Monthly Archives: January 2017

Thoughts on Oxygen – Part 2

Based on genetic evidence across all life it appears that the earliest organism called LUCA, short for Last Universal Common Ancestor, contained a wealth of cellular components that handled molecular Oxygen otherwise known as O2. This in light of the fact that there was scant Oxygen present in the atmosphere, a fraction of a percent compared to the current concentration of 21 percent. Why?

Most likely is the fact that Oxygen is a very reactive gas, and it reacts by snatching electrons away from other molecules. This creates two other kinds of chemical compounds, free radicals which are electrically neutral but very reactive, and cations which are positively charged ions which also are reactive. When Oxygen or a few derivative molecules react with other components of cells or tissues they cause damage which can lead to cell death and even death of the whole organism.

One description of growing old is little more than the accumulation of cellular damage due to exposure to Oxygen. Just one example is that Oxygen reacts with a component of our skin called collagen. Over time the damage leads to reduced elasticity. This results in “brittle” skin which is more easily damaged by physical abuse. The skin also loses its tone and becomes saggy. These are oxidation reactions just like the rusting of iron and cooking oil becoming rancid. When you burn something you are oxidizing it, hence growing old is slowly burning up.

The earliest anaerobic single celled organisms had a myriad of cell components to protect themselves from oxidative damage even in an atmosphere which contained little oxygen. Today most of what we recognize as living things such as plants and animals, are aerobes. We require Oxygen to drive the processes by which we generate energy. We need the energy to do all the work of our bodies. To detoxify poisons in our liver. To move us from couch to dinner table and back. To fuel the nerve impulses to our brain that allow us to read newspaper columns.

Interestingly, our brains consume close to 25 % of all the Oxygen we use. Compare that to the heart muscle which only uses 12 % or the kidneys which need only 7 % of our Oxygen. The question now is how did we go from Oxygen being a deadly poison when life operated anaerobically (without oxygen) to our current state where it is demanded? The answer lies in a number of evolutionary advances. Those cell components that were used to protect anaerobic organisms were shifted in function by random mutations to do the job of aerobic metabolism. The advantage is that if you can control the reactivity of Oxygen, you can put it to good use to do the work of the body, but only if you control it.

Evolution does not require new constructions from whole cloth. Slight changes in a macromolecule allow it to be repurposed. Life is complex, but not so complex it requires a designer. Evolution only requires random mutations and a long time scale.

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.