherever it was, shaking my head and thinking, This is important.

And now I have the feeling again.  NewScientist (30 May 2015, paywall) reports on the sudden deaths of saiga antelopes:

The animals began dying from an unidentified cause around 10 May. The death toll soared within days to 27,000, at which point the Kazakh government requested help from the secretariat of the convention. A team of vets, led by Richard Kock of the Royal Veterinary College in Hatfield, UK, flew out on Friday.

“It’s very dramatic and traumatic, with 100 per cent mortality,” Kock told New Scientist from Betpak-Dala in central Kazakhstan. “I know of no example in history with this level of mortality, killing all the animals and all the calves.” The animals die through severe diarrhoea and difficulty breathing.

100% mortality?  That’s extremely worrying.  Saiga antelope are a critically endangered species,

… that originally inhabited a vast area of the Eurasian steppe zone from the foothills of the Carpathian Mountains and Caucasus into Dzungaria and Mongolia.

They also lived in Beringian North America during the Pleistocene. Today, the dominant subspecies (S. t. tatarica) is only found in one location in Russia (steppes of the northwest Precaspian region) and three areas in Kazakhstan (the Ural, Ustiurt and Betpak-Dala populations).

They also having this charming appearance:

Scientists had come to watch the calving scene, but, according to WBUR, NPR’s Boston, MA station,

… but instead, what they witnessed was the end of life—with the carcasses of tens of thousands strewn over the terrain. Steffen Zuther, acting director of the Association for the Conservation of Biodiversity of Kazakhstan, was among the first witnesses on the scene. On May 10 and 11 and in the days that followed, he observed the devastation: whole herds lying dead—the carcasses of calves curled up at the bellies of their dead mothers.

Nature has a briefing on the event, including some interesting background:

Saigas are known to be prone to massive, as yet unexplained die-offs. These usually occur when the females come together to calve in the spring. In 1984, such an event in the Ural Mountains resulted in the loss of 100,000 animals — 67% of the local population. There were several smaller scale die-offs in the 2000s. But this year’s mass-death event among animals living in the Betpak-Dala region of Kazakhstan is much more significant as entire herds are dying.

“I have worked in veterinary diseases all my career and I have never seen 100% mortality,” says Richard Kock, a wildlife veterinarian at the Royal Veterinary College in Hatfield, UK, who flew out to Kazakhstan last month to assist with efforts to make sense of the devastation. “We had a herd of 60,000 aggregated and they all died. That is extraordinary.” …

The cause is unlikely to have been an infectious agent that was transmitted from one animal to the next. “Epidemiologically, you cannot get a directly transmitted disease to kill a whole population in seven days,” says Kock. “I’d say it’s a polymicrobial disease,” he says. This involves pathogens such as pasteurella and clostridia that are often present in the body but have seized an opportunity to run riot.

The pathogens may have been responsible for the deaths, but something must have caused the saigas to fall victim to them. Given that two discrete sub-populations some 300 kilometres apart suffered similarly and simultaneously, it seems likely that an environmental factor is part of the story.

The speculation, so far, appears to be purely concerning biological factors.

cdub24 @ The Daily Kos has a post entitled “POLL finds 80% of Republicans AGREE with BERNIE SANDERS“, which links to a post at PoliticsUSA:

Sen. Bernie Sanders is often characterized by the media as an out of the mainstream presidential candidate, but a new CBS/New York Times poll revealed that 80% of Republicans agree with Sanders on the issue of getting money out of politics.

The CBS/NYT poll found that:

– 80% of Republicans believe that money has too much influence in our politics.

– 54% believed that most of the time candidates directly help those who gave money to them.

and etc., all related to campaign finance.

So, we can look at this and say, Wow, isn’t this amazing, maybe we should elect Bernie and get things DONE.

But here’s the thing: Presidents are Executives.  They Execute the law.  They don’t make the Law.  They may make War, but even then they are supposed to retroactively get permission – and risk getting booted out, if the Legislature is up to doing its job, rather than playing tribal politics.

The Legislature makes the law.  And that’s where just about all the positions of Bernie’s would need action.  (Constitutional Amendments also start in legislatures.)

So this sort of headline is all hot air and no red meat.  It can be used to embarrass your favorite conservative relative, if that’s your conception of politics – tear up the family and friends, that sort of thing.

But what it really needs to be is the extension of a hand to the family and friends and the remark, Hey, I hear your Representative isn’t in step with the conservative movement, yeah, that one that happens to think there’s too much money in politics, that corruption is rampant – what do you think should be done to correct or replace your Representative?

As entertaining as I find the modern conception of politics to be, the use of embarrassment, contempt, and scorn are the first materials to use – when burning bridges.  What do you think should be used when building bridges?

On this topic, Rolling Stone magazine published a piece by Hannah Gold I missed just about a year ago.  It covers the relationships between private prisons and higher education:

American universities do a fine job of selling themselves as pathways to opportunity and knowledge. But follow the traffic of money and policies through these academic institutions and you’ll often wind up at the barbed wire gates of Corrections Corporation of America (CCA) and GEO Group, the two largest private prison operators in the United States. …

Institutions of higher education have now become a part of what sociologist Victor Rios has called the “youth control complex”—a tightly bundled network of institutions that work insidiously and in harmony to criminalize young people of color. Here are five ways that universities buy into private prison companies.

Slightly conspiratorial, slightly cobbled together – but useful information, all the same.  Hannah finds five connections: The classic investments in private prisons corporations; the use of criminal record information to bar students with records from admission; presence of private prison company executives on the Boards of Trustees of educational institutes; the use of unsavory security giant G4S for campus security; and funding university research.  As a simple minded software engineer, here’s what comes to mind as I read the piece, structured by point:

1. Regarding educational investment/divestment: This is the most important and understandable – but exists on the assumption that the readers are liberals who already understand the inappropriateness of private prisons.  Perhaps there’s an accompanying piece that covers it; but, if not, then the “outraged liberal” tone of the piece comes off as tone-deaf.  How many conservatives are against private prisons?  No luck finding any polls on that precise question; AFSCME has an undated poll that claims only 28% of US citizens are in favor of private prisons, 51% against.  Given the lack of date, I have trouble with credibility – and with the source of the poll.

All that said, higher ed campuses are certainly one of the best places to start protesting against private prisons, as students rarely have vested interests in private prisons and therefore can honestly evaluate, and then act, on issues.  A fallacious focus on the efficaciousness of the divestment should not be permitted; it is the symbolic aspect of the action which is important, the statement that private prisons are inappropriate to democracies.  Naturally, this should be an educational moment – not only for the students, but for the administration, the Board of Trustees, and, of course, the citizenry at large who has, in the average case, not given the issue a moment’s thought.

2. Regarding requiring criminal offense history: A ticklish subject.  Even though the typical college student is no longer a fresh high school grad, we still would prefer the college experience be free of risk (a ridiculous statement itself, but there it is).  However, it’s difficult to think of any reason beyond that to deny someone an education.  Hannah’s point is that requiring that history legitimizes

a juvenile detention system which locks away more young people than that of any other industrialized nation, and institutionalizes inequality and racism in America (black youths are incarcerated at a rate five times that of their white peers; Latinos at two to three times the rate).

However, not asking for it does not delegitimize it; and, further, by not banning violent offenders from, at least, campus, you may be endangering other students.

3. Regarding private prison executives on Boards of Trustees:  I take this as indicative of the responsible body’s ignorance of the issue.  They can also exert undue influence on the institution, which may obscure research that might otherwise undermine private prisons.

4. Regarding campus security: Someone has to provide it.

5. Regarding funding research: This is an important point, given the phenomenona of funding bias and appeal to authority.  For those citizens who’ve not become familiar with the issue, the simple imprimatur of, say, Princeton (or Liberty University) on a piece of research which justifies private prisons can be a legimitizer in many people’s minds.

*   *   *

Eugene Volokh @ The Volokh Conspiracy contributes an overview of research on the efficiencies of prison methodologies, which reduces to the complaint that it’s hard to do and virtually no one has performed such research.  He usefully points to a 2012 Bureau of Justice Bulletin, which in Appendix Table 15 lists how many prisoners resided in private prisons in 2011 – indicating that, at the time, 19 states did not use private prisons.  The highest, at that time: Montana at 40% of total prison population.

But Eugene’s work (and those of whom he surveys) seems a wasted effort.  While to a devoted opponent of private prisons, research on efficiencies may seem another tool in stopping private prisons, I do not think it’s a wise tactic, for you are now risking the sin of biased research, if you reach a finding that supports your position, and risk the sin of omission of relevant facts if the finding is against you, and you choose not to use it (since you really can’t, except in passing).  The point must be kept in focus: are private prisons appropriate in a democracy?  Until and unless that argument is terminated against you, the efficiencies are meaningless: no improvement in efficiency can erase an ethical transgression, but if there is no transgression, quite often efficiency can be improved, or can be used to select which approach to use.

(h/t Kevin McLeod)

The Islamic Revolutionary Guard Corps (IRGC) continues their political push against the deal, reports AL Monitor‘s Arash Karami.  The faculty of a University allied with the IRGC has issued a couple of statements:

The letter accused some officials of advocating a policy that “is opposed to the fundamental principles of Imam [Khomeini] in foreign policy” and ignores “the daily crimes of Israel, America and Saudi Arabia.” The letter rejected that a hard-line foreign policy would allow the West to create an image of Iran seeking war or would increase Iran phobia in the West. Foreign Minister Mohammad Javad Zarif has on various occasions criticized the Mahmoud Ahmadinejad administration for its harsh rhetoric, blaming him for increasing Iran’s international isolation and adding to a negative world image of Iranians. …

The letter warned officials that “before it’s too late, to return to the real path of the people” and those who don’t “are not far away from the eyes” of the IRGC. The rare letter and its harsh language has surprised many, especially since it came one week after an Imam Hussein University public relations statement May 24 that expressed support for Khamenei’s May 20 comments at the university about refusing inspection of military sites or to allow Iran’s nuclear scientists to be interviewed as part of a comprehensive nuclear deal.

The National Council of Resistance of Iran reports,

IRGC Brigadier General Gholamhossein Qeybparavar, the commander of IRGC forces in the Fars province said on Saturday: “You would be wrong to dare to want to inspect our military centers and whoever does look at IRGC centers we will fill his throat with molten lead.”

The Christian Science Monitor has a different view, though:

“I think under the surface a lot of the different businessmen who are connected to the [IRGC] are putting pressure on Rouhani and his team to make sure these [nuclear] deals go through, because it’s hurting their pockets very deeply,” says Narges Bajoghli, a PhD candidate at New York University who interviewed some 150 members of the Guard and affiliated Basij militia over nine years of research.

“Of course, they have an interest in making themselves seem like a very strict organization, but I think when you go into the belly of the whole thing, you realize it’s not like that, especially since they’ve been involved in business,” says Ms. Bajoghli.

While hard-line Iranian politicians oppose any nuclear deal that requires compromise, and dislike even talking to the US and Western powers, whom they accuse of seeking regime change, the IRGC top brass in early April publicly backed the nuclear talks like never before.

“Up until today the nuclear negotiation team have defended the Iranian nation’s rights well, and the nation and IRGC is grateful for their honest efforts,” said IRGC commander Mohammad Ali Jafari.

But the support came with a dose of tough talk. This period of negotiations was a definitive year for Iran, Maj. Gen. Jafari said, and “the enemy” – the United States – was “wrongly thinking” it could change Iran’s behavior through talks and sanctions. Lifting all sanctions was the main demand of the talks, he said, in addition to preserving Iran’s right to uranium enrichment and nuclear development.

However analysts say the IRGC is far from monolithic, and that its own confrontational rhetoric often masks a pragmatic side.

So does LobeLog:

In over nine years of on-the-ground research with different factions of the Revolutionary Guard and Basij, I have found that an underlying concern for many, regardless of political leaning, is a desire to create an Iran with more opportunities for their children, and that means the removal of sanctions and better relations with the world.

After the 2009 crackdown in Iran, I interviewed over 150 members of the Revolutionary Guard and Basij. Seventy-five percent of those I interviewed vehemently disagreed with the conservative turn in Iranian politics during the presidency of Mahmoud Ahmadinejad. Most wanted an easing of relations with the West.

Perhaps a split within the IRGC?  Adroit maneuvering within the political mists of a country effectively several times older than the United States?  It’s all quite interesting.

The conversation about future drug policy continues:

Well, sure, actual legislators who have paid staff ought to be hiring smart, educated, creative staff who are well-versed (or can become so) in the issues to advise them. But does that actually happen? Especially if the hiring boss is a flaming idiot who does not believe in science? Of course not. They hire yes-men and political operatives who are there solely to get the re-elected, and/or stick to the ideology, rather than examine the actual facts. And I still argue, you want a representative who has some native intelligence himself, in order to correctly put both their own staff’s opinions and the public’s into proper perspective. I don’t think the challenge of voting on those issues you mentioned is particularly daunting for someone well- and broadly- educated and well-read.

It’s true, no one can be an expert on everything. And the Venturas of the world are useful, indeed. In your example, he at least realized his lack and was willing to get expert input. All too often, that’s not the case. The expert input comes from the people who contribute most to the re-election campaign.

It’s still my position that we are in a mess because we are governed and “led” by people who are mostly imbeciles, who couldn’t otherwise succeed on their own except by taking advantage of other people (i.e. they seem to have one big skill — the one to schmooze and lie convincingly).

I agree that there are too many folks led by their ideologies, rather than by experts; but then, the whole ‘expert’ game itself is a conundrum that has not yet been solved.

The term limits idea continues to be attractive; the arguments against it presume an active, acute citizenry who can perceive incompetent representatives and refuse to elect them on repeat opportunity.  However, it can be difficult to perceive that, between working for a living and a plethora of irrelevant information conveniently hiding important information.  And, then again, sometimes the electorate simply shares the same superstitions as do their representatives.

It appears corporations have better vision than politicians.  Sami Grover at TreeHugger.com gathers up information about coal starting to fall out of favor, and not just in China:

From Bank of America quitting coal mining to an Australian utility that’s committed to eventual decarbonization, the idea that we might be transitioning away from fossil fuels is rapidly gaining traction in some surprising quarters.

But what fossil fuels will we quit first?

That’s where things are likely to get interesting. Just take this piece from the Wall Street Journal talking about how oil giants are pushing for more gas as a medium-term strategy to cut carbon emissions, with Shell and Total quitting coal mining as part of this effort.

A FB reader responds to the possibility of having a drug factory in our homes:

It’s going to be a brave, new world in not many years, for this and other reasons. Unfortunately, the USA and I imagine most other countries do not select their leaders, politicians and legislators for their intelligence, education, creativity or ability to lead. Especially in this country, the “elite” educated people are frowned upon to the point where that very term is a disparagement and symbol for bad things. When it comes to managing things like yeast-based opiate synthesis, it’s going to take a lot of intelligence and creativity and leadership to keep it from becoming a magnified scourge. Legislators ought to be reading SF, things like William Gibson and far wider, just to get some wild ideas about just how future things might pan out, as well as including the scientists and scholars. But that won’t happen. We will still elect the guy who sends selfies of his penis to women he is not married to.

While I’ll grant that sometimes our legislators are less than we might find desirable, and that the right wing is particularly deplorable over the last 20 years, it’s not necessarily up to leaders of a nation of ours to come up with creative solutions to new problems – but to gather up the thoughts of smart people, winnow out those that won’t work, and implement those that will.  That’s why then-candidate Jesse Ventura could get away with saying, “I don’t know”, because he’d follow it up with, “But I’ll hire the smartest person I can find to answer that problem.”

Have you ever (rhetorical q) tried to imagine being a legislator yourself?  Of having to cast votes on policy concerning Ag, Finance, Legal System, investigate judicial nominees, Defense, Surveillance domestic and foreign … AND represent your district?  Well, you do it with the help of your staff.  Same staff should also be doing research on these hard questions and coming up with proposed solutions, the names of experts who can testify …. so, to some extent, if former Rep. Weiner is competent at taking that sort of approach to new problems, then I don’t really care if he amuses himself with selfies of his penis.

Of course, arguing that such behavior indicates a fundamental immaturity inappropriate to a leader would be appealing to me.  Then I’d remember just how much Winston Churchill drank.  The pecadilloes of leaders, effective or not, are legion, and sometimes I wonder if they’re a necessity, a relief valve, rather than a contemptible habit.

… is down the hallway, on the left, next to the pool table.  Michael Le Page reports on home brewing your own opiates for NewScientist:

A growing number of drugs, scents and flavours once obtainable only from plants can now be made using genetically modified organisms. Researchers want to add opiates to that list because they are part of a family of molecules that may have useful medicinal properties (see “The yeast route to new painkillers“). Plant yields of many of these molecules are vanishingly small, and the chemicals are difficult and expensive to make in the lab. Getting yeast to pump them out would be far cheaper.

Yeasts capable of doing this do not exist yet, but all the researchers that New Scientist spoke to had no doubt that they soon will. “The field is moving much faster than we had previous realised,” says John Dueber of the University of California, Berkeley, whose team has just created a yeast that makes the main precursor chemical needed to produce opiates. Until recently, Dueber had thought that the creation of, say, a morphine-making yeast was 10 years away. He now thinks a low-yielding strain could be made in two or three years.

While applauding the disruption, and possible dissolution, of drug gangs, I’m more than a little unsettled at the thought of teen age boys experimenting with the creation of opiates in their own homes.  No doubt, so is the DEA:

“It would be as disruptive to drug enforcement policy as it would be to crime syndicates,” says Tania Bubela, a public health researcher at the University of Alberta in Edmonton, Canada. “It may force the US to rethink its war on drugs.”

Nature elaborates:

Various international conventions and national laws are designed to prevent diversion to illegal markets. Countries that manufacture opiates commonly use large, secure industrial facilities. Australia further enhances security by growing a thebaine-rich poppy variety; thebaine is toxic to ingest and is not easily converted into morphine. It is difficult to predict how the main international body, the International Narcotics Control Board (INCB), would react to a new production system for opiates. The INCB is unlikely to slash current opium-production quotas and disrupt current legal opiate-trade patterns to accommodate yeast-based production. This would limit the ability of new producers to enter the market.

Meanwhile, yeast-based opiate synthesis could have a significant effect on illicit markets. Currently, opiates are sold illegally through two main channels. First, prescription pain medications such as oxycodone and hydrocodone are pilfered, prescribed improperly or prescribed legitimately but then sold on illegally by patients. Second, illegally cultivated opium poppies in countries such as Afghanistan, Myanmar, Laos and Mexico are processed into heroin and distributed by criminal networks that sell them at street prices several dozen times the production costs⁸.

Nature‘s recommendations?

Engineering. Yeast strains should be designed to make them less appealing to criminals. For example, strains could be engineered to make only opiates with limited street value, such as thebaine. Alternatively, weaker strains could be engineered to make it harder for people to cultivate and harvest opiates outside established laboratory settings. Strains could be engineered with unusual nutrient dependencies, for instance. Such methods of ‘biocontainment’ have been developed in Escherichia coli. Opiate-producing yeast strains could also contain a marker, such as a DNA watermark, that makes them more readily identifiable to law-enforcement agencies.

Screening. Because there is some — albeit low — risk of criminal syndicates synthesizing opiate-producing yeast strains using published DNA sequences, commercial organizations that make stretches of DNA to order should be alerted. The sequences for opiate-producing yeast strains should be added to the screening criteria used by these providers. Overseen by two voluntary consortia, the International Association of Synthetic Biology and the International Gene Synthesis Consortium, these criteria currently cover only pathogens.

Security. Efforts should be made to keep opiate-producing yeast strains in controlled environments that are licensed by regulators. Physical biosecurity measures — including locks, alarms and systems for monitoring the use of laboratories and materials — could help to prevent the theft of yeast samples. Laboratory personnel should be subject to security screening. Similarly, assigning liability and penalties may dissuade researchers from sharing strains with anyone who is not legally authorized to work with them.

Regulation. The current laws covering opiates, such as the US Controlled Substance Act and its worldwide equivalents, should be extended to cover opiate-producing yeast strains, to make their release and distribution illegal.

It does occur to me to wonder if these recommendations would be counter-productive – could the next great painkiller be found by a bio-hacker at the local junior college?  Granted, getting it through the FDA approval process seems unlikely – but there it is, that brand new drug that, rumor has it, will stop that relentless agony you – or a loved one – is going through.  Think about it.

I personally think the sober recommendations of Nature will fail – it only takes one researcher willing to take a risk for desperately needed cash (or whathaveyou) for an export from a lab to occur; and, of course, researchers may actively work for criminal gangs.  However, the opposite is a prickly cactus to hug.  The first dead teenager might sink the project.

This may open up an interesting market opportunity for firms to specialize in running FDA tests for drugs they have not developed.  I suspect they already exist, but I could not come up with any names.  They would supply capital and expertise in exchange for a cut of the profits – if any.  Expensive?  Yes.  However, these expenses may start to come down as we get better and better at evaluating toxicity and efficacy.

The blog at Scientific American also covers the issue.

In North Carolina, educators win a victory, as noted in Indiana’s The Republic:

North Carolina lawmakers violated veteran teachers’ constitutional rights by passing a law that would remove job protections they’ve earned, the state’s Court of Appeals found Tuesday, but the court rejected efforts to restore newer teachers’ pathway to the protected job status.

Under the 2013 law, legislators sought to move away from a system that protected teachers from firing or demotion after they passed four years of probation and earned “career status.”

Veteran teachers argued that the law violated constitutional rights protecting contracts and preventing governments from taking a person’s property.

The NCAE fights back and wins a victory on a 2-1 ruling, but it’s not the state’s Supreme Court.

A joint statement from state House Speaker Tim Moore and Senate leader Phil Berger said legislative leaders are reviewing the opinion and considering their options.

“While we are disappointed with today’s ruling, we appreciate the thoughtful dissent,” they said.

The Charlotte Observer notes:

Six teachers and the Association of Educators sued, and last year Superior Court Judge Robert Hobgood ruled that taking tenure from teachers was an unconstitutional taking of property rights.

The decision did not apply to teachers who had not earned tenure. Supporters of phasing out tenure called the ruling “judicial activism.”

(h/t a North Carolina Educator)

In other news, other citizens of NC protest the dubious actions of their leaders, as the Charlotte Observer reports:

Critics of the Republican-controlled state legislature gathered Monday night to induct several North Carolina lawmakers into a different kind of hall of fame: the Moral Monday movement’s Hall of Shame. …

The group displayed posters with photos of Mecklenburg state representatives Bill Brawley, Rob Bryan, Charles Jeter, Jacqueline Schaffer, and Sens. Bob Rucho and Jeff Tarte.

Rucho was covered previously here.

Treehugger.com‘s Katherine Martinko reports on ADHD in France:

A shocking 9 percent of U.S. kids are diagnosed and medicated for ADHD, compared to 0.5 percent of French kids. What’s causing the big difference?

Several years ago, a fascinating book came out called Bringing Up Bébé. Written by an American woman named Pamela Druckerman who lives and raises her kids in France, the book explores the many ways in which the French, as a whole culture, parent differently than the Americans (and Canadians, since that’s where I live and see the many similarities in parenting styles).

The biggest difference between France and the United States is the approach to routine and structure in children’s lives. While the French implement a strict daily routine from the very beginning and expect their children to fit into a parent-determined lifestyle, American families are usually child-centric, with parents accommodating their children’s needs and desires.

This stereotypical American parenting style, however, may have a serious downside. An article in Psychology Today attributes the relatively low levels of ADHD in French children in part to the presence of structure in their lives. Because their parents insist that they learn self-control from an early age by enforcing limits and are supported in this by the education system, fewer French children develop behavioral problems that reach the point of requiring medication.

After reading Benen’s blog, I’m enjoying quite a bit of schadenfreude. What a bunch of hypocrites, and who is the one man still married to his first wife? Clinton. Hastert’s years of bribery to hide his “indiscretion” or crime (depending on the age of the high school student), plus breaking federal banking laws to keep those brides anonymous — well, that’s some serious icing on the schadenfreude cake. I can’t wait to see him do the perp walk.

Oh, I wish I was an editorial cartoonist … I’m seeing the Walk of Hypocrites: stone statues of hypocrites throughout the 90s.  Here’s Clinton, with a moderate sized statue, followed by Gingrich, Hastert, Livingston, and all the rest of them – with much larger statues.  And some Mom with her kid, trying to explain …

Politics of the Iran nuclear deal continue to swirl with a visit to Iran by the Taliban of Afghanistan.

Maybe. Abbas Qaidaari of AL Monitor reports:

On May 19, the Tasnim News Agency, which has ties to the Islamic Revolutionary Guard Corps (IRGC), was the first to break the story: “A political delegation of the Taliban led by Tayyeb Agha has traveled to Tehran and held talks with certain Iranian security and military officials. They had also previously visited Iran during the Islamic Awakening Conference.”

 

In Iran and Afghanistan, media outlets quickly reported this news, which generated curious reactions. The Ministry of Foreign Affairs spokeswoman, Marzieh Afkham, said, “I am not aware of any such visit. We should follow up on this and find out which sources have published this news and based on what information.” The government spokesman, Mohammad-Bagher Nobakht, stated, “I am not aware of any such visit. It does not make any sense, and in any case I do not confirm that this visit has taken place.”

So the IRGC welcomes the Taliban while the main government is unaware of the visit?  According to the article, the Taliban murdered 9 Iranian diplomats in 1998, nearly triggering an invasion.  Indeed, Abbas claims,

In 2001, in the wake of 9/11, Iran provided logistical and intelligence support to the United States during the international coalition’s military campaign targeting the Taliban, al-Qaeda’s ally, in Afghanistan.

If true, I was not aware of that support.  This 2010 paper by a Dr. Sadat, a specialist in the region, and Lt. Col. James Hughes, USAF, hosted by the Middle East Policy Council, confirms:

Following the 9/11 attacks, Iran assisted the U.S. invasion of Afghanistan and participated in international efforts to establish a new Afghan government. A senior Iranian diplomat describes the decision making in Iran immediately after the 9/11 attacks: “[W]e consciously decided not to qualify our cooperation on Afghanistan or make it contingent upon a change in U.S. policy, believing, erroneously, that the impact would be of such magnitude that it would automatically have altered the nature of Iran-U.S. relations.”⁹ U.S.-Iran cooperation was unprecedented, but in the years that followed, the George W. Bush administration chose not to continue substantive diplomatic dialogue with Tehran on Afghanistan unless Iran changed its behavior toward nuclear development.¹⁰ Perhaps in 2002, the United States could afford to ignore Iran’s interests in Afghanistan. Eight years later, however, as the first decade of the twenty-first century closes, the situation has changed. There are indications that rogue elements within the Iranian government, presumably the Revolutionary Guard Corps, are providing support to the Taliban in response to perceived threats from the United States.¹¹A U.S. strategy that fails to incorporate Iran’s constructive role in Afghanistan, while weakening its destructive role, may not succeed and could further jeopardize future relations. Although engaging Iran will not be easy, Afghanistan provides an opportunity for both countries to achieve some practical strategic objectives independent of other more entrenched foreign-policy disputes.

The remark about the Revolutionary Guard is interesting.

How does this affect the nuclear deal?  Abbas comments,

The outcome of this event could affect Tehran-Kabul relations and also cast a shadow over the nuclear negotiations between Iran and the five members of the UN Security Council plus Germany (P5+1). The Iranian government needs the nuclear agreement more than ever, so it also must keep tensions low with the P5+1. On the other hand, IRGC [Islamic Revolutionary Guard Corp] officials oppose the negotiations and are trying to raise obstacles. A visit from the Taliban just might be an obstacle meant to prevent Rouhani’s administration from moving forward with its regional and international policies.

I wonder if the IRGC takes its role of guardian of the Islamic Revolution so seriously that it would overthrow the elected government using charges of treachery.

Continuing the theme of short notes on my current computing project, and how I don’t have time to work on it, I can now report that I’ve achieved, in this iteration, what I’d achieved in the previous, which is to say the current code base passes the (slightly modified) auto-regression tests I’ve been writing.  Because I used the supplied EBNF to build the parser, it also means I’ve surpassed (theoretically – not verified) the parsing capability of the previous iteration.  It’d be nice if I could find a publicly available test suite.

The debugging approach described in my previous missive has also worked well.

The auto-regression test suite, however, needs a complete re-think.  The lesson there is one all coders should know: test suites need to be thought out as well as what they are testing.  And I didn’t do that.  Bad Hue, go lay down by your dish.

Next steps: Continue working on the “well-formedness” and validation parts of the processor; expand the auto-regression test suite.

All this for a compiler which may never be completed, nor ever be widely used.  Tilting at windmills entered a new age when open source software started up, all those years ago.

Steve Benen at MaddowBlog engages in more than a bit of schadenfreude following the recent indictment of Dennis Hastert, former Speaker of the House.  He references the work of Orin Kerr at The Volokh Conspiracy in summarizing the indiscretions of a number of Republican personalities who chose to vote for the impeachment of President Bill Clinton over his indiscretions with Monica Lewinsky, and then closes with this:

During the impeachment proceedings, I specifically remember testimony from Princeton scholar Sean Wilentz, who told House Republicans that, in the future, they would be seen as “zealots and fanatics,” adding, “History will hunt you down for your cravenness.”

If you, like myself, were not a Republican at the time, and found the uproar to be more than a bit puzzling, then perhaps you, too, glory a little in the schadenfreude over Gingrich (carrying on with an aide), Livingston (affair), Hyde (affair) and now Hastert (alleged sexual contact with a boy).

But you also have to wonder about the nature of these men, particularly if  you are interested in story-telling (and, about that, another post in another time).  Are they so obsessed with power that the hypocrisy of their actions isn’t apparent?  These guys are smart, surely they can see that.

I recall a story from, I believe, Senator Barbara Boxer, concerning another, very senior Senator from her freshman days in the Senate.  She described him as having a self-image of being right next to God.  Perhaps being at the center of government, these Representatives felt they could do no wrong?

Or, more prosaically, they simply hated Clinton?  President Clinton has a history of taking the issues of his political opponents and making them his, to the point where they become lethal weapons against his opponents.  Add in that he is undoubtedly one of the smartest politicians around, and perhaps it’s just raw envy and anger.

This was the time where ideology began to get the better of the GOP, where governing wisely became a secondary – or tertiary – activity, where being in power was the thing, and principle was optional (see the spending habits of Congress, vs what they proclaimed as ideology, 2000-2006).  This chart courtesy The Daily Kos:

Perhaps, even as I grind my teeth over what might have been, this is simply the result of amateurs running government.

Recalling Supreme Leader Ayatollah Ali Khamenei’s proclamation that Iranian military bases are off-limits with regard to nuclear installation inspections, Lawfare‘s Yishai Schwartz comments:

… some members of the P5+1 appear no less unyielding, with the French foreign minister telling his lawmakers, “France will not accept (a deal) if it is not clear that inspections can be done at all Iranian installations, including military sites.”

At first glance, Iran’s hesitation at allowing international inspectors access to its military sites might appear reasonable. But the history, law, and language of non-proliferation agreements lie squarely on the side of France. Concessions on this issue—even in the form of subjecting certain inspections to the approval of some kind of “joint commission”—would not only dramatically weaken any deal, but would actually constitute a major departure from long-standing principles of nuclear controls. …

Of course, no country liked the idea of foreign inspectors poking around their military bases. But each realized that the comprehensiveness of inspectors’ reach was crucial to the entire system. If there would be inspections-free zones, there could be no guarantee that states’ nuclear programs were peaceful. …

Throughout the years of sanctions and negotiations, Iran has chafed at restrictions and repeatedly demanded to be treated just like any other state. But in insisting on a special exemption denying IAEA access to military site, Iran is actually demanding special, privileged treatment. The fact that the p5+1 would even consider subjecting such visits to a “joint commission” of the IAEA represents a significant, and dangerous, departure from previous practice. The logic of the oversight system rests on the assumption that the IAEA Board of Governors holds ultimate authority to decide where its inspectors go, and that the Security Council serves as its enforcement mechanism. Playing with these details would gut the entire structure.

This is rather interesting in that last week Lawfare suggested the Iran deal could go off the rails without it being a disaster:

After a number of conversations with some of these critics, however, I’m increasingly convinced that there is an alternative, albeit a poorly articulated one. To be sure, it has question marks and uncertainties—and the deal currently being hammered out may yet offer the best balance of risks and benefits. But there is another side of the ledger. Here, then, is a roadmap to that alternative path.

First, American negotiators would have to allow the current round of negotiations to fail, but without blowing up or reneging on any already-made commitments. Doing so should not be too difficult. There are enough unresolved issues that adopting a hard (and reasonable) line on, say, the timing of sanctions relief or the reach of inspections would either force Iranian capitulation (good) or lead to an impasse—which from this perspective would be fine as well.

Perhaps Khamenei is paving that road for them.  Yishai Schwartz continues:

The competing interpretation (and this is something about which far too few of the deal’s critics speak concretely) is that Iran will make some noise, but will actually seek a temporary stop-gap accommodation. It may build a few more centrifuges and reduce inspections by a marginal amount, and in return, the White House and its allies would mildly tighten some existing sanctions. Kirk-Menendez will remain on the shelf and Iran’s breakout time will continue to hover near the three-month mark. There will be Iranian violations and American threats, but both sides will keep their provocations below a certain escalatory threshold, and diplomats will resume talks under an arrangement roughly similar to the JPOA.

And, basically, a status quo.  The important point to note is that Iran doesn’t have resources equivalent to the world’s, so status quo for us merely leaves us with irritating political questions (Obama doesn’t get the legacy he wants), while the Iranian government has more existential questions to consider, between this and its food and water problems.  Of course, one is tempted to say that the Iranian government will find a way to stay on top.  But then, I felt the same way about the East German government, as did just about everyone else – until they collapsed.

Helping me wander about left field, my Facebook correspondent responds:

By “recover from damage” I meant in such a way that mankind could continue to live comfortably and sustainably on this planet. We’re wrecking it for ourselves, and for millions of species we have and are exterminating. But life will go on, on this planet, with or without us. Many species will adapt. So it’s just self interest. I’d like to not have to worry if my grandkids are going to be wiped out by pestilence or war or hunger or thirst simply because current day peoples are too stupid and short-sighted. We are a part of nature, sure. But we’ve got more influence over our natural world than all the rest of the species put together.

Yes, I suppose so, although I can’t help but note the AntBlog, back in 2010, has made some notes concerning total biomasses:

Worldwide biomass estimates for individual species are very difficult to come by. The most rigorous estimates are for humans and domesticated animals. There are probably a little more than 6.7 billion humans alive right now, and together, we might weigh as much as 335,000,000,000 kg (or 737,000,000,000 lbs.) This figure is based on an average human weight of more than 100lbs, though (50kg, to be exact). I don’t know how accurate this estimate is, especially considering that about 1/3 of us are children. There are supposedly around 1.3 billion cattle in the world, and, put together, they may weigh almost twice as much as our species.

The only non-domestic, super-abundant species for which serious attempts have been made at estimating biomass is a type of shrimp that lives in the cold waters around Antarctica: the Antarctic krill, Euphausia superba,. They are the primary food for many fish and baleen whales (suborder Mysticeti). In a really interesting study (click here for more) Atkinson and colleagues (2009) calculated the world biomass of krill to be between 117 and 379,000,000,000 kg (note that the upper estimate is slightly above what people have suggested for the total human biomass). Truly, these organisms are successful. They might be the only wild species that could compete with Homo sapiens for the title of “species with the most biomass.”

However, we can’t forget that as much animal biomass as there is, there is even more plant and bacterial biomass. Probably at least ten times as much as the biomass of all animals put together. Scientists still argue about which has more biomass on earth: bacteria or plants. Worldwide, they both probably have about the same amount of Carbon, but Bacteria probably contain about 10 times more Nitrogen and Phosphorus (read more here ) Like ants, though, there are many many species of bacteria and plants, and I don’t know of any studies that attempt to estimate world-wide biomass for a single species of either.

But I’ll agree with you ahead of time, it’s not really relevant – just very interesting.  What are all those bacteria up to, anyways?

Continuing this topic, North Carolina legislators discover that business will, indeed, pay attention to legislation which appears to ignore scientific realities, as Sami Grover on Treehugger.com reports:

Does $20K buy you a Senator these days?  Or did their lobbyists simply make such a strong presentation that he felt that he had to break the rules?  From the News & Observer:

In light of the questions, Democratic Leader Dan Blue of Raleigh told Rucho he wanted a “division” of the vote, which would allow for an individual tally rather than just by voice. Rucho refused, and when Blue asked him by what rule he was refusing, Rucho said it was his prerogative as chairman and then called for the vote.

The rules the Senate adopted earlier this year say the presiding officer shall conduct a division if it is called for prior to the vote, which in this case it was.

After the meeting, Rucho emphasized to Blue that he had the authority not to allow a division.

I have no idea what sort of punishment can be meted out to a committee chairman who won’t follow the rules.  Removal from the chairmanship?  Kicked out of the legislature?  But if the Republicans are in control, would anyone even dare to bring up the idea?

NewScientist (23 May 2015, paywall) interviews Slawek Tulaczyk concerning how to stem the rising of sea levels:

Are you talking about geoengineering ice streams to control sea level rise?
Yes. When we talk about geoengineering we usually mean bringing down levels of carbon dioxide or controlling Earth’s reflectivity to sunlight. We haven’t yet considered putting the brakes on ice streams and glaciers, but we should be considering this possibility. Last month in Nature, new results corroborated previous evidence showing that the loss of mass from polar ice sheets accelerated in the last decade (DOI: 10.1038/nclimate2635). …

How might we slow down the flow of ice?
One mechanism has to do with decreasing the amount of water at the base of the ice stream, to increase the friction between the base and the bedrock. Basically, we’d need to remove water by increasing drainage. Paradoxically, that may require something counter-intuitive, like drilling a hole from the top of the ice stream to the base and injecting water. You would have to work out how the sliding of the ice would respond to the injection of additional water, but in certain scenarios, the excess water would create a new, bigger channel beneath the ice, and this would help drain the water that’s already there faster than before. Typically when you drive water out from beneath a glacier, you are making it harder for ice to flow.

There are other ways. One would be to prevent warming ocean waters from reaching the ice sheets.

What do you mean?
One reason why many ice streams and glaciers are flowing faster into the ocean is because warming waters are melting the floating ice shelves that surround them and normally act as buttresses. We think that warm water is channelled in through deep troughs in the continental shelf.

And you are saying we can prevent this warm water from reaching the ice?
That’s right. You should be able to build submarine barriers. I’m not suggesting huge concrete structures; you can build something that has the right density to float 300 to 400 metres underwater. You attach some kind of barrier to the floats. The currents in these troughs are not very strong and the barriers don’t have to stop the flow of water, just slow it down. And you could have openings in them to enable life to pass through.

Over at Glacier Hub, Dan Kandy considers how to build new glaciers:

How do you make a glacier? You can transport tens of thousands of tons of ice from a place where retreat is fast to a pre-prepared location where retreat is slower; you can set up barriers around an existing ice field, increasing snow accumulation and transforming the area into a small glacier; or you can cover an existing one with a “geotextile” sheet or rocky debris to slow ablution. A minimum of three years is required for some of these methods, according to [Cedomir] Marangunic, [sic]

While stimulating the growth of new glaciers or slowing the retreat of established ones sounds great, project must simulate a “natural process” and avoid damage to local ecosystems, according to Marangunic, who claims this as a priority for his projects.

Also at Glacier Hub, Tsechu Dolma reports on a conference concerning the shrinking glaciers of Mt. Hood:

That method was created by Chewang Norphel, a civil engineer in Ladakh, India, who pioneered a way to “grow” glaciers in the Himalayas. A short film about Norphel’s mission to create small glaciers in Nepal, “Beyond Prayer”, shows the retired engineer describing his technique, which relies on the redirection of streams in the winter to cool areas, and constructing breaks to slow the flow of water. The water freezes along the mountain slope at regular intervals. During the winter, an ice sheet covers these frozen pools, creating small, artificial glaciers.

“When it comes to Alzheimer’s, iron may not be good ferrous”

Augh!  NewScientist loves its headlines, but that one just makes me ITCH!

Anyways, it’s about a study in Australia:

Researchers at the University of Melbourne in Australia followed 144 older people who had mild cognitive impairment for seven years. To gauge how much iron was in their brains, they measured ferritin, a protein that binds to the metal, in their cerebrospinal fluid. For every nanogram per millilitre people had at the start of the study, they were diagnosed with Alzheimer’s on average three months earlier.

(NewScientist 23 May 2015, paywall, and the headline is only in the print edition.)

The Egyptian correspondence leads to an off-topic point on my part.  First, I’ll reiterate the correspondent’s innocent remark:

I was channeling Jared Diamond when I wrote that — a non-optimistic version of Jared, that is. Right — 100 years ago we were divinely (innocently?) naive and innocent. And the earth could recover from the damage we had done. Today, at 7 billion plus strong, it’s a far worse story — but we like to pretend it’s not there or not so bad. You should read Diamond’s “Collapse”. It’s long and wordy, but very informative.

… but the entire “recover from the damage” remark is interesting in its implication that there’s an ideal “natural” state which we humans have damaged.  I don’t  believe there’s ever an ideal natural state in isolation from humanity, nor do I generally feel we humans are somehow outside of Nature.  Until we re-insert the human viewpoint into the conversation (and I believe that it’s very important that the viewpoint be explicitly stated), there are simply states, which can be characterized in any number of ways – species diversity, population densities, mineral presence, etc.  Once we restate with the human viewpoint (or interest), then it’s possible to credibly say, “Well, it’s ruined for human occupation because of xyz …”

Perhaps it’s all a fine point, but to me there’s this confusion of the first statement implying that the Universe was made for humanity’s use – because we attach value statements to state perturbations of Nature – while, to me, the proper detached viewpoint requires not attaching a value statement to an observation until the proper interest – humanity’s – has been established.  The implicit – and unstated – assumptions can really twist a deductive series until the final conclusion doesn’t really bear any connection to the original set of observations, particularly if prescriptives are suggested.

The Egyptian correspondence continues:

I was channeling Jared Diamond when I wrote that — a non-optimistic version of Jared, that is. Right — 100 years ago we were divinely (innocently?) naive and innocent. And the earth could recover from the damage we had done. Today, at 7 billion plus strong, it’s a far worse story — but we like to pretend it’s not there or not so bad. You should read Diamond’s “Collapse”. It’s long and wordy, but very informative.

I’ll put it on the list.  My suspicion, however, is that either the peace movement or the epidemiologists are going to lose – and a lot of us will suddenly die.  As creatures of Nature, we may find ways to modify the rules of Nature, but outright breaking them may be beyond our capacities.