Islam is Not a Religion of Peace

Nor is it a religion of war. A review of the Quran.

Muhammed is the Apostle
Of God; and those who are
With him are strong
Against Unbelievers, (but)
Compassionate amongst each other.
 (48:29)

As scripture, the Quran stands head and shoulders above its relatives in some respects. It is clear, (if tediously long and repetitive), not given to parables and riddles. Nor is it given to obscure genologies and mythical tales (other than a few retold from the Jewish and Christian traditions). It is explicit on many points, giving rules for behavior and hammering home its points about who and what are good and bad. Its general world view is also refreshingly simple. The world's beauty and gifts, especially the wonders of biology, are clear signs of the one god, and one would have to be an idiot or worse to doubt them and thus the Apostle's message, which comes directly from god.

And among His Signs
Is the creation of the heavens
And the earth, and the variations
In your languages
And your colors: verily
In that are Signs
For those who know.
 (30:22)

(The version I am using dates from sixty-eight years ago, well before the political correctness that beset the field since 2001. It is also a version that reads very well and is abundantly annotated. The text runs to 1800 pages.)

The Quran's provinance is also far more secure than those of the other scriptures, being assembled within twenty years of Muhammed's death by order of the rulers of the community. The ancillary Hadith is less secure, but that is another matter. Muhammed's existence is also far better attested than that of the other prophets, from Jesus back to Moses, Abraham, Noah, Adam, and into the mists of time, many of whom, if not all, are mythical, or very heavily mythicised. Muhammed had a very active and well-recorded life, full of commerce, revelation, warfare, and preaching. Indeed, he took special exception to the deification of Jesus, making it a tenet of Islam that Jesus as one of the prior apostles was a normal man with (some) divine inspiration. One might note in passing, however, that the seemingly universal practice of Muslims to never refer to Muhammed without wishing peace be upon him amounts to a furtive deification / sanctification of the apostle. He is most certainly in the finest possible position of heaven by this doctrine, and hardly needs assistance of any kind from the sinners here below.

The Muslim doctrine, aside from a few defects that I will get to, is also a highly moral one, which repeatedly invokes a very simple formula for community membership- belief in god and obedience to his apostle, virtuous moral action, modesty and circumspection in all affairs, and charitable giving to the poor. There are other incidental tasks, such as praying, food restrictions, and the hajj, (incidentally, Islam is about the only modern religion still employing animal sacrifice, which takes place during the hajj), but the basics are admirably simple and doubtless contribute to the attraction of this religion to so many people, and to their self-understanding that it is an almost self-evident doctrine. The Quran also enjoins believers to give charity with open arms and a positive attitude- something that our current Republicans might do well to emulate, our tax system being, in essence, precisely the kind of alms and charity distribution system (plus a little jihad) that Islam envisions.

But some of the desert Arabs
Believe in God and the Last Day,
And look on their payments
As pious gifts bringing them
Nearer to God, and obtaining
The prayers of the apostle.
Aye, indeed they bring them
Nearer (to Him): soon will God
Admit them to His Mercy:
For God is Oft-Forgiving,
Most Merciful
 (9:99)

Unfortunately, Muhammed was faced with a lot of disbelievers in his time, as is reiterated on virtually every page. They are assigned to hell in innumerable ways, sometimes mild, sometimes excruciating. But the repetition of this theme is striking, seeming to signify some insecurity about the clarity and confidence otherwise expressed. Its endless repetition also functions as a sort of hypnotic mantra. Sometimes he takes the mild approach, assuring listeners that, despite the apparent success of unbelievers in this life, with riches and sons, god will mete our their just deserts in the afterlife. But frequently, hatred gets the better of him, and unbelievers are reviled where they are, threatened with various horrible fates in this world, and subject to terror by the (always virtuous) believers. He recurs frequently to the tales of Noah, Moses, Lot, et al. to make clear that unbelievers stand a very good chance of being struck down in this life, en masse, God-willing.

Those who reject
Our Signs, We shall soon
Cast into the Fire;
As often as their skins
Are roasted through,
We shall change them
For fresh skins,
That they may taste
The Penalty: for God
Is Exalted in Power, Wise.
 (4:56)

There is also an odd lack of certainty sometimes, as though the speaker, though being god, isn't entirely sure of some facts or events events. He recounts (18:22) an old Christian story of boys who happened upon a cave and fell asleep there, for a few centuries, only to find on waking that the Christianity that was reviled by the Roman authorities before is now the state religion. Only, the teller of the tale isn't sure whether there were three boys, or five, or seven. It doesn't inspire confidence, frankly. Likewise, he retells the immaculate conception story of Mary having been impregnated by god, but later claims that Jesus was a normal man like all others, not in any way a deity. And that nor did god ever have a son. Logically, it doesn't quite make sense, especially as told by an omniscient being, but makes more sense as a sop to tradition.

Have We not created
You from a fluid
(Held) despicable? 

The which We placed
In a place of rest,
Firmly fixed, 

For a period (of gestation),
Determined (According to need)? 

For We do determine
(According to need); for We
Are the Best to determine (things). 

Ah woe, that Day!
To the Rejectors of Truth!
 (77:20-24)

More generally, the book claims to be full of truths, but the information communicated is meagre. Belief is extolled ad nauseum, as is truth, but no scintilla of knowledge not commonly known at the time is related. This is especially notable in its celebration of biology and the heavens, which are given repeatedly as strong signs of god and his beneficence. Where is the knowledge of breeding, of evolution, of development, and of genetics? (Hey, how about a funny biology song?) The author claims simply that god has made everyone, and can make or unmake people at will. Where is the knowledge of the history of biology and scale the universe? The birth of Adam is recounted as the origin of humanity, in the story of the garden of Eden. As a source of knowledge, the Quran comes off poorly indeed. Imagine how mind-blowing it would have been for an ancient scripture to tell the true story of our origins and nature, taking it as a lesson on the great preciousness and rarity of our existence, and the momentous stewardship we have been granted.

Praise be to God,
Who hath sent to His Servant
The Book, and hath allowed
Therein no Crookedness: 

(He hath made it) Straight
(And Clear) in order that
He may warn (the godless)
Of a terrible Punishment
From Him, and that He
May give Glad Tidings
To the Believers who work
Righteous deeds, that they
Shall have a goodly Reward, 

Wherein they shall
Remain forever:
 (18:1-3)

There are also some theological confusions. God is free of all wants (14:8, and elsewhere), but at the same time wants all kinds of adulation and submission, wants unbelievers to spend eternity in Hell, wants moral behavior in peace and martial behavior in war, indeed, has transmitted a book full of wants.

Pagans and unbelievers are assigned to hell on virtually every page. But they also are promised ill fortune in this life, though sometimes they might do just fine, as god is just staying his hand till some more convenient moment. Indeed, sometimes they are so rich with money and sons that it drives believers positively apoplectic, and to doubt that they are on the right side after all. The Quran tries its best to quiet such doubts, asserting time and again that whatever the current situation, (and however detestable the unbelievers, and whether they may be crushed and destroyed in this world as many other whole tribes have been before by earthquake, flood, or fire, or the sword, or ...), god sees all and will send them to the fire when they die. If not before.

The Santa Claus nature of all this is unmistakable. Charming in its simplicity, but intellectually not at a very high level. God sees all, and will balance all accounts in the final judgement. All the good actions of this life will be rewarded. Except that unbelief seems to cancel them all out. Unbelievers in the Quran can never be good. They are perverse, lying, deceitful, blind, arrogant, mocking ... the list is endless. So the doctrine never has to grapple with the problem of positive moral behavior among non-Muslims. This applies apparently both to the time of death, and to a final judgement, which is mentioned, along with bodily resurrection of the believers, as an evident bow to the Christian system, but is not very well fleshed out, if you will excuse the pun. I could never tell whether I, for example, would go to hell immediately upon death, or whether that would await a general judgement day. The whole thing is, theologically, a jumbled mishmash of past beliefs, and looks much more like a psycho-mechanical contrivance for belief propagation than it is a search for, or convincing explanation of, truth.

O ye who believe!
Ask not questions
About things which,
If made plain to you,
May cause you trouble.
But if ye ask about things
When the Quran is being Revealed,
They will be made plain to you,
 For God is Oft-forgiving,
 Most forbearing.

 Some people before you
 Did ask such questions,
 And on that account
 Lost their faith.
  (5:104-105)

This god is also the most passive-aggressive character in all literature. The signs of his existence are no more than the mundane / glorious / mysterious conditions of nature, which admittedly in Muhammed's day, merited virtually unlimited awe. But if you don't believe in him, (and, notably, obey his humble Apostle), he will get you when you are least aware, and haul you off to everlasting hell fire. On the one hand, the whole Apostle thing comes off as a ego trip without parallel, while on the other, if god were so merciful and powerful, why would Satan (Iblis) be given leave to mislead so many hearts for so much time- why would anyone listen to him and not to god? It makes little sense, other than as a mapping of psychological archetypes onto an imaginary cosmic drama.

This brings up a significant moral point, which is that one would think that with such a fate in store, unbelievers would merit more compassion than they seem to get in the Quran. Why indulge in so much hatred if their fate is so sure and terrible- if they are building in this world their furnace in the next, by all their immoral deeds, unbelief, and mockery? Again, one gets the distinct sense that the theology is not really all that secure, and that the hatred is a very this-world phenomenon oriented to the oldest trick in the book, convincing people to believe in invisible beings, unbelievable doctrines, and the goodness and success of one's own group, led & ruled by God's representative on earth. All for the most admirable reasons, of course, but in a contemporary world that is so dense with other beliefs, yet at the same time contains a billion and half Muslims typically in communities with no contact with unbelievers at all, such attitudes are unhealthy, to say the least. Muhammed himself practiced precisely what he preached and lived a blood-soaked life, killing his enemies right and left, in Medina (expelling all the Jews along the way), Mecca, and in the larger conquests through the Arabian peninsula up to the end of his life.

Which brings us to jihad. This struggle against unbelief is fundamental to the message of the Quran (indeed, one wonders about some influence from Zoroastrianism, with its relentless black-white outlook) and one question is whether it is formulated in military terms in the text itself, or only in the ancillary Hadith. There are many sections about war, usually focused historically on the early battles of Muhammed which are plainly life or death struggles for the faith. War is definitely the answer, and the pagans are reviled and attacked in the most absolute terms. God expresses himself through the success of his believers in arms.

But the Quran also claims to be a very general text, being the last and final revelation, so its lessons are not simply confined to their historical moment, but apply to all the faithful still today. This makes for a messy theology. The practice of going out hunting for unbelievers to forcibly convert is not explicitly promoted, as far as I could read, despite all the hatred directed at them. Indeed, Muslims are instructed to live in community with each other and to leave areas where they are a minority (i.e. Mecca during the exile in Medina). At the same time, the struggle against unbelief is to be unremitting, so the more explicit directive to military jihad that one finds in the Hadith is very consonant with the Quran in this respect. And of course the historical record of Muhammed's career and the ensuing centuries, when Muslim armies swept the known world, makes the point more eloquently still. Overall, it supports the idea that jihad is properly understood in the original sense, to be a military conquest of unbelievers until the whole world takes up the one true faith.

Be not weary and
Faint-hearted, crying for peace,
When ye should be
Uppermost: for God is
With you, and will never
Put you at a loss
For your (good) deeds.
 (47:35)

The Quran, for instance, promotes terrorization of unbelievers, as though the theology of hell were not already disquieting enough. It also allows polygamy, which, in my opinion, leads inexorably, if indirectly, to war by the excess males of a society. Females captured on battle were, and, if one is to believe reports about ISIS, remain, fair game to jihadists. In Muhammed's day, one can put a somewhat more generous construction on this policy, as a way to provide for widows in a violent, militaristic age. But then his marriage to Aisha (one of his thirteen wives) suggests something quite different ... a Koreshean zeal for a more youthful additional wife.

If ye fear that ye shall not
Be able to deal justly
With the orphans,
Marry women of your choice,
Two, or three, or four;
But if you fear that ye shall not
Be able to deal justly (with them),
Then only one, or (a captive)
That your right hands possess.
That will be more suitable,
To prevent you
From doing injustice.
 (4:3)

Incidentally, married life was not without its problems. In one chapter, he complains about wifely insubordination and threatens to divorce them all:

It may be if he [Muhammed]
Divorced you (all),
That God will give him
In exchange Consorts
Better than you,-
Who submit (their wills),
Who believe, who are devout,
Who turn to God in repentence,
Who worship in (humility),
Who travel (for Fiath) and fast,-
Previously married or virgins.
 (66:5)

But back to the main theme of what to do about unbelievers:

Therefore, when ye meet
The Unbelievers (in fight),
Smite at their necks;
At length, when ye have subdued them,
Bind a bond
Firmly (on them); thereafter
(Is the time for) either
Generosity or ransom:
Until the war lays down
Its burdens. Thus (are ye
Commanded): but if it
had been God's Will,
He could certainly have exacted
Retribution from them (Himself);
But (He lets you fight)
In order to test you,
Some with others.
But those who are slain
In the way of God,-
He will never let
Their deeds be lost.
 (47:4)

There are various mercies and controls put on war against unbelievers, such as the acceptance of conversion on its face, and the directive to not be vindictive in victory, and to attack only in defense, not in offense. But the plastic nature of victimization narratives is such that, as we observe all over world, groups can always construct some way in which they are under attack and thus justify attack. Christians in the US moan constantly how victimized they are by those arrogant atheists, etc. Indeed the insufferable arrogance of the unbelievers is a constant (and rather ironic) theme in the Quran.

Your God is One God:
As to those who believe not
In the Hereafter, their hearts
Refuse to know, and they are arrogant. 

Undoubtedly God doth know
What they conceal,
And what they reveal;
Verily He loveth not the arrogant. 

When it is said to them,
"What is it that your Lord
Has revealed?" they say,
"Tales of the ancients!" 

Let them bear, on the Day
Of Judgement, their own burdens
In full, and also (something)
Of the burdens of those
Without Knowledge, whom they
Misled. Alas, how grievous
The burdens they will bear!
 (41:22-25)

The Quran is an interesting blend of Jewish and Christian theology (Mostly Jewish, however, which accords with Muhammed's principal influences). Muhammed comes off as something of a Paul-like character, reshaping the somewhat foreign theology of Judaism for a new audience, language, and age with forceful, confident, and ceaseless proselytizing. The schizophrenic, two-faced nature of god is extreme, as he is called terrible, awful, and judgemental in the same breath as he is the most merciful. Clearly the audience for this message was intensely tribal, and the transposition of the old family & tent tribalism into a new religious tribalism of believer vs unbeliever was as historically momentous as it was psychologically astute and intellectually vacuous. In our own day, it continues to be the nail upon which multitudes of Muslims, disaffected as they routinely are by their own defective systems of civil society and government, hang their hopes and hatreds.

But there was one enormous oversight in all of Muhammed's hundreds of pages of detailed directives and repetitive trash talk, which was the matter of succession. Muhammed never revealed the identity of, or method of choosing, the next leader, let alone all the successive leaders of the community. This despite the huge significance he placed on the community, its coherence, and its leadership. This failure has haunted Islam from the day of his death, when the wrangles and ultimately civil wars over Ali, Abu Bakr, and Shiism began. The founders of the United States, in contrast, stand head and shoulders over Muhammed in that they authored a durable mechanism of peaceful succession and of government in general. A beneficent god could surely have managed as much for Muslims.

"The Kharijites argued a true believer would have trusted his fate not to diplomacy but to ongoing warfare and God will decide." .. from a Western commentary.

Unfortunately, Islam has vacillated between legitimacy by blood and legitimacy by battle, per the most ancient template. It is incidentally odd that the theocratic model we find in Iran has been so rarely employed, in light of Muhammed's example. In any case, this continues to be a glaring weakness of the Muslim world and especially of ISIS, Al Qaeda, Taliban, and other fringe groups that send up fatwas and set up caliphates that get nothing but scorn from mainstream Muslims (unless they succeed ... nothing succeeds like success!). The charisma of the moment, yoked to fanaticism, fundamentalism, and terror, may be able to scatter a dysfunctional and totally corrupt government as found in Iraq or Syria, but its staying power against well-functioning, legitimate, (not to mention open, truth-seeking, and democratic) societies is going to be extremely modest.

They will recline on Carpets,
Whose rich inner linings
Will be of rich brocade: the Fruit
Of the Gardens will be
Near (and easy of reach). 

Then which of the favors
Of your lord will ye deny? 

In them will be (Maidens),
Chaste, restraining their glances,
Whom no man or Jinn
Before them has touched; 

Then which of the favors
Of your Lord will ye deny?
 (55:54-57)

In the end, we have to ask how much Islam per se is responsible for the features of the Muslim world that keeps it in the news on such a regular basis. Many argue that religion has no significant effect, for it can and is interpreted quite flexibly depending on the material circumstances of the society. We would have to look to our own actions from the Crusades, colonialism, and recent US foreign policy to locate the reasons why some Muslims are so bitter about modernity and ready to take up arms anywhere they can fight infidels or set up fly-by-night caliphates.

Obviously, there is some truth to that view. The spectrum of Islamic interpretation is vast, from the Sufis to the Salafists. The Quran supports numerous views, and offers some compassion in amongst the rest. But I think that ideology is also critically important. We do not absolve the Nazis by accusing the Versailles treaty of driving Germans to  world war and genocide. Ideology drives world affairs, as the narrative force that shapes our responses to material conditions. No ideology, no Inquisition, no cold war, no racism in the US, no Crusades, no "holy land", no patriarchy, etc. ad infinitum. As the Quran exemplifies, people will find ideologies to suit them, (or have them forced down their throats), but if those ideologies claim to be rational, yet are not rational, the seeds of their own critique, if not destruction, can be sown. At least one can hope.

Fighting is prescribed
For you, and ye dislike it.
But it is possible
That ye dislike a thing
Which is good for you,
and that ye love a thing
Which is bad for you.
But God knoweth
And ye know not.
 (2:216)

For instance, one of the momentous issues in Islamic ideology is its stance towards the modern world. Which is not easily compatible with traditional Islam. Globalism breaks down cultural borders, infecting everyone with consumerism, liberal political philosophies, women's liberation, and religious skepticism. The commerce and especially the oil-addiction of modernity has made some Muslim nations unimaginably wealthy, while more generally, the advent of colonialism, interacting with the technological and intellectual power of the West, has put Islamic culture in a poor, embattled, even subservient, position. The Egyptian philosopher Qutb came to a shocked and fundamentalist conclusion- that modernity is the mortal enemy of Islam. Quran and Sharia must be the sole answer to all of mankind's problems.

"The concept of the imperceptible is a decisive factor in distinguishing man from animal. Materialist thinking, ancient as well as modern, has tended to drag man back to an irrational existence, with no room for the spiritual, where everything is determined by sensory means alone. What is peddled as 'progressive thought' is no more than dismal regression."

Let not the Unbelievers
Think that they can
Get the better (of the godly):
They will never frustrate (them). 

Against them make ready
Your strength to the utmost
Of your power, including
Steeds of war, to strike terror
Into (the hearts of) the enemies,
Of God and your enemies,
And others besides, whom
Ye may not know, but whom
God doth know. Whatever
Ye shall spend on the Cause
Of God, shall be repaid
Unto you, and ye shall not
Be treated  unjustly.
 (8:59-60)

The Saudi rulers in particular have blended this ideology with their wealth and Wahhabist religious structure into a globe-straddling ideological machinery of fundamentalist madrassas that groom the cannon fodder of jihad. Yet Attaturk, a generation before, came to the opposite conclusion, frog-marching Turkey into a quasi-secular, modernizing state. What is it to be? A great deal depends on the fairness and decency the rest of the world can bring to the table. But more depends on the readings that Muslims give themselves of their central text, history and traditions. The war for the ideological / theological soul of the Muslim world is highly consequential. And the core text is not, on the face of it, particularly helpful towards a tolerant, cosmopolitan, and peaceful reading.

It may be that God
Will grant love (and friendship)
Between you and those whom
Ye (now) hold as enemies.
For God has power
(Over all things); And God is
Oft-Forgiving, Most Merciful. 

God forbids you not,
With regard to those who Fight you not for (your) Faith
Nor drive you out
Of your homes,
From dealing kindly and justly
With them: For God loveth
Those who are just.
 (60:7-8)

• An Islamic theologian on the value of theology and the fundamentalist turn. "Islamic theology is based on an ethical rather than speculative imperative. Many Qur’anic verses and hadiths show that iman or “true faith” is obligatory and rewarded by paradise, and that kufr or “unbelief” is wrong and punished by hell." This shows, unsurprisingly, that a search for truth is not really part of the program.
• An advanced discussion of ISIS and the Muslim world, on POI.
• Shiite cleric sentenced to crucifixion in Saudi Arabia.
• Christianity ... can be taken several ways as well.
• Maher on Islam. And more, more, more, more, more.
• What do regular Muslims think?
• Is the Quran an example of "derp"?
• And now some very peaceful news, from Indonesia.
• The unending irony that is Pakistan: "An anonymous senior Pakistani security official stated: 'It is a worrying development that the TTP is regrouping close to the border right under the nose of the Afghan security forces.'"
• Wesley Clark on policy: "We just can’t believe that we were responsible for creating it. We weren’t. The money that went into ISIS came from Saudi Arabia and Qatar, and it came particularly from the work of the Saudi leadership trying to find an opposition to Bashar Assad in Syria."
• Fear is a political act, and a media goldmine.
• Gosh- what happened to the middle class?
• GOP heads to new lows. Suppression or outreach, that is the question.
• What is the nature of our current form of capitalism? And of our political economy?
• And what's the problem with Europe? "The Eurozone’s current problem arises because one country - Germany - allowed nominal wage growth well below the Eurozone average, which undercut everyone else.... Within a currency union, this is a beggar my neighbour policy."
• Krugman on Japan- now is no time for false fiscal responsibility.
• Notes and data on inequality.
• The Fed can set long as well as short rates.
• Economic graph of the week. Our economic prospects continue to decline.

Regulatory Dynamism in Evolution

While the proteins stay mostly the same, the management evolves much faster.

When looking at evolution in the genetic code, we tend to focus on the most conserved elements which can take us the farthest back in time. Essential proteins like metabolic enzymes that we recognizably share with bacteria, or the translational apparatus of ribosomal RNA and related proteins, shared in all life forms. But to look at more rapid and recent evolutionary processes, one has to look at other parts of the genome which churn a lot faster and can be, incidentally, far more difficult to discern.

General illustration of regulation of gene transcription; DNA is the black/green line, the yellow lozenges are histones, and protein regulator binding sites are red. Various regulators bind near and far upstream of the gene, (whose start site of transcription is shown by the arrow, bottom right), all conspiring to promote or retard formation, placement, and activation of the initiation complex of proteins (blue) that includes the RNA polymerase.

The DNA sites that direct transcription tend to be such fast-changing genetic elements. They are short, often redundant, degenerate (able to accommodate various errors) and modular, meaning that they can occur in various positions and orientations with respect to their target gene and still work. Their shortness means that they can be born by mutational accident, and also that they are hard to recognize by text-comparison methods.

Human-mouse comparison of three protein regulators, (GATA, MAX, cMyc), and a brief stretch of DNA they bind to (red and blue). The blue MAX site in the middle was born in the primate lineage, while the others are recognizably conserved. From the top, the general coordinates of the genomic region, over this gene, EPB41, which encodes a protein that provides special flexibility to erythrocyte blood cells. Then various annotated features (colored bars) looking for regulator binding sites, then graphs of the physical binding data for each regulator (colored graphs).

They are also enormously important for evolution and biology in general. There are many hundreds of gene regulating proteins encoded by the genome, each of which bind to some DNA site, typically 6 to 16 base pairs long. These protein+site complexes constitute the first line of gene regulation, and, though virtually every possible aspect of biology can be bent to regulatory uses, typically the most sensitive and influential mechanism of gene regulation.

"... there are an estimated ~1700–1900 TFs [transcription factors, or regulators] in the human genome."

A recent paper discussed a new-ish method to study the phylogeny of such sites. The first step is to use a modern technology to find such sites, physically purifying such individual regulatory proteins while they are still bound to DNA in a cell, and later sequencing the underlying DNA snippets. This allows, for a single regulatory protein, all its target sites in a genome to be mapped (at least the sites being used under the condition used to grow the cells for the experiment, in this case erythroblast cell lines). The researchers did this (or actually got data from others) for several different transcriptional regulators in human and mouse cells.

 Then they used sequence comparison methods to deduce the history of these sites in the lengthy time of divergence between the two lineages, over the sequenced genomes of baboon, chimpanzee, rat, squirrel, tarsier, and other species. They used not only sequence conservation of the sites, but larger-scale studies of how the genomes relate to each other, called synteny analysis. This depends on large regions of diverged genomes being, at least on a patchwork basis, descended from each other, even if some of the sequences they contain are not so recognizable. Over time, various accidents in recombination and replication cause genomes to slowly re-arrange relative to their ancestors.

Synteny comparisons of human and chimpanzee (top) and human and mouse (bottom). The colors from one genome's chromosomes are projected / sprinkled as they correspond to the other genome. The Y chromosome tends to have a lot of junk or unrecognizable sequence.

The finding of this paper that is of general interest is: "Notably, between ~58–79% of all human TFBSs [transcription factor binding sites] had inferred origins after the human-mouse split." This is far more rapid change than one would see in encoded proteins, of which about 80% are recognizably shared between mice and humans. It follows that the regulation system, which controls where, when, and how much genes are expressed, is far more variable through evolution, than are the products of those genes. This makes sense when we see the slight variations over human populations and among closely related species that tend to concern relative sizes of bodies and parts, slightly more or less some some feature, coloration, etc. It fits very well with the typically gradualist nature of evolution, operating on thousands of genes and hundreds of thousands, if not millions, of their regulatory sites all in parallel over populations and time.

"For all six factors analyzed, the majority of human TFBSs [transcription factor bound sites] bound in vivo were originally absent in human-mouse common ancestor, which is consistent with previous cross-species comparisons noting substantial divergence in ChIP-seq protein-binding events across the two species and similar comparisons presented here, and is also comparable to detailed analyses conducted in Drosophila using alternative approaches" 

"Genes located nearest to hominid-specific binding sites were more frequently enriched for neural and sensory-related functions, and were in many cases involved in neurological pathways (Table S2). CTCF, MYC, and SOX2 target gene sets were all enriched for GO categories involved in sensory perception, while GATA1, MYC, ETS1, and MAX were enriched for neural development and differentiation categories."

• Terrorists win ... in the US.
• And in Afghanistan.
• Annals of feudalism: the no-compete "agreement".
• A jobs shortage, not a skills shortage.
• The next financial crisis may come sooner than we think, at least to poor people.
• In praise of helicopter money.
• The shame of "rocket scientists" who work in finance / fraud.
• This week in WSJ: "... the Obama economy ..." The definition of chutzpa and hypocrisy is to cause an economic catastrophe, then do everything in one's ability to stifle effective action against it, then blame the other party for the result.

Thought Experiments in an Equal Pay World

Imagine ... what if everyone could get a job, and every job paid exactly the same? 

The labor market is highly problematic. It doesn't value people or work fairly, rewards destructive behavior (pollution, lawyering, lobbying, finance), and fails to reward socially constructive work (teaching, nursing, mothering, cleaning, farming). It tends to reinforce social hierarchies that have roots in patriarchy and class, perpetuating patterns that have questionable social value. Salary decisions are typically quite distant from business considerations, as CEOs have amply demonstrated, (both on their own behalf and over their minimum wage minions), depending more on the social and power relations of the parties involved.

There are also the persistent issues of gender and race inequality in hiring and pay- conditions that were supposed to have been solved by now, but which rear their heads again and again because of biases in the social system, if not in humanity itself. There is also the appallingly low pay provided by some of our biggest companies and industries (Walmart and farm labor come to mind) that rely on taxpayers to keep their shoddily paid employees fed, clothed, and housed. One way to solve all these problems would be to stipulate that all jobs pay the same wage. That average pay is currently about $44,322 per year, full time, in the US.

And if one is interested in addressing economic and social inequality in a comprehensive way, all the (progressive) solutions on the taxation side are trying to capture a horse after it has left the barn. The power that employers have now to pay rock-bottom wages to workers while paying themselves like kings means that they will likely have the means to make up for any tax increases. One solution is to insure that the labor market favors workers consistently, making jobs available to all, and using plenty of fiscal spending in times of slack private investment. But that simply works within the system, a system that is run, via our political and financial elites, by the incumbent powers of class and wealth, from which labor friendly policy is as likely to come as pennies from heaven.

Let's start with some easy issues first. How would currently high-paying professions be staffed if they were not paid differentially? Such work as financial engineering, dentistry, or medicine. Or CEO, lobbyist, sports star, political consultant, movie actor? The current system is, frankly, obscene in this regard. Would NBA teams not be able to field players if they did not paid them like kings? Probably, and one might get players who actually want to play, and they would be selected just as stringently, because the ancillary benefits of fame, status, and pleasure would remain, and the limited number of teams (and audiences) would remain likewise. More obscure fields like oil drilling, sales and marketing, dental hygienist, etc. might be more difficult to fill. But are they really paid that well? Typically not. It would probably just take some modest interest and training to attract people who otherwise might end up as farm workers or janitors, with less pleasant work conditions.

Similarly, the challenge and personal rewards of professions like medicine would remain and attract perhaps an even better class of trainees than they do now. Professions such as finance whose mind-numbing and pointless nature is now relieved only by their high pay might indeed contract, and frankly that would be a very good thing. So we would enter a world where students study what they are interested in, and enter professions that suit them, which select them on every basis of training and qualification as now, but without the lure of unusual monetary reward or penalty.

How about the low-wage work on which so much of the economy depends? Firstly, easily half of this work is completely useless. Unlivable wages allow many employers to hire far more people than needed, (fast food, retail; imagine being a walmart greeter), flood markets with low-margin franchises, and avoid efficiencies and mechanization. Labor shortages commonly spur efficiency gains. Secondly, a great deal of effort otherwise spent fighting against and dealing with unions might be saved by an equal pay regime. But in the end, paying people decently should come ahead of the consumer's ability to command the cheapest goods and services.

Entrepreneurialism is a somewhat more ticklish problem. How should we encourage business formation, innovation, family businesses, investment, and all the other energies of the free enterprise system if greed is no longer the central motivator? I think a general answer to that is to separate corporate and personal income on a stringent basis. If one wants to start a company that does great things, fine. One can grow it to globe-straddling size, but one can not pay oneself more than any other employee. That goes for bonuses, shares, etc.. all the remuneration that is now fair game would be strictly controlled, via the tax reporting system, and perhaps other enforcement, to one simple salary.

This relates to the problem of how investment would take place. Personal savings from such a system would probably be modest, and insufficient for the capital needs of the economy. People would generally be more dependent on (and willing to pay for) government programs to manage life-cycle savings, catastrophic contingencies, education, etc. I think one way to deal with the investment issue would be to allow special corporations (one might even call them "banks"!) and corporate entities like non-profits and educational institutions to have investment holding roles. Thus there would be a large ecosystem of investors and investments that do not significantly touch /affect personal income, but run large-scale investments in private enterprises due to the good judgement and personal values of the people involved. If the managers were unsuccessful, they might be demoted from their C-suites to street sweeping, but their personal income & sustenance would not be affected. One's social standing (and values) would be a much stronger aspect of motivation than greed, as would the personal satisfactions of the work one does. This would perhaps hearken back to the conditions in Antiquity, (occasionally, at least), when leading people and families competed to contribute to the state, not to leach from it, due to an intense sense of honor and reputation.

How about parenting? A fair system would pay for child care, whether done by parents or outside caregivers. So perhaps a parent could be paid through the first five years of a child's life if the parent decided to stay home, ideally at a full salary. This would make the decision to work or stay home shaped by personal preferences, such as career goals, rather than about finances. The same would go for care-giving to elderly parents and relatives, subject to some kind of certification that it is a full time occupation.

Perhaps the most difficult aspect of such a system is the impetus towards a black market, to under-the-table payments, gold-plated executive suites that pay in helicopter rides, escort services, etc. In our political system, with all the principles and deterrents against corruption, corruption remains rampant, indeed functionally legalized. Similar pressures would be inevitable in a tightly controlled equal pay system. Communist systems routinely elevated powerful people into great effective wealth, whatever their nominal salary. The best I could propose is again a strict separation between corporate and personal books, with transparency and strict regulation of what goes where. The current system of business tax deductibility, for example, requires extensive itemization and reporting, all to create an appalling drain on the public coffers, for the benefit of those need no such benefit. In the end, we organize society to limit some freedoms, (killing, fraud, theft), so that other and better freedoms may flourish. And perhaps the freedom to pauperize / feudalize your fellow citizens might not be as valuable as the freedom to have a decent and equitable life.

And how would this universal pay be set? It would be a broad economic policy exercise that fits closely with MMT (macro)economics. The tuning could be quite simple- if inflation threatened, pay would not be raised, while recession or deflation would be easily solved by raising the standard salary. Ultimately, its level and its value would be set by overall GDP and productivity, but the government, as the creator (and destroyer) of the currency, could easily make more or less of it and spend it in the form of salaries or other projects to fine-tune through any economic variation. Variations that, naturally, would be rare if not unheard of in this proposed society.

It is a thought experiment to imagine a system less besotted by greed, class, and injustice, more valuing of human e-qualities. One has to doubt its feasibility, but I believe it is a relevant ideal, or perhaps counter-ideal, for our time.

• Worship of money and those with it, cont.
• The middle class is kaput.. how did this happen in a democracy?
• Gates on Piketty. 
• "One side insists that the only important question is whether the truth-claims of religion are actually true; the other side says that question doesn’t even matter, and then wonders what “truth” is, anyway. It’s the overly literal-minded versus the hopelessly vague."
• More on austerity.
• Could we bring extinct animals back? But without habitat or stable climate, what would be the point?
• Reality, as usual, has a liberal bias.
• Meltdown in Iraq- the final chapter of Bushistic incompetence.
• Bolivia- a happy case study of good governance and fiscal policy ... and throwing out the IMF.
• On the impunity of finance.
• Annals of feudalism ... Conoco bullies its employees.
• The US deficit is low ... too low, as deflationary concerns drive the markets, and especially the specter of Europe melting down.
• Sleep is really, really good for your brain.
• Death might not quite as bad as imagined, either.
• Insanity and religion ... not always either / or.
• ISIS propaganda image of the week. Move along ... nothing Freudian here.

Organizer Without a Brain: the Centrosome

The microtubule organizing center of eukaryotic cells, which guides mitosis and nucleates cilia.

One of the more immediate wonders of biology is the division of cells and the organized march of chromsomes that accompanies it, girdled by a beautiful web of microtubules. These microtubules all emanate from something called the microtubule organizing center (MTOC), or centrosome, which is itself strictly duplicated during cell division. It all looks so alive. Yet the process is one of molecules each doing their little thing in blind fashion to make a greater and very dynamic whole.

In this image of a large eukaryotic cell, DNA is stained blue, microtubules are stained green, and the centrosome is stained red / orange. At some point during the mitotic process, the kinetochores (possibly the pink/lavender spots) would line up strictly along the midline between the two centrosomes.

Centrosomes are special to eukaryotes- there is no trace of them in bacteria. They also have no DNA or other sign of being descended from some symbiotic or other bacterial forebear, unlike the mitochondrion or chloroplast, perhaps even the peroxisome. (Though some researchers find they contain a few special RNAs and argue for an endosymbiotic origin on that basis.) Yet they are quite complex organelles, based on the same tubulin that composes the microtubules of the cell generally, but with hundreds of other proteins added in. They organize not only the microtubule asters that drive mitosis, but also form the basal bodies of cilia- the flaggella of eukaryotic cells, again composed of microtubules. These cilia in turn have important, though only recently-discovered roles in mechanisensory and chemical signaling.

The centrosome and its component centrioles. The micrograph cross section shows parts of each centriole from one centrosome.

The centrosome is composed of two centrioles, one of which is the mother, and the other the daugher. At each cell cycle, they split apart and each grows another daughter centriole to reconstitute a full centrosome. Each centriole resembles a microtubule, which is a tube of nine paired tubulin tubules, but has an extra set of tubules, so nine triple tubules of tubulin. At the base of each centriole is something called a "cartwheel", which is made up mostly of a non-tubulin protein (Sas6) that forms a nine-fold symmetric ring that nucleates growth of the centriole, which in turn nucleates growth of the microtubule.

Detailed structure of microtubules (top) and the centriole (bottom). Note the two pairs of tubules in the microtubule, but triplets in the centriole, or basal body. The third tubule appears to template or make space for the dynein arms, which are the motors that allow cilia, for instance, to wave and move.

Models of the molecular structure of the "Cartwheel" protein complex, which  (d) templates and nucleates the centriole structure. Microtubules (purple) fit to the outside spokes of the cartwheel (blue). In the electron micrograph (e), three cartwheel stacks can be seen at the bottom, at the base of the centriole, and higher up, with lower electron density, the microtubule.

"Studies using human cells have revealed a mechanism that regulates cartwheel assembly through controlling the amount of SAS-6 in the cell. SAS-6 starts to accumulate at the end of the G1 phase and decreases in anaphase through proteasomal degradation mediated by APC/CCdh1 [19]. When the SAS-6 level is artificially increased by overexpression of non-degradable SAS-6, excess procentrioles are formed on the mother centriole."

Another electron micrograph of the centrosomes and their microtubule junctions.

The main component of all these structures is tubulin, the building block of all microtubules, which, along with actin, make up the cellular cytoskeleton of eukaryotes. Actin is smaller and free to form more flexible structures, (as well as being used to form the structural scaffold of muscle action), while microtubules make bigger structures (in cellular terms) like that which spans the whole cell for division, making cilia / flagella, and conducting cargoes along the enormous distances of nerve cell axons. Not all eukaryotes have centrosomes, (notably plants and yeast don't), but all have some form of microtubule nucleating center, (MTOC), of sometimes more modest construction. While microtubules are made of alpha and beta tubulin, the centrioles have a third form, gamma tubulin, which only exists at the nucleating base, not in the bulk structure.

Diagram of nucleation from a cartwheel (red) to a centriole (blue).

Unfortunately, less is known about how all this works dynamically than about its structural components. A recent paper covered two key proteins (Cnn and DSpd-2, in fruit flies) that seem to be all that are required to turn a bare centriole into a busy MTOC with hundreds of other proteins in a nimbus around it (the pericentriolar material). These key proteins are controlled by phosphorylation which is a common element of the cell cycle, and when turned on, come into the most interior precincts of the centrosome/centriole, and then migrate slowly outwards, with new molecules arriving at the center as long as the cell is in the requisite state.

"Mimicking phosphorylation allows the PReM domain [part of Cnn] to multimerize in vitro and Cnn to spontaneously assemble into cytosolic scaffolds in vivo that can organize MTs. Conversely, ablating phosphorylation does not interfere with Cnn recruitment to centrioles, but inhibits Cnn scaffold assembly. We speculate that, like Cnn, DSpd-2 can assemble into a scaffold and that this assembly is regulated in vivo so that it only occurs around mother centrioles."

At the other end, a good deal more is known about how microtubules attach to the kinetochores (structures at the center of chromosomes -at DNA centromeres- that anchor them to the mitotic spindle). This is not really in the scope of the post, but again, phosphorylation of key proteins is the theme, as is regulated assembly and disassembly of the microtubule itself. Disassembly right where it abuts the kinetochore causes shortening, thus tightening of the whole spindle, as long as the kinetochore has properly captured microtubules on/from both sides, i.e. both centrosomes, which is another complicated and phosphorylation-regulated process.

Example of a model for microtubule dynamics during one part of mitosis, with microtubules in purple,  (and unconnected microtubules in yellow, cell edge in gray), the centrosome in pink dots, and relevant motor proteins in green and salmon. The point is that, if relevant motors and attachment functions are regulated and happen at the right times, the system can accomplish complex tasks.

It is worthwhile to note that while the replication of the centrosome and its component centrioles is strictly regulated with the cell cycle, the same core system is used to create the basal bodies of cilia, and can create organizing centers from scratch. It does not require a pre-existing centrosome (unlike mitochondria, chloroplasts, and cells, which always come from pre-existing respective cells or cell-ish organelles). Sometimes, the basal body is the same as the centrosome; when cell division is done it migrates to the membrane. But many cells have multiple cilia, and each one has a newly created basal body at its base, whipped up without the complicated replication process. So it appears that replication is more a regulated restriction of MTOC creation than it is a necessary precondition of MTOC birth.

The science of the microtubule nucleation systems is still underway, but the direction is clear, as in any other area of molecular biology that has been laid bare to date. Molecules of some complexity, equipped with various means of regulation, such as regulated transcription and synthesis, outright destruction, interaction with various partners, or covalent modification like phosphorylation, neddylation, methylation, palmitoylation, GPI-anchoring, etc., can find their places and times of action in chemically explicable ways within a cell that is a vast, if microscopic, machine.

• A relevant review of centrosomes, and a second, and a third.
• Motors on the microtubules.
• Freedom & security flows from law, not from the barrel of a gun.
• But paranoia is patriotism and apple pie.
• Economics can say a few things about recent events.
• To save Lehman or not?
• Poor, poor, AIG.
• Quackonomic vocabulary.
• Inequality and the freezing of upward mobility, in Venice.
• Government by the corrupt, for the corrupt.
• Startups not all they are cracked up to be.
• The European economy is disastrous across the board.
• Krugman on the crisis.
• Requiem for the incandescent light bulb, though for its corrupt business practices, who knows?

Environmentalism is anti-American

Book Review of the biography of Rachel Carson, "On a farther shore".

Are we part of nature, or above it? Did god give it to us for our domination, or did we wriggle from its bosom to the condition of (bare) consciousness and power that threatens to undo the patient work of millions of years of evolution? Thousands of years ago, we had already killed off all our immediate ancestors in the hominid line and countless other species of megafauna. Now we have taken over most of the arable land of earth, comandeered much of the fresh water, polluted the rest of it, as well as the oceans, killed off many more species, doubled the concentration of CO2 in the atmosphere and the fixed nitrogen in the biosphere, and are facing ocean acidification and dramatic climate heating as an irreversible future fate.

But two generations ago humanity (and that would be the US) created the most immediately alarming and noxious dangers of all- nuclear weapons with their attendent radioactivity, and a fusilade of biocides and other poisons emerging from the postwar chemical industry- pesticides, herbicides, plastics, drugs, "food" additives, cleaners, etc. After a cavalier start to the era, when Las Vegas visitors turned out with their sunglasses to watch nuclear tests, the far-reaching dangers came increasingly to public consciousness, resulting in the above-ground nuclear test ban treaty of 1963, and the establishment of the EPA in 1970 and banning of DDT in 1972.

The reduction of nuclear radiation has been enormously successful, with negligible impact from current uses. The Chernobyl and Fukushima nuclear disasters have been the sole, and very large, blots on a very good record of radiation control (negligible amounts were released in the Three Mile Island disaster). Whether we want to use more nuclear power or not for the sake of climate change is a reasonable question.

Our record on control of biocides and other environmentally harmful chemicals, on the other hand, is far less impressive. Their use is less individually dramatic than that of nuclear technology, but their scale is mind-boggling. Every home and garden center hosts a biocide department that reeks to high heaven. DDT may have been banned, but an endless supply of other biocides have been concocted that are applied over the best land to kill all insects on it. The holocaust is ongoing.

"In 2006 and 2007, the world used approximately 5.2 billion pounds of pesticides"

Rachel Carson played a large role in our budding environmental awareness, both in her early work in books like "The Sea Around Us" that celebrated the beauty and interest of the natural environment, and in her last prophetic work on the dangers of the new pesticides, "Silent Spring". This biography is a worthy testament to her drive and talent which formed out of very unlikely materials (being a self-made professional woman in the 1950's) an earth-shaking message.

Indeed she could even be regarded as a significant religious leader, inspiring love for the world, and issuing prophetic warnings about its mistreatment at the hands of humanity, due in part to a lack of spiritual awareness, or misdirection. Humans have an innate religious sensibility about nature, and all the old religions treat it with reverence. The Celts had their sacred groves, worship of trees, and custom of bringing holly and mistletoe to their dwellings at the winter solstice. Unfortunately, the monotheisms, with their worship of a blown-up self-image, put nature into the shade as something to be dominated, something lost anyhow (Eden), even dirty and unclean. The unholy mix with post-war technologies allowed the dream to become a reality ... to "purify" the world of insects, vermin, disease, and all kinds of uncleanliness.

Obviously there is a great deal of good in cleanliness. But we learn that even our own health benefits from some amount of infection and dirt, lest our immune system idly turn its attention on our own tissues by mistake. Which is not to mention the wider ecological benefits of moderation and species diversity, and particularly in less wanton destruction of insects and other unheralded organisms that may not be the "stars" of our nature shows.

While we have banned the most noxious chemicals, (thalidomide, DDT, aldrin, lead arsinate, etc.), our systems and policies are simply not up to the task of protecting ourselves or the environment in a more comprehensive way. They are not precautionary, but rather wait for some dramatic harm to come to light before starting studies and investigations that take forever. The neonicotinoid insecticides are still being applied by the ton, despite their clear harm to bees (not to mention to all other insects).

Why? Principally, it is the agricultural and chemical interests, and their conservative allies, that fight chemical control policies every step of the way. There was once a time, when the EPA was founded, when conservatives were true to their name and cared about conservation, not only of their power, but of the environment as well. Those times are long gone, as the interests of the 1% diverge increasingly from those of the rest of society, indeed of humanity in general. Their loud patriotism tells us that government is bad, taxes always too high, scientists are all lying, and corporations always tell the truth. The worship of self has turned from a projected image of god to the even worse god of Mammon.

"It had only taken a few short centuries to move from a time when we gazed out at the ocean and wondered what was over the horizon. Now, she said, "our whole earth has become only another shore from which we look out across the dark ocean of space, uncertain what we shall find when we sail out among the stars." Based on the experience of her own generation- which had brought the world to such a dangerous crossroads- Carson said it was now time for the inheritors of earth and it many difficulties to finally prove human mastery not of nature, but of itself. "Your generation," she said, "must come to terms with the environment."

• Wildlife is in dramatic decline.
• Bees are in especially dramatic decline ... collapse.
• Fly less to fight climate change.
• On the psychology of evil, corruption, ideology, contradiction, hypocrisy, and other forms of humanity.
• In the new economy, nice guys finish last.
• Cute kids ... these days.
• The recent US military campaign has little immediate effect. ISIS keeps gaining ground, and "One estimate puts the number of overall desertions for the Iraqi Army at over 90,000."
• How and why the Fed shores up the global dollar system.
• But banks run the Fed, so of course ... the Fed serves Goldman.
• Goldman, Lehman, Enron.
• AIG as a money-laundering bailout. "Alternatively, maybe Mr. Geithner simply felt that Goldman and the like had a more legitimate claim to billions of dollars in funds than the taxpayers who were footing the bill."
• Bonanza gets one in against the bankers (Episode 284, The Trackers)
• Pray our way, or the highway.
• To screw workers, employers talk out of both sides of their mouths.
• This week in the WSJ, annals of irony: "But does anybody in the government feel it is necessary to be truthful about anything anymore?"   
• Economic graph of the week.. just how dramatically our economy has changed over the last 60 years. We've already had a class war, and we lost.

Prosecutors Gone Wild

Truth is the first casualty of bureaucracy. Review of "Licensed to Lie".

Sidney Powell is a defense lawyer and erstwhile prosecutor who got tangled up in defending one of the Enron cases, launching an unwelcome odyssey into prosecutorial malfeasance. Her book is an excoriation of the prosecutors, Justice department, courts, and justice system as a whole as it took shape under the Bush Administration and continues under Obama. She summarizes everything in a final chapter that helpfully names names in bold type.

The case was the "Barge" trial, which accused a set of Merrill Lynch functionaries of colluding with Andrew Fastow to conduct a sham transaction whereby Enron "sold" a set of electric generating plants (on barges in Nigeria) to Merrill Lynch so that Enron could book a sale, while actually guaranteeing that Enron would buy the Barges back in a matter of months. The point was to help Enron temporarily cook its books and goose income. In the whole spectrum of Eron cases, and certainly in terms of harms alleged, this one was quite minor.

The defense disputed the entire case, and maintained that the transactions were actual sales, and that no one in Merrill Lynch did anything wrong. Powell's particular client, whom she picked up at the appellate level, was James Brown. His testomony was consistent on this and related points, both in grand jury testimony and at trial ... that his understanding was that the transaction was legal, if inadvisable.

Unfortunately, the defense was not allowed to use all of Brown's testimony, or much testimony from elsewhere, because the prosecution played keep-away with the evidence in the case, intimidated relevant witnesses, and pursuaded the court to adopt bizarre legal theories, jury selection processes, and jury instructions. Prosecutions generally have a duty to give the defense any exculpatory or even relevant information, called the "Brady" materials. Since the government typically runs the investigation, the prosecution is the party with all the evidence. Defendants do not have the resources or the powers to do as much investigating. This natural assymetry is supposedly resolved by the "Brady" rule. But of course, prosecutions are sorely tempted, and have every motivation, to hide such material if they find it inconvenient to their case. As they would.

It is a fundamental issue of whether the legal system exists to find truth, or whether it exists to win prosecutions. In the Enron cases, the government was under extreme political pressure to win, and to put some scapegoats in jail. The public, and especially the public in Houston where all the trials were held, was in no mood to split legal hairs about procedure. They wanted blood. Powell's tale is remarkably engaging, even gripping, for a narrative about US appellate processes that in this case dragged on for almost a decade. Her client served one year in jail, railroaded in by prosecutorial shennanigans that are, frankly, breathtaking.

First, the legal theory of the prosecution was, in part, that Brown and colleagues, by supposedly arranging a sham transaction, had deprived Enron shareholders of "honest services". This was a novel, even non-sensical, doctrine, and was reversed on appeal. Secondly, the prosecution alleged that, by its theory of the case, Brown had lied to the investigators and juries, thus perjuring himself. Thirdly, they alleged that all the evidence attesting to the legal nature of the transacation was ass-covering, belied by separate verbal promises they alleged had been made by Fastow and others to Merrill.

The problem with all this was that their own evidence pointed in the opposite direction. Fastow's own interviews mentioned explicitly that he had offered only a best-efforts promise to re-market the barges to other companies (which was indeed done and did occur, and was legal). But those interviews were suppressed by the prosecution, which relied on non-direct evidence from secondary players whom it pressured to testify according to their theory by threats of indictment. Fastow had already agreed to turn state's evidence in return for a reduced sentence (10 years, reduced eventually to six years, which was shockingly minimal in light of his masterminding the entire Enron debacle. He also probably retains some of his ill-gotten gains.)

Indeed, eventually Powell and colleages obtained detailed transcripts and notes from the Brown prosecution where the prosecution (or prior investigators) had highlighted in yellow the precise exculpatory testimony that would have easily acquited Mr. Brown and belied the entire theory of the prosecution. It was thus made quite plain that the prosecution had committed (and continued to cover up) gross misuse of their powers, which had the effect of destroying several innocent people's careers. Even after this information came to light, the judge in the original case continued to unwaveringly support the prosecution, blatantly ignoring defense arguments of gross malpractice, and despite having been overturned on several crucial issues on appeal.

This would have remained a typical defense attorney cry into the void except that another case came along during the same period featuring several of the same higher level officials in the Department of Justice- the case of Senator Ted Stevens. Similar tactics were used to develop a false theory of the case, hide exculpatory testimony, and railroad his jury to conviction (I hasten to add that I have no political sympathy with Stevens or indeed author Powell, who seems a red-as-they-come Texas Republican).

The (appellate) judge in that case did what the Brown judge did not do, which was, (in addition to reversing the case), to blow the whistle on the prosecution and call for a special prosecutor to investigate the Department of Justice's prosecution. The resulting report laid bare blatant abuse of the Brady rule and other forms of malfeasance- the same pattern that Powell was experiencing in her case. Unfortunately, this report neither took the highest levels of the Justice Department into its scope, nor had an discernable effect on any Department employee. Except for one: Nicholas Marsh, a low-level prosecutor on the Stevens case committed suicide as the investigation was underway. All the others either landed in cushy private firm jobs, or were promoted to higher levels in the government. One became a White House Counsel to Obama.

There are good political reasons to incentivize certain prosecutions. The late financial meltdown was clearly undermotivated in the prosecution department- no one went to jail for clearly illegal as well as phenomenally damaging acts and practices. Whole industries riven with illegal practices have been held harmless for their actions. There may also be a lack of legal tools to perform such prosecution and render justice. For instance, none of the fines that the Department of Justice has extracted from the various banks (investigations and findings that have remained secret, thus useless in the cause of justice) came from individuals. They come from the future earnings and innocent shareholders, not from the managers who actually performed the illegal actions and destroyed their companies and / or the economy at large, and who even in all likelihood remain in their jobs. Perhaps the legal structure to hold the responsible officers to account, not to mention claw back their ill gotten gains, does not exist (yet, though the Sarbanes-Oxley laws were supposed to have resolved some of that, yet were not deployed for the financial crisis non-prosecutions)

Whatever the case, the answer is not to run an illegal prosecution against minor actors who committed no crime, in a kangaroo court. Our country is better than that. What is equally disturbing is that this continued from one administration to the next, clearly signalling a fundamental lack of accountability in the department's bureaucracy and an unwillingness by the new administration to put its mandate into action. In so many instances, the Obama administration has kept the actors, and practices, of the old intact, prosecuting whistleblowers rather than listening to them, deporting and mistreating immigrants in droves, and keeping the military-industrial-espionage complex humming. The change has been much less than promised.

Powell's money quote: "Blind judges do not render blind justice."

• A Holder retrospective.
• Hope in Afghanistan, or endless dysfunction? "A thousand beggars can live under one quilt, but two kings cannot share a kingdom."
• Not just military-industrial, but now military-industrial-espionage complex.
• Rent extraction by finance. Is what they do useful? Or is it sheer embezzlement?
• The government is losing all the revenue that goes instead into tax avoidance.
• Pat Robertson: our genocide better than your genocide.
• Right wing Christians ... reality is not a strong suit.
• Climate, schmimate- science will deal with it, right?
• Guns 'n apple pie- and don't let Gabby Giffords tell you different.
• Yes, you are dying ... and truth is the answer.
• Germany vs the Euro, cont.
• That magical number two.
• Pension funds got suckered into the hedge fund scam. And who pays? Not the retirees.
• Yes, the inflation fight is not really about inflation.
• Reality is outstripping perceptions of the new feudalism.
• One more reason the 70's were a dreadful decade- it was when economics went awry.
• The psychology of free will.
• Again, just what is an economy good for?
• "As Krugman goes on to note, the nation’s 400 richest households, who paid more than 50 percent of their income in taxes at midcentury, now fork over less than one-fifth of their income."

What is the Opposite of PTSD?

On the Arthurian and Homeric battle hymns.

I have been reading Mallory's tales of King Arthur, and wondering at the lovingly described jousting, ado-ing, dueling, damsel-saving, and battling. Why so much space devoted to minute variations of the most tedious material? Why is Sir Launcelot the main character of the romance, not King Arthur? Why such a flood of testosterone?

We have heard a great deal about PTSD, where ex-soldiers can't get scenes of trauma out of their heads. We also have just been through the anniversary of World War 1, with ongoing head-scratching about why the cosmopolitan and civilized countries of Europe let themselves descend into the depths of hell. A generation with PTSD resulted, especially in France, which supinely rolled over in the next war, unwilling to face up to the developing reality.

Mallory reminds us (as Homer did long before) that war is joyous. Men live most vividly in war, and always have. They (I am generalizing wildly on a postulated average) have evolutionary settings that care for others and engage in all the other positive morals of quotidian life, but in addition, are fixated on power, danger, honor, competition, and ultimately, war. Those who succeed through these trials come out glowing with pride, as did our greatest generation, at least many. They are feted by others, lionized, valorized and given all good things, especially social power. Not for nothing was John Kennedy's administration named "Camelot". The tellers of tales have no better material, in the culture that this process produces- the patriachy.

PTSD is the dark side of this psycho-socio-genetic legacy, especially now that chivalrous rules of engagement no longer apply, and the horrors of war come upon everyone, winner or loser. Few came out of the trenches of WW1 with glowing pride, and few again come out of our recent wars in Iraq or Afghanistan so crowned with honor and success. The US military occupies an uncomfortable tension between the mechanization, routinization, and sanitization of war, vs the need to keep its soldiers motivated and charged-up for battle.

This leads to the currently most notorious lovers of honor, chivalry and blood- the islamists of IS, Al Qaeda, et al. To read the autobiography of a Taliban leader, there was no better time, nothing more vivid, than the time he spent killing infidels (or just rival factions) and bonding with his band of brothers. So it is on all sides. The question is ... not who is violent, but who is fighting for positive ends for the human community at large. Who is upholding an ideology and system that serves the general good rather than creating chaos?

The chivalric system had its good points. The Arthurian tales are filled with good knights fighting bad knights who imprison, rape, and plunder. It was a nascent form of state legitimacy, under an aristocratic oligarchy. Now we have higher standards of legitimacy, cast in terms of universal democracy and human rights. But Islam is not in the same mind-space, still fixated on patriarchy if not theocracy. Its idea of chivarly and human rights are quite different (indeed far more traditional) from those current in the West.

But is this true of the population at large, or is it only true of the extreme, the disaffected, the anti-West, and the callous rulers who use any convenient ideology to direct resentment away from themselves? That is the question that the West, and the US in particular, has been grappling with as we try to spread "democracy" in a Middle East where democracy is such a strange flower; where legitimacy flows from scripture, tradition, and turban rather than from a legalistic, post-enlightenment philosophy.

It wouldn't be a pressing issue, except that we all happen to live on the same planet. While those in the West struggle to keep the joy of war confined to the football field or the videogame, and locked within a disciplined military, elsewhere it flourishes in age-old existential terms, freed, ironically, by the chivalrous and respectful reluctance of leading powers to use the virtually infinite military violence they have at their disposal.

• Being a warrior today.
• Fanatical religiosity ... but why in the US military? (Correction)
• Better living, through plastic.
• Allied with Al Qaeda, Iran, and Hezbolla, against IS ... can it get any stranger?
• More in the annals of violent self-pity: Russia.
• Yes, it was, and still is, all Bush's fault.
• To zero carbon with a carbon tax. And for free.
• Arrested for manner of walking ... the Ferguson case and police ass-covering.
• Plato and the GO-PAC of his time.
• Bad justice, continued ... bribery and corruption are OK.
• Krugman for the Nth time.. economists failed us miserably.
• And are still failing ... the irony of Germany vs Keynes.
• The ratings agency cesspool? Still there.
• Fraud in business ... a normal condition.
• This week in the WSJ, annals of climate denial: "While the past two decades have seen progress in climate science, the field is not yet mature enough to usefully answer the difficult and important questions being asked of it." ... "Even though human influences could have serious consequences for the climate, they are physically small in relation to the climate system as a whole. For example, human additions to carbon dioxide in the atmosphere by the middle of the 21st century are expected to directly shift the atmosphere's natural greenhouse effect by only 1% to 2%."

The Origin of Life

Some papers on the earliest steps from geology to biology.

One of the great questions, second only to the origin of the universe (multiverse) and perhaps the nature of thought in the brain, is how life got started on Earth. (Leaving aside, of course, the even more daunting question of peace in the Middle East.) Of the three, the mind is well on its way to definitive solution, and the origin of the universe is rather unlikely to ever be solved, or at least there is no prospect that I can see, despite enormous advances in cosmology. The origin of life occupies a middle ground, so far off in time that certainty may be impossible, but bounded enough by our knowledge of the ambient conditions and their rich aftermath that detailed and plausible theories can be, and have been, advanced.

The papers reviewed here are not new, (dating from from 1997 and 2003), but provide background for my post two weeks ago about the divergence of Archaea and Bacteria, and constitute what I think remains the leading hypothesis for the origin of life (elaborated in more recent papers 1, 2, 3). (Other recent origin of life refs 1, 2, 3, 4, 5.) This hypothesis situates the scene of action at thermal vents at the ocean floor, where highly reduced and alkaline geological fluids percolate up into an ocean that was, at that time, far less oxidizing than today, but still, due to the prevalence of CO2, several logs more oxidizing and acidic than the geochemical fluid.

As still seen today, this fluid deposits rich chimneys of iron sulfide wherever it emerges, in a porous matrix that could host untold chemical complexity. And there are / were a full spectrum of more moderate vents, with lower temperatures and less harsh chemistries. These locations attract theorists of the origin of life because they provide a great deal of potential energy, in a form that life still uses: the electro-chemical gradient in the form of acid / base (protons) and oxidation / reduction (electrons).

They also provide the key elements (sulfur, iron, nickel, tungsten) that are needed, and the kinds of enclosed, yet semipermeable, spaces that would be needed to accumulate the compounds needed as proto-cells. So the 1997 paper by Russell and Hall delves into the kind of proto-metabolism that the energy gradients and structures at these locations might have provided. The Earth was saturated with CO2 at the time, as free oxygen had not yet been photosynthesized into existence.

But let's take a step back and ask what is needed for life. The basics are a membrane or some other compartment to keep inside and outside apart, an energy source, a metabolic system to harness that energy to create the molecules on the inside, like complex carbon molecules of our form of life, and a genetic replication system that controls the metabolism and other characters, so that they can be selected via Darwinian evolution.

Not all of these things have to happen at the same time, and the goal for figuring out how geology generates life is to locate conditions where as many of the earliest requirements are present for free in the geological environment, and deduce what had to happen at which stage thereafter. A great deal has been made of the RNA world (references 1, 2, 3, 4, 5, 6, 7, 8, 9, 10) as a near-certainty in the progression from proto-life to the last common ancestor of all life. Our ribosome, for one thing, carries its clear signature. But this is a very late stage in the origin of life. The RNA world presupposes metabolism, a cell structure, and a replication system, even while it gives rise to a translation system that sets forth on the protein- and DNA-centric course we are on today.

So, energy is a must. Nothing can happen without it, but it can take many forms, from lighting discharges to sunlight, to chemical gradients from stable geological sources. As discussed in the previous post, chemical gradients remain the bread and butter of cellular energy, and are the most likely original form, leading to the hypothesis that undersea hydrothermal vents are an excellent candidate setting for consistent gradients of pH and redox, among other chemicals, approximating our current chemiosmotic metabolism.

Overview of Russell & Martin theory, with CO2 reduction occurring in mineral "bubbles" at the hydrothermal / oceanic interface.

Prior to biological, lipid-based membranes, such vents also supply porous rocks and somewhat sealed bubbles of rock that could serve as chambers or "cells" for pre-biotic chemistry. And lastly, they provide the actual enzymatic chemicals that remain at the core of our coupled redox metabolism- condensed iron and sulfur complexes that conduct electrons between proteins and across membranes while pumping protons in the opposite direction or reducing carbon compounds.

Example of a contemporary iron-sulfur  (Plus nickel) cluster that forms the heart of many enzymes that reduce (or oxidize) carbon compounds, in this case carbon dioxide to carbon monoxide, given water and a proton acceptor such as ferredoxin, another iron-sulfur protein.

What was the most elementary metabolism? Somehow, carbon compounds must have been reduced from the high level of CO2 and CO on early Earth to the sugars and polymers that form the basis of life, such as ATP, NAD, ribose, and the various metabolic intermediates of the Krebs cycle (which we use to break down food to CO2). The authors present a reverse Krebs cycle as the founding metabolism, where carbon compounds are built up (i.e. reduced) using electrons as well as catalytic surfaces furnished by Fe-S minerals mediating between external acid to internal alkaline conditions.

Basic energy scheme where a chemical gradient is used by iron-sulfur compounds to do enzymatic work, such as hydrogenating (reducing) CO2.

"It is the interfacing of the alkaline hot springs with the acid ocean that brings about the precipitation of an iron monosulphide (mackinawite) membrane. Electrons could have been transferred across such a membrane. Also the hydrogenating potential of the mackinawite could have been enhanced by the presence of nickel (Kouvo et al. 1963; Vaughan 1969; Morse & Arakaki 1993)." 

"Iron monosulphides such as mackinawite can contain up to 20% nickel (or cobalt and copper), probably tetrahedrally bonded between the sulphur-sulphur layers (Vaughan 1970). The FeS membrane considered here may have only adsorbed a few per cent of nickel, enough to force the cleavage of the hydrothermal hydrogen at the nickel site with the production of a transient hydride. The left-over proton would be neutralized with hydroxide in the protocytoplasm. The electrons could be transported through the membrane along the iron layer situated along (001), conducting
toward the final electron acceptor such as Fe(III) on the outside of the membrane. The atomic hydrogen could then hydrogenate the CO2 molecules bound on adjacent iron sites."

"In particular, Shock (1992, 1996) has carefully calculated the metastabilities of carboxylates, ketones and alcohols as inorganic carbonate in seawater mixes with hydrothermal solutions, with their fugacities buffered by both quartz–magnetite–fayalite (QFM) and the more oxidized pyrite–pyrrhotite–magnetite (PPM) mineral suites. The fugacity of carbon dioxide is taken as 10 bars, the presumed atmospheric pressure in the Hadean (Walker 1985; Kasting et al. 1993). ... Shock (1996) demonstrated that the possible synthesis of organic molecules between 50 and 250degC is sensitive to the fugacity of the hydrothermal solution, which must be buffered by QFM for all inorganic carbon to be converted to organic molecules. This is still a conservative choice, since 4.2 billion years ago the redox state of the mantle was probably two or three log fO2 units below that of the quartz–fayalite–magnetite buffer (Arculus & Delano 1980). Remarkably, Shock (1996) demonstrated that at temperatures below about 150degC, the longer chained polymers (dodecanoate is the longest chain considered so far) will theoretically be most represented of all the organic molecules, and that they could be generated at no energy cost."

An imagined reverse TCA or Krebs cycle, where carbon compounds are grown from humble beginnings using the free energy of the redox and pH gradients at the vent structures. What would guide the soup in any direction or to any particular compounds (including chirality) is not clear.

Given the right conditions, things might have proceeded quite rapidly ... millions of years would not be needed.

"The far-from-equilibrium conditions in which these geo- chemical processes and mechanisms operated would have been widespread for a limited period of Earth history, and would have provided ample opportunity for such a unique sequence of events leading to the minimal cell, the common ancestor of all life on this planet. Although coupled to a long-lived hydrothermal system, the actual gestation period for organic synthesis and the self-assembly of organic protocells capable of fledging and replication from within the iron monosulphide hatcheries would have to have been rapid, and may have taken weeks or months, rather than the millions of years normally assumed for the emergence of life."

The second paper takes the story onward through subsequent steps of probiotic evolution, where the metabolism becomes more ramified with phosphate (on ATP) as another energy currency, and  nascent protein and RNA enzymes develop out of the organic soup. And finally the mineral membranes are supplemented and replaced by organic ones, given some ion channels and membrane-bound enzymes to carry out metabolism. This sets the stage for escape as free-living organisms.

Cartoon of the general model of Russell and Martin, with organic pro to-metabolism generating carbon compounds which then undergo chemical evolution towards the RNA world, and eventually to organic membranes and cell walls that allow complete escape from the mineral womb at the hydrothermal vent setting.

I can hardly convey the entire theory, and at an outline level it seems reasonable. But what was the force or principle that made the carbon compounds become more complex and self-organize into an RNA world with enzymes and coding / reproduction schemes? That remains a major question (but see the collection of RNA world references cited above). Energy alone, even when channeled in some approximation of the later major microbial metabolism to a profusion of organic molecules, does not, on the face of it, direct complexity or productive competition between mineral bubbles. (The authors have a later paper that claims that conditions "forced" life to emerge, but its details are not available, and the argument seems geochemical, not biological, so it does not seem to address the competitive issue.) We can refer to the anthropic principle to say that whatever led to us must have survived somehow, but that is a far weaker theory than one that drives events based on the chemistry of the time. So I think these concepts are a strong start to a theory of the origin of life, but as yet far from the whole thing.

• Above the law- why pardoning Nixon set a bad precedent.
• Realism and Ukraine.
• "There was so much more reason for the U.S. to respond to 9/11 by invading Pakistan than there was Afghanistan."
• Who should pay for Detroit?
• "For middle-class Americans trying to save for retirement in a 401(k), bank fees take about $2 of every $5 over a lifetime of investing."
• Japan continues its curious ways of monetary sovereignty.
• The Chicago school thinks deflation is not so bad.
• MSM getting a little lefty!
• Our divided country- is speech speech, or is money speech?
• Did Apple solve payment security via biometrics?
• Quiverfull education.. a bit oxymoronic.
• Watch out: Deepak is really pissed, and has a nonphysicalist ontology on his side.
• Enron echoes "In short, Congress has consistently eroded the disincentives designed to keep corporate managers from lying to their shareholders and creditors"
• This week in the WSJ: Even someone at the Hoover institution recognizes the lack of prosecution, and the utter corruption of the financial system. "We also point out that when the Fed finally acted, it not only rescued the banks, it also bailed out their shareholders as well as the executives who had helped steer the banks and country into the crisis. In contrast, when the government rescued General Motors, it forced shareholders and bondholders to take huge financial losses and executives to be fired."