Author Archives: rdmyers75@hotmail.com

Philadelphia prison population might be cut by a third

I found this news pretty surprising:

Philadelphia’s prisons hold on average more than 7,000 inmates each day – the highest incarceration rate of any major American city.

The powers that be want to cut it by more than a third, 34 percent to be exact, during the next three years.

Part of that will call for addressing racial bias in the justice system… “Folks cannot get what they need in the way of drug treatment, counseling, job training, social skill training behind bars,” said Mayor Jim Kenney.

The article goes on to quote judges who agree with this. It’s certainly good news. If so many people involved in the system agree that one-third of people in prison are there because of racial bias, are nonviolent, and don’t need to be there, and it can really be fixed so quickly, what took so long?

 

designing genetic circuits

This article in Science describes design of circuits that can be translated directly to DNA sequences, which when built will perform the function of the circuit.
Programming circuitry for synthetic biology

As synthetic biology techniques become more powerful, researchers are anticipating a future in which the design of biological circuits will be similar to the design of integrated circuits in electronics. Nielsen et al. describe what is essentially a programming language to design computational circuits in living cells. The circuits generated on plasmids expressed in Escherichia coli required careful insulation from their genetic context, but primarily functioned as specified. The circuits could, for example, regulate cellular functions in response to multiple environmental signals. Such a strategy can facilitate the development of more complex circuits by genetic engineering.

electric cars

This article argues that electric cars could be about to take off in a big way, and draws an analogy to the disruption of the cell phone industry caused by the iPhone.

In 2007, Nokia was the biggest and most fashionable name in cell phones, with an unassailable lead in hand-held technology. Things had been so good for so long that company executives saw little chance for any competitive challenge–phones were a tough business, they said, and Nokia was reaping the harvest of decades of hard work that no one else could hope to match.

That June, Steve Jobs introduced the iPhone. And seven years later, Nokia—worth a quarter of a trillion dollars at its apex—abjectly sold off its much-diminished phone division to Microsoft. The price was $7 billion, less than 3% of its former value…

On March 31, his Tesla Motors unveiled its long-promised Model 3, a $35,000 electric car that will go 215 miles per charge… In addition to GM’s Chevy Bolt, Nissan will produce a second-generation Leaf with the same 200-mile range and approximately $35,000 price; it will come in 2017. Before that, Toyota will deliver its Prius Prime, a plug-in hybrid; and BMW already has its pure electric i3. The other major carmakers are piling in as well by the end of the decade.

Before the iPhone, some of the best recent examples of disruption are the digital camera displacing the film camera (much to Kodak’s surprise) and the internet all but destroying the newspaper industry. And you could argue that these are no more revolutionary than the advent of automobiles, electricity, steam, and so on back through history. But the point is big technological advances happen in fits and starts on a regular basis, and will continue to do so however surprised and complacent we may continue to be.

Standard Alternative Energy

In a slight irony, The Rockefeller Brothers Fund has joined the fossil fuel divestment movement.

Given the RBF’s deep commitment to combating climate change, the Fund is now committing to a two-step process to address its desire to divest from investments in fossil fuels. Our immediate focus will be on coal and tar sands, two of the most intensive sources of carbon emissions. We are working to eliminate the Fund’s exposure to these energy sources as quickly as possible. Given the structure of some commingled investment funds and investments in highly diversified energy companies, we recognize there may continue to be minimal investments in our portfolio in those energy sectors, but we are committed to reducing our exposure to coal and tar sands to less than one percent of the total portfolio by the end of 2014. As we take the steps to divest from coal and tar sands investments, we are also undertaking a comprehensive analysis of our exposure to any remaining fossil fuel investments and will work with the RBF Investment Committee and board of trustees to determine an appropriate strategy for further divestment over the next few years.

In working to align our endowment investments with our mission and programs, we will adhere to the longstanding mandate of our board of trustees that our assets be invested with the goal of achieving financial returns that will enable the foundation to meet its annual philanthropic obligations, while maintaining the purchasing power of the endowment, so that future generations will also benefit from the foundation’s charitable giving. In uncertain and volatile markets, these financial goals are not easy to achieve. Therefore, our divestment from fossil fuels, which is now underway, will be accomplished through a careful process of evaluating our exposure and a phased approach that proceeds as quickly as is prudent.

where are the tigers?

Wild tiger populations are critically low, but have actually ticked up a bit. Here are the numbers: There are 12 countries thought to have wild tigers, with a global estimate of 3,890. There were 13 until Cambodia recently announced that theirs were gone. India has by far the most, with an estimated 2,226. The next largest populations are only 433, in Russia, and 371, in Indonesia. The rest generally have around a hundred or less.

antibacterial soap

The tide may be finally turning against anti-bacterial soap. Not only does it not improve health, it becomes lodged in your nose and allows antibiotic-resistant germs to breed there.

In the meantime, however, researchers seem to be digging up more and more dirt on the chemicals, particularly triclosan. This antimicrobial is widely used in not just hand soaps, but body washes, shampoos, toothpastes, cosmetics, household cleaners, medical equipment, and more. And it’s just as pervasive in people as it is in homes and clinics. Triclosan easily enters bodies by ingestion (think toothpaste) or skin absorption. It’s commonly found in people’s urine, blood, breast milk, and even their snot.

A 2014 study led by microbiologist Blaise Boles of the University of Michigan in Ann Arbor tested 90 adults and found that 41 percent (37 people) had triclosan-laced boogers. Antimicrobial-snot paradoxically doubles your odds of having the potentially-infectious Staphylococcus aureus bacteria up your nose.

In rats exposed to triclosan, Dr. Boles and his colleagues found that triclosan exposure made it more difficult, not less, for the rodents to fend off Staph invasions. Triclosan seems to make the bacteria “stickier”—better able to adhere to proteins and surfaces. That stickiness could be why Staph is so good at hunkering down in the schnoz, setting the stage for future infections.

The article goes on to say they are having an adverse effect on wastewater treatment processes, and possibly on aquatic ecosystems downstream although that doesn’t seem conclusive.

The way I think of clean chemistry, we can break substances into three categories: (1) those we know are useful, non-toxic and safe (basic soap, for example), (2) those that are useful but we know or suspect they may not be safe (laundry and dishwasher detergents for example), and (3) those that are useless and we do not know if they are safe (antibacterial soap is a perfect example!). Saying no to category 3 should be the easy part! They should be banned, and leaders of companies that push these products should be held accountable. The hard part is finding substitutes from category 1 that are just as effective and cost-effective as the ones in category 2. We put up with category 2 because the functions are important enough to us that we are willing to put up with the risks. But consumers are not good judges of that risk, and companies not only are willing to sell them dangerous products, they are willing to use cynical marketing campaigns to boost demand for them.

soil and carbon sequestration

This open-access article in Nature makes a surprising claim – that much better management of agricultural soil could offset a significant portion of annual carbon emissions from all sources (not just agriculture), while also being good for ecosystems and food security.

How important, in total, is this large, varied set of land-use and management practices as a GHG mitigation strategy? One of the challenges in answering this question is to distinguish between what is technically feasible and what might be achieved given economic, social and policy constraints. A comprehensive global analysis of agricultural practices combined climate-stratified modelling of emission reductions and soil C sequestration with economic and land-use change models to estimate mitigation potential as a function of varying ‘C prices’ (reflecting a social incentive to pay for mitigation). They estimated total soil GHG mitigation potential ranging from 5.3 Pg CO2(eq) yr−1 (without economic constraints) to 1.5 Pg CO2(eq) yr−1 at the lowest specified C price (US$20 per Mg of CO2(eq)). Average rates for the majority of management interventions are modest, <1 Mg CO2(eq) ha−1 yr−1. Thus, achieving large global GHG reductions requires a substantial proportion of the agricultural land base (Fig. 2). Although the economic and management constraints on biochar additions (not assessed by ref. 19) are less well known, ref. 67 estimated a global technical potential of 1–1.8 Pg CO2(eq) yr−1 (Fig. 2).

A more unconventional intervention that has been proposed is the development of crops with larger, deeper root systems, hence increasing plant C inputs and soil C sinks. Increasing root biomass and selecting for root architectures that store more C in soils has not previously been an objective for crop breeders, although most crops have sufficient genetic plasticity to alter root characteristics substantially and selection aimed at improved root adaptation to soil acidity, hypoxia and nutrient limitations could yield greater root C inputs as well as increased crop yields. Greater root C input is well recognized as a main reason for the higher soil C stocks maintained under perennial grasses compared to annual crops. Although there are no published estimates of the global C sink potential for ‘root enhancement’ of annual crop species, as a first-order estimate, a sustained increase in root C inputs might add ~1 Pg CO2(eq) yr−1 or more if applied over a large portion of global cropland area (Fig. 2).

Thus, the overall mitigation potential of existing (and potential future) soil management practices could be as high as ~8 Pg CO2(eq) yr−1. How much is achievable will depend heavily on the effectiveness of implementation strategies and socioeconomic and policy constraints.

I tried to get a quick answer on global annual emissions in Pg CO2(eq), and failed. Now I’m out of time. I’ll figure it out some other time.

Robert Paxton on Trump

Back on the “Trump is a fascist” topic, I think I recently took an article by Robert Paxton, an expert on who is a fascist, and used it to try to make the case that Trump is a fascist. Well, from an interview in Slate here is Paxton himself on the topic:

First of all, there are the kinds of themes Trump uses. The use of ethnic stereotypes and exploitation of fear of foreigners is directly out of a fascist’s recipe book. “Making the country great again” sounds exactly like the fascist movements. Concern about national decline, that was one of the most prominent emotional states evoked in fascist discourse, and Trump is using that full-blast, quite illegitimately, because the country isn’t in serious decline, but he’s able to persuade them that it is. That is a fascist stroke. An aggressive foreign policy to arrest the supposed decline. That’s another one. Then, there’s a second level, which is a level of style and technique. He even looks like Mussolini in the way he sticks his lower jaw out, and also the bluster, the skill at sensing the mood of the crowd, the skillful use of media…

I think there are some powerful differences. To start with, in the area of programs, the fascists offer themselves as a remedy for aggressive individualism, which they believed was the source of the defeat of Germany in World War I, and the decline of Italy, the failure of Italy. World War I, the perceived national decline, they blamed on individualism and their solution was to subject the individual to the interests of the community. Trump, and the Republicans generally, and indeed a great swath of American society have celebrated individualism to the absolute total extreme. Trump’s idea and the Republican plan is to lift the burden of regulation from businesses…

The other differences are the circumstances in which we live. Germany had been defeated catastrophically in war. Following which was the depression, which was almost as bad in Germany as it was here. Italy was on the brink of civil war in 1919. There were massive occupations of land by frustrated peasants. The actual problems those countries addressed have no parallel to today. We have serious problems, but there’s no objective conditions that come anywhere near the seriousness of what those countries were facing. There was a groundswell of reaction against the existing constitutions and existing regimes.

So the original fascism was openly anti-democratic, about subordinating individuality to the state, and it seems unlikely for any American politician to openly campaign on these ideas. Does that matter? It was also about going back to perceived glory days when the state was much stronger and people were more united. In that sense, it makes sense that in the U.S. a fascism would be based on our national myth of rugged individualism and the equal opportunity to “pursue” happiness, which maybe implies that if you have the natural talent and/or make the effort you deserve to succeed, while those who lack those things do not.

And anyway, the original Italian brand of fascism was not really based on ideology – it was more style over substance as described here by Umberto Eco:

If we still think of the totalitarian governments that ruled Europe before the Second World War we can easily say that it would be difficult for them to reappear in the same form in different historical circumstances. If Mussolini’s fascism was based upon the idea of a charismatic ruler, on corporatism, on the utopia of the Imperial Fate of Rome, on an imperialistic will to conquer new territories, on an exacerbated nationalism, on the ideal of an entire nation regimented in black shirts, on the rejection of parliamentary democracy, on anti-Semitism, then I have no difficulty in acknowledging that today the Italian Alleanza Nazionale, born from the postwar Fascist Party, MSI, and certainly a right-wing party, has by now very little to do with the old fascism. In the same vein, even though I am much concerned about the various Nazi-like movements that have arisen here and there in Europe, including Russia, I do not think that Nazism, in its original form, is about to reappear as a nationwide movement…

Nevertheless, even though political regimes can be overthrown, and ideologies can be criticized and disowned, behind a regime and its ideology there is always a way of
thinking and feeling, a group of cultural habits, of obscure instincts and unfathomable drives. Is there still another ghost stalking Europe (not to speak of other parts of the world)? …

Italian fascism was certainly a dictatorship, but it was not totally totalitarian, not because of its mildness but rather because of the philosophical weakness of its ideology. Contrary to common opinion, fascism in Italy had no special philosophy. The article on fascism signed by Mussolini in the Treccani Encyclopedia was written or basically inspired by Giovanni Gentile, but it reflected a late-Hegelian notion of the Absolute and Ethical State which was never fully realized by Mussolini. Mussolini did not have any philosophy: he had only rhetoric. He was a militant atheist at the beginning and later signed the Convention with the Church and welcomed the bishops who blessed the Fascist pennants. In his early anticlerical years, according to a likely legend, he once asked God, in order to prove His existence, to strike him down on the spot. Later, Mussolini always cited the name of God in his speeches, and did not mind being called the Man of Providence.

Speaking of style over substance, I’ll link to one more article that I found fascinating, describing a theory that Donald Trump honed his skills at firing up a crowd through his involvement in U.S.-style professional wrestling. Now, I do want to say that I find it slightly offensive to imply, as I think this article does, that fans of certain low-brow entertainments and sporting events tend to be stupid and impressionable, with fascist tendencies. I think most rational, tolerant adults can compartmentalize reality and entertainment in two parts of their brains, and choose to enjoy entertainment and sporting events with no effect on our politics or civil lives. It’s relaxing. You get the joke, the same as if you chose to be entertained by a night of standup comedy where completely outrageous things are being said. But with Trump, you get the idea that not everyone gets the joke.

Here’s one last link I want to provide, just for my own later reference. This is a Fresh Air interview with the author of a new book on Franco’s Spain, which is a part of the pre-World War II European fascist story and a major gap in my personal education.

launching the cosmic-ray neutron probe…


Okay this isn’t really about an evil plot to dominate the world. It’s about measuring soil moisture.

Estimating field-scale root zone soil moisture using the cosmic-ray neutron probe

Many practical hydrological, meteorological, and agricultural management problems require estimates of soil moisture with an areal footprint equivalent to field scale, integrated over the entire root zone. The cosmic-ray neutron probe is a promising instrument to provide field-scale areal coverage, but these observations are shallow and require depth-scaling in order to be considered representative of the entire root zone. A study to identify appropriate depth-scaling techniques was conducted at a grazing pasture site in central Saskatchewan, Canada over a 2-year period. Area-averaged soil moisture was assessed using a cosmic-ray neutron probe. Root zone soil moisture was measured at 21 locations within the 500 m  ×  500 m study area, using a down-hole neutron probe. The cosmic-ray neutron probe was found to provide accurate estimates of field-scale surface soil moisture, but measurements represented less than 40 % of the seasonal change in root zone storage due to its shallow measurement depth. The root zone estimation methods evaluated were: (a) the coupling of the cosmic-ray neutron probe with a time-stable neutron probe monitoring location, (b) coupling the cosmic-ray neutron probe with a representative landscape unit monitoring approach, and (c) convolution of the cosmic-ray neutron probe measurements with the exponential filter. The time stability method provided the best estimate of root zone soil moisture (RMSE  =  0.005 cm3 cm−3), followed by the exponential filter (RMSE  =  0.014 cm3 cm−3). The landscape unit approach, which required no calibration, had a negative bias but estimated the cumulative change in storage reasonably. The feasibility of applying these methods to field sites without existing instrumentation is discussed. Based upon its observed performance and its minimal data requirements, it is concluded that the exponential filter method has the most potential for estimating root zone soil moisture from cosmic-ray neutron probe data.

Roombot

This is a great solution to a problem everyone who has worked in an office has had. As a Generation Xer, I am not yet senior enough to intimidate those younger employees who have actually reserved the conference room I am illegally occupying. At the same time I still have a grudging respect for my own elders, so I can’t march in and tell the CEO to get the hell out of the conference room I have reserved, like a truly fearless Millennial would do.