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Reactive nitrogen lockdown

22 February 2020 - Ecologism

When farmers bring their own scientists to a negotiation.

As already mentioned in an earlier blog The Netherlands is facing a reactive nitrogen crisis. It put the country in a active reactive nitrogen lock-down with building permits for large infrastructure projects revoked and something like a farmers revolt. How did this happen? As part of a European agreement called Natura 2000 141 locations in the country are designated ecologically protected areas and the government is obliged to look after them. That would not be a challenge but the biggest threat to these locations is an abundance of reactive nitrogen. Too much of it kills of for example sensitive heath and favors ordinary grasses. One thing is clear: the country is producing too much reactive nitrogen and emissions must be curbed. But who to blame? Builders, heavy industry and traffic create NOx and from agriculture ammonia is emitted. Welcome to an interesting numbers game.

If the government is to rescue the Nature 2000 area's it first needs to find out who emits what and how much of that what ends up in one of these 141 locations. Then it can either close down the identified operations or force them to clean up their act. The Dutch RIVM is a large government research institute (1700 employees) and some time ago they did the numbers: the biggest reactive nitrogen producer is agriculture (46%) followed by what crosses the border (32%) and then traffic (6%). Industry is a tiny 1%. Government acted accordingly by not invading out neighboring countries (read Rhine-Ruhr) to switch off pollutants there but instead singled out Dutch agriculture and to a smaller extent building. As a symbolic gesture the speed limit for automobiles nation-wide will be reduced from 130 to 100 kilometers per hour starting next month.

The RIVM verdict does not sit well with the farmers. They are facing tough measures and will have to invest heavily in their businesses in order to reduce emissions. A lot of them will be forced to shut them down completely. The ensuing farmers revolt and protests (one of them held in front of RIVM headquarters) may not have accomplished anything yet but this week the farmers struck back at the RIVM scientists by bringing their own scientists Link. Enter Geesje Rotgers (investigative reporter) and Richard Zijlstra (geo data analist) representing Mesdag-Zuivelfonds, a research institute and innovation platform or a lobby group depending who you ask. Their key complaint: the RIVM numbers game has flaws and farmers are singled out as the bad guys for the wrong reasons. Here is why. The figure of 46% concerns the reactive nitrogen emission for the entire landmass (Link) but the farmers argue that only the amount of reactive nitrogen ending up in Nature 2000 area's are relevant.

Before they could begin their own numbers variation they had to take RIVM to court for the release of emission data sets(Link) but this week geo data scientist Richard Zijlstra presented his results: he arrives at 25% for agriculture, 18% foreign, industry 6% and traffic is now 41%. The value for agriculture is much lower, one of the arguments is that ammonia emitted on a farm migrates over a distance of 100 meters at the most, that is often still within the boundary of the farm itself. This is in itself an interesting science question that this blog has attempted to tackle but but research appears to exist only on vertical atmospheric migration patterns but not on horizontal patterns. The figure for traffic is much higher, Mesdag-Zuivelfonds notes that a lot of busy highways and shipping cuts right through Natura 2000 areas. Industry is also higher, Mesdag-Zuivelfonds questions the quality of the RIVM data because it relies on self-reporting of emissions by the industrial companies and smaller companies are exempt from reporting anyway.

The RIVM response was threefold. Yes, they do have deposition data specifically for each Nature 2000 area which do not deviate in a significant way from the national data. The Mesdag-Zuivelfonds data analyst has been using a data set that lacked proper resolution and the calculations included protected lakes that do not have a reactive nitrogen problem.

After a week of publicity the media have solidly sided with RIVM. It does not help that Mesdag-Zuivelfonds is viewed as a lobby group and not a innovation platform. The data were not presented as a single proper report, we have a press release, a video, a powerpoint and a whopping 600 MB pdf that cannot be downloaded because it cannot be scanned for viruses. So much for communication skills.

On the other hand the RIVM can complain Mesdag-Zuivelfonds used the wrong data set but it is the data set they have handed over in the first place. A high-resolution data set is not going to help Mesdag-Zuivelfond anyway because it will lack the serious computing power typically available only to large institutions such as RIVM. The RIVM remark that reactive nitrogen deposited in a lake is harmless may very well trigger a new scientific debate.

Update 03 March: Mesdag and RIVM have discussed matters. Mesdag will start new calculations, RIVM will provide additional datasets if required. Mesdag has acknowledged it made errors in their calculations, RIVM has acknowledged it made a mistake in their calculations. Agriculture contribution now 41% from 46%. The power of peer review! (

Update 05 March: an official committee of scientists have advised the government that the methodology used by RIVM to track reactive nitrogen can be trusted. (volkskrant). RIVM should however according to the committee seriously increase the number of physical measuring stations around the country. This has always been a key point of contention with the farmers who argue that the simulation models do not accurately reflect data collected in the field. Big win for the farmers there. The newspaper The Volkskrant notes that it does not help that the chairman of the committee has past employment with RIVM. On the other hand the committee included a known RIVM critic. The national media declared the RIVM the winner.

Update 05 March: The Mesdag geoneer Zijlstra on his Twitter account provided a link to the OPS source code at github. Not sure if it went open-source just today. Interestingly this software has been around since 1989 and a lot of national policy making depends on it. Our geoneer is delving into the code as we speak.

Remdesivir latest

08 February 2020 - Antipandemics

remdesivir synthesis With large parts of China in a lock down on account of the Wuhan corona virus the hunt is on for a defense, a treatment or a cure. A lot of attention is directed at vaccines as in regular flu but with development work, testing and production a working vaccine in the hands of medics can be months away. Another potential avenue is a synthetic antiviral. It is not that we are lacking them, examples of commercially available drugs are Baloxavir marboxil, Peramivir, and Zanamivir. The 2003 SARS pandemic eventually petered out and has been treated with antivirals in general as yet no vaccine exists. In the 2005 H5N1 Pandemic the antiviral Oseltamivir (Tamiflu) became a household name. Governments were stockpiling it but years later it was determined Tamiflu is not that efficient. Middle East respiratory syndrome (MERS) was first diagnosed in 2012 and never went away with new cases reported every year. Same story here: no vaccine and no virus-killer wonder drug.

A compound making the rounds in 2020 China is remdesivir, an existing antiviral drug that has already proven to be effective against Ebola and Marburg. Remdesivir has been successfully tried on a patient in the US as reported in the New England Journal of Medicine on 31 January (DOI).
In a letter to Nature on 4 February a group of researchers from Wuhan (Wuhan Institute of Virology) and Beijing (National Engineering Research Center for the Emergency Drug) report that remdesivir and chloroquine are effective in vitro. They infected Vero cells with the isolated corona virus and measured cytotoxicity in a cell counter kit and the proliferation of new viruses with RT-PCR. They were also able to visualise the viruses in immunofluorescence by adding a so-called Goat anti-Rabbit antibody labeled with a Alexa Fluor formulation.

Remdesivir is a adenosine analogue, basically a purine and a ribose. The molecule can insert itself into viral RNA making the virus crash. The compound was developed by Gilead Sciences (the Oseltamivir people) years ago and a patent describing the synthesis is US73474980. Chloroquine has been around for decades and is basically an antimalarial drug. It interferes with the fusion of a virus and a cell.

Meanwhile the Wuhan researchers appear to have taken out a patent for remdesivir as an corona virus specific drug (link). This is problematic as Gilead has already patented the compound for this purpose in 2016 including in China (Link). Several days ago the company announced a clinical trial to be conducted with 270 patients in Beijing (Link) Another clinical trial announced by the president of the Chinese Academy of Medical Sciences will be held in Wuhan (Link).

Update 10 February. Earlier The Lancet study published 31-01 mentions oseltamivir (DOI) . A Nature comment mentions favipiravir, ribavirin and galidesivir and explain their attack mode (Link).

Update 13 February. New study had remdesivir tested in animals exposed to the MERS coronavirus (DOI). Research group includes Gilead people. Strange use of the word "inoculation" because the experimental monkeys were for sure infected. Remdesivir was found to be effective administered before and after the onset of infection. Chinese company BrightGene Bio-Medical Technology is reported to be ready for remdesivir production (Link). No patents but the company has patented Oseltamivir work in the past.

Update 14 February: Wired has the full story on the clinical trials taking place (link). Two antivirals intended for HIV, lopinavir and ritonavir will also be trialed. Like remdesivir they also work by messing with a key enzyme produced by the virus. No word of chloroquine trials yet.

Update 18 February: Chloroquine successfully tested in clinical trial. Report from Chinese state-owned website here and confirmation from Belgian virologist Marc Van Ranst in news report here (in Dutch).

Update 20 February: Just read in The Guardian that the WHO is not backing chloroquine? They are betting on lopinavir / ritonavir and remdesivir.

Hydrogen from seawater

02 February 2020 - The energy transition

Hydrogen is an efficient energy carrier. In many countries it can replace natural gas for heating and cooking in households with minor modifications to the existing infrastructure. It can also power cars and it can be used to store energy. The gas is relatively safe to use because its low density will in the event of a leak make it rise quickly and disperse. On the other hand it can enbrittle metals and it ignites easily, compression and liquefaction is expensive. For the Tokyo 2020 Olympics hydrogen will be shipped in from Australia to provide energy for the entire event. Even the Olympic torch will be powered by hydrogen. Too bad this particular hydrogen is produced from low-grade coal making it not exactly environment-friendly.

Ideally hydrogen is produced from solar or wind energy and the conversion then takes place via electrolytic water splitting. Everything is settled then? Not so easy. Water splitting requires a lot of water and there is not enough clean fresh water around if hydrogen is to be used on a massive scale. Seawater then? There is a catch. Whereas fresh water electrolysis gets you oxygen on the anode and hydrogen on the cathode. With seawater chlorine gas also evolves on account of the dissolved sodium chloride. In fact all industrially produced chlorine is made from brine electrolysis. Then what to do with all that chlorine? You can convert all of it to household bleach and distribute it for free making Earth the cleanest planet in the universe or .... find a way to suppress chlorine formation in electrolysis or try something else altogether with seawater. With that in mind, what has been happening in research labs around the world? Time for a quick update.

In 2018 Vos et al. (DOI) tackled the problem of chlorine evolution head-on. The oxygen half-reaction is thermodynamically more favorable but is kinetically slower (involving 4 electrons and not 2). A coating of manganese dioxide on a iridium oxide electrode was found to impart selectivity in the oxygen reaction versus the chlorine reaction. The manganese layer is passive and porous and inhabitable for chlorine ions. In this work as a stand-in for seawater a sodium chloride solution was used but less concentrated than the real thing. The article mentions scientist John Bockris who already in 1970 worked on water electrolysis and coined the term "hydrogen economy". Readers be warned, his alleged secret catalysts never materialized, his later work on cold fusion and forays into alchemy met with controversy.
In another 2018 effort (Hsu et al. DOI) the iridium oxide electrode was coated with a cyanometalate layer. The water was actual seawater and was sourced from West Coast Park in Singapore, the more than thorough supplemental information even has a photo of the collection site. An efficiency of 20% was reported. Amikam et sal. (2018, DOI) have investigated in another way the suppression of the chlorine formation. They found out that conducting the electrolysis (artificial seawater, nickel electrodes) with added sodium hydroxide not only eliminated this side reaction but also salted out sodium chloride through the common ion effect. Solutions can be surprisingly simple.

Artificial seawater ((1 M KOH with 0.5 M NaCl) was again used in a 2019 study (Kuang et al. DOI) with this time an electrode based on a nickel-iron hydroxide coating on a nickel sulfide coating on a porous nickel foam.

Another contender for hydrogen production from seawater is photocatalytic water splitting, no need for electrodes here, just add a catalyst, aim a light source and hydrogen again should evolve. Research has come up with a bunch of catalyst systems, a recent example is metal-doped strontium titanate perovskite (Sahrma et al. 2019 DOI). In this particular effort sea water (Tamsui River in Taiwan) was also tried but it behaved badly compared to fresh water.

One adventurous 2019 research article (Kim et al. 2019 DOI) has the promise of simultaneous carbon dioxide consumption, electricity generation and hydrogen evolution in seawater (sea of Ulsan). To good to be true? In the proposal a carbon dioxide feed continuously acidifies a seawater platinum cathode compartment, the other compartment is an alkaline solution with a zinc electrode. This constitutes a working galvanic cell with accumulation of potassium bicarbonate , a spent zinc electrode and hydrogen gas production. Too good to be true.

Aluminum metal is a known redox partner for water but the oxide outer layer poses a problem and aluminum salts have to be regenerated. In a 2017 effort (Lu et al. DOI) the liquid gallium-indium alloy galistan (think thermometer) is proposed as a remedy for use of Al with artificial seawater. The alloy destroys the oxide layer and can be reused.

Hydrogen can also be replaced by hydrogen peroxide as fuel carrier. The production of this compound from seawater was demonstrated by Mase et al (2016 , DOI) with a tungsten trioxide catalyst. This seawater was made from commercially available red sea salt and with respect to experimental reproducibility preferable over real seawater.

Someone is yelling methanol. If it is not going to be the hydrogen economy or the hydrogen peroxide economy there is always the methanol economy and Hogerwaard et al. have been viewing a bucket of seawater as a bucket of future methanol. A 2019 analysis (DOI) envisions artificial islands stacked to the brim with advanced solar technology and electrodialysis units. In this technique seawater is desalinated using an electrode to force the sodium ions past an ion-exchange membrane. Hydrogen gas production is a side effect in commercial desalination plants based on electrodialysis but in a combined dialysis / electrolysis process the main aim becomes hydrogen production and in addition because hydrogen ions replace the sodium ions the formation of carbon dioxide is also accelerated. In a final step hydrogen and carbon dioxide combine to form the methanol.