Gaussling’s (k + 1)th Epistle to the Bohemians. A Liberal Speaks.

This is an updated re-release of an old post from Dec 10, 2010. I have applied a bit of polish and a spit shine, but not much. Since I wrote this, political correctness has morphed into wokeness.

==========

I keep hearing comments by conservative people who are obsessed by what they call political correctness. In these commentaries, some kind of sarcastic parody is made regarding an alleged trend to ban the use of the phrase “Merry Christmas”.  Neoconservatives latch onto this like barnacles on the bottom of a tramp steamer. Inside their heads they imagine that a cabal of liberals are scheming to take their guns and their religion from them.

At the most recent liberal cabal meeting, we decided to let the gun owners keep their damned guns. There was a vote, however, where a proposal was made to require gun owners to take turns cleaning up the blood and guts after a shooting and to pick up the funeral costs.

Ok, that was a joke. Actually, we voted on something else.

If other liberals are like me, then not only do we not want to deprive them of their damned firearms and religion, minimally we would simply like to be out of shooting range.

Christmas has a secular component and practice that even a bitter, crusty, non-religious liberal like myself can feel comfortable with. But as far as possible insensitivity to Christians, they’ll just have to get over it.

In my limited sphere I don’t know of a single liberal who is trying to replace “Merry Christmas” with “Happy Holidays”. The only time I hear of it is when a conservative repeats it sarcastically as a token of disapproval. Only conservatives carp about this.  It’s a red herring promulgated by that famous dead yapping cur himself, Rush whatshisname, in the name of ratings.

——————

I’m moved to comment on what makes some people liberal.  A recent article in Slate was written by a conservative, Daniel Sarewitz, who seems to be genuinely perplexed at the apparent trend of scientists, or at least academics in general, to be liberal. It is though he is talking about a smallpox epidemic.  While I have no idea as to the conservative/liberal ratio of scientists and academics, I can say that from my perch on a small and obscure branch of the tree of science, scientists tend to be overall a bit left leaning. However, make no mistake, there are plenty of conservatives in the group as well.

Indeed, many of the industrial chemists I am in contact with are libertarians, religious conservatives or just plain-vanilla orthodox conservatives. So, from my limited data set,  Sarewitz’s complaint appears a little specious to me.

He probably refers to the life and eco-sciences, earth science, astronomy, big-time-physics, etc. I suspect that the balance is different in these fields.

But why would scientists trend towards a liberal viewpoint?  I have some ideas. First, the scientific approach to the world relies on study, measurement and analysis.  Scientists tend to study analytically or, to use another term, critically. Critical study of the physical world requires a willing suspension of belief. A formal education in science takes the student through many, many opportunities to see how scientific knowledge was acquired by successive approximations and sometimes led into fruitless cul-de-sacs. A scientist must keep a loose grip on theoretical viewpoints because experimental results frequently contradict fundamental assumptions. Fame and glory in science goes to those who tip over the apple cart of concepts and theories.  All scientists are excited at the prospect of looking at something in a new way or bringing a puzzle into sharper focus.

“But, it’s just a theory …” I hear this ignorant comment frequently. A theory is just a model of a particular aspect of reality that is then strengthened or weakened by experiment. It is not uncommon for theories to be tossed aside in the junk pile when data or a better theory comes along. Science advances by successive approximation. One does not “believe in” a theory. It is not a “devotional” thing. You agree with it to some extent or you dispute its accuracy. It’s an “analytical” thing. A theory does not have to be completely accurate to be useful. Even a faulty theory may provide certain perspectives that are useful.

Many conservatives whom I know also appreciate study and measurement. Numbers people are greatly influenced by numerical data regardless of their political stripe. But in the religious realm there is often a trend towards devotional study rather than critical study. Devotional study is about finding a greater understanding of doctrine or greater fidelity with a catechism of beliefs.

Religionists upset with the notion of the separation of church and state often assert their right to be heard and to express their religiosity in public spaces.  Some might take this as a simple matter of freedom of speech. And if that is all the religionists want, that would be fine. But if you look closely, they don’t want just speech, often times they want government endorsement of their doctrine. They want equal time in the public schools. They want to bring the civil sphere into alignment with their beliefs. “Go ahead and teach Darwinian evolution, but Creationism should get equal time.” Creationism is just a Christian conservative flavor of denialism. It is the denial of evidence in favor of a magical world of spirits and things that cannot be physically evaluated.

Religious services are about the veneration of the sacred. The word “sacred” means that which is beyond question or understanding.  In a real sense, holding something sacred is to set apart a concept or doctrine from critical analysis. Religionists are not interested in a public critical analysis of their precepts. They are interested in broader devotional coverage, i.e., the fruits of evangelism.

It isn’t unusual for a liberal person to be compelled to do critical analysis of their basic beliefs over a lifetime.  The very notion of spiritual sacredness is antithetical to one who seeks analytical truth. The policy that some belief systems are beyond analysis is simply a form of thought control and is more suited to the iron age than the present. Being a nontheist I hold human life sacred. I’m very partial to kindness too. But this does not require that I believe in a supernatural universe.

For a great many people, college is a time and a place for intellectual experimentation and exploration. It is a place where you can have chance or purposeful encounters with new ideas, people and careers that were beyond your previous horizon. The university is an institution where critical analysis of the great world systems takes place. The active examination and betterment of our world is the realm enjoyed by the progressive.  Progressives push the boundaries of knowledge and thought. Sometimes focused analysis reflects well on our human or national institutions and sometimes it does not. But knowledge hidden is knowledge abused. That universities are loaded with liberals is a natural outcome of the youthful intellectual adventure the students are taking. It is a journey of discovery of the self and one’s place in it. It can be both joyous and a bit disappointing. New lands and new boundaries are there to be found.

The current efforts by American conservative Christian nationalists to scour out all traces of liberalism in education is worrisome and frankly, a little stupid. The assault on New College by the governor of Florida is a dark example of state government taking a giant step backwards by imposing one-sided political controls on a public resource. This in itself shows that American education has failed a great many people. America has generally failed in citizen’s knowledge and practice of civics and the long, troubled path of history to the present.

Just take a long look at the MAGA movement. Make America Great Again. When was this actually? If you look below the surface in any period of US history, you’ll find political problems and upheavals galore. There have always been social struggles in our history. Formerly venerated American Heros like Buffalo Bill Cody and the near extinction of the buffalo. General Custer and what he was really doing at the little Bighorn. Or the revered westward expansion with the Gold Rush and migration of the pioneers which were part of our celebrated manifest destiny. These were national enthusiasms that have been endlessly celebrated and woven into textbooks for generations of school kids.

The ugly truth to much of the actions of our ancestors is that a great many innocent people died as settlers began to occupy North America. Land was stolen, European diseases were spread, native Americans were murdered and robbed of their land and resources and their children were reprogrammed in government schools. Survivors were herded into reservations with little in the way of amenities or natural resources that we take for granted. Treaties were made and broken. This is also part of our history.

There is no benefit in self-flagellating ourselves over the sins of the past. However, what we need to do is to take note of the mistakes of the past and steer a better path to the future.

Do I believe that American conservative thinking and liberal thinking are equally right? Not at all. I’ll take progressive liberalism any day.

Standing up for what you believe

I’ve long had difficulty with the validity of advice that says “always stand up for what you believe.” Superficially, it is inspirational to those working in a difficult and discouraging situation. It is meant to convey encouragement that a person should strive not to give up on a difficult goal. Keep chipping away at the problem. You can eat an elephant, but only by one bite at a time. There are many aphorisms that tie into this sentiment. A crisp analysis of this is not like a problem in algebra, you know, a problem with a unique solution. If you share the person’s subjectivity, then perhaps there is no problem.

Standing up for what you believe is often used to proclaim a refusal to give up some action or view. It can telegraph moral clarity and devotion to an ideal.

What are we to think when a leader stands up and proclaims that they intend to stand firm on their convictions? Irrespective of whether or not you agree with them, doesn’t their proclamation to stand fast say something about flexibility in the face of contrary evidence or logic? If new thinking comes along, wouldn’t we want a leader who can turn the boat around to a better heading?

We don’t want wishy-washy or indecisive leaders- don’t we really want action based on the best thinking? In a democracy it is our job to put the best thinkers in the important slots.

The weakness of this advice comes into view when you consider whether any given goal is “worthy” or not. Is there objective information or reason supporting going after a goal or maintaining a belief? Even if a belief or goal is objectively valid, is it something worth committing your life to? Will it really lead to the desired end? On the personal level, someone may be convinced that a goal is indeed worthy and is backed with good intentions, tight reasoning or what appears to be justifying evidence.

A person may be genuinely convinced that their goal or belief is worthy irrespective of objective fact or analysis. They would be making a subjective decision to stay on the path for reasons of comfort or aesthetics. As long as your path is not harmful to those around you, why not?

People possessed of divine certitude in their politics or religion, for example, will often claim that a particular hill really is worth dying on. They are willing to defend their beliefs to their last breath, a few in the literal sense but most metaphorically speaking. Righteous though they may seem, are we obliged to stand by and let the firmly held but baseless or insane beliefs of others swerve our democracy into an autocratic swamp of fringe beliefs and looney political theories?

The societal problems are supposed to be addressed by voting based on rational thought and conveyed through freedom of speech. Today in the US, large and well-funded forces are focused on eliminating time-tested elements of democracy based on firmly held beliefs.

The practical difficulty in the US is that monied interests have the cash to buy media time to persuade the masses. Repetition of untruthful assertions and fearmongering are highly effective. Recruiting and inciting people into the dark side of politics is all too easy as the GOP has shown for decades. And yes, I’m taking sides.

This is my theory: From the view at 30,000 feet we can broadly divide thinking into two manifolds- analytical thinking and devotional thinking. Analytical thinking is that in which conclusions or practices are based on consideration of established secular principles, measurable evidence and the science behind cause and effect.

Devotional thinking is rationale based on adherence to doctrine- be it religious or political. A particular doctrine guides a person’s beliefs, emotions and actions or conclusions, maybe even in the face of contrary evidence.

Analytical thinking is my preference but it can go awry. Conclusions may be drawn from faulty evidence or previous thinking that is factually incorrect or poorly conceived. Worse, human thinking is subject to stranding in the cul-de-sac of confirmation bias. Many of us get stuck in this appealing comfort zone indefinitely. Beliefs or opinions are often cherished and difficult to release.

So, what do you say to a person who adheres to a belief that can be objectively contradicted with arguments based on data or rational analysis? How far along are we obliged to indulge a person in a faulty belief? Should we be supportive and encourage them to “stand up for what you believe” knowing full well that they are on a fool’s errand or their belief leads to actions troublesome for others?

This is where politics comes in as useful. In principle, poor thinking can be outvoted. A majority of poor thinkers with bad ideas is a problem as history shows. Assuring the survival of liberal democracy takes continual monitoring. Oh yes, the continuance of liberal democracy is axiomatic in my view.

No doubt this ground has been plowed by philosophers for centuries. But, I don’t call myself a philosopher.

Is it really our place to correct a person’s belief? Who am I to reset an adult’s thinking? If someone is operating on the basis of incorrect information, like a definition or a piece of data, it could be argued that correcting them would be an act of kindness. If someone is just full of harmless baloney, then perhaps they should be left to wander through life as is.

This situation has been part of the human condition forever. Everyone has the right to be an idiot now and then. But what happens when their idiocy becomes a problem for others or too self-destructive to stand by and watch in civil society?

Speaking for myself only, I’m inclined to ignore those who espouse ignorant or magical beliefs. I’ll steer clear of the flat-earthers or Baptists, for instance, as not worth the effort to engage. With homeopathy believers, in a moment of weakness I might engage with some words about basic chemical principles relating to dose/response relationships. With the anti-vaccine crowd … this a tough one. All too frequently I go non-linear and become scornful of those harboring misplaced fear or anger towards vaccination. I’ll start gibbering and sputtering if I don’t quit thinking about it.

Speaking of goofy beliefs, I’ve had a longstanding issue with most religions, the big 3 in particular. To me, standing up for something that derives from magical thinking and no evidence seems foolish. Writings of dubious origin and translated or edited over the millennia could be as source of fiction or a mixture of truth and fiction. Followers of religion operate under the belief that their religious doctrines are set in stone and are the basis for all moral behavior.

Religion finally boils down to being a theory of the universe. The big 3 religions have always struck me as transparently anthropomorphic rationalizations of the universe using iron age thinking. I used to engage with others on this for fun but it’s nothing but aggravation now.

Does science give us the ultimate view of the universe? We only get pieces of it directly. The universe most of us know is substantially based on our what our brains perceive via stimulation of the nervous system. What we can see is limited to a very narrow slice of the electromagnetic spectrum, maybe one octave wide. Light waves exist many octaves distant on either side of the visible range. On the high energy side, there is the gamma ray universe shining brightly from nuclear reactions in stars and other objects. On the low energy side is the radio universe shining away by larger scale mechanisms. Adjacent to the visible spectrum is the x-ray and ultraviolet spectrum. On the opposite side are infrared and microwaves. All can reveal insights based on how they interact with matter. We exploit imaging, spectroscopy and mathematics to understand the universe outside of the solar system.

But maybe the reality we experience is just a type of baseline hallucination that we think of as our “normal” consciousness.

Science is unable to help with the desire to know the supernatural. Science requires observation, quantification, measurement and analysis. I suppose that if you could start classifying and counting miracles per square kilometer, you could begin to understand the effects of location and type of miracle. Anyway …

Gosh. It seems that I’ve painted myself into a corner.

Meta Making Progress Towards a Science Fiction-Like Dystopia

A piece in the Washington Post by Prashnu Verma appeared reporting progress with Meta’s Cicero artificial intelligence (AI) system. The thrust of the report is that Cicero can play a game called Diplomacy better than humans. The article is worth reading- I know nothing about AI so all I can do is link readers to the article.

Quoting from the Post article-

“Researchers at Meta, Facebook’s parent company, have unveiled an artificial intelligence model, named Cicero after the Roman statesman, that demonstrates skills of negotiation, trickery and forethought. More frequently than not, it wins at Diplomacy, a complex, ruthless strategy game where players forge alliances, craft battle plans and negotiate to conquer a stylized version of Europe.”

Further down …

“It’s a great example of just how much we can fool other human beings,” said Kentaro Toyama, a professor and artificial intelligence expert at the University of Michigan, who read Meta’s paper. “These things are super scary … [and] could be used for evil.”

The nations of the world have civil and criminal laws to discourage and punish people who use their natural intelligence to commit crimes and misdeeds. What about those who use- or unleash- AI to achieve ends that would otherwise be ruled as unethical or even illegal? Pet owners can be held liable for the damage their pets do. Why shouldn’t AI owners have at least the same liability? Could a court order the alteration of an AI’s algorithms in a way that would shut down objectionable or unlawful “behavior”.

If the work product in the application of any intelligence includes action, then where does that leave an AI that can make decisions independently? When could we let it loose to do things that may affect people in novel circumstances? And what kind of ethical responsibility do programmers have in anticipating negative outcomes and acting to arrest them? Lots of questions.

One of the consequences of technological advance has always been the elimination of jobs. That is, getting the same or better results with a lower headcount. It represents cost savings and added margins for an organization. AI will be a valuable tool in the eternal drive for faster-better-cheaper.

AI will almost certainly change many experiences in life. AI systems will manage and replace people in the workplace. It is likely to improve multitasking in many job descriptions, boosting productivity over human counterparts. AI will produce a more effective sales force because the art of persuasion will become much more highly refined. Just what we need- craftier salespersons humping our legs for a sale.

On the positive side, AI has the potential for executing better judgement in many situations. For example, law enforcement could be polished to a point where many errors in judgement can be avoided. This applies across the board in all activities.

AI will also enable criminal intent. The ability to execute crimes will be improved with better judgement, knowledge and fewer mistakes.

Soon, if not already, wars will be guided and fought between AI systems. Cold war type activity could be refined to produce better intelligence and undercover schemes to outwit the other side. Leaders could put AI to use in the darker side of governance. It could be used to keep better track of individuals and information related to them. It could also be used to apply punishment to people without the messy issue of personal morals.

Any dark human activity you can imagine can be made more effective with the application of AI. If it can be tried, it will be tried.

Twittered

So, after a long period of abstinence I recently added the Twitter to my daily feed from the interwebs. In a moment of weakness my resistance to Twitter folded like a lawn chair. Almost immediately I began to notice that my background level of social/political anxiety had increased.

On the plus side, I was pleasantly surprised to see all of the interesting chemistry-related content that appeared from day one. How did Twitter know that I really dig organic/organometallic chemistry having never experienced my internet shadow directly darkening their servers? I guess because I told them so. My shadow did darken their floors. In signing up, I did select a number of interests and this accounts for my connection to chemistry feed.

What is startling though is that they already had a good inkling of my philosophical and political leanings from day one. I do not recall disclosing this. While it is indeed an echo chamber, there are many tweets that articulate notions and ideas that I’ve had trouble putting into words myself. Clearer thinking is always a plus.

The side effect of hearing all of the “agreeable” echo chamber content is that my world view is more broadly negative and my general level of peaceful equilibrium has diminished. There is a constant rattling noise of cogent observations about negatives. While thankfully I do not receive tweets from Margorie Taylor Greene or her ilk, I do get many tweets with excoriating comments on her latest outrageous utterings and pathetic stunts. This just keeps me front and center with this malignant political movement #45 is leading.

There are certainly many negatives to be found in American history and culture. People from all quarters are plainly aware of this. What is less frequently shouted across the interwebs are the positives from our technologically advanced democratic republic. Okay, technology has indeed produced net negatives like nuclear weapons and anthropogenic climate change. But there is a vast wealth of good that has come from our culture as well. We dare not lose sight of this for fear of perishing from the ever-growing circular firing squad that we find ourselves in. Returning to fundamental principles is often a good exercise.

The positives we have produced are too numerous to count. But, how about this- why don’t we each strive to be grateful about some particular benefit every week? Yes, it seems pollyannish. I get that. But let’s train our minds to seek gratitude. This week I’m going to be grateful for our electrical distribution system. We’ve all grown quite accustomed to it and it continues to provide elevation in our quality of life.

Liberalism and its Discontents

An interesting review of a book titled Liberalism and its Discontents by political scientist Francis Fukuyama of Stanford University appeared in the internet magazine Quillette recently. The author of the review, Seamus Flaherty, is a writer and historian. The article struck me, as a moderate liberal, as a fair analysis of historical liberalism and where it might be going. I won’t rattle on about the article except to say that the final paragraph below sums up nicely some informed thoughts about liberalism. Flaherty writes-

“According to Fukuyama, the best we can hope for is a liberalism aware of its flaws, a liberalism that “prioritizes public-spiritedness, tolerance, open-mindedness, and active engagement in public affairs,” is unembarrassed by national identity and cultural tradition, seeks to devolve power to the lowest feasible levels of government, and accepts human limits and promotes the virtue of moderation. A liberalism, in short, which seeks to compensate for its own ineradicable shortcomings. In so saying, Fukuyama sounds a lot like a reticent Red Tory or Blue Labourite—a critic of liberalism who is not anti-liberal—an impression created throughout his new book. Now, that is “progress.” What Fukuyama succeeds in showing us is that liberalism need not be commensurate with the extremes of individualism or wokeism. His version of liberalism repudiates both.”

A final comment about vocabulary. In looking up an unfamiliar word found in the article, I encountered the words that describe my world view quite well. Meliorism: the idea that progress is a real concept leading to an improvement of the world. It holds that humans can, through their interference with processes that would otherwise be natural, produce an outcome which is an improvement over the aforementioned natural one. Yeah, I like it.

An organic chemist looks at evolution

I wrote this essay a few years ago but did not publish it. I don’t remember why. This is not written for evolutionary biologists. For better or worse, here it is.

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 were quite authoritative and highly skilled in the rhetorical arts. 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 weakness’s of Neo-Darwinism. The thrust of his argument centered on the disagreement among scientists meme 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 trick used by creationists to cast doubt on the science of evolution.

Pro-creationist adherents have learned that they do not have to prove evolution is incorrect. 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 is not portrayed in the historical context relative to modern molecular biology. When I hear creationists discuss evolution, the discussion seems to remain with the work of Darwin. I would maintain 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 taken the chance to unsheath some mechanism to respond by rejiggering its genetics in a way that would lead to survival of subsequent generations. A more accurate description might be that fortuitous genetic mutations in the past have allowed the organism to survive challenges presented by a changing environment. There is a critical qualifier, however. The lucky mutation must be survivable and facilitate the continued reproduction of the critical trait to subsequent generations. Mutations occurring after the possibility of reproduction lead only to an evolutionary dead end.  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 throw an idea on the table. Perhaps writers and public figures should deemphasize Darwin’s work and emphasize the mutability of the genome.

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, plausibility is a tough sell to students, teachers, and the rest of the lay public. Darwinism is a tidy package with an appealing story. However, without mention of its mechanism it resembles magic. Evolution at the molecular scale can offer mechanisms and measurements. 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 mutability of genes.

Another troublesome aspect of explaining evolution is the plausibility of random change leading to organisms of greater complexity. The notion that the human eye or hand is the result of random change is simply too incredible for non-sciency people to accept. 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 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. Randomness as a successful driver seems so implausible.

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 plausibility of random change 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? What exactly is it that is random? This is difficult even for scientists, let alone the lay public. Let’s consider some relevant aspects of the world of the molecule.

Axiom 1: The initiation of life may be a quite different chemical mechanism from the reproduction of life.

The origin of life and the evolution of life are different processes. The physical conditions and available substances amenable to evolution necessarily 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 adverse conditions to contend with in general (bio)chemical synthesis. Biochemistry is largely aqueous chemistry with all of the constraints and degrees of freedom that follow: Solubility, Gibbs free energy, transition states, polarity, acidity, 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 happen. Rather than be overwhelmed by them, they could be considered as a finite number of channels in which a limited range of inputs 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 at some range of favorable trajectories. The mobility necessary for atomic and molecular interactions to occur is available in fluids but not 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 is substantially a solution phase phenomenon.

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 is based on the physics of electric charges and the best description of how and where electrons spend their time. This is successfully described by quantum mechanics.
3. Because of physics and more to the point, quantum mechanics, the electrons which do the chemistry are capable of a finite variety of allowed states according to selection rules.
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 set of characteristic groupings within a molecule that are energetically preferred and thus common. The groupings are called moieties or functional groups. Examples are stable 5 and 6 member rings of atoms (pentagons and hexagons), carbon chains long and short, single, double, and triple chemical bonds. The variety of connected atoms in living systems include carbon-oxygen, carbon-carbon, carbon-nitrogen, carbon-sulfur, carbon-phosphorus, 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 ways. The 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 attract certain hydrogen groups to make something called a hydrogen bond. This behavior lends water solubility to biomolecules.
6. Certain groupings of molecules can intimately comingle indefinitely in the liquid state, but other groupings spontaneously separate into separate “phases” or layers to minimize contact. Consider oil and vinegar and how they spontaneously separate for minimum contact in salad dressing. Molecules that have a charged end and a long water insoluble end may form organized structures called micelles in water. It bears a resemblance to the cell wall. It is an example of spontaneous organization because it is energetically favorable.
7. The assembly, behavior, and disassembly of biomolecules follows finite, definable chemical interactions. Synthetic biomolecules are indistinguishable from the biological version.
8. A limited number of liquids are compatible with living systems. Life as we know it requires that molecules are mobile during certain periods. Living things reproduce and grow. This requires changes that are only possible if molecules can move within the system. Movement happens within a fluid system.

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 routes and end-states are energetically preferred. Things that have only specific behaviors are things that will always behave or react in a particular set of ways to give a limited range of products. Products from molecules that react along alternative 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.

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 characteristic to 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 behave. The interactions in which a biomolecule can behave is channeled through a limited number of pathways due to the nature of the chemical pathways that are energetically favorable. The universe is surely chaotic, but not entirely so. Organization in biomolecules, or should we say a finite number of energetically favored structures, are the result of the limited number of ways that molecules can interact under terrestrial conditions.

Is is a common assertion by creationists that the odds of a hand or eyeball spontaneously forming could result from random interactions is 1 in some extremely large number. To the contrary, there is a case to be made that the hand or eyeball is the result of a series of natural molecular collisions, each constrained to a limited range of reaction possibilities over a very, very long period of time. What’s more, a molecule at room temperature is colliding with another molecule at maybe a frequency of 10^12 or 10^14 per second*. Scale that up to 1 million years and you have a tremendous number of opportunities to produce change.

* These frequencies may be off a bit, but it is what I seem to remember.

Gaussling’s 15th Epistle to the Bohemians. Thoughts of a Secularist Liberal Scientist.

If you knew me personally, you’d know that as a reductionist my profile can be reduced to that of a liberal atheist scientist with marginally good manners. I broke the shackles of magical thinking in high school after reading a few books by Bertrand Russell and Carl Sagan. Though I have not been the same since, I have come to sympathize a bit with Quakers and their predilection for peace.

My religious upbringing was quite ordinary for a young Iowegian lad in the 1960’s. Confirmation in the Lutheran Church (Missouri Synod) in 8th grade followed by a short stint as a reluctant acolyte. The church seemed firmly footed in bedrock as an institution and adept at indoctrinating the young. In catechism studies I tried to understand the authoritarian system that is outlined by Martin Luther and the strange collection of narratives that make up the King James Bible.

There were abstractions that didn’t make sense then and are still a mystery to me today. The concept of the Holy Trinity always seemed suspiciously anthropomorphic. Then there is the crucifixion as a kind of “ghostly sorting mechanism” for salvation. It stands out against the backdrop of natural phenomena like physics and biology- mechanistic systems which seem to suffice for everything else. Finally, there is God’s seemingly endless requirement for worship and admiration which has always struck me as a vanity unnecessary for a supreme being. The whole scheme reeks of iron-age anthropology.

I remember the day it happened. I was praying for something or other. Trying to have a little spiritual time with the Big Guy. It finally dawned on me that I was talking to myself and in doing so, wishing for some particular outcome to happen. All those years. Praying and wishing were indistinguishable. I’ll admit, I was never one to volunteer a lot of praise to God. Heaping praise on a deity seemed patronizing and wholly unnecessary. Surely if God could elicit wrath, then he’d certainly pick up on being flattered.

Well, in the end, so what? Another tedious atheist commits apostasy. Like most people in US culture, my moral basis was built on what has been described as Judeo-Christian morals or ethics. It’s hard to avoid. But just as the earth does not rest on a foundation, I am not limited to sensibilities derived only by the sons of Abraham in a far earlier age. My culture and my brain tell me that theft, murder, and the other spiritual crimes (sins) are bad for the common good. That respect for others has a pleasurable and sensible aspect that threats of eternal damnation do not improve on.

The reductionist in me can’t resist the following assertion. Deistic religion reduces to cosmology. In the end, a religion offers a theory of the universe. It is a kind of physics that defines relationships between the prime mover and his (?) bipedal subjects imbued with mystical sensitivities. It claims to define the outcome of the disposition of a soul, whatever that may be.  I don’t even believe in the existence of the mind, much less a soul.  As a form of physics, religion lacks means by which theories can be tested. Quantitation of a spiritual element is an idea that has yet to see practice. It seems to lack predictive capability to estimate an outcome that can be validated. It is definitely not a science. It is not about matter or energy. It is about how to conduct ones life against a backdrop of divine authority and within a box of behaviors.

But our brains seem to be constructed in a manner such that religious/spiritual notions are nearly irresistible. Billions of people have claimed to feel its draw and testify to its merits. The projection of anthropomorphic imagery in myth is common in diverse cultures.  The Abrahamic religions congealed from cultures that were apparently unaware of the concept of zero. Where heaven is death with a plus sign, hell is death with a negative sign. To an atheist death is just zero. It has no sign or magnitude. It is unconsciousness and devoid of the awareness of pain or pleasure. Zero sensory processing. It is neither exaltation nor agony. Just zero. Entropy prevails. Such an outlook is hardly appealing enough to gather followers. It is grim and without hope of graduation to eternal bliss.  The take home lesson is to live in the moment, not the future.

Who am I to argue with millennia of religious thought? I don’t know. All I can say is that even as a cancer patient, I remain refractory to the pull of religious and mystical thinking. So it was and so it is.

Post script.

Divinity students! Relax. I’m no threat to your faith. My conclusions on this life of ours offers no ceremony and precious little fellowship. I can say that I’ve had an eye-full of the clockwork of this universe. Adherence to evangelical doctrines could not have provided the amazing insights. And for that I have no regrets.

Tempest in a Teapot. Philosophy-v-Physics.

A minor snit has broken out between outspoken physicist Lawrence Krauss of Arizona State University and, well, the philosophers of the world. Krauss has become a darling of the cable TV world of NatGeo and the Science Channel. It seems that you can’t swing a dead cat without knocking over the same dozen television astronomer/cosmologists and quantum physicists. This rotating crew of scientists are filmed on various locations straining to explain the universe in terms of string theory, dark matter, and quantum wierdness using language with a Fog Index of 8 or less.

I’m not slighting these folks in the least. Using the English language to convey the essence of these concepts is difficult, as is preventing the reflexive use of the remote control by viewers with the attention span of a house cat.

Anyway, Krauss has managed to inflame those philosophers who pay attention to popular science.  His latest book, A Universe from Nothing: Why there is Something Rather than Nothing, has precipitated this argument. I don’t care about the merits of his argument here. The reader is invited to dive in.

What I am writing about is the social and intellectual mistake Krauss made. Like all physical scientists, he is a reductionist. The drive for a ToE, Theory of Everything, is the ultimate act of reductionism. His assertion that philosophy is obsolete in the face of discoveries in physics and the emergence of big subassemblies of a ToE has been received with dismay by philosophers.  A large fraction of people (adults, anyway) are hardwired to be receptive to mysticism and no amount of handwaving, no matter how logical and crisp, is going to cause the bell curve to skew substantially away from cherished mystical beliefs.

Krauss has fallen into the same trap as those in the 19th century who may have declared that physics was pretty much complete with Newtonian mechanics. While quantum mechanics provides a template for the description of how particles behave constrained to a region of space, it fails as a replacement for philosophy. That is, quantum mechanics and cosmology do not provide any concise analysis on how people should treat each other, how to conduct a worthwhile life, or how to interpret what the meaning of quantum mechanics is in your life.

This is the realm of philosophy and religion and these kinds of questions must be freshly examined by each generation born into this strange universe. The meaning of existence is not yet settled science.

Plasma

Today I found myself peering at the lovely lavender glow of opaque argon plasma through the viewing screen of a gleaming new instrument. The light-emitting 8000 K plasma sits apparently still alongside the conical metal skimmer. Somewhere a Dewar was quietly releasing a stream of argon into a steel tube that was bent in crisp military angles into and through walls and across the busy spaces above the suspended ceiling. Another cylinder quietly blows a faint draught of helium into the collision cell. A chiller courses cooled water through the zones heated by the quiet but savage plasma. Inside a turbo pump labors to rush the sparse gases out of the mass analyzer and into the inlet of the rough pump and up the exhaust stack.

Up on the roof, the heavy and invisible argon spills along the cobbles of roofing stones until it rolls off the roof onto the ground where the rabbits scamper and prairie dogs yap. The helium atoms begin their random walk into space. The argon shuffles anonymously into the breeze and becomes part of the weather.

All of the delicate arrangements; all of the contrivances and computer controls in place to tune and play this 21st century marvel. And a wonderment it is. The ICPMS obliterates solutes into a plasma state and then taps a miniscule stream of the heavy incandescent argon breath that trickles into the vacuous electronic salsa dance hall of the quadrapole.  All the heat and rhythm for the sake of screening and counting atomic ions. What a exotic artifact of anthropology it is. And it all began in a rift zone in Africa millions of years ago.

Anti-SOPA Solidarity

In solidarity with yesterdays protest against internet censorship, my porch light remained dark last night. What is normally a shining beacon of hope in the neighborhood was last night a mute and dark void.  This pocket of frigid darkness sat in silent protest to those who would presume to stunt the billion webbed neurons of this nearly-sentient being we refer to as The Internets. So it was and so it shall be.

Thus spake Th’ Gaussling.