A Few Thoughts on Oxygen – Part 1

Until late in the 20th century scientists hypothesized that the earth’s early atmosphere was highly reduced, in a chemical sense. What atmospheric elements were present were bonded to hydrogen. This followed from the well-known fact that hydrogen is by far the most abundant element in the universe . Hence, other elements were more likely to be chemically attached to Hydrogen than anything else. Any carbon would be present as methane CH4, nitrogen would be present as ammonia NH3 and oxygen in the form of water OH2.

Scientists in the early 1950s (Stanley Miller-Urey) used this assumption in experiments looking for mechanisms for the beginning of life. They created an atmosphere composed of these reduced gasses and then induced chemical reactions among them using UV light (which would have been abundant ) and/ or Electric arc (simulating lightning.) They found that the could produce several “life precursor” molecules such as amino acids (to form protein), purine and pyrimidines (to form nucleic acids), and simple sugars (to form carbohydrates.)

I gave many a lecture discussing the Miller-Urey experiments, which with current understanding of what the early atmosphere was like, were wrong. Evolution of life most likely required the same simple precursors to be present but they must have come about by other mechanisms. The current wisdom as to the composition of the early atmosphere suggests in was more in line with the composition of volcanic gasses. This is based on more recent geochemical studies. Carbon would have been present in its oxidized form, CO2. Nitrogen would have been present as the diatomic gas N2, sulfur as SO3.

The only feature of the previously assumed early atmosphere and the current hypothesis is that the presence of any free oxygen (O2) was very limited, maybe a fraction of one percent of the total atmosphere. Currently it is about 21 percent.

Regardless of the competing hypotheses about the composition of the atmosphere life most likely began and then evolved in the absence of any significant amount of Oxygen for a couple of billion years. Because of the specificity of the genetic code it has always been assumed that all life is related and the earliest ancestor of all life is called LUCA – the Last Universal Common Ancestor.

What did LUCA look like? How did she make a living? Surely she was a single celled organism replicating by cell fission. Information from mother to daughter cell was transmitted by DNA replication, so the enzymes attendant to this task are shared by all her descendants. She had to have been an anaerobe as there was scant oxygen in the atmosphere at the time. What about the other cell machinery?

When certain components of cellular machinery are found across all life, it must be that LUCA had these components. Oddly, for an anaerobe, LUCA appears to have had a broad range of macromolecular structures which are for handling oxygen. What is that all about?


A couple of decades ago and without having taken at least a high school chemistry course most would not have heard of Lithium, nor use it in their daily lives. Now however it dominates the battery world. Disposable Lithium metal batteries power all sorts of devices which require the packing a lot of power in a small space . In addition to AA and AAA batteries, Lithium metal batteries power virtually all the “coin” batteries in small devices such as hearing aids and watches. Lithium metal batteries also have an illicit use as a reagent in the synthesis of methamphetamine but that is another story.

Lithium metal batteries pack about twice the punch as Lithium ion batteries for a given size. More important for many applications is the fact that Lithium ion batteries are rechargeable, greatly increasing their utility. Everything from cell phones to plug-in hybrids (electric cars which can be charged at home or work) utilize the rechargeable aspect of lithium ion batteries.

Lithium is a metal but the periodic chart is populated by scores of metals, in fact the majority of elements in the universe are metals. What makes Lithium unique is it’s charge to weight (and volume) ratio. Lithium metal is the lightest metal and can exist as a stable ion. This means it is capable of giving up or accepting an electron, a necessary function of a battery. Think of a charged battery as reservoir of electrons. When a battery powered device is turned on a circuit is completed which allows the electrons to flow. This is the electric current which does what ever work of a device was built for, be it lighting a light bulb or powering an electric automobile.

As the reservoir of electrons is depleted the battery loses power. Rechargeable batteries are capable of reversing the loss of electrons by pushing electrons back into the battery.

Rechargeable batteries are at the heart of numerous university, government, and private research facilities for two obvious reasons. First, electric powered transportation is the future but contemporary batteries have a limited range. Equally limiting is the long recharge times required. To replace internal combustion engine powered cars, battery powered electric cars and going to have to have a several hundred mile range and a few minutes recharge time. That is a tall order.

So is there enough Lithium out there to meet the increasing demand? Do we have supplies here in the US or do we have to buy it from other countries? Can we afford it? All valid questions. Lithium is present in the earth’s crust at about 20 parts per million (PPM.) This doesn’t sound like much but it more than more commonly known metals such as Lead and Mercury.

Currently we import about 80% of our Lithium needs, but recent prospecting has turned up brine deposits in Wyoming which may provide for our need for sometime into the future. Ultimately the world’s richest deposits of economically recoverable Lithium are in the Atacama desert on the Pacific coast of Chile. Unrelated factoid – the Atacama is the driest place on earth.

Exxon valdez cleanup

Trump, the Environment, and the Cabinet

It would appear that president-elect Trump thinks our air and our water are too clean and If he is successful we are likely to have less of both (and there is no reason to assume he won’t be successful due to the republican majorities in both houses of congress.)

Oddly, in 2009 he signed a letter along with numerous business leaders to President Obama encouraging him act. “”We support your effort to ensure meaningful and effective measures to control climate change, an immediate challenge facing the United States and the world today” … and further “If we fail to act now, it is scientifically irrefutable that there will be catastrophic and irreversible consequences for humanity and our planet.”

Now his pronouncements are just the opposite. In 2010 he said that Al Gore should have his Nobel peace prize revoked because he decided that global warming was a hoax. His evidence du jour was the fact that it was winter and snowing. Later still he expanded on the hoax idea claiming that not only were the world’s scientists conspiring to promote a hoax but apparently doing so at the bidding of the Chinese who invented the hoax in the first place.

So when Trump takes office in January which one will show up ? Will it be the Trump of “catastrophic and irreversible consequences for humanity …” or the more contemporary Trump of 2015: “it’s a hoax, it’s a hoax. I mean, it’s a money-making industry, okay? It’s a hoax.” Some how it is not surprising that Trump sees money as the only motivation.

Based on a few cabinet nominations it looks like the recent Trump will show. Scott Pruitt, nominee to head the Environmental Protection Agency is currently the Attorney General of the state of Oklahoma, the politics of which are dominated by the oil and gas industry. In this position he has sued the EPA numerous times to block the EPA from enforcing regulations aimed to protect our air and water. If the Senate approves the nomination, it will mark a sea change at EPA. Every previous administrator at EPA has worked to protect the environment and relied on sound science.

Another critical cabinet position is the Secretary of Energy, currently headed by a theoretical physicist with a PhD, Ernest Moniz. The Energy Department oversees not only our overall energy policy but also controls our nuclear armaments. Trump’s pick is Rick Perry former Governor of Texas and a friend of the fossil fuel industry. In 2008 Perry ran for president. One of his planks was the elimination of the Energy Department. With no small irony, during a debate he was asked to name the departments he intended to eliminate. He only had to remember the names of three departments, but he remembered only two – Energy was not one of them.

Although the mission of the state department is only tangentially related to the environment, Trump’s selection speaks volumes. Nominated for Secretary of State is none other than the CEO of Exxon-Mobile, the world’s largest player in the fossil fuel industry. Rex Tillerson as head of Exxon-Mobile had planned a 500 billion dollar deal with Russia to drill for oil and gas in the Arctic. When Russia annexed Crimea and was implicated in shooting down a commercial airliner over Ukraine, sanctions from the US and other western powers made the artic drilling deal null and void. Mr. Tillerson noted at a news conference in 2015 that he looked forward to lifting the sanctions on Russia. Drill baby Drill.


Generally the citizens of red states take in more from the feds than they pay out in taxes. Conversely blue states pay out more than they take in. There are exceptions, red Kansas pays out more than it takes in and blue New Mexico takes in more than it pays out.

Both Trump and the Republicans in congress have repeatedly stressed their plan to repeal the Patient Protection and Affordable Care Act (Obamacare.) Will it be replaced? If So what will replace it? House majority leader Kevin McCarthy said “”Nothing’s been decided yet but I would move through and repeal and then go to work on replacing.” There are several competing ideas floating around, all of which will mean less support for healthcare.

The medicaid expansion is certain to go, eliminating healthcare support for about 14 million people nation wide. Most republican plans drive people with pre-existing conditions into very expensive high risk pools, essentially eliminating insurance for those with lower incomes. Most republican plans will return to annual and/or lifetime limits – exceed your limit and you no longer have insurance at any cost.

People will continue to get sick, insurance or not. In fact without the preventive care measures built into Obamacare, they likely will get more sick. Without reasonable healthcare protections, they won’t be able to afford to go to a clinic for treatment of a cold. They will wait until on death’s bed with pneumonia before they go to the hospital for treatment but can’t pay with dollars they don’t have.

So our population will suffer more serious health care emergencies, increased medical bankruptcies will lower payments to hospitals and staff, and smaller rural hospitals which operate on narrower margins will close their doors, further decreasing access to health care for much of the state’s working poor.

And it won’t stop with just healthcare. Expect cuts to any number of federal programs including food stamps, housing subsidies, subsidies for transportation, etc.

Here in Arkansas we are one of the net takers receiving more in federal dollars than we pay in taxes. Over 684,000 votes were cast for Trump. Around a half a million voters and their children will lose some or all of their healthcare support. Another half a million more could lose some or all of their nutritional support (foodstamps, WIC) including children. What do you think a Venn diagram of Trump voters and beneficiaries of federal largess would look like? Considerable overlap?

The real irony in all this is that the republicans’ lust for smaller government will negatively impact their voter base in the red states. The more prosperous blue states will have their treasuries buoyed by the reduction in federal tax payments. They can use that money to provide for the health and welfare of their citizens. The less prosperous red states will be allowed to continue on a downward spiral with lower wages, poorer health and an every person for themselves paradise. Be careful what you wish (vote) for.

Parasite Powers

In nature there is an abundance of examples of two organisms living together. These can be two plants, two animals, or a plant and an animal. Regardless, the relationship is called symbiotic.

If both organisms benefit from the relationship it is called mutualism. Coral reefs are built by a two organisms that both benefit from their relationship – a coral polyp is an animal that has a plant called zooxanthella living within it. In a commensal relationship such as the mites that live in our eyebrows, one organism benefits without any impact on the other. Humans are the unaffected host for the commensal follicle mite.

The relationship with the greatest “yuck” factor is parasitic, where one organism suffers while the benefits. A broad array of worms, insects, mites, etc plague both plants and animals, sometimes with lethal effects. Complex strategies have evolved over millions of years to allow a parasite to take advantage of the host.

The ability of some parasites to manipulate the behavior of the hosts in nothing short of amazing. The example of the horsehair worm is illustrative. The adult form of this organism, phylum Nematomorpha, is a free living aquatic organism. As the name implies it is long skinny worm. Its life cycle starts as an egg in freshwater. The egg hatches to a larva which lives on the bottom of a lake or stream. Larvae eaten by fish or snails are a dead end, but if consumed by an aquatic insect it can encyst in the body of the insect. When the insect matures, into a mayfly for example, the encysted larva make its way to land. If, after the insect dies, it is eaten by a cricket the hairworm larva has found its destined host.

All this is incidental so far. The real trick is when the larva matures to a juvenile., It has to make its way to water, but crickets don’t normally go to water. Crickets infected with hairworms however change. They seek out water and willingly jump in only to drown, thus releasing the worm back to the aquatic environment. Zombie crickets.

How about zombie ants? The lancet fluke lives in the liver of a cow. To propagate the fluke produces eggs that end up in the animals manure. The eggs get eaten by snails first, then they are passed from the snails to ants – ants like snail slime apparently. An infected ant is then directed by maturing flukes to go find the tallest blade of grass and climb to the top and die. Along comes a cow which grazes the tender tips of the grass. In the process it ingests the dead ant with the flukes, and in so doing completing the life cycle of the fluke.

Even plants and fungi are part of the zombie game. A fungus which inhabits a mustard plant causes the plant to to halt flower production and instead produce small bright yellow leaves that appear to be flowers. These fake flowers contain the reproductive parts for the fungus which are then transmitted to other mustard plants by foraging bees.

Humans have parasites, the only question is, is our behavior being manipulated? Are we zombies?

Trump’s Environment

The votes have been counted and we have a result. Donald Trump will be our next president. For the second time in the last 16 years a Democrat drew more votes than the Republican only to lose to the vote in the electoral college. Secretary Clinton out polled Mr Trump by 2.8+ million votes, more than a 2 % margin.

If President Trump follows through on only a portion of what Candidate Trump said, it will be trying times for the world climate and the environment. Based on his dismissive attitude towards global warming, it is likely that the Paris Accord signed by Obama will be scrapped. World leaders meeting currently in Morocco are constructing the details of how to implement the international law. The objective is to reduce carbon emissions to prevent the temperature of earth from rising more than 2 degrees Celsius (3.6 degrees Fahrenheit)

Whether he makes a pronouncement to abandon the accord or not, his avowed policy of expanded use of fossil fuels, coal in particular, will make meeting carbon reduction goals impossible. The US has pledged to reduce carbon emissions by 27 % compared to 2005 levels. The United States alone is responsible for over 20% of total global carbon emissions, and our target will reduce our share proportionately.

The only thing that may constrain his proposed expansion of the use of coal is economics. Cheap natural gas has undercut the price of electric generation from coal. Burning natural gas to produce electricity produces lower carbon emissions per unit of energy produced, hence replacing coal with natural gas will result in lower emissions.

Inaction has two damaging effects. First, not meeting our goal will seriously impair the attempts to stabilize the climate. The US and China alone account for nearly half of the global warming gasses. For us to not participate means one fifth of the global goal won’t be met.

Not participating also has a profoundly negative impact on international relations. Like it or not we live in a global economy and the only way a global economy works is if we all play by the same rules. Many other international laws protect us through other country’s participation: Whaling, fishing, hazardous waste disposal, illicit drugs, and the list goes on. Do we really want to tell the rest of the world we don’t care?

Meanwhile to our north, Canada will begin taxing carbon as a mechanism to reduce carbon emissions. An initial tax of 7.62 dollars Canadian per metric ton of carbon. At this rate it would add about a dollar to the price of a barrel of crude oil, currently around 44 dollars. Each year until 2022 the price will go up by 7.62 dollars till the tax reaches 38 dollars per ton. All fossil fuels – natural gas, oil and coal will be taxed.

We could do the same, in fact previous republican administrations have called revenue neutral carbon taxes a free enterprise way to manage the cost of pollution.

Crude Movements

It seems that oil pipelines are in the news of late. Some of the new pipelines are to deal with the expanded production of crude oil here in the US. New and better technology – hydraulic fracturing (fracking) and directional drilling have resulted in the need for transportation of that oil, pipelines generally being the cheapest.

We produce about 10 million barrels of crude oil per day and import another 10 million barrels from sources all over the world. Most of this is turned into fuels such as gasoline and diesel fuel and only a pittance for non-fuel petrochemicals.

But are pipelines the best way to go? Other methods to move the crude oil from where it is produced to where it is refined include barges, rail cars and tank trucks. What is the best way to do it? It depends entirely on what metric you use to measure “best.”

If you simply want to compare the least oil spilled when normalized for amount of total oil transported per distance moved (ton/mile) the ranking is barges and tankers are better than rail is better than pipeline is better than truck.

If your metric is human deaths and property destruction we get a different rank: barge is better than pipeline is better than rail is better than truck. How about environmental damage? Because aquatic environments are more sensitive the ordering becomes: Rail is better than truck is better than pipeline is better than barge.

Oh but it gets more confusing, because so much of the crude oil moves by pipeline, about 70%. Another 23% by barge and tanker, trucking 4% and rail transport a mere 3%.

If a decision were made to go to more trucking for example the change for the better (or worse) would not necessarily be linear. More trucking would mean more congestion, hence an increased risk of untoward events even after adjusting for total oil moved.

There is already some evidence of the non-linearity of change. From 1975 to 2012 trains were much shorter and had very few spills, but the recent oil boom means a higher proportion of oil moving by train. Because of longer trains and more frequent crashes, more oil was spilled in 2013 alone than the previous 37 years.

It is just not a simple “what is the best.” This conundrum is reminiscent of a senate hearing back in the 1970s. Ed Muskie was conducting a hearing as to the risks of the supersonic Concorde flying over the United States. The committee’s chief scientist said, “Senator, we’re ready to testify,” and Muskie responded, “Okay, tell me what the answer is. Is this going to be a danger?” The scientist responded “I’ve got these papers here that definitely tell us this is going to be a danger.” Muskie was ready to conclude right there, but then the NAS scientist interjected, “On the other hand, I have another set of papers over here that says these papers aren’t good enough to know the answer.” Incredulous, the senator looked up and yelled, “Will somebody find me a one-handed scientist?!”

A one-handed scientist may produce a simple answer, but it won’t necessarily be the only or best answer.

Australian Outback via The Ghan

Australia has about 75% of the area of the United States, roughly 3 million versus 4 million square miles. The real difference is in population. Australia with under 25 million is less the 8 % of the US population, about 320 million. Most the residents are on the coast, with the east and south coasts the more populous.

The first humans in Australia, the Aborigines, arrived around 50,000 years ago. European exploration and subsequent immigration came much later than that of the Americas. The British established a penal colony in southeast Australia in the late 18th century and population gradually grew thereafter. Exploration and habitation of the coasts greatly preceded the central region, the outback, known for the vast expanses of arid to semi arid deserts.

dragon lizard

dragon lizard

By early in the nineteenth century journeys through the outback were aided by caravans of camels imported initially from India and Pakistan. Caravans of up to 70 camels each carrying nearly a half ton of goods each, were driven by teams of Afghans who apparently excelled in camel herding. The camel caravans were used to supply remote mining sites, a few sheep stations (ranches) and to aid the construction of the first telegraph lines from the north to the south of Australia.

7 foot tall termite mound

7 foot tall termite mound

Today the Afghan herded camel “trains” no longer ply the desert. To a large degree they have replaced by rail service. As the camels were no longer needed they were simply released to the wild to fend for themselves. There are now estimated to be over a million feral camels.

The Ghan

The Ghan

Sections of a rail line began as early as 1858, but completion of the line connecting Darwin in the north with Adelaide in the south wasn’t completed until late in the twentieth century. The almost 1800 mile trip can be completed nonstop in 48 hours. A popular passenger rail service called the Ghan (after the Afghan camel drivers) now makes the trip with side excursions over 4 days.

Darwin , Northern Territory

Darwin , Northern Territory

We boarded the train in Darwin, capital of the Northern Territory (NT). Darwin on the northern coast has a tropical climate, lying about 12 degrees south of the equator. From there we headed south for several hours before arriving in Katherine, NT. Nearby is the Nitmiluk National Park. The Katherine river flows through the park where it has cut deep gorges in the Sedimentary rock, dated to 1.2 billion years old.

Katherine River

Katherine River

Farther south is the quaint town of Alice Springs, essentially the geographic center of Australia. It is equidistant to Darwin and Adelaide, 900 miles each way. Desert climates can be severe. Summer high temperatures can reach 120 degrees, and winter lows, especially on clear nights can dip well below freezing.

Near Alice Springs

Near Alice Springs

South of Alice Springs is the town of Coober Pedy, renowned as the richest source of opals in the world. The climate is so extreme here that over half the town’s inhabitants live underground to escape the heat.

Opal Mines

Opal Mines

The end of the line on the southern coast of Australia is Adelaide, the capital of the state of Southern Australia. It is the most centralized city in Australia with over 70% of the state’s population in the greater metropolitan area.

Great Barrier Reef and Daintree Rainforest

Port Douglas, Queensland, Australia is located in a semitropical region on the northeastern side of the continent. A major claim to fame here is the Great Barrier Reef which lies only a few kilometers off shore.

The Great Barrier Reef (GBR) is the single largest structure on the planet made by living things.
The organisms that make up the reef are some of the smallest living things – coral polyps and photosynthetic algae. The GBR consists of several thousand separate reefs and about nine hundred islands. It extends as an arc some 2300 kilometers along the east and northeast coast of Australia and north towards Papua New Guinea in the Coral Sea.

bob in the Coral Sea

bob in the Coral Sea

Because of the enormous value of tourism to the region, much is done by governments to protect this UNESCO World Heritage Site. Diving and snorkeling in and around the reefs is a big tourist industry but those doing so are not permitted to touch, much less damage the coral. If a ship wants to “park” in the vicinity of the reef, they can only do so by attaching to an established mooring spot rather than dropping an anchor.



Although the reef is generally protected from direct human depredation, global warming is taking a toll. Coral reefs are suffering “bleaching.” This is a phenomena where the symbiotic algae, zooxanthellae, abandon the coral due to warming or more acidic ocean waters, both of which are due to global warming. Without the symbionts, the coral polyps die off and the result is colorless, dead reef.

Equally interesting onshore is another World Heritage site, the Daintree National Park. It is an ancient rainforest (annual rainfall around 110 inches.) A variety of plants found in this rainforest trace their ancestry to the earliest land plants. Primitive tree ferns, giant cycads, and the earliest angiosperms (flowering plants) exist here essentially unchanged from the Cretaceous era, the age of the dinosaurs.

The park is drained by the Daintree river, named after an early explorer of the area. The water is brackish for several miles upstream of its mouth on the coral sea and is home to the salt water crocodile. These ancient reptiles can get to over 23 feet long and weigh in at over a ton. They are the world’s largest living reptiles. dsc00808

Also among the largest animals in this forest is the endangered Cassowary, a six foot tall flightless bird. The males at four feet tall are smaller than the females. They take on the job of brooding the eggs and caring for the chicks.



The proximity of the off-shore reef and inland rainforest make this area an unrivaled tourist destination, attracting an international clientele. Because of the semitropical climate, there is little seasonal variation in weather. All in all it is a wonderful site for a south Pacific vacation. Next up the Australian Outback. Stay tuned.

Booming Solar


Sustainable energy is currently the most rapidly expanding form of energy in the United States. The same is true here in Arkansas. Whereas we are not well set for wind as our neighbors are to the west, solar panels (PV) that generate electricity are effective, and getting cheaper by the day. Solar arrays now cost less than half of what they cost just 10 years ago.

The price is now so low as to be competitive with more conventional power sources such as coal and natural gas, and infinitely cleaner. Current solar capacity (as of 2015) is 20.1 megawatts (MW.) This is an unbelievable 640 % increase over all PV power installed up through 2014. The new power installed in 2015 is dominated by utility scale power, 15.4 MW. Commercial industries and businesses installed 0.24 MW and the residential sector 0.46 MW. This represents a 56 million dollar investment in clean energy and jobs.

Solar power has come of age, not just for people wanting a little power for an off-grid cabin in the woods, but residents tied to the grid, industries, and especially power companies. One real advantage of solar power is its scalability. If a power company needs to expand their energy supply a small amount, they can add a small solar field. If they need a lot of power, they install a bigger field. No alternative has this scalability. You just can’t build a (cost effective) small coal or nuclear plant. Not even natural gas fired turbines are as scalable.

The L’Oreal plant in North Little Rock will install several thousand PV panels, about 1 MW’s worth. In March 2016 a private-public consortium consisting of two Arkansas Electric Cooperative Corporations, and Aerojet Rocketdyne will install a 12 MW solar field near East Camden. The largest install this year will be an 81 MW solar farm to be installed by Entergy near Stuttgart.

Generally installs of home solar arrays are booming also. Most cost effective for the consumer is a grid-tied net metered array. This system allows the home owner to remain connected to the grid in addition to the solar panels. When the sun shines the panels provide energy to the house, but when the sun is not shining, the home can draw power from the grid just like any other home.

PV systems can be sized to provide all or any fraction of the power needed for the home. If a particular array actually produces more energy than can be consumed in a given month, the law allows the excess to be carried over to a month when energy is needed.

The consumers gain is however the power companies loss, and they don’t like it. They lose profits by not selling as much electricity and even worse net metering threatens the vertically integrated structure of the business. They are the power generators, the wholesalers, the distributors and the retailers, and they want to keep it that way. Other states, notably Arizona and Oklahoma, have instituted additional fees for home solar which will severely limit the development of truly distributed clean energy.

The Public Service Commission here in Arkansas is empowered by law to set rates and rate structures of electric utilities. Over the next year they will be conducting studies to determine if changes are needed (read additional costs to home solar users.) The utilities will be arguing that they have to claw back their profits to remain in business. Stay tuned.