Bad Faith

"Skepticism" about vaccines, or about evolution... isn't skepticism at all.

This was going to be a post about the Ediacaran epoch, which is a fascinating time, spanning the hundred million years before the Cambrian, when animals began to appear in the fossil record. First tentatively, as sessile sheets of tissue, then later as beautiful motile segmented discs (below), and later still as something a bit more aggressively shaped. All this is yet another (as though more were needed) justification of the overall scheme of evolution developed by Charles Darwin, who knew about what in his time was already a distinct and puzzling lack of animal fossils below the Cambrian strata. If one seeks data in good faith, and while pursuing a well-reasoned hypothesis, one is bound to find something interesting! Incidentally, David Attenborough and the BBC gave an excellent treatment of this era.

The beautiful, and slightly motile, Dickinsonia, from the mid-Ediacaran, about 560 million years ago.

Yet there are some who don't see things that way. Over at the Discovery institute, they don't discover anything, but they do write blogs taking potshots at science. No fossil is enough, no explanation is acceptable. There is always a question left to answer, a gap that has not been filled, wherein God can be squeezed. It is the essence of bad faith, arguing not from reason and evidence, but from a pre-existing truth that must be defended at all costs, particularly against an inveterate enemy which ignores them so assiduously. An enemy who publishes, and publishes, and for whom the God hypothesis is not even worth mentioning in the quest to explain how things happen. Who regards them and their arguments as beneath contempt.

Well, needless to say, they were all in for Trump. If one likes to argue in bad faith, why not vote for the master? The new administration doesn't seem to have much stomach for the Darwinian evolution culture war of decades past (though there are three years to go.. who knows!?). But they have been doing their best to destroy science in the US and put China in the lead for good. Whether it is climate science, medical science, space science, it is all being gutted. Diplomats and other experts? Who needs them? We have discarded our allies, and our best friends are now Victor Orban, Vladimir Putin, Muhammad bin Salman, and Bibi Netanyahu. Fairness and legality at the Justice Department? Who needs that? The theme is kicking intelligent, moral people in the teeth, to bring in a callous, greedy and corrupt new dispensation for the US. One of the more alarming and consequential elements of this campaign has been against vaccines. All the real scientists were thrown off the advisory panels, replaced with vaccine "skeptics". 

We in the US have a long history with vaccines. The revolutionary war featured solicitations for soldiers already vaccinated against (or recovered from) smallpox, the most frightening scourge of the army's camps. Later on, Washington approved mass vaccination for the army. Vaccination in that day (variolation) was no easy matter. It involved introducing someone else's smallpox into an opened vein, and taking all the risks of infection. It was lethal 1-2% of the time, but those were better odds than the 25% death rate from normally contracted small pox. These people knew how to assess risks, and took the vaccination risk to forestall the greater risk. Then there was the polio vaccine, in the 1950's, that wiped out another scourge. One would think that getting a vaccine made in record time that promptly resolved the Covid pandemic and saved millions of lives would have been greeted with a bit more appreciation. But no, it was all too easy to take that science for granted, and adopt bad faith arguments against that and other vaccines.

Today's vaccines still carry risk, though minuscule compared to variolation. The odds are incredibly good. It takes no brains at all to judge vaccines worthwhile. But we have "skeptics". Why do we have them? For the same reason that we have Donald Trump, or have believers in religion. Humans are gullible and seek easy truths over hard ones. It is easy to feel squeamish about getting an injection. It is easy to believe that a con man with enormous self-confidence and wealth has some degree of competence. And it is easy to believe that we as humans are special with some special someone running the universe who cares about our fate. Those are the easy truths, archetypally ingrained, apparently. It takes higher intellectual standards and discipline to look at reality and accept that many easy truths are not true at all. 

For all their religious faith, (and indeed because of it), the religious people who pervade the current administration, Supreme Court, and culture war strongholds routinely argue in bad faith. They are pre-selected for their ability to believe stupid and wrong things. They are not sincere in looking for evidence, or making logical arguments. They put forth laughable legal arguments. They hardly even bother to explain why the "endangerment finding" on CO2 is wrong on the merits. They care about loyalty ahead of competence. And do not even understand what might be systematically wrong about raging corruption. When faith (in their charismatic leader, or their warped religious convictions) comes first, intellect takes a back seat. That is the fundamental rule of this new dispensation in the US, and it will be damaging us for a very long time.

• Clowns in high places.
• History repeats, the second time as farce.
• An AI winter?
• To touch, or not to touch, in curling.
• The rich just keep getting richer.
• For three justices, the law has no meaning whatsoever.

We Have Rocks in Our Heads ... And Everywhere Else, Too

On the evolution and role of iron-sulfur complexes.

Some of the more persuasive ideas about the origin of life have it beginning in the rocks of hydrothermal vents. Here was a place with plenty of energy, interesting chemistry, and proto-cellular structures available to host it. Some kind of metabolism would by this theory have come first, followed by other critical elements like membranes and RNA coding/catalysis. This early earth lacked oxygen, so iron was easily available, not prone to oxidation as now. Thus life at this early time used many minerals in its metabolic processes, as they were available for free. Now, on today's earth, they are not so free, and we have complex processes to acquire and manage them. One of the major minerals we use is the iron-sulfur complex, (similar to pyrite), which comes in a variety of forms and is used by innumerable enzymes in our cells. 

The more common iron-sulfur complexes, with sulfur in yellow, iron in orange.

The principle virtue of the iron-sulfur complex is its redox flexibility. With the relatively electronically "soft" sulfur, iron forms semi-covalent-style bonds, while being able to absorb or give up an electron safely, without destroying nearby chemicals as iron alone typically does. Depending on the structure and liganding, the voltage potential of such complexes can be tuned all over the (reduction potential) map, from -600 to +400 mV. Many other cofactors and metals are used in redox reactions, but iron-sulfur is the most common by far.

Reduction potentials (ability to take up an electron, given an electrical push) of various iron-sulfur complexes.

Researchers had assumed that, given the abundance of these elements, iron-sulfur complexes were essentially freely acquired until the great oxidation event, about two to three billion years ago, when free oxygen started rising and free iron (and sulfur) disappeared, salted away into vast geological deposits. Life faced a dilemma- how to reliably construct minerals that were now getting scarce. The most common solution was a three enzyme system in mitochondria that 1) strips a sulfur from the amino acid cysteine, a convenient source inside cells, 2) scaffolds the construction of the iron-sulfur complex, with iron coming from carrier proteins such as frataxin, and 3) employs several carrier proteins to transfer the resulting complexes to enzymes that need them. 

But a recent paper described work that alters this story, finding archaeal microbes that live anaerobically and make do with only the second of these enzymes. A deep phylogenetic analysis shows that the (#2) assembly/scaffold enzymes are the core of this process, and have existed since the last common ancestor of all life. So they are incredibly ancient, and it turns out to that iron-sulfur complexes can not just be gobbled up from the environment, at least not by any reasonably advanced life form. Rather, these complexes need to be built and managed under the care of an enzyme.

The presented structures of the dimer of SmsB (orange) and SmsC (blue) that dimerize again to make up a full iron-sulfur scaffolding and production enzyme in the archaean Methanocaldococcus jannaschii. Note the reaction scheme where ATP comes in and evicts the iron-sulfur cluster. On right is shown how ATP fits into the structure, and how it nudges the iron-sulfur binding area (blue vs green tracing).

A recent paper from this group extended their analysis to the structure of the assembly/scaffold enzyme. They find that, though it is a symmetrical dimer of a complex of two proteins, it only deals with one iron-sulfur complex at at time. It also binds and cleaves ATP. But ATP seems to have more of an inhibitory role than one that stimulates assembly directly. The authors suggest that high levels of ATP signal that less iron-sulfur complex is needed to sustain the core electron transport chains of metabolism, making this ATP inhibition an allosteric feedback control mechanism in these archaeal cells. I might add, however, that ATP binding may well also have a role in extricating the assembled iron-sulfur cluster from the enzyme, as that complex is quite well coordinated, and could use a push to pop out into the waiting arms of target enzymes.

"These ancestral systems were kept in archaea whereas they went through stepwise complexification in bacteria to incorporate additional functions for higher Fe-S cluster synthesis efficiency leading to SUF, ISC and NIF." - That is, the three-component systems present in eukaryotes, which come in three types.

In the author's structure, the iron-sulfur complex, liganded by three cysteines within the SmsC protein. But note how, facing the viewer, the complex is quite exposed, ready to be taken up by some other enzyme that has a nice empty spot for it.

Additionally, these archaea, with this simple one-step iron cluster formation pathway, get their sulfur not from cysteine, but from ambient elemental sulfur. Which is possible, as they live only in anaerobic environments, such as deep sea hydrothermal vents. So they represent a primitive condition for the whole system as may have occurred in the last common ancestor of all life. This ancestor is located at the split between bacteria and archaea, so was a fully fledged and advanced cell, far beyond the earlier glimmers of abiogenesis, the iron sulfur world, and the RNA world.

• Triumph of stupidity and corruption.
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• But they should be getting closer.
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• Who wants a concentration camp?

The Federal Reserve is an Executive Agency

On the logic of the unitary executive, and the Supreme Court.

As our system of Federal institutions melts down, one actor deserves particular blame and disgrace. That is the Supreme Court. The extreme right majority have time and again tossed consistency, precedent, and logic to the winds in order to legislate their extreme view of executive power, which unfortuitously coincides with that of the current president. They have funneled dark money into the political system, equated money with speach, refused to address the glaring problems of gerrymandering, granted the president blanket immunity, and allowed the president to eviscerate civil service protections and independent agency structures specifically constructed by the legislature. And they have often used the shadow docket to do this dirty work, not even deigning to offer explanations at all, pursuasive or not.

Now they are tying themselves into pretzels to carve out an exception for the Federal Reserve, another independent agency that the president wants under his thumb. But it isn't so easy. The Federal Reserve clearly carries out executive functions, regulating banks, and setting interest rates, mostly by cooperating with the Treasury Department in the management of government debt. Is the Fed a court? Obviously not, as their criteria for action are economic conditions, guided by a mere two parameters- the dual mandate. They flexibly respond to conditions on the ground, in order to manage the US economy and currency. That sounds like an executive function to me. Is the Fed a legislature? They do not seem to enact laws, other than under their regulatory guise. But there are countless other agencies that promulgate rules. If that were the mark of a legislative institution, the court would have had to have made a wrong turn somewhere.

No, the Fed is just as executive as any other agency, and the court can not, by special pleading, argue otherwise. Therefore, either the Fed comes under the president's malign influence, or all the other agencies that Congress in its wisdom provided with measures of independence should have those structures respected as well. 

The significance of what the court is doing here is enormous. First, in their haste to give the president anything he wants and to execute a desire, apparently burning in the breast of John Roberts since the Nixon administration, to construct an imperial presidency, the court has repeatedly authorized the counter-legislative actions of the president to eviscerate agencies such as the labor relations board, the consumer financial protection agency, FTC, AID, and many others. This constitutes the reversal of Humphrey’s Executor v. United States, which laid the groundwork of regulatory agency structures. Second, the court is now casting about for rationales to not do the same to the Federal Reserve, out of an understandable practical desire to not have the country and its economy completely melt down. 

Both threads of action lack basis, and essentially constitute exactly what the court has heretofore so bitterly complained about- legislating from the bench. But of course, when Republicans do it, it is OK. The obvious solution is for the Supreme Court to climb down from its unitary executive horse, reverse its own shadow decisions, and accept that regulatory agencies can be structured by Congress with measures of independence to preserve the public interest precisely, as now, in the face of hostile and intemperate executives. 

Across the constitutional landscape, the problem is not that the executive is too weak, it is that Congress has ceded too much of its power to the executive. Just last week, when faced with Democratic demands that homeland security be brought to heel as a civilized agency, Republican Senators floated the idea of beseeching the President for a new executive order or two. It is incredible. Through the New Deal, World War 2, and the Cold War, the executive branch grew enormously, almost beyond the capacity of Congress to conceive of, let alone oversee. Yet in the Constitution, article 1 is by far the longest, most detailed, and most extensive. Congress has the ability "To regulate Commerce with foreign Nations", "To establish an uniform Rule of Naturalization", "To provide for organizing, arming, and disciplining, the Militia, and for governing such Part of them as may be employed in the Service of the United States", etc. etc. and on and on. Congress makes the rules and provides the structures within which the executive works. Indeed, "To make all Laws which shall be necessary and proper for carrying into Execution the foregoing Powers, and all other Powers vested by this Constitution." It sure seems that Congress is able, as envisioned throughout article 1, to structure executive agencies as it sees fit. 

The constitutional section on the executive branch is, in comparison, exceedingly brief, only requiring reports to congress, command of the armed forces, and the making of treaties, with the consent of Congress. He or she also gets the veto power and makes a variety of appointments, to the courts and the executive branch. That is pretty much it. All else is left to interpretation and conjecture. While the President has wide appointment powers, it is not given the he or she has equally wide dismissal powers. That would be something well within the lawmaking capacity of Congress to regulate. It is apparent from this text that Congress makes all the rules and oversees the operation of the government as a whole, in the broadest terms. Congress is the body that makes the best decisions, that are most accountable to the people, in a deliberative and careful way. Thus the most important decisions are reserved to it. It is also notable that Congress has the power to impeach officers of each of the other branches, a power none of them have over Congress. It is only the people, and Congress itself, which can remove or discipline its own members.

The need for an executive is a practical matter, for someone who is present all the time (does not adjourn for long periods), and who, by his or her nature as a single person rather than a committee, can make hasty decisions in those areas that require it. And not every area of administration, needless to say, requires such an approach. Just because the Presidency is patterned on the relations between Britain's parliament and its king (which had itself developed by that point, given the civil war, beheadings, etc. to a complex system of power sharing) does not mean that the President has infinite latitude. Far from. 

It is thus apparent from this structure and from the history from the earliest times that Congress can make institutional structures of many kinds, in its quest to do whatever is necessary and proper. The first Bank of the United States is an example of one such structure, totally divorced from the President (and perhaps overly independent, as it later turned out). Not every executive function needs the immediate attention of the President, or benefits from his or her political meddling. Sometimes the structures necessary and proper for carrying laws into execution make use of experts, or bipartisan appointees, or public-private partnerships, or tenured appointees. Right now, the Justice Department stands out as an area that particularly needs better statutory protection from the whims of the executive. The Consitution itself provides for modes of shared appointment, as when Senate approval is needed for high executive officials, or long tenure, such as for Supreme Court justices. Such methods of reining in the dangerous and highly political powers of the presidency are clearly consistent with the text, history, and spirit of the Constitution. If those methods are not working, or one does not like them, change the laws, do not unlegislate them from the bench.

• NATO is falling apart.
• Krugman has some harsh words on Warsh.
• Insults and cruelty will continue until you like me.
• Science and football helmets.