Monthly Archives: June 2015

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?