Donny and Vlad

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Yet another mournful lamentation on Putin and Trump.

Yesterday, 2/22/22, Trump had words of praise for Putin’s move into Ukraine with “peace keeping” forces. He used the word “savvy” in his praise of the tactic. This is in addition to his spoken admiration of Putin in past years. But he also said that if he were in office this wouldn’t have happened. Trump’s acolyte, Tucker Carlson, seems to be issuing forth the same kind of spew. So, what is Trump really saying?

During Trump’s term he proved to be cool on NATO and America’s place in it. So much so that he spooked EU countries. By most accounts, he had little if any recognizable foreign policy and left a great many important posts unfilled in the State Department. Foreign affairs just didn’t capture his interest. Yet, he says he could have prevented Putin’s invasion if he hadn’t been cheated out of the presidency. I guess the invasion is maybe the fault of Biden supporters.

I have come think of Trump as a wannabe despot who admires Putin the despot (and others) as one professional may admire the work of another. Putin as leader is accustomed to having considerable control of Russia. Trump was in control of numerous private companies and thus not accountable to public shareholders. Both characters are used to the exercise of unquestioned power. Maybe it’s not surprising that there is mutual admiration.

Will Trump followers be disappointed by his open admiration of Putin? It seems doubtful. His supporters have an evangelical zeal for the man. A great many of his followers are conservative evangelical Christians who believe that Trump’s appearance on the scene meshes with their end-times theology. His appearance is related to the beginning of the apocalypse of prophesy. These supporters believe that the man is here due to supernatural forces that must play out and cannot be dissuaded.

If this is your belief, then it must be comforting for you. For the rest of us, it is an incoherent and destructive kind of nonsense. How can it be that the same religion that preaches love and gave us the Beatitudes would also give us a leader the likes of the ethically disabled Trump. Somehow the creator of the universe, the one who set the galaxies spinning and knows the movements of every flea in the tail feathers of every sparrow, gave us a malignant narcissist like Trump. It is not a question shrouded in religious mystery. It is what it appears to be- absurd. Ambitious and destructive characters like Putin and Trump have appeared regularly throughout history. And through the lens of history we can make some good guesses as to what they can do. Both are threats to democratic civilization in their own way and must be contained.

As to the original question, what did Trump mean by his comments, I don’t know. He makes things up as he goes and lies profusely. I don’t think that even he knows what he means.

Witches in Church

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Wow. This video has just appeared on the internets. Not only is Tennessee pastor Greg Locke off his rocker, but listen to the crowd clap and cheer. The pastor seems ready to confront the accused witches in the congregation with a stream of bile, angry accusations and promises of divine retribution. These people are our family and neighbors who have fallen for a charismatic leader spewing nonsense.

Civilization is a millimeter thick. It seems to have worn completely through to the bone in Tennessee.

Locke is just one example, granted. What is especially alarming, though, is the enthusiasm with which the congregation receives this information absent any evidence. They seem thirsty for a mystical experience and to witness divine intervention. The preacher-man is very persuasive and could possibly inspire someone to commit an act of violence. This kind of intellectual frailty is another example of why church and state should remain separate at all levels.

When future historians view this pandemic

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Some historians in the future will focus on this time period and try to make sense of the social and political turmoil we’re now experiencing in this endemic of COVID-19. Many US citizens are in conflict with knowledgeable authorities who are trying to limit the spread of this viral disease. As of this writing the endemic has not yet fully played out.

There are several particularly good questions that must be investigated- How should we view a culture that can’t bring itself to cooperate internally in the prevention of a communicable disease that has so far caused more than 900,000 deaths? Would one expect that roughly 1/3 of the adult population in a highly advanced culture such as ours would refuse to cooperate with the most minor measures to prevent the spread of contagion? That is, wearing a light weight mask when around others. Standing apart just a little bit and washing your hands a little more. These are simple requests yet they appear to be outrageous forfeitures of liberties to many people in the USA.

What kind of civilization is this where an appreciable fraction of the citizens refuse to act in the direction of self-preservation of the population? When shouting about personal rights to not wear a mask or get vaccinated outweighs the rights of the majority to remain infection free?

As bad luck would have it, the endemic coincides with a far right wing-leaning conservative political movement in the USA. This crowd had issues with the government anyway. They are especially furious that experts within various health agencies have issued instructions and mandates on containment of the disease.

We might have thought it obvious that when presented with a highly infectious virus that is spread through the air, it would be in our self-interest to voluntarily control where infectious breath goes, dial back our movement a bit and increase interpersonal distances temporarily in order to avoid mass infection and mass casualties. One might also think that given the long and highly successful use of vaccines, volunteering to get a shot would seem reasonable and also be in our self-interest.

The US constitution is silent on personal freedoms in a time of contagion as it is on many other things. I interpret that as wiggle room to figure out solutions for the problems of our time that serve to further the cause of survival against a mindless but efficient virus.

One of the purposes of government has always been to protect ourselves from each other. What we’ve experienced when government has tried to intervene is loud hysteria and political pressure from an infectious vocal minority who are actually dying from COVID at a higher rate than the vaccinated public. Aggravating matters greatly, some of the opponents of masking and vaccination have very large commercial platforms from which to broadcast self-serving misinformation. It has been obvious for a long time that this is done to increase viewership and profit from the misinformed. Capitalist organizations are using their broadcasts to increase the bottom line on the backs of the volatile misinformed.

At the moment, it doesn’t look like persuasion with solid information will work with the anti crowd. Do the rest of us have to wait around until these folks, many of whom are fervent authoritarian Trump supporters, just live out their lives and die hoping that they don’t crash democracy along the way?

Is this really the direction that the American experiment goes? What kind of country are we? I thought that I had a good grasp of that. I was wrong.

For Students. Thoughts on Chemical Process Scale-Up.

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Chemical process scale-up is a product development activity where a chemical or physical transformation is transferred from the laboratory to another location where larger equipment is used to run the operation at a larger scale. That is, the chemistry advances to bigger pots and pans, commonly of metal construction and with non-scientists running the process. A common sequence of development for a fine chemical batch operation in a suitably equipped organization might go as follows: Lab, kilo lab, pilot plant, production scale. This is an idealized sequence that depends on the product and value.

Scale-up is where an optimized and validated chemical experimental procedure is taken out of the hands of R&D chemists and placed in the care of people who may adapt it to the specialized needs of large scale processing. There the scale-up folks may scale it up unchanged or more likely apply numerous tweaks to increase the space yield (kg product per liter of reaction mass), minimize the process time, minimize side products, and assure that the process will produce product on spec the first time with a maximum profit margin.

The path to full-scale processing depends on management policy as well. A highly risk-averse organization may make many runs at modest scale to assure quality and yield. Other organizations may allow the jump from lab bench to 50, 200, or more gallons, depending on safety and economic risk.

Process scale-up outside of the pharmaceutical industry is not a very standardized activity that is seamlessly transferable from one organization to another. Unit operations like heating, distillation, filtration, etc., are substantially the same everywhere. What differs is administration of this activity and the details of construction. Organizations have unique training programs, SOP’s, work instructions, and configurations of the physical plant. Even dead common equipment like a jacketed reactor will be plumbed into the plant and supplied with unique process controls, safety systems and heating/cooling capacity. A key element of scale-up is adjusting the process conditions to fit the constraints of the production equipment. Another element is to run just a few batches at full scale rather than many smaller scale reactions. Generally it costs only slightly more in manpower to run one large batch than a smaller batch, but will give a smaller cost per kilogram.

Every organization has a unique collection of equipment, utilities, product and process history, permits, market presence, and most critically, people. An organization is limited in a significant way by the abilities and experiences of the staff who can use the process equipment in a safe and profitable manner. Rest assured that every chemist, every R&D group, and every plant manager will have a bag of tricks they will turn to first to tackle a problem. Particular reagents, reaction parameters, solvents, or handling and analytical techniques will find favor for any group of workers. Some are fine examples of professional practice and are usually protected under trade secrecy. Other techniques may reveal themselves to be anecdotal and unfounded in reality. “It’s the way we’ve always done it” is a confounding attitude that may take firm hold of an organization. Be wary of anecdotal information. Define metrics and collect data.

Chemical plants perform particular chemical transformations or handle certain materials as the result of a business decision. A multi-purpose plant will have an equipment list that includes pots and pans of a variety of functions and sizes and be of general utility. The narrower the product list, the narrower the need for diverse equipment. A plant dedicated to just one or a few products will have a bare minimum of the most cost effective equipment for the process.

Scale-up is a challenging and very interesting activity that chemistry students rarely hear about in college. And there is little reason they should. While there is usually room in graduation requirements with the ACS standardized chemistry curriculum, industrial expertise among chemistry faculty is rare. A student’s academic years in chemistry are about the fundamentals of the 5 domains of the chemical sciences: Physical, inorganic, organic, analytical, and biochemistry. A chemistry degree is a credential stating that the holder is broadly educated in the field and is hopefully qualified to hold an entry level position in an organization. A business minor would be a good thing.

The business of running reactions at a larger scale puts the chemist in contact with the engineering profession and with the chemical supply chain universe. Scale-up activity involves the execution of reaction chemistry in larger scale equipment, greater energy inputs/outputs, and the application of engineering expertise. Working with chemical engineers is a fascinating experience. Pay close attention to them.

Who do you call if you want 5 kg or 5 metric tons of a starting material? Companies will have supply chain managers who will search for the chemicals with the specifications you define. Scale-up chemists may be involved in sourcing to some extent. Foremost, raw material specifications must be nailed down. Helpful would be some idea of the sensitivity of a process to impurities in the raw material. You can’t just wave your hand and specify 99.9 % purity. Wouldn’t that be nice. There is such a thing as excess purity and you’ll pay a premium for it. For the best price you have to determine what is the lowest purity that is tolerable. If it is only solvent residue, that may be simpler. But if there are side products or other contaminants you must decide whether or not they will be carried along in your process. Once you pick a supplier, you may be stuck with them for a very long time.

Finally, remember that the most important reaction in all of chemistry is the one where you turn chemicals into money. That is always the imperative.

An organic chemist looks at evolution*

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(Revised 7/28/22) I wrote this essay a few years ago but did not publish it. This is not written for evolutionary biologists. It is written for folks who may struggle with hopeless conversations with creationists and deists.

[I apologize ahead of time for the lack of images. The editing software makes pasting images quite problematic.]

On weekends I check in on C-SPAN 1 and 2 to see what folks are talking about. A couple of weekends ago on Earth Day there was a C-SPAN 1 broadcast of an April 19th, 2017, panel discussion on the ” March for Science and Threats to Science.” The segment was hosted by The Heritage Foundation and featured a number of well-dressed folks who presented themselves as being authoritative and were highly skilled in the rhetorical arts. It was a curious thing that the Heritage Foundation chose this topic to weigh in on.

The discussion followed various lines of conservative analysis of the 4/22/17 March for Science and touched on the New Atheism, Neo-Darwinism, with allusions to a supposed endemic misanthropy of some March for Science participants. One of the panelists was a fellow named Stephen C. Meyer who is a senior Fellow and founder of the Discovery Institute. Meyer is a very articulate and persuasive proponent of creationism. His contribution to the discussion was a recitation of the pro-creationist argument on the weaknesses of Neo-Darwinism. The thrust of his argument centered on the alleged disagreement among scientists in the field of biological evolution and how this delegitimizes the whole concept. This line of argument is a common (dare I say standard?) rhetorical detour used by creationists to cast doubt on the science of evolution.

Creationism adherents have learned that they do not have to prove evolution is incorrect to religious followers. After all, you can’t prove a negative. They need only make a case for disagreement in the scientific community of its veracity or infer scientific misconduct. As a friend once quipped, they stir up a dust cloud and then complain because they can’t see anything.

Darwin and the story of the expedition of the HMS Beagle is a tale of 19th century discovery that is inspirational and iconic. Too often, however, Darwin’s writings on natural selection are not portrayed as a prelude to modern molecular biology. When I hear creationists discuss evolution, the discussion seems to remain with the work of Darwin. It is plain to see that if Darwin and Lamarck had not developed their work on natural selection, modern molecular biologists would have had to postulate evolution themselves.

Public discussion of evolution in the limited context of Darwin is frequently burdened with misinterpretations and half-truths by adherents and deniers alike. It is not unusual for people to become confused by the use of imprecise language when discussing evolution-as-Darwinism. For instance, I’ve heard knowledgeable people assert “… the species evolved (such and so) in order to adapt …”. Well, yes and no. The species may well have over time evolved some adaptation. However, the words “… the species evolved …” may be misinterpreted by some as meaning that a species, when presented with some survival challenge, may have activated some mechanism to rejigger its genetics in a way that would lead to survival of subsequent generations. A more accurate description might be that fortuitous, survivable genetic mutations in the past have allowed the organism to squeeze by challenges presented by a changing environment. Mutations occurring after the possibility of reproduction lead only to an evolutionary dead end. Above all, Evolution is blind going forward. Descriptive language must be built around that concept.

Rather than consuming time and bandwidth reciting the history and elements of Darwinism, the reader is invited to pick this up elsewhere. Instead, I would like to remind folks that chemical mechanisms give rise to evolution and this should be touched on fairly early. Perhaps writers and public figures should deemphasize Darwin’s work a bit and emphasize the mutability of the genome through the mechanisms of organic chemistry. I realize that non-chemists may be uncomfortable with doing this, but surely something can be said.

If we consider that the large scale structural morphologies of organisms are an emergent phenomenon and arise as a result of molecular and cellular scale structures, then we can begin to see evolution much like a performing symphony orchestra is comprised of many instruments, each with characteristic effects. The overall effect is the sum total of all the contributing instruments. Evolution then becomes a matter of changing the score a bit here and there to produce variants. The notion of life as an emergent phenomenon is itself evolving to a high level of theory. See: Pier Luigi Luisi, The Emergence of Life: From Chemical Origins to Synthetic Biology 2nd Edition, 2016, Cambridge University Press.

With 19th century Darwinian theory, we are limited to observing evidence of change at the macroscopic level but with no credible mechanism for the manner of change or a cause for initiating a change. Without a mechanism, the plausibility of evolution is a tough sell. Darwinism is has an appealing story. However, without mention of its mechanism it resembles magic. The evolutionary model at the molecular scale can offer mechanisms with well known chemistry. I would offer that Darwinism could be treated in a historical context, but a transition to the level of molecules appropriate to the intended audience should happen. Evolution rests on the moderate instability of DNA.

More than a few moments of chemistry.

DNA is a long polymer chain molecule that consists of two cross connected strands wrapped in a right-handed double helix like a spiral staircase or threads on a screw. (Note: A helix has handedness, that is, a helix is not superimposable with it’s mirror image, just like a pair of gloves) Each strand consists of a chain of sugar-phosphate-base monomers where phosphate-sugar linkages are the polymer backbone and each sugar has a dangling “base” fragment attached.

The base fragment contains nitrogen atoms that may or may not have hydrogen atoms attached. The base fragment may also have an oxygen atom with no hydrogens attached. Nitrogen (N) atoms with a hydrogen (H) are electrostatically attracted to a nitrogen without a hydrogen and weakly connect as an N-H-N linkage between strands. There also may be an oxygen (O) atom present in the base that is attracted to a nitrogen atom with a hydrogen atom attached and connect as an O-H-N linkage between strands. This electrostatic attraction with weak sharing of a hydrogen atom is called a hydrogen bond. Hydrogen bonds are highly prevalent in biochemistry. Hydrogen bonds are what hold the two DNA strands together. Many, many weak hydrogen bonds along the length of the strands make a securely connected DNA double helix.

The term “sugar” needs a bit of clarification. In chemistry the term “sugar” is more precisely referred to as a saccharide or synonymously, carbohydrate, and has the general formula Cm(H2O)n, where m and n may or may not be the same number. Sugars also classify as polyols meaning that they may have high water solubility. Sugars contain C-O-H (alcohol) groups which gives them the water solubility and the possibility for tremendous diversity in chemical connectivity. Sugars can exist and function as small molecules or in a polymerized form. They may exist on their own or connected to proteins or lipids (fats). The range of connectivities that sugars may form is extremely large. Sugar functions range from an energy source such as glucose or starch, to structural components like cellulose, to binding sites for chemical recognition between substances or life forms. It is hard to overstate the importance of sugars in biochemistry.

Along the length of each strand are phosphate ester bridging groups with each phosphate having two P-O-C linkages connected to a sugar called deoxyribose. It is this deoxyribose sugar fragment that has the dangling base fragments mentioned above. The remaining two atoms connected to phosphorus are a negatively charged oxygen ion and neutral oxygen double bond to phosphorus. Another way to say it is that there is a negative P-O– ion and a P=O double bond. This remaining feature of phosphate helps lend water solubility to the polymer and suppresses attack by negative ions like hydroxide that might take apart the ester linkage. All in all, phosphorus has 4 oxygen atoms and 5 phosphorus-oxygen bonds attached to it. The combined withdrawal of negative electron charge from all 5 P-O bonds renders it susceptible to hydrolysis and cleavage, disconnecting the phosphate backbone linkage. It is thought that the P-O– feature serves to slow down degradation by deflecting attack by hydroxide, H-O–. The phosphate esters of DNA are water stable in the long term under ordinary temperatures and pH. However, in the presence of specific enzymes, phosphate linkages can be broken or assembled.

A quick word about acids and bases in chemistry. The most general category of acids and bases comes from the Lewis acid/base theory. A Lewis acid is an atomic or molecular species that can accept an electron pair. A Lewis base can donate an electron pair. A Lewis acid or base may be charged or neutral. A subset of this is called the Bronsted-Lowry acid/base theory. A Bronsted acid is a donor of H+ (a proton) a Bronsted base is an acceptor of H+.

A sugar connected to a base is called a nucleoside. A nucleoside with a phosphate unit is called a nucleotide. Genetic information in DNA is “stored” as a sequence of nucleotides linked by phosphate ester bonds. It takes three adjacent nucleotides- called a codon– to code for the placement of one specific amino acid in a protein. DNA contains the sequencing pattern for the production of proteins, both structural and enzyme. Addition, loss or misplacement of a nucleotide in the DNA strand will lead to an error in protein assembly. It is called a mutation and may or may not be disruptive to the function of the protein. A mutation in DNA may or may not survive the reproduction cycle of the cell. If the mutated DNA survives, it becomes part of the genetic makeup of the organism and is passed along through subsequent generations.

In a cell, proteins have structural, regulating and transport functions or serve as enzymes to catalyze chemical transformations that might otherwise require harsher conditions or would otherwise be too slow. A mutated protein structure or enzyme could be less effective, more effective or there might be no effect at all in its function. There may or may not be an effect on the survivability of the organism. A mutation could be fatal or it might provide an advantage to survival if not presently, then in the future. It could also be that many mutations are needed to produce a change that affects survival and reproduction. The many factors that cause genetic mutations are the true drivers of evolution. Mutations could arise from DNA interaction with a chemical or by both particle and photon radiation.

Evolution moves forward at the level of molecules.

The balance between too much or too little stability of the phosphate linkages and hydrogen bonds is critical to life as we know it. These linkages are stable enough to resist hydrolysis in the aqueous environment of the cell to afford a safe, though not absolute, long-term repository of genetic information. But the linkages are also weak enough to allow the necessary chemical transformations on DNA in “normal” cellular chemical and thermal environments. There is an excellent paper by F.H. Westheimer, Science, New Series, Vol. 235, No. 4793. (Mar. 6, 1987), pp. 1173-1178, on the properties of phosphate in DNA which can be found at this link.

As described above, the DNA molecule is stable just enough under normal physiological conditions but not overly so. DNA is a molecule that must be able to periodically come apart to discharge its duties and then reconnect for long term storage. A highly stable DNA molecule, one that is highly resistant to change, would be very difficult to use for reproduction or protein building. The DNA molecule must be unstable enough to take apart under positive control, but not so unstable as to decompose and disperse by coming apart easily. If each chain of the double helix were linked by covalent bonds stronger than phosphate ester linkages, then the chemistry of chain disassembly could be a much more energetically costly and slower proposition.

A troublesome aspect of explaining evolution is that inevitably, the question of random change leading to organisms of great complexity comes up. Creationists will go on about how preposterous it is that the human eye or hand could be the result of random change. For them, it is an intellectual cul-de-sac that, in parallel with their religion, only validates “creation implies creator”. To folks firmly affixed in comfortable ignorance or concrete reasoning, the notion of non-living, disorganized matter somehow spontaneously organizing to form elaborate life forms is beyond comprehension. This argument is often brought up as a coup de grace against evolution. The generation of orderly structures within a seemingly random soup of atoms and molecules seems so implausible.

The idea of randomly moving molecules giving rise to ordered organisms from absolute randomness is a dead end. Random collisions between molecules do take place, but only a limited range of consequences can happen between colliding atoms and molecules. This is due to the inherently specific chemical reactivity of atoms, ions, and molecules. Atoms and molecules can only react in a collision so many ways under given conditions to afford a stable chemical change. Helium can bang into virtually any other element on the periodic table all day long at terrestrial conditions and nothing interesting or useful will happen because helium is chemically inert. But when carbon dioxide molecules collide with water, for example, it can form carbonic acid which may lead to a whole collection of stable metal carbonates. In this case, random molecular collisions lead to a limited set of outcomes. Metal carbonates tend to be stable and poorly soluble in water so they precipitate to form solids. Random collision does not mean chemically random outcomes.

Random collisions lead to a finite range of chemical outcomes.

The formation of stable substances results in the evolution of heat. A single molecule having a bond forming chemical reaction will heat its immediate surroundings and the heat will diffuse away into the bulk matter in contact with the reacting molecules. This heat causes nearby molecules to vibrate, rotate and translate, giving rise to an increase in temperature. It might even accelerate nearby chemical reactions. As the heat energy moves away from its source, it is lost to an ever-increasing mass and is thus diluted. When diluted over greater mass, the remaining energy’s ability to raise the temperature of matter diminishes until only the background temperature is measurable. If a large number of molecules undergo a reaction, each contributes to the total energy release, there is less dilution of the energy and the temperature of the bulk material will rise. This is an example of how energy is lost into the random motions of surrounding molecules. The formation of the metal carbonate resulted in the irretrievable loss of energy to the environment.

In the process of life on earth, the act of forming organized structures- such as in metabolism- comes at the great expense of creating disorder elsewhere. An example is the metabolism of glucose. Energy is extracted from glucose to energize the molecular mechanisms of metabolism and forms water and carbon dioxide in the process. Some of thermal energy from the formation of carbon dioxide and water is used to heat the components of the cell and maintain the rate of metabolism through body temperature. The rest is lost to the environment. Structure isn’t popping out of nowhere without a penalty. Life creates great disorder in certain parts of the process.

Perhaps Darwinism is better expressed as only an introduction to the story of molecular evolution.

Standing in the way of a mature understanding of evolution is the perceived plausibility of random influences giving way to greater complexity. What exactly do we mean by random? Does random change imply an infinite range of categories of influence and outcome? Let’s consider some relevant aspects of the world of the molecule.

Axiom 1: The initiation of life may require a quite different set of chemical transformations and chemical environments than the reproduction of life. The origin of life and the evolution of life are different chemical processes. The present physical conditions and available substances amenable to evolution likely diverge from those present when and where life arose.  Origins and subsequent evolution must be pulled apart into separate arguments for the sake of clarity.

Axiom 2: Evolution is a molecular phenomenon. In order to have macroscopic change there must be microscopic change. The DNA molecule is well established as the repository of stable organizational information necessary for the construction and operation of living things. If change characteristics are to be passed along through successive generations, then DNA has to change accordingly. DNA is ordinary matter and subject to the constraints of chemistry and physics. A part of being subject to chemical change is the effect of multiple inputs to contend with in general (bio)chemical synthesis. Biochemistry is largely aqueous organic chemistry with all of the constraints and degrees of freedom that follow: Solubility, Gibbs free energy, transition states, polarity, pH, concentration, catalysis, stability in an aqueous environment, reaction rates, stoichiometry, time, temperature, and reduction/oxidation potential.

All of the parameters listed above represent variables with their own range of values that must be in alignment in order for life to begin and propagate. Rather than be overwhelmed by them, they could be considered as a finite number of channels in which a limited range of inputs can give rise to a limited range of outputs.

Axiom 3: Atoms and molecules must collide in order to react. A generalization in chemistry is that atomic and molecular interactions require the components to collide within some range of favorable energies and trajectories. The mobility necessary for atomic and molecular interactions to occur is much more available in liquids than solids. If molecules are held in place in a bulk solid phase, then they don’t have the opportunity to bump into one another just right and interact.

The most abundant element in the universe is hydrogen. Water, H2O, is comprised of the most cosmically abundant element bonded to oxygen, the most abundant terrestrial heavy element.  A planet that has water with a climate and pressure amenable to the liquid phase is a planet that has a start on supporting life. Life as we know it is substantially a solution phase phenomenon. Solid phase life seems to be fundamentally excluded because of the lack of mobility of molecules giving rise to the process of life. Admittedly, this is a bias of this earthling.

Axiom 4: There is a menu of limitations in the behavior of molecules.
1. The set of atoms necessary for constructing life on earth is of limited number and variety.

2. The behavior and properties of a given atom or molecule is based on the physics of electric charges and how and where the outermost electrons spend their time in a molecule. This is successfully described by quantum mechanics. Atoms, molecules, and chemical reactions can be accurately modeled with computer software using quantum chemical concepts.

3. Because of physics and more to the point, quantum mechanics, the outer electrons which participate in the chemistry are capable of a finite number of allowed states.

4. There is a limited set of ways that a given atom can attach to other atoms to make chemical bonds under ordinary terrestrial conditions.

5. Molecules are made of atoms. These atoms naturally form a limited set of characteristic groupings within a molecule that are energetically accessible and common. The groupings are called moieties or functional groups. Carbon forms a large part of the skeleton of most biomolecules. Carbon’s inherent properties allow for a vast number of stable molecular structures either limited to carbon or connected to other atoms like hydrogen, oxygen, nitrogen, sulfur. The variety of connected atoms in living systems include carbon-oxygen, carbon-carbon, carbon-nitrogen, carbon-sulfur, oxygen-phosphorus, oxygen-hydrogen, carbon-hydrogen, nitrogen-hydrogen, sulfur-hydrogen, and maybe a few more. Atoms can connect or disconnect, but in a finite number of mechanisms. The some atoms that make up biomolecules have certain features that make them amenable to dissolution in water. In particular nitrogen and oxygen have non-bonding electron pairs that electrostatically attract certain hydrogen groups to make a hydrogen bond. This behavior lends reactivity and water solubility to biomolecules.

6. Some groupings of molecules can intimately comingle indefinitely in the liquid state, but other groupings spontaneously partition into separate “phases” or layers to minimize contact. Consider oil and vinegar and how they spontaneously separate for minimum surface contact. Molecules that have a charged end and a long water insoluble tail may form organized structures called micelles in water. It bears a close resemblance to the cell wall. It is an example of spontaneous organization because it is energetically favorable and easily formed.

7. The assembly, behavior, and disassembly of biomolecules follows finite, definable chemical interactions. Synthetic biomolecules are indistinguishable from the biological version, so interactions can be reproduced in the lab.

8. A very limited number of liquids are compatible with and participate in the biochemistry of living systems. Life as we know it requires that molecules are mobile. Living things metabolize and reproduce. This requires changes that are only possible if molecules can move within the system. Movement happens within a fluid system and water fits the bill wonderfully. Water can even facilitate some interactions and inhibit others. Critical chemical events that are only possible in water is another limiting channel to the permutations of non-living matter leading to living matter.

The list above sketches out some limitations that atoms and molecules are subject to. It is useful to note that the atoms and molecules of life are subject to constraints that prevent them from behaving in a completely random fashion. Molecules in general will not form in every conceivable connective permutation under terrestrial conditions. Particular reaction pathways and end-states are energetically preferred. Things that have specific properties are things that will always behave or react in a particular set of ways to give a limited range of products. Molecules that can react along multiple pathways will favor the end-state of the fastest pathway. That means that there is exclusion of some molecular products. This is another loss of randomness overall, but at the expense of energy bleeding off into the environment at some point in the process.

Contrary to your camp counselor’s advice, not just anything is possible. What makes the universe sensible and relatively stable is the fact that objects and events interact or unfold in ways stemming from the characteristics of their building blocks. What follows from the limitations of objects and events is that many forms of behavior or channels of interaction are therefore excluded. That is, there are not an infinite number of ways that a biomolecule can be assembled or behave. The interactions in which a biomolecule can behave is channeled through a limited number of routes due to the nature of the chemical pathways that are energetically favorable. The universe has chaotic aspects, but not entirely so. Recurring forms of biomolecules are the result of the limited number of ways that molecules can interact under terrestrial conditions.

It is a common assertion by creationists that the odds of a hand or eyeball spontaneously forming could result from random interactions is 1 in 10 to some large exponent. The thing is, these biological structures didn’t form spontaneously or over short periods. They are the result of a long series of natural molecular structure-forming collisions, each constrained to a limited range of reaction outcomes over a very, very long period of time. Heat energy moving into a substance is dispersed into translational, vibrational and rotational motion. The number of collisions a molecule suffers per second is a very large number. Consider that a small molecule like hydrogen is having ~10^10 collisions per second or vibrating at a frequency of 10^12 to 10^14 per second. Every collision has some finite chance of causing a chemical change. Scale that up to 1 million years and you have a tremendous number of opportunities to produce complex molecular structures that successfully manifest as a change in macroscopic features in an organism. The arrival of a species to the present time comes at the cost of innumerable dead ends back into the distant past.

Genetic mutation is observable and can be engineered with widely available technology. Genome engineering is now a recognized discipline. The mutation of the COVID virus to it’s many variants is a recent example of molecular change. These mutations resulted from changes in the molecular structure and shape of the viral spike proteins. This is the scale at which the gears of evolution grind forward.

* This is a revised version of a previously released essay.

Chemical safety as social science

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Chemical manufacturing safety is challenging to oversee consistently over time. A given manufacturing facility has many kinds of hazards, some common and some specific to plant activity. Specialized operations will produce hazards that manifest in ways ranging from obvious to obscure to counterintuitive. For those tasked with keeping operations free from injuries and mishaps, the hard part may be to keep everyone vigilant constantly.

I often compare safe practices to the handling of a rattle snake. Every time you pick up that snake, you have to be just as careful as the last time. Over time you may learn to predict or anticipate threatening snake behaviors, but you do not get to bank safety credits for past cautious behavior. Furthermore, it is necessary for you to change some of your basic behaviors around the rattler. For instance, you may want to alter your posture when standing near the snake so, if you lose your balance, you fall away from the snake, not onto it. Or, you may decide to bring the snake out only when there is not a crowd around you for fear of spooking the animal. A wrangler can cite many techniques to adopt when handling this venomous creature.

My views of safety policy and practices have evolved over time. In the academic and industrial lab facilities I have worked, safety policy varied from “don’t get hurt” to academic departmental policies with the unofficial “for god sakes don’t let a student get hurt” to highly professional facilities using “we reserve the right to dismiss you” if your accident involved a violation of policy. In these chemistry jobs I have functioned as a dairy processing lab chemist, student assistant, grad student, postdoc, assistant professor, chemical sales manager, senior scientist and process safety chemist. There has been some variety.

What allowed my successful navigation through these experiences with body parts intact? Skill from good training and a large shot of luck. And having been cautious by nature when it comes to hazardous energy and chemical hygiene doesn’t hurt.

In my estimation there is a large social/psychological component to safety anywhere. Safe operations in a chemical plant requires an alignment of behaviors that lead away from mishaps due to all manner of influences, predictable or otherwise. To oversee safety at a facility, one must use facts and the power of persuasion to convince people to behave in ways that might seem needless or unnatural. There is a large social component to safety. That said, the threat of dismissal doesn’t hurt.

In a US chemical plant, operational staff commonly undergo safety training on hiring and refresher training thereafter on a periodic basis. If an adverse event happens relevant staff may undergo a refresher training session as policy dictates. The range of safety topics will depend on the kind of activity happening at the facility.  Safety training has the goal of bringing and keeping staff up to par on recognition and prevention of some kind of undesired event that plays out as a near miss or an incident.

A core subject in chemical manufacturing facility is the matter of hazardous energy. Hazardous energy is manifested in numerous ways: High pressure, high temperature, electrostatic, rapid or runaway heat of reaction, compressed springs and energy of motion. Hazardous energy can emerge from the familiar and the unfamiliar.

Dangers emerging from “ordinary” hazards, i.e., the hazards everyone is accustomed to, can perhaps be most vexing. How does one convince people not to become complacent with familiar hazards, particularly those of low frequency high consequence?

Frequent training and thorough root cause analysis of actual incidents is probably the best approach to suppressing complacency. One need look no further than the military for an example. Military personnel undergo frequent training with an emphasis on situational awareness. A particular strength is the existence of protocols for many exigencies and the mandatory adherence to that protocol. The obvious problem of the military approach to training is that it is not aimed at producing material goods for a competitive market. Businesses cannot afford to lavish much downtime to training. Civilian safety training in business is conducted but at nothing like the frequency or scale that the military uses to maintain readiness.

A useful tool available to industrial safety is layer of protection analysis (LOP). There are companies that offer custom LOP services/instruction and outside assistance is often a good thing. Other resources exist as well. There are two kinds of layers- administrative and engineering. Administrative layers of protection include the process instruction document, various SOPs and work instructions, training as well as eyes-on active management. Engineering layers of protection refers to the equipment which protects against the effects of an excursion.  Each layer will have empty spaces where they are not protective. The idea is to lay down layers where the empty spaces do not overlap. Most would agree that engineering LOP are preferred over administrative LOP.

The terms “dangerous” and “hazardous” are often used interchangeably. I would argue that the word danger be reserved for the situation when all of the layers of protection around a hazard have been removed. This is an important distinction because our lives are filled with hazards that don’t fill us with dread fear. We tolerate this only because we contain hazards with layers of protection which prevent the consequences of the hazard. In order to keep working in an industrial setting, we all must come to terms with the contained hazards on site. Workers predisposed to chemophobia must become comfortable with the LOP in place, yet remain vigilant for uncontained hazards. The alternative for them is to work elsewhere.

Incidents should be followed closely by a Root Cause Analysis, RCA. There should be an SOP that specifies this action. With any luck, an expert conversation in the subject matter at hand will spark the insight of someone leading to the identification of failure modes related to the incident. The RCA will identify which dominoes fell in the event and will highlight the weak points and hopefully find the initiating event. Finding the incident initiating event is always a goal.

It is important to evaluate the existing LOP after the RCA and every effort should be made use the event to strengthen systems. The notion of LOP should be present early in the process of writing instructions for the manufacture of materials. Each batch or process instruction document should be critically evaluated and signed off by a variety of experienced people. This would include R&D chemists, chemists and engineers involved in process scaleup, Environmental, Health and Safety, production supervisors and plant managers. All can be reminded to evaluate the production document with LOPA in mind.

Inevitably, incidents and near misses stemming from unanticipated failure modes will occur. To provide added protection against the unexpected, imaginations need to be stimulated by conducting a PHA- Process Hazard Analysis. This must be done before a process is begun. It is a formal brainstorming session conducted by a committee of subject matter experts evaluating every step in a chemical process at the production scale for possible failure scenarios. These will be chemical, mechanical or safety systems related. In the PHA you ask the question: What happens if this component or action fails in the process? It is a detailed what-if map of the failure or event with potential consequences. Each potential consequence must be evaluated for risk and harm. Software is available to help people guide themselves through the process.

Finally, it should be noted that once the incident investigation is complete, learnings from the event should be applied going forward and archived where the results can be readily found.

Orphan Wells

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Recent news tells of the federal government’s intent to spend $1.15 billion to cap orphan gas and oil wells in 26 states. For its part, the American Petroleum Institute issued a statement “We welcome the administration’s efforts to address orphaned wells,” said the API spokesperson. I should hope so.

My question is, what kind of person/organization would walk away from a gas/oil well that isn’t capped? It seems like there should already be structure in place to prevent or remedy this. Leaving behind open wells that could be venting hazardous natural gas should be defined as willful negligence and subject to criminal penalties for the company officers. This behavior is an affront to those of us in the chemical industry who strive to comply with good operating practices and environmental compliance 24/7/365.

Learnings from a career in chemistry.

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I will be retiring from industrial chemistry in early 2023. Retirement has snuck up on me, to be honest. I suppose like most 64 year-olds I have trouble recognizing myself in the mirror. The joys and battle scars from my youthful early career are still fresh in my memory even as I turn the corner into the doddering years. I still recall most of the sights and smells and people in the years leading up to the present. I was lucky to meet many good people and unlucky enough to encounter a few problematic jerks. One of my earliest lessons was that not every scientist is one of your brethren. Science contains a bell curve of people- skewed to the good side for the most part, but there are always toxic characters around seemingly bent on making life difficult.

My entry into chemistry was a bit of an accident. I entered college as a physics major and Air Force ROTC minor at the age of 22. Naively I thought that my freshly issued pilots license and an intended physics degree would grease the skids into a flying career in USAF. Boy was I wrong. If anything there was palpable contempt for the pilots certificate. The curious attitude was if you didn’t learn to fly in the USAF then you weren’t shit. Turns out that I was also nearsighted so I was automatically disqualified from a pilot slot. My view in turn became that if you can’t fly jets why be in the USAF?

I took freshman chemistry in the summer for the physics major, then in the fall of my freshman year I started organic chemistry just out of curiosity. I was always puzzled about how drugs work and organic chemistry seemed to be the key. It turned out that organic chemistry was uniquely suitable for my type of ape brain. Soon I switched to a chemistry major and out of ROTC and never looked back at the smoldering crater of my flying career. That said, airplanes are still a passion of mine.

From this end of my career I can look back and see some mistakes I made in the past. First, while I chose a good PhD advisor, I may have aimed too low for the postdoc. It limited my opportunities for a better academic career. Always aim high.

I had a succession of four (count ’em) 1-year sabbatical replacement jobs before I got a tenure track slot at a small midwestern college (with an NMR). One year into my tenure track academic position I drove my career straight into a tree by having an escalating argument with the tenured chemistry department chair. After a long and successful career before my arrival, he tragically became a drunk and a failure in the classroom, he came to treat department faculty with disrespect and was an autocrat. All of this was well known in the department. My mistake in handling the personality conflict was to push a little too hard for near term change in department norms rather than playing the long game by waiting for his retirement. Unfortunately there was no support from the Dean despite the chair’s history of bad behavior. Seeing no help from admin, at Christmas break of the second year I took the first industry job offer I got and left the college. There was no hope for a new contract. I consider this episode to be my fault entirely for not being savvy enough to play the politics right. It was a mistake I would not make again. Oh yes, he died a year after I left.

Lesson No. 1. Learn to engage in politics calmly and ethically. Be patient and smart about it. Abstaining entirely from politics is the politics of victimhood. Like the old saying goes, if you put two people in a room you have politics. If it’s going to happen anyway, you may as well be good at it.

Believing that my teaching resume was fatally disfigured by this absurd episode, I resolved to move into industry. I joined a startup company that was bringing out new technology for commodity-scale polylactic acid (PLA). I was hired to find new catalysts for the cyclodimerization of lactic acid to lactide (the monomer) and comonomers that would lower the glass transition temperature of PLA. PLA homopolymer has a high glass transition temperature that leads to brittleness under ambient conditions. It was a great job and I took a fancy to polymer chemistry. Unfortunately, 11 months after I joined the company folded and I was on the street. Bringing a new polymer into the market at the commodity scale requires a powerful position in the polymer market which we didn’t have. Worse, we had persistent problems with low molecular weight as the money was running out.

Lesson No. 2. Beware the siren song of startup companies. They often fail.

Losing an academic job and an industrial one in a short interval had me eating a big slice of humble pie. These were dark times. In order to feed the family I took a job as an apprentice electrician working commercial construction sites. I had a good boss and the work was interesting. This phase lasted 6 months.

Not wanting to move across the country again I looked for a local job as a PhD chemist. They were scarce. Passing by pharmaceuticals, I took a risk and got a job in chemical sales at a small local chemical plant. Initially I assumed that my career as a scientist was over. As it turned out, that wasn’t true. Most of the chemistry there was multistep organic synthesis so I fit right in. This job would put my chemistry education to use in ways I hadn’t anticipated. We had diverse customers scattered across the world and marketing and customer sales and service required more than just a conversant level of chemistry knowledge in this small market. Very often being able to speak with equal confidence to both scientists and purchasing managers was a necessary skill in making the sale. And the job required some travel to far flung locations which was very stimulating.

Lesson 3. Don’t assume that your career should look like your dissertation project. Be open to possibilities.

Along the lines of Lesson 3, it is worth mentioning that in the course of a chemistry career the chemist might run into the choice of remaining in the lab or transitioning into the business end. The chemical industry requires some business leaders to have a knowledge of chemistry. This should be obvious. The problem is that relatively few chemists enter the job market with solid business credentials. By contrast, chemical engineers evolve their careers by solving chemical manufacturing problems and designing projects within very tight economic constraints. Whereas chemical scientists have a world view that mainly has two axes- space and time- engineers see the world in terms of 3 axes- space, time, and economics. Engineers are trained to bring capital projects in on time and within budget. This facility with projects and economics provides for the facile promotion of engineers to top management positions. My observation is that lab chemists without training in business generally seem to have less career buoyancy than engineers within chemical organizations. Of course there are exceptions. An MBA for a chemist can have real value in upward mobility and lifetime earnings. I’ve seen it happen numerous times.

Lesson 4. The world of chemical business is very interesting and challenging. Give it some consideration.

One way to migrate from the lab to an executive level for a chemist is to become a chief technology officer. This can be a very consequential position in an organization bearing a heavy load of responsibilities. Executive level chemistry jobs can take you into the thin air of business development and the chance to work with a large assortment of executives and managers from other organizations. It is worth aspiring to.

Lesson 5. Polymer chemistry is very interesting. For all you small molecule people out there, try it. You might like it.

But with all of this said, my view now is that I should have tried harder for a flying job in the airlines.

Applied Science

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Like most sciency individuals who graduated from the university/research complex in the US, I planned on a life of doing science. And I did for a few years as a post-doc and assistant prof. But eventually I left academia for the industrial side of the scientific enterprise. There was a period of getting oriented to the commercial arena of chemical technology. But, after seeing the boost in pay, the abundance of lab equipment and the prospects for travel, I quickly adapted.

In industry, scientists are hired to solve problems. And there are usually problems galore. But unlike academia where the entire spectrum of chemical methodologies are available for use, in industry we are often constrained to use in-house technology and standard operating procedures. This in-house technology can consist of proprietary materials and methods, specific substances that are compatible with environmental, health, & safety requirements (OSHA & EPA), or that reaction chemistry which is suitable for scale-up. Suitability can be based on compatibility with materials of construction or the practical operational constraints of existing equipment. Oh, I forgot to mention process safety. Manufacturing at large scale brings safety problems that academics may have little familiarity with.

In-house technology can be broad or narrow in scope. It can be practiced openly in the public domain, reside under just trade secrecy, or under patent protection and a spritz of trade secrecy. Progress in academia is about sharing knowledge and publishing as a measure of productivity, all the while educating students. In industry, the productivity of a scientist is measured as best profit margins on new or old products and technical service to customers. Whereas, an academic is expected to propagate knowledge, we in industry are obligated to keep everything under wraps. Disclosure can be a career ending mistake. This seems like an oil and water compatibility problem.

The differing imperatives, commercial secrecy vs public domain, make the cooperation between industry and academia fraught with difficulties. What is in it for an academic or grad student if they are not able to get a publication out of their labors? A big grant possibly but few publications to show the rank and tenure committee. Will patents get you tenure or a full professorship? I don’t know. Would students be able to use proprietary information in their dissertation? It’s questionable. The matter of proprietary information, inventorship, and assignment of ownership makes cooperation between industry and academia a complex problem for the lawyers.

I live under a rock but perhaps the readers might know of fruitful alliances in the lab between the two chemistry domains- college chemistry faculty and industry. I suppose in circumstances where a company has been started by a professor, productive alliance could happen more easily. 

 

Flying Cars

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I’ve been thinking a lot about flying cars lately. The promoters of these cars have said nothing about what would happen if these things became popular. How would one qualify to operate one? Presumably the FAA would get responsibility for regulatory oversight of this new air traffic. What airspace would these flying cars be allow to fly in? Would they have to be automated? Would you dare fly without a backup pilot on board?

While driving on a busy road, look at how people drive. I’m sure you’ll agree that there might be a large fraction of folks who should not be allowed to control a flying vehicle. Just how much air traffic congestion could/should we tolerate overhead? The issues get stickier the more you think about it.

Currently there is extensive training and 3 tests to pass to get a basic airman’s certificate. Of course these vehicles could hit the market with full automation and without a licensed pilot. But that doesn’t mean there won’t be the need for a backup pilot for some period of time. After all, modern airliners are heavily automated but pilots are still required. And, do we really want them to land just anywhere even though that is a selling point? Perhaps there will be selected places where they can land, you know, like an airport.

I doubt that we’ll see flying cars replacing significant ground commuter traffic even into the distant future. I think they’ll get a recreational vehicle status and will be limited -economically- to wealthy status seekers, show-off executives, or the state.

Eventually, the police and FBI will want them them as well. And criminals.