Iran: Object Lesson of the Enlightenment

Review of Iran: A Modern History, by Abbas Amanat. Part 2- the contest between autocracy, democracy, and theocracy.

Has history ended? Did all countervailing ideologies give up and yield to democracy as the universal form of government and does peace now reign? Apparently not. Indeed, democracy is embattled in many areas as it has not been in decades- even in the US, whose institutions are under sustained attack by a renascent autocratic / plutocratic coalition. Iran has exemplified the contest between the ideals of democracy, human rights, state stability, authority, and religious sentiment in ideologies of government over many centuries. It has been positioned at some remove from, though in durable if not tragic contact with, the European cultures that fostered the Enlightenment in all its aspects. What has been their impact, and what are we to make of the current result?

Amanat provides a magisterial overview of Iran's recent history, (recent meaning since 1500, which leaves out a vast portion going back to antiquity and beyond), focusing on its political systems as they range between autocracy and revolution, growth and decline, consolidation and decadence. Iran was heavily influenced by Europeans starting in the mid-1800's, as the great game got underway. While Russia was unapologetically autocratic, making its menace clearly lineal with previous contests against other invaders, Britain, and later the US, brought a new level of hypocrisy as imperial powers founded on Enlightenment ideals and practices, which were, however, not for foreign consumption.

The Qajar monarchy in the 1800's managed a weak position relatively well, keeping Iran intact and largely sovereign, if also continually corrupt, indebted, and backward. But finally, the modernist winds were too strong, and a constitutional revolution established a constitutional monarchy and parliament in 1906, then again in 1909. This parliamentary system never fully found its footing, however, tussling with the Shah for power, and buffeted through disastrous invasions and occupations during world war 1. It was sort of a Weimar Republic, never attaining full power in military or political terms.

But it embodied the idea of a Western-style, constitutional, democratic system. The addition of an Islamic advisory council was an afterthought and never seriously implemented during this era, since the ulama, or community of clerics, was generally content with its long-standing role of loose collaboration with the secular power, tending to a narrow sector of jurisprudence over religious, business, and personal matters, on a somewhat freelance basis. While the Shi'i clergy had occasionally led protests and fostered limited political activism in the face of gross injustices and suffering from their base among the small merchant class and urban poor, the idea of becoming a full partner in government, or its comprehensive adversary, did not cross their minds, since government was fundamentally unclean and not worthy of theology, short of the return of the twelfth Imam. The clerics were also fully invested in the somewhat corrupt system, having gotten quite rich from their segment of the economy.

But the trauma of the Pahlavi era, broken in the interval between father and son by a hopeful but chaotic constitutional period under Mohammed Mosaddegh, set the clergy- at least some of it- on a more activist path. Both Shahs were dedicated modernizers, dismissive of religion and destructive to the livelihoods and institutions of the clergy. Along with other islamists in the Sunni world like Qutb, they (that is, the less quietist elements, spearheaded by Ruholla Khomeini) started generating a comprehensive critique of modernism, the Pahlavi apparatus, and the West as antithetical to Islam, which it quite obvoiusly was and remains. They found that they still had enormous political power and public sentiment on their side, not among the intelligentsia, but among the common people who had been coming to the mosques, and requesting judgements, and paying their dues all along. All this was seized by Khomeini, who in 1963 gave fiery sermons denouncing the Pahlavi regime, and was duly detained, almost executed, and then exiled to Iraq. The Shah ran an economically successful few decades, but also a brutal secret service and a grandiose view of himself and the dynasty so severely out of step both with native sentiment and with the democratizing / human rights trends in the West, suddenly put on the top of the table by Jimmy Carter.

Faithful Shi'ite Iranians were interested in more spiritual fare than what the Shah offered, and the clerics, through Khomeini, gave them visions of an ideal society, rectified through "dear Islam" to resolve all the injustices and degradations of the Pahlavi era. In return, Khomeini was first elevated to the unprecedented status of "Grand Ayatolla", and then ultimtely to "Imam" status, which had never been done before, the twelfth Imam having been the last of the set, now in occultation. So the revolution rolled on with inexorable power, but also with inexorable revolutionary logic, piling up bodies and hypocrisies as the imperatives of staying in power overwhelmed all other scruples. For example, Amanat mentions with some acidity that, while centuries of Shi'i jurisprudence may not have foreseen the problems of writing a constitution, running foreign policy, or operating a secret service, it had long dealt, and dealt with care and discretion, in contract and property law. But all that went right out the window as the new government "inherited" or expropriated countless businesses and personal properties, took over all major industries of the country, and distributed their management to family members, cronies and loyalists.

Diagram of the Iranian government, from the BBC.

It is through the lens of the constitution and the cobbled institutions that have arisen in Iran that we can see the dialectic between Enlightenment principles and Islamic principles. Khomeini promised a democracy, where power would no longer be monopolized by a somewhat mad Shah. But it also had to be an Islamic democracy, "guided" by the clerics to retain purity and justice. The logic of all this resulted in a thoroughly theocratic state, where there is an interlocking set of instutions all run by the clerics, from the Supreme Leader to the Guardian Council, Assembly of Experts, and Expediency Discernment Council. Each are supervisory, with various veto and appointment powers, leaving the popularly elected parliament with little real power or even representative complexion, since its candidates are routinely disqualified by the Guardian Council for not being conservative enough.

In practical terms, this means that the system maintains just enough democracy to foster some hope and buy-in from some of the populace, while keeping complete control in the hands of the clerics. Will this end in utter corruption of both religion and government? It is difficult to say, but Iran has more of a functional democracy and republican system than many other Muslim countries, which is sadly not saying much. Those who reflect on the very origins of Islam and Shi'ism can readily see that theory of government is not a strong suit of this tradition. I see Khomeini as a demagogue- a Trumpian figure who promised the stars, offered a telling and comprehensive critique of the Pahlavi system, and had a genius for turning a phrase. But he did not promise a coherent and democratic program of governance, rather a messianic dream and relentlessly divisive politics. In the revolutionary process, he always played to the base, favoring extreme positions. A base whose core, there as here, is a religious element of great patriarchial conservatism and dismissive of intellect and compassion. He was fully behind the hostage-taking students, for instance, which solidified support at home while making Iran a pariah abroad.  Hate, of course, was and continues to be central to the Iranian theocracy, from the Great Satan (us), to the little Satan (the Iraq of Saddam Hussein), to the communist Tudeh party, to the Baha'i religion, which they particularly revile and persecute.

At first, the clerics worked with liberals to fashion a written constitution (a significant concession to modernity and Western ideas) and a civilian government. But as time went on, the many contradictions of this approach became apparent, since if the people were given real power, the clerics would lose theirs- that was a lesson of the first constitutions of the early 1900's, and again during revolutionary process in the 1970's and 80's, which saw many contestants for power. The clerics only won due to their cohesion and their ability, time and again, to move the masses with demagogic and messianic appeals.

So the Iranian clerics ended up in unknown territory, creating a government that had no Persian or Koranic precedent, other than putting clerics in charge of everything (including at the top, the monarch-for-life Supreme Leader), and hoping that their own formation, training, and institutions will keep them uncorrupted. At one dire point in the revolution, a hanging mullah suggested that his rather under-supported decisions didn't matter that much, since God would sort it all out in the end, sending those who deserved it to heaven. But by that logic, he should have killed himself first. It is always curious how those who supposedly believe in religion and the glories of its afterlife turn out to have a strong regard for their own lives in the here and now. One would think that meeting one's maker would be a more positive goal, rather than being a mere scrim for power politics in this fallen world.

Iran gets ranked just above China in the democracy index.

Anyhow, Iran has ended up with more torture, more executions, more war, a bigger secret service, a more intrusive state, and less freedom, than the Pahlavi era. It turned out that Islam is not a guarantee of good, let alone moral, governance. Islamic countries generally occupy the lower rungs of the democracy index, and other indexes of development and happiness. This while Islam portrays itself as a religion of peace, of mercy, and of the most exacting jurisprudence and scholarship. The revolutionary government of Iran dabbled in liberalism, and wrote up a semi-democratic constitution, and faced a culture of great diversity and intellectual depth. But in the end, authoritarian logic won out over traditional Shi'i quietism and over most Western trends, creating a sort of Shi'i Vatican writ large, with opaque committees of old bearded men running everything, with additional torture chambers and gallows.

Iran offers an object lesson why the interlocking lessons of the enlightenment are so important- why withdrawing religious projections, drama, and righteousness from the state, in favor of civic secularism, yields a more rational and humane way of life. Why even the most long-standing and cherished religious traditions and "scholarship", while they may serve as selective institutions to weed out the stupid and socially unskilled, are not conducive to the search for objective truth or even a marker of moral superiority.

All that said, the French revolution began with enlightenment principles, which did not prevent a similar revolutionary logic from sending it to appalling depths of brutality, injustice, and authoritarianism. Yet it also spread more liberal, anti-monarchical values throughout Europe during the Napoleonic era, and ended up, after decades of historical development, with true democracy in France and Europe. The whole point of political theory in the Enlightenment was to allow such development via a fundamental humanism and humility in the civic sphere and the state. Its antithesis is messianism of various sorts, from communism to Shi'i theocracy, (even atheist enlightenment, when driven to extremes!), which drives polarization, extremism, and totalitarianism. Iran may yet develop in a softer direction, after what is now forty years of theocracy, but that would take a substantial change of heart on the part of the current ruling class, and perhaps a reduced allergy to Western ideas.

• Happy Quds Day!
• Changing conceptions of masculinity...
• Right wing legal community is going over the deep end.
• It is not clear that California is ready to re-open. Graph of the week:

Iran: Pawn in the Great Game

Review of Iran: A Modern History, by Abbas Amanat. Part 1- the great game and a history of victimization.

The lure of victimization narratives is a little hard to pin down, though it is universal. No matter how much power Republicans acrue, they always seem to feel victimized by the still-ascendent liberal culture, by rational or compassionate argument, and indeed by anyone who disagrees with them. Victimization is an assertion of moral righteousness, sometimes proven more pure and righteous in its defeat by forces of darkness than by its triumph. Christianity is a victimization narrative par excellence- of a savior tragically unrecognized in his own day, callously sold out and executed by the ruling powers, but ultimately, though the intercession of miracles, energetic preaching, and what have you, ready to save you if only you too believe this story. Victimization can be as callous and unthinking an ideological postition as its opposite- domination- excusing any extremity and moral lapse in the service of the restoration of what was lost or been suppressed. Indeed, victimization narratives exist in a complex dance with domineering ideologies, and are frequently used by them, as suggested above. The Nazis, after all, were victimized by the Jews.

But how much more intoxicating is all this if you really are a victim? Iran, in its long history, has played many roles. But over the last few centuries, that of victim has been predominant. Its early cultures, before and after the Indo-European invasions of the second millenium BC, usually played second fiddle to the Sumerian, Assyrian, and Babylonian cultures to the west. Then came the high point of the Persian Achaemenid Empire in the mid-first millenium BC, which spread over the entire Middle East, from Afghanistan to Egypt and Greece, and was memorialized extensively in both Greek and Jewish literature. Cruelly truncated by the invasion of Alexander the Great, Persia then went through extended domination by the Greeks in the Seleucid Empire, followed by somewhat cosmopolitan domination by the Parthians, a Scythian tribe from the East, before regaining most of its former extent under the Sassanian Empire, which was truly Persian in origin and culture again. Only to be brutally crushed by the Arab invasion. Gradually, Persian culture re-asserted itself, forming the backbone of the Islamic Golden Age, which whithered amid the Mongol invasions and a reversion to doctrinaire Islam. One hardly knows which oppression to bemoan first.

The Azadi tower. Take that, Brandenburg gate! This is perhaps the most durable and iconic bequest of the second Shah's rule, adopted by all sides in Iran, whether protesting for or against the powers that be.

The coronavirus lockdown has brought me one consolation, which is this lengthy tome on Iranian history, borrowed just before the boom came down, and which the library shows no sign of wanting back. Amanat takes up the story at 1500 CE with the rise of a militant Shiite ruler, Ismail I, who set the tone for Iranian culture up to today: a full-on victimization passion play, with oppressors ranging from Abu Bakr and Yazid I to the United States, heart-rending mourning, and self-flagellation. The story of Iran is one of a small country with big ambitions, which it occasionally fulfills. Why didn't Persia remain a large empire and culture, like Rome did, even after its formal fall? On the one hand, there were too many other competing cultures about. The Persians could not quite put together a world-leading coalition. The Achaemenids, under Cyrus the great, came closest, setting a cosmopolitan standard that was widely attractive and powerful. At least the Jews gave it good press. But it fell apart amid civil war and the usual bane of early empires- dysfunctional or non-existent methods of transferring power. The Safavid dynasty, begun in 1501, set Shi'ism as the national religion of Iran. This had the twin effects of being highly motivational to the "base", while being rather isolating vs the wider world, including the Sunni majority across Islam. The course was thus set for Iran to be a small-to-mid-sized power, a box they are still trying to break out of today, to little effect.

Over the last few centuries, Iran's major antagonists have been the much greater empires of Russia, Great Britain, and the US. While there have been occasional raids from, and forays to, the East, towards Afghanistan and India, generally relations in that direction have been calm, and Persian culture has had significant influence in Afghanistan and Mughal India. On the other hand, expansionism and colonialism from the West and North have been devastating. Iran was barely able to hang on to its territorial and cultural integrity at the worst of times. Russia dealt Iran a comprehensive military defeat in 1826, took parts of the North, and threatened the rest of the country. Through the nineteenth century, Iran tried its best to play the big powers off against each other, playing its part in the great game. But just as often, the British and Russians would make their own agreements to carve up the local countries into spheres of influence, if not zones of occupation. They also engaged in destructive loans, saddling Iran with unpayable debts and increasing foreign ownership of its infrastructure, customs, and other means of paying them back. Russia sponsored a pro-shah coup in 1908. Britain especially forced Iran into a series of bad trade deals, privileged treatment, and forced imports, killing off the Iranian silk industry, among much other economic and cultural damage. And once Britain smelled oil, and switched its navy from coal to oil, (during world war 1), its regard for the integrity and interests of Iran fell even further. Russia and Britain each occupied large parts of the country during both world wars, without so much as a by-your-leave.

What saved Iran was an unexpected favor from Russia. The communist revolution led to an immediate evacuation of Russia's occupation of Northern Iran and cancellation of its debts, and, at least for a brief period, much friendlier relations. But it also led to simmering communist political and guerrilla insurgencies for the next century. Iran kept being knocked about between the great powers, with the US taking an increasing role during and after world war 2. The US had previously been one of the friendlier countries to Iran, providing critical financial advice and political support during its constitutional phase, during the Shuster appointment as treasurer, back in 1911. And the US was naturally thought to be supportive of constitutionalism, rule of law and democracy. But world war 2 changed all that, making the US more or less the inheritor of the British empire. When the first Reza Shah government finally collapsed and a nascent constitutional system arose, one of its first and most popular pieces of business, under Mohammed Mosaddegh, was nationalization of the oil industry. Britain, which ran the Iranian oil fields outright, sharing a paltry 16% with Iran, was outraged. The US, caught in the middle, was unfortunately more sympathetic to Britain than Iran. The US offered a 50% deal, in line with others in the region. This would have been a good compromise, but Mosaddegh had painted himself into a corner. And made many enemies across the political spectrum, not being, at base, a particularly good politician. His ouster, amid a coup staged explicitly by the Iranian military, but with support from the British and Americans, was not a big surprise at the time. Only in retrospect, after the subsequent regime of the second Shah dragged on, decade after decade, with unstinting US support, no matter the excesses of the secret services or oppression of the people, and with the backdrop of the US's brutal wars in Vietnam and Cambodia, did the narrative of the great Satan take shape. It was an understandable, yet also facile, and ultimately misguided response to yet another episode in Iran's long and often tragic history of international relations.

We won't get into the next parts of the story in this post, but reflect that size matters in international relations. The Shah stuck with the US through thick and thin, creating a rare stable environment for Iran internationally. No one questioned Iran's sovereignty, or its position in the cold war. None of its neighbors attacked. But when that sponsorship fell apart amid the Islamic revolution, and Iran started pissing off each of its neighbors near and far, things did not go so well, and remain perilous today. On the other hand, the US played a large part in the Shah's failure to manage internal affairs, losing sight of our principles (as we also did in Vietnam, then again in Iraq) and blindly funding a despot. Our best cases from this period were the various countries (South Korea, Indonesia, Philippines, Taiwan) that got away belatedly, through popular protests, out of US-sponsored dictatorships and towards democracy. Is that the best we could have done?

• Some notes on Iran's process of conversion to Islam.
• Studies in Shiite propaganda.
• Another dysfunctional country failing to deal effectively with the virus.
• And now, for a bit of science.

Origin of Life- RNA Only, or Proteins Too?

Proteins as Participants in the Origin of Life

After going through some momentous epochs in the history of life in the last two weeks (the origin of eukaryotes, and the nature of the original metabolism), we are only part of the way to the origin of life itself. The last common ancestor of all life, (LUCA), rooted at the divergence between bacteria and archaea, was a fully fledged cell, with many genes, a replication system and translation system, membranes, and a robust metabolism based on a putative locale at hydrothermal vents. This is a stage long after the origination of life, about which our concepts remain far hazier, at the chemical interface of early Earth.

A recent paper (and prior) takes a few more speculative shots at this question, (invoking what it calls the initial Darwinian ancestor, or IDA), making the observation that proteins are probably as fundamental as RNA to this origination event. One popular model has been the "RNA world", based on the discovery that RNA has some catalytic capability, making it in principle capable of being the Ur-genetic code as well as the Ur-enzyme that replicated that same code into active, catalytic molecules, i.e., itself. But not only has such a polymathic molecule been impossible to construct in the lab, the theory is also problematic.

Firstly, RNA has some catalytic ability, but not nearly as much as it needs to make a running start at evolution. Second, there is a great symmetry in the mechanisms of life- proteins make RNA and other nucleic acids, as polymerases, while RNA makes proteins, via the great machine of the ribosome. This seems like a deep truth and reflection of our origins. It is probable that proteins would, in theory, be quite capable of forming the ribosomal core machinery- and much more efficiently- with the exception of the tRNA codon interpretation system that interacts closely with the mRNA template. But they haven't and don't. We have ended up with a byzantine and inefficient ribosome, which centers on an RNA-based catalytic mechanism and soaks up a huge proportion of cellular resources, due to what looks like a historical event of great significance. In a similar vein, the authors also find it hard to understand how, if RNA had managed to replicate itself in a fully RNA-based world, how it managed to hand off those functions to proteins later on, when the translation function never was. (It is worth noting that the spliceosome is another RNA-based machine that is large and inefficient.)

The basic pathways of information in biology. We are currently under siege by an organism that uses an RNA-dependent RNA polymerase to make, not nonsense RNA, but copies of itself and other messages by which it blows apart our lung cells. Reverse transcriptases, copying RNA into DNA, characterize retro-viruses like HIV, which burrow into our genomes.

This thinking leads to a modified version of the RNA world concept, suggesting that RNA is not sufficient by itself, though it was clearly central. It also leads to questions about nascent systems for making proteins. The ribosome has an active site that lines up three tRNAs in a production line over the mRNA template, so that the amino acids attached on their other ends can be lined up likewise and progressively linked into a protein chain. One can imagine this process originating in much simpler RNA-amino acid complexes that were lined up haphazardly on short RNA templates to make tiny proteins, given conducive chemical conditions. (Though conditions may not have been very conducive.) Even a slight bias in the coding for these peptides would have led to a selective cycle that increased fidelity, assuming that the products provided some function, however marginal. This is far from making a polymerase for RNA, however, so the origin and propagation mechanisms for the RNA remain open.

"The second important demonstration will be that a short peptide is able to act as an RNA-dependent RNA polymerase."
- The authors, making in passing what is a rather demanding statement.

The point is that at the inception of life, to have any hope of achieving the overall cycle of selection going between an information store and some function which it embodies or encodes, proteins, however short, need to participate as functional components, and products of encoding, founding a cycle that remains at the heart of life today. The fact that RNA has any catalytic ability at all is a testament to the general promiscuity of chemistry- that tinkering tends to be rewarded. Proteins, even in exceedingly short forms, provide a far greater, and code-able, chemical functionality that is not available from either RNA (poor chemical functionality) or ambient minerals (which have important, but also limited, chemical functionality, and are difficult to envision as useful in polymeric, coded form). Very little of the relevant early chemistries needed to be coded originally, however. The early setting of life seems to have been rich with chemical energy and diverse minerals and carbon compounds, so the trick was to unite a simplest possible code with simple coded functions. Unfortunately, despite decades of work and thought, the nature of this system, or even a firm idea of what would be minimally required, remains a work in progress.

• Thus, god did it.
• Health care workers can be asymptomatic, and keep spreading virus over a week after symptoms abate.
• Choir practices are a spreading setting.

Turning Biochemistry on its Head in Search of the Origin of Life

Early earth was anoxic. That means that metabolic reactions ran backwards, compared to what we regard as normal.

Following up on last week's post on the origins of eukaryotes, I ran across a brilliant body of work by William Martin and colleagues, which explores both that and the related topic of the origin of life, all of which took place on an early earth very different from our own. Perhaps the most fundamental theme in any biochemistry course, especially when it comes to metabolism, is controlled oxidation. We in our bodies recapitulate the action of fire, by transforming (reduced) hydrogen-rich carbon compounds (carbo-hydrates, fats, etc.) to the most oxidized form of carbon, CO2, which we regard as a waste product and make- from our food, and now by proxy out of our ramified economic metabolism- in prodigious amounts. Our rich metabolic inheritance essentially slows down and harnesses this energy-liberating process that, uncontrolled, runs wild.

But early earth was anoxic. There was no free oxygen, and this metabolism simply could not exist. The great oxygenation event of roughly 2 to 3 billion years ago came about due to evolution of photosynthesis, which regards CO2 as its input, and O2 as its waste product. Yet plants metabolize the other way around as well, (often at night), respiring the reduced carbon that they painstakingly accumulate from CO2 fixation back to CO2 for their growth and maintenance. Plants are firmly part of this oxidized world, even as they, in net terms, fix carbon from CO2 and release oxygen.

An energy rich, but reducing, environment, full of sulfides and other hydrogen-rich compounds.

In a truly anoxic world, the natural biochemical destination is reduced compounds, not oxidized ones. The deep-ocean hydrothermal vent has been taken as a paradigmatic setting, at least as common on the very early earth as today. Here, reduction is the order of the day, with electrons rampant, and serpentinzation a driving mineral process, which liberates reducing power, and generates methane and hydrogen sulfide. This is one home of anaerobic life- an under-appreciated demimond of micro-organisms that today still permeate deep sediments, rocks, hydrothermal vents, and other geologic settings we regard as "inhospitable". An example is the methanogens- archaea that fix CO2 using the local reducing power of hydrogen, and emit methane. Methane! A compound we in our oxygen atmosphere regard as energy-rich and burn in vast amounts, these archaea regard as a waste product. The reason is that they live where reduction, not oxidation, is the order of the day, and they slow down and harness that ambient (chemical gradient) power just as we do in reverse. This division of aerobic vs anaerobic, which implies metabolisms that run in opposite directions, is fundamental, accounting for the hidden nature of these communities, and why oxygen is so toxic to their members.

By now it is quite well known that not only was the early earth, and thus early life, anoxic; but the broadest phylogenies of life that look for our most distant ancestors using molecular sequences also place anaerobes like methanogenic archaea and acetogenic bacteria at the earliest points. Whether archaea or bacteria came first is not clear- they branch very deeply, and perhaps earlier than any phylogenetic method using the molecular clues can ever tell. Thus the archaeal progenitor of the eukaryotic host appears to have been anaerobic, and may have entered into a dependence with a hydrogen-generating, methane-using bacterium which had already evolved an extensive metabolism compatible with oxygen, but not yet dependent on it. It was only later that the oxygen-using capacity of this partner come to such prominence, after oxygen came to dominate the biosphere so completely, and after the partner had replaced most of the host's metabolism with its own enzymes for heterotrophic use (i.e. fermentation) of complex carbon compounds.

This overturns the image that was originally fostered by Darwin, in a rare lapse of prophetic skill, who imagined life originating in a quiet sunlit pool, the primordial soup that has been sought like a holy grail. The Miller-Urey experiments were premised on having complex compounds available in such a broth, so that heterotrophic nascent cells just had to reach out an choose what they wanted. But these ideas above end up proposing that life did not begin in a soup, rather, it began in a chemical vortex, possibly a very hot one, where nascent cells built an autotrophic metabolism based on reducing/fixing carbon from CO2, (the dominant form of carbon on early earth), using the abundant ambient reducing power, and local minerals as catalysts. Thus the energetics and metabolism were established first, on a highly sustainable basis, after which complexities like cell formation, the transition from mineral to hybrid mineral/organic catalysts, and the elaboration of RNA for catalysis and replication, could happen.

Much of this remains speculative, but one tell-tale is the minerals that underpin much of metabolism. Iron-sulfur complexes still lie at the heart of many electron transfer catalysts, as do several other key metals. RNA is also prone to oxidation, so would have been more robust in an anoxic world. More generally, this theory may widen our opinions about life on other planets. Oxygen may be a sign of some forms of life, and essential for us, but is hardly necessary for the presence of life at all. Exotic places with complex chemistries, such as the gas giant planets, may have fostered life in forms we are unfamiliar with.

• Maybe, there are too many of us.
• Order vs justice.
• American institutions, dying of bureaucratic sclerosis, politics, and corruption.
• What serious contact tracing would look like.

Mother of us All- the Eukaryotic Ancestor

A new archaeon looks very much like an early transitional form between archaea and eukaryotes.

Even more than the invention of photosynthesis or the transition to multicellularity, the transition from bacteria to eukaryotes was perhaps the most dramatic and momentous evolutionary event after the origination of life. Bacteria are everywhere, and still dominate the biosphere in many respects with an unparalleled range of biochemistries. But they have severely limited prospects, being so streamlined in their genetic and sexual practices that they seem unable to escape their single-celled, remorselessly competitive fate.

Eukaryotes are known to have originated in the fusion of at least two different bacteria-like microorganisms, one perhaps an amoeba-like hunter, the other the bacterium that became our mitochondrion. Plus another that in plants became the chloroplast. There are several theories about the details, of which several propose metabolic symbiosis- that the original exchange between the mitochondrial progenitor and its host was actually not amoeboid engulfment, but quite gradual and voluntary, uniting a methanogenic partner that used small organic compounds and hydrogen as its inputs- making methane- with a methanotrophic host that produced various organic compounds from methane plus CO2 without complaint.

But once joined, eukaryotes did so much more, generating countless innovations in cell organization, sex, genetic control, organelle subspecialization, membrane management, cytoskeletal structure, among others, that it is hard to believe this event ever happened, and difficult to reconstruct its steps. In this regard, it is similar to the origination of life, where several obstacles (enclosure of a cell with selective transport, replicative mechanism, and metabolic power, perhaps among others as yet unappreciated) all had to be surmounted in some fashion before something that we would call life existed- a process that remains a topic of wide-ranging speculation.

But the starting point for eukaryotes seems to have been an archaeon- a member of the third major kingdom of life discovered only in the 1970's, which are unicellular like bacteria, but have many distinct molecular and genetic mechanisms that are more closely related to eukaryotes than to bacteria. These seem to be our nuclear ancestors, with a lot of bacterial genetic material added later on, either from the early mitochondrial symbiont, or from other transfers, which enriched their biochemical range. The big questions are- what caused the unification of these two life forms, and why did it result in such an extensive profusion of other innovative traits? A recent paper (review) is devoted to the first question to some degree, discovering a new archaeal species that is the closest yet to such a transitional form.

"We confirmed the presence of 80 eukaryotic signature proteins, which are also observed in related Asgard archaea."

To do this, they cultivated deep marine sediments from around Japan in an oxygen-free bioreactor, feeding methane (plus a bunch of antibiotics, to kill off any bacteria) in order to cultivate organisms that are notoriously hard to cultivate. They were looking for anaerobic archaea that die in oxygen, and live off of methane, which they get typically from partner bacteria. The hydrogen that the former (methanotrophs) produce from methane is toxic in large amounts, so having a partner to use it and give methane in return is a partnership made in heaven. Those partners (at first, methanogens) eat hydrogen and CO2, or other small organic molecules and produce methane. The new methanotroph is not just picky about conditions it will grow in, but extremely slow-growing, doubling in the best of conditions in about 20 days. These are not E. coli! Indeed, the whole project took a decade.

The idea to culture such obscure and obdurate organisms comes from two sources. First were existing hypotheses about how eukaryotes got started, in the form of metabolic collaborations described above, between disparate micro-organisms, centering on the use and exchange of methane and hydrogen, in addition to electrons and other compounds. Second were surveys of marine sediments and many other habitats for raw DNA, which has been sequenced in vast amounts. Such DNA is obviously a messy mixture, but given enough patience and computer power, one can re-assemble many interesting distinct genomes out of it, and some transition-like genomes have been glimpsed in this way. But what could be the corresponding organism? That was the question.

The author's phylogenetic tree across all kingdoms, using ribosomal proteins, highlighting the new organism's (red) position as sister group between archaea and eukaryotes. Note how relatively deep the divergence (X-axis) is between bacteria at the bottoms, and all other life forms.

One key analysis was to put this new organism into a phylogenetic tree, using the incredibly well-conserved sequences of the ribosomal proteins. The diagram above shows that the new organism, dubbed MK-D1, sits right at the threshold of the eukaryotic group, just as one would expect for an ancestor. It constitutes, to date and in molecular terms, the closest organism to eukaryotes that is not one itself. The diagram also shows, yet again, the vast molecular gulf between bacteria (at the very bottom) and archaea, which occupy most of the middle. While eukaryotes (top) are clearly a sister group of archaea, it is the divide between archaea and bacteria that is the most profound within the whole biosphere.

These new organisms are unexpectedly small- tiny, indeed. They are not the huge phagocytic amoeba that have often been imagined engulfing hapless bacterial partners about to be taken hostage. No, the methanogenic partners that are co-cultured by these researchers are far larger, by roughly ten-fold. But the new methanotroph has some interesting behaviors, such as putting out extensive cell projections and curious vesicles. It also has, as expected, a variety of genes that characterize eukaryotes, such as actin, profilin, Ras, G-beta like protein, TPR motifs, Zinc finger and HTH proteins, core transcription proteins like TFIIB, SMC, Ankyrin motifs, histones, SNARE-like proteins, signal recognition factor.

Micrographs of the new organism, MK-D1. Left is a high-magnification electron micrograph showing membrane vesicles budding off the main cell. Scale, 200 nm. Right is a scanning electron micrograph of two or three cells with dramatic projections emerging, plus some previously budded vesicles lying about. Scale, 1 micron.

Of course, this organism exists now, a couple billion years after its imagined ancestor occured in a lineage that we speculate was related to one that led to eukaryotes. So it is a stretch to make this diagnosis of a transitional form. Except that relict forms seem to litter the biosphere, such as the stromatolites that still crop up in Australia, and the vast hordes of bacteria and archaea that remain the metabolic engines of the biosphere, in perpetual competition, yet also largely frozen in their lifestyles and roles.

When free oxygen was introduced into the biosphere by nascent photosynthesis, starting roughly two and a half billion years ago, the putative methane-exchanging organisms all needed extra partners to detoxify it, for instance bacteria which oxidize (using O2) organic compounds to CO2. This, finally, was the motivating force for the partnership with the true mitochondrion, which performs the same service today, providing enormous amounts of energy along the way. The transition from the loose partnership cultured by the current researchers to the one that truly gave rise to eukaryotes is a bit murky under their class of hypotheses, but there are other hypotheses that make a more direct job of it.

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