You may wish to read:

• Ebola, Rats, Lice, and History, and Hans Zinsser Part 1
• Ebola, Rats, Lice, and History, and Hans Zinsser Part 2
• Ebola, African Doctor, and HIV, Part 3
• Ebola: Fire head of CDC ?
• Why I Support Dr. Anthony Fauci
• COVID-19 and The Satan Bug, a John Sturges Movie

While dogma that life has a single ancestor has softened somewhat, the manifest presence of Darwin’s evolution implies that species radiate from a common ancestor in a branching pattern sometimes referred to as the Tree of Life. Before the advent of tools for DNA analysis, the  relationship of complex organisms on that tree was educated guess based upon comparison of  body plan and other traits, together called phenotype.

This was never an option for viruses. Though they became visible with the advent of the electron microscope in the late 1930’s. the images revealed little of functional significance.  Some viruses are pleomorphic, with the same species exhibiting a variety of forms.

A virus resembles a computer program that hijacks a computer. A computer program does not depend upon how it is displayed; it is pure information. Except for a few recently discovered exceptions, which bring some of their own tools to the job, a virus analogizes very well with a program, with the cell as the infected computer.

So how can we get a meaningful classification? These criteria don’t work:

• How a virus infects a cell.
• Mechanism by which it produces disease.
• Severity.
• Incubation period.
• Infectivity.
• Symptoms.
• species infected, et al.

They don’t work because, no matter how many traits are considered,  they don’t reduce to a small number of classes. Reduction is the basis of modern science, and this idea, based on apparent observation, is not reductive. David Baltimore’s scheme solves this.  Most viruses fit cleanly into seven categories, defined by the carrier of the genetic material, and how it reproduces.

Ebola, Hantavirus, and Influenza are Baltimore Class 5, with a negative-sense, single-stranded RNA (–ssRNA) genome. Virus evolution is too messy  to assert one ancestor from which these viruses descended, but it is likely that many or most viruses of a single Baltimore class evolved by a combination of radiation and recombination of genetic material. The Tree of Virus Life has branches that swap parts.

This is  particularly likely with Class 5 viruses, because  single strand RNA is unstable, with repair procedures that are usually  faulty. The genome is constantly changing. In the case of influenza, only a small percentage of replicated  virions are actually  capable of reproduction. See (NIH) Biological activities of ‘noninfectious’ influenza A virus particles.

I wasn’t able  to find a figure for total number of virions in a flu patient (as opposed to just the nose), but for a very rough idea, we might use the estimate for COVID of  1 to 100 billion; see (NIH) The total number and mass of SARS-CoV-2 virions. How does all this replication work, when it does?  The virus must first copy its genome, producing messenger RNA that will direct the cell ribosomes to make more virus. The enzyme RdRp is the agent. It works in haste, with no proofreading. If the original strand of RNA which served as a template breaks, RdRp bounces around the cell looking for another. The chance that it finds a proper replacement is not good. This is like doing brain surgery in a dive bar.

This Frankenstein process, template switching, is routine for Baltimore Class 5. If the resulting substitution is large enough, it is called reassortment. If the cell is simultaneously infected with another strain, or conceivably, species of virus, there is a very tiny chance that the resulting virions are viable, and an even smaller chance that the switch confers an advantage. But the number of virions per infection, and the number of infections, are so huge, that occasionally, the resulting virus is something truly monstrous.

Template switching is a  documented way for this to happen. Spontaneous mutation at a point in the genome, genetic drift, is another. But there are also instances when genetic material has been transplanted by no known mechanism.  It is almost as if a bomb went off in the cell, the exploded pieces came raining down, and reassembled into something viable.

The most likely result is a fitness defect; the virion is nonviable, or can’t compete. What are the chances that something monstrously novel will result, something not recognized by the adaptive immune system, perhaps a virus that would kill everybody? These stand in the way:

• The innate immune system possessed by all healthy humans . Requiring no training to recognize novel pathogens, this has been honed to a pitch since the dawn of life.
• Small size of most viruses. This  limits the size of the viral genome. Virtually all viruses are one-trick ponies, with one way to attack a cell, one way to reproduce, and one way to propagate.
• Fitness defect. A virus which is very good at one thing might be at a competitive disadvantage in some other way. This could explain the  so-far failure of bird flu to adapt to humans. Or it could be simply a matter of time.
• Genetic diversity of the host, in this case,  human. The pathological machinery of a virus specializes to a host with a narrow range of genomes. Genetic diversity within a species obstructs the ability of a virus to kill everybody.

For the most important reason, see this series: COVID Resurgent: Of Hares and Foxes; Primer for Policy Makers, Parts 1 to 4. In short, a virus which exterminates all possible hosts has nothing to live on.

Nevertheless, there is no hard boundary on how lethal a virus can be. Suppose a cell is simultaneously infected with Hantavirus, Influenza, and Ebola, all of which belong to Baltimore Class 5.  Do this a trillion trillion times. The worst that can result is unknown.

In Let Us be Thankful for Vaccines, I wrote

What is the limit of virulence? Without the need to preserve some hosts for future infection,  is there a limitation to all viral machinery? Is it Ebola or a rabies virus, packaged for airborne delivery? Can stealth aspects be added, as observed with COVID-19 ? What of a constellation of virusoids that co-infect and extend the virulence of the engineered virus?

As a universal killer of all life, the Satan bug is almost impossible. Fiction takes dramatic license.  Life fights back with genetic diversity. But the border of reality is unknown. Vaccine technology has made great strides. The methods of trialing a vaccine have not; they do not reflect knowledge at molecular level that was unknown in the whole-virus live-or-killed vaccine era.

This time, the cost in lives of the prolonged vaccine trials will be in the low millions, or tens of millions. It could have been much worse.  (Atlantic) Hic sunt dracones. There be dragons.

Quoting from (CNN) Fauci’s new 2022 timeline for Covid fight,

A decade ago, there were DARPA programs for rapid vaccine production to defend against biological warfare. The  programs were successful in rapid production of vaccines of variable quality, for deployment against dire threat. But the loop was never closed; identification  of dire need was never pursued. The process infrastructure for identification of dire need remains vacant.

***Hic sunt dracones***

Quoting the New York Times,

Officials noted that the suspect never made it into the hotel ballroom, where President Trump and hundreds of journalists were gathered for the White House correspondents’ dinner.

Not so fast. Quoting (NY Post) Witness describes the moment gunman Cole Allen was taken down after White House Correspondents’ Dinner shooting , which quotes Erin Thielman,

“As soon as my son answered the phone, I said, ‘Hey, bud,’ and I heard three loud bangs,” she recalled to The Post. “It was gunshots. I looked to my left. I saw Secret Service with their pistols drawn, probably just had shot. Like right in front of me, he was a foot away,” she said of the suspect, Cole Allen, 31, after Secret Service took him down. “The would-be assassin fell face-first, and his hands were out in front of him.

Why did Allen fall to the ground?

• It has been established that he was not shot.
• He could have heard a command, though Thielman doesn’t mention hearing one.
• He could have been tackled, which Thielman has not mentioned.
• He could have imagined he had been shot, which often causes an instinctive fall.
• He could have lost his balance, or tripped.

Had Allen not fallen, had he entered the stairs proper, he would have had to navigate a landing, a 180 degree turn, the bottom landing, and a 90 degree turn to face the ballroom door. Had he not tripped, with sufficient speed, the first landing would have provided cover from Secret Service agents attempting to down him with gunfire. And fast he was, considering how far ahead he was before he  fell. Once in the ballroom, the risk of civilian casualties becomes huge.

Why did this happen? This was a continuation of recent complacency. The Secret Service doubtless anticipated that a heavily armed assassin might try to storm the checkpoint. They did not anticipate that an individual would prioritize speed. There was nothing to slow Cole down; the reaction time at the checkpoint was slowed by the balancing requirement of public safety with the use of deadly force.

The fix is simple. The checkpoint should have had a portable turnstile, or a back-and-forth path of the kind used to organize long lines, which would have slowed Cole down to enable proper scrutiny. It is so simple, it’s a kind of test.  Will the press will properly engage the  the Secret Service about how sharp they are?

After all, it was their dinner.

A better headline for Iran Blockades the Strait Again; Negotiations Break Down; Iran Has Upper Hand.

(CNN) Iran renews restrictions on Strait of Hormuz as peace talks approach a critical juncture. Quoting,

• Strait closure: Iran says it is once again shutting down the Strait of Hormuz, blaming the US for “breaches of trust” during the ongoing ceasefire. The move may threaten momentum toward a peace deal between the two countries.

The above is a bit watery. On November 3, 2026, the U.S. will still be at war with Iran. The basis is the innate character of the Iranian regime, which cannot be altered. This has been discussed in fine detail in previous posts; here is the summation:

• There is a fundamental misapprehension of the nature of the enemy, which it is thought can be pressured to behave as a rational actor.
• The overarching war strategy has been to create conditions for a rational actor (according to our definition) to emerge, to accede to U.S. demands.
• The  Iranians believe they can manage the privations of the oil blockade better than the West.
• The Iranians believe they can manage civilian suffering with oppression.
• Control of the Strait is a weapon for which the U.S. has no effective countermeasure.
• The IRG anticipates that November will see the sunset of U.S. operations. That is not long in the scheme of things. They anticipate that as the date approaches, Trump will declare victory and disengage.

The enemy is not a rational actor as we understand it. We don’t have to look outside Western civilization for examples. In the closing days of WWII, in the two week Battle of Berlin, 92,000–100,000 German soldiers and 125,000 civilians  lost their lives. Why was the Wehrmacht unable to concede the inevitable?  Fear of Russian revenge was one factor. The personal loyalty oath of Wehrmacht officers to Hitler has direct analogy to Iran’s authoritarian theocracy, however warped it may be by the IRG. A third reason: In the extremity, they had no  time to think.

Even if there exists a moderate faction, it is almost a mathematical theorem that radical elements will dominate, displacing moderates.  Radicals tend to be meaner and more violent than moderates; hence radicals kill more moderates than moderates kill radicals. See (Brinton) The Anatomy of Revolution. Corollary. This cannot change from external pressure. Social order can only be changed up close, as by an occupying force.

It doesn’t matter whether Vance or Rubio negotiate. For Iran, negotiations are nothing more than a smokescreen. To avoid strategic defeat, completely different tactics are required.

There are many ways to classify war. One is intensity. High intensity is the preferred modality for advanced powers, leveraging technology and industry to minimize casualties. Low intensity is the only option available to insurgencies, and remains an option for developing countries. It has been so successful that one wag advises throwing out all the textbooks on counterinsurgency, because they were written by the losers. Afghanistan, Vietnam, and  the 2003 Iraq occupation that followed invasion were asymmetric, where the U.S. / allied effort was mostly high  intensity, against low-intensity insurgent opponents.

With isolated exceptions, such as the occupied Philippines during WW2 (see Wendell Fertig), the Green Berets in Vietnam / small scale ops elsewhere, and an abortive effort in Syria during the Obama administration, U.S. history shows a strong preference for high intensity warfare. Iran is perhaps the most audacious, with an all-air approach that maximizes intensity per combatant. Optimistic predictions were likely based on Iran’s preference for the same.  Simultaneous decapitation and destruction of Iran’s high-intensity base would leave it with “no cards to play.” They actually have a whole other deck. We can “bomb them back to the Stone Age”, as was attempted in Vietnam, only to find they have backup spears, furs, and flints. This is one of Clausewitz’s choices. We don’t decide what the Iranians need to fight. They do.

It was anticipated that, even with an Iranian “backup deck”, the regime would collapse. Here logic was replaced by faulty intuition. Quoting from What Are the Mullahs of Iran Thinking?,

An insurgency is vital to seize power; otherwise it will simply lapse to surviving elements of the current regime.

High intensity warfare has another limitation. It deprives the adversary of time to change their mind.  Readers who have spouses are doubtless familiar with the tactic of wearing down, or being worn down, conceding over time what is unthinkable in an instant.

The alternative. We need to flip the script, with the current maximal intensity reduced to something like what Israelis call “mowing the lawn.” This can be a hybrid approach; we don’t have to go all the way in that direction, but the level must be sustainable indefinitely. But how does the switch open the Strait?

Negotiation with Iran has been proven not to work. So replace it. The broad success of B.F. Skinner’s operant conditioning, with animals as diverse at rats and humans, suggests Iranians are not likely to be immune. See Advice for a New Secretary of State, Part 6; How to Use a Skinner Box. Quoting,

We want the Russians to cease subversion of our political process via social media and fake news.  B.F. Skinner’s numerous publications explain in general terms how this should be done. Now let’s get specific.  A U.S. response, what Skinner calls the reinforcer,  to inhibit the Russian operant,  should:

• • • Occur quickly after the operant, preferably overlapping the operant itself.
    • Be  implemented according to Skinner’s research on schedules. This rules out actions that are one-shots, without the possibility of unlimited repetition.

The reinforcer is transit of the Strait, a set of rules that determine how often, how much, and where-to Iran may transit the Strait in response to successful  transit by U.S. allies. The rules do not have to be simple; they can be capricious and punitive, but they must be consistent. The rules must represent the cheaper alternative to aggression. The Skinner box buys the Iranians time to think.

The alternative also buys  time to establish an insurgency. It is potentially politically durable, removing the Iranian anticipation that they only have to hold out until political pressure in the U.S. terminates U.S. action.

Quoting from (CNN) Trump agrees to two-week ceasefire with Iran; Strategic Deadlock,

Some time before the last battle, when things become obvious, four trends are possible:

• • • • We’re winning, and we know it.
      • We’re losing, and we know it.
      • We’re winning, but we think we’re losing.
      • We’re losing, but we think we’re winning.

One possibility was left out, the current situation of strategic deadlock. Both parties can sustain the conflict almost indefinitely.

Both the present and the future remain in doubt.

(CNN) Trump agrees to two-week ceasefire with Iran.

Open source often must rely on after-the-fact deduction. Quoting from Iran Conflict Myths; Seven Fallacies,

Myth 1. The press, and various open source authorities, such as retired military, voice strong and contradictory opinions at how this war is going. The data required to inform these opinions is not available in open source. Political spin dominates. What about the war planners who have the data? Their accuracy is impaired by the chaos of war. Some time before the last battle, when things become obvious, four trends are possible:

• • • • We’re winning, and we know it.
      • We’re losing, and we know it.
      • We’re winning, but we think we’re losing.
      • We’re losing, but we think we’re winning.

One possibility was left out, the current situation of strategic deadlock. Both parties can sustain the conflict almost indefinitely.

In this swirl the foremost question was, could the U.S. open the Strait of Hormuz? In the past few weeks, this has become the missing demonstration of U.S. power, a requirement rather than an option. If it were possible, the destruction of Iran’s electrical grid would not have been made the substitute. Execution would deprive the U.S. of even the most tenuous support of allies, with additional restrictions on the use of bases, and preeminently, loss of congressional support.

This is the way open source intel works. We cannot directly evaluate the feasibility of war plans, seen or unseen. We know that in the 1990’s  when Iran had lined the shore with ponderous Chinese Silkworm missiles. there were plans to dig them out, with an estimated time for the task of two weeks. The Strait was still approachable by naval vessels, which could competently deal with the Silkworm. Since that time, faster, smaller, more accurate missiles require much greater separation. A single Iranian missile is not guaranteed a hit; the math of repetition works against a navy.

So we can now infer that in at least one way, Iran has the upper hand. We can also infer something about the broad strategy. It was thought that air strikes would degrade Iran’s war-making capacity to insignificance, rendering Iran incapable of concentrating forces along the coast of Hormuz. This may have been partly successful, but the problem of concentrated missile fire at compact area, such as a small island, remains. The 1-2 ton warhead of an Iranian ballistic missile can demolish any field bunker Marines might build.

What options does Trump have? Choices of abandonment or modification remain open. 

• It has been suggested that he could declare victory and disengage. This is a hard sell.
• He could switch to a  low intensity approach.
• He could hold Iranian tankers  hostage in an ocean corral off Oman and sell their oil, using the revenue as a carrot.
• There are ways to disable a power grid which are more easily repairable than destroying power plants.
• He could promote an insurgency, the absence of which is the greatest flaw of the plan.

While POTUS cannot completely duck this situation, he cannot be expected to understand military plans in detail.  His judgement depends on really smart, well balanced administrators, devoid of strange beliefs and agendas. Military science, in combination with intelligence and diplomacy, informs us of what is possible, what is desirable, and what is avoidable.

To POTUS: Changes must be made. You probably know what you have to do and who to do it to.

***How to Succeed in Business Without Really Trying***

See Iran’s Next Move? The SAM Trap.

(CNN) Smerconish: Now that we’re in Iran, we cannot afford a premature exit. Subtitle: Smerconish examines the current state of the war with Iran, and the necessity of securing the Islamic Republic’s enriched uranium.

Examining the inconsistent ways the Administration has expressed goals of U.S. action, Smerconish settles on the conceptually simplest one: seize a hard, dense metal, enriched uranium, that facilitates  great harm. If only this could substitute for the messy business of upending a regime of terror by men with guns and replacing it with a nice bunch of people with no guns!

Quoting Iran Conflict Myths; Seven Fallacies,

Myth 2.  U.S. objectives can be achieved without regime change. A  popular phrase associated with U.S. objectives is “once and for all“, permanent de-nuclearization and de-missilization.

This myth results from a confusion of physical infrastructure with mental infrastructure. It is feasible to raze the industrial base of Iran; it is not  feasible to nullify Iran’s work force. Engineering is a very high status profession in Iran,  even more than in the U.S. How long would it take to build new infrastructure, considering China would sell them brand new factories on easy credit?…razing Iran’s industrial and military infrastructure would buy at most a decade.

Smerconish does not specify whether the uranium stockpile is to be surrendered or seized. The first assumes something about the IRG that may not be true. Quoting Why Trump is Optimistic about Iran Conflict; Role of Technology; Flexible Goals, substitute uranium for bases:

Hence a purely kinetic solution to Iran’s missile bases may not be possible.  A trade may be envisioned. Destruction of Iran’s industrial base is feasible. At some point, the surviving power structure may be amenable to sacrificing the bases in exchange for remaining infrastructure. This assumes some minimal commonality of values. Sometimes there is, sometimes not. North Vietnam is most pertinent. This ingenious culture valued infrastructure, yet was completely willing to sacrifice it for a political goal. The self-destructive Taliban are even more extreme.

So what if they won’t give it up? Then we have to go in and get it. That would require transporting hundreds or thousands of troops through airspace that has recently proven unsafe. It also requires that the Iranians are dumb. The IRG is not full of brilliant minds, but it take little to imagine a booby-trapped fortress, where thousands of tons of rock comes crashing down on Special Forces. The uranium can be dug out at the Iranians’ leisure. For a dramatization, see Could U.S. Special Forces Seize Iran’s Enriched Uranium from Secret Cave?

Suppose we take the uranium. Is that the end of the question? No; the IRG would prefer to make the Bomb themselves, but that is largely a matter of pride. North Korean nukes are vastly more sophisticated, much more powerful, smaller, and, I daresay, for sale at  the right price.

We are left with the only true  defense  against nuclear proliferation, Nice People.

This argument between Michael Smerconish in the Philly Burbs and Bob Morein in the Philly Burbs may be a subject matter first for the Philly Burbs. How about them Eagles?

What follows is not predictive of how this war will turn out. Seven fallacies of press and pundits are discussed. If you are employing one or more, consider reformulating your argument.

Myth 1. The press, and various open source authorities, such as retired military, voice strong and contradictory opinions at how this war is going. The data required to inform these opinions is not available in open source. Political spin dominates. What about the war planners who have the data? Their accuracy is impaired by the chaos of war. Some time before the last battle, when things become obvious, four trends are possible:

• We’re winning, and we know it.
• We’re losing, and we know it.
• We’re winning, but we think we’re losing.
• We’re losing, but we think we’re winning.

Those who think  their predictions are so accurate as to certainly be among the first two should review their records of the Ukraine conflict.

To evaluate the military effort, the first data required are  air attack attrition rates of launchers, missiles, and drones, per day, and remaining stockpiles, including error bars. If the  data is good, it can be used to game  further options, possibly revealing a path to a positive strategic outcome.

Myth 2.  U.S. objectives can be achieved without regime change. A  popular phrase associated with U.S. objectives is “once and for all“, permanent de-nuclearization and de-missilization.

This myth results from a confusion of physical infrastructure with mental infrastructure. It is feasible to raze the industrial base of Iran; it is not  feasible to nullify Iran’s work force. Engineering is a very high status profession in Iran,  even more than in the U.S. How long would it take to build new infrastructure, considering China would sell them brand new factories on easy credit?

The answer comes from China itself. In 1972, when Nixon visited China, that country had political impediments to economic development far more severe than Iran today. It was frozen in a Maoist orthodoxy that prohibited economic development. In 1978, when Deng Xiaoping assumed power, capital accumulation was finally encouraged. In 2010,  only 32 years later, the industrial output of China passed the U.S.  But China lacked Iran’s skilled work  force, so razing Iran’s industrial and military infrastructure would buy at most a decade.

Myth 3. “Imminent threat” is the proper measure to determine the validity of U.S. deployments. When a threat becomes  imminent, it is  is often too late to prevent serious consequences.

Myth 4. The Strait of Hormuz is irreplaceable in world commerce. See New Pipelines for the Middle East; Bypassing the Strait of Hormuz . Some commentators have pointed out that other bulk commodities, such as fertilizer and petrochemicals, also transit the strait.  In the U.S. all bulk commodities other than oil, and some oil too, go by rail.  Is it difficult to build a railroad in Arabia?  Before World War I, the Turks built the 810 mile Hejaz railway on the west side of the Arabian peninsula, which ran from Damascus to Medina. A freight line  on the east side of the peninsula, along with pipelines, to Salalah in Oman, would devalue the strait.

Myth 5 (possible). A quick end to hostilities, even if Iran is left with considerable capacity to regenerate, is preferable to a drawn-out conflict. This is driven by blockage of the Strait. If the Strait is devalued, we can take our time and options open up,  with opportunity for Kissinger’s diplomacy backed by force. The longer the time frame, the more possible regime change becomes.

Myth 6. Bypassing the Strait with pipelines and freight rail is too expensive. It’s actually much cheaper than fighting a war: $10M/mile for a pipeline, $5M/mile for a single freight track. You do the math.

Myth 7. Iranians can overthrow their captors without guns. Anchors conditioned by senseless gun violence in the U.S. barely manage to sputter “and guns” at the end of their homilies.  I got over this by sheer force of logic. You can too.

(CNN) Iran building up defenses of Kharg Island to protect against potential US ground attack, sources say.

A very effective countermeasure exists.

(AP)  Trump says Iran gave the US a gift ‘worth a tremendous amount of money’.

As to what the gift is, here is a reasonable guess, with the attractiveness of reciprocity:

Iran will permit the transit through the Strait of Hormuz of oil equal in value or quantity to the 140 million barrels of Iranian oil  stranded at  sea now subject to sanctions relief. Against a background of endless negotiations, renewals will be contingent on U.S. strikes cessation, and unverifiable Iranian concessions.

Iran takes the initiative in relief of the markets, while the U.S. can only obstruct the markets. International opinion, including allies, swings sharply against the U.S. Continuation is contingent on cessation of hostilities. The result, vindicating the mullahs, is discussed in

What Are the Mullahs of Iran Thinking?

This action by  Iran  results in a return to a frozen conflict. This is the low risk option. It leaves Iran in a position to block the Strait at will.

The alternative U.S. option, preserving the original strategic objectives, involves seizure of several strategic Iranian islands. It potentially frees the Strait from Iranian threat, while exposing occupying troops to continuous, low intensity fires.

Which option would you take?