Saturday, August 27, 2011

Breaking DNA to save itself

The structure of an enzyme that disentangles DNA- by passing strands through each other.

A single break in a cell's DNA is, typically, lethal. The cell will wait and wait for repair to happen, but if it doesn't, boom- it commits suicide. This is one of the quality controls that cancerous cells lose, in order to carry on despite the broken chromosomes they typically contain, among many other mutations. It is one of many homeostatic and quality control mechanisms that manage our cells. Another enforces that all DNA is completely replicated before cell division begins, and a different one enforces that all the condensed chromosomes are congregated neatly at the middle of the cell in mitosis, before separation and division can proceeed.

Yet we have enormous amounts- eight feet- of DNA in each cell, wrapped up in knarly bundles that can't possibly be maintained tangle-free, even with nice rollers to curl on (histones) and scaffolds to fold into (chromosomes, when condensed). On top of that, DNA is helical and additionally twisted, requiring unwinding to be read by RNA polymerases, and much more extensive unwinding to be replicated. What we find inside our cell nuclei is a mess. So naturally, we have several enzymes dedicated to untangling DNA- winding and unwinding it, and in extremis, when a knot can't be unwound, an enzyme that passes strands through each other, cutting the gordian knot.

These are topological problems, so the enzymes are called topoisomerases, catalyzing transitions between topological states. The current paper describes an atomic structure of topoisomerase II, which cuts DNA, allows another strand to pass through the cut, and then reseals the original strand. Quite a dangerous proposition! The experimenters used an anti-cancer drug (etoposide) to lock the enzyme in an interesting halfway state of cut DNA, helping them grow the crystals of protein that provided the structure.

Remember that the diffraction pattern of X-rays passed through a crystal allows mathematical reconstruction of the arrangement of the crystal's atoms, given enough order in that crystal, and enough intensity from the X-rays, typically provided by synchrotrons these days.

X-ray diffraction pattern of an arbitrary crystal. The center is where the main X-ray beam goes through, and the surrounding dots are reflections from the atomic crystal planes. With a lot of math, one can reconstruct the crystal's atomic structure.
In cancer cells, the DNA is particularly messed-up, cell devision is rapid, and the quality control mechanisms that tell the cell to halt and wait for repairs when the DNA is broken are gone. So this drug encourages more and more DNA breaks, to the point that active cancer cells get fatally damaged, even without the specific suicide system that is sensitive to single DNA breaks in normal cells. The cancer cells are given the rope to hang themselves.

But I am more interested in the magic of the topoisomerase II enzyme. (Topoisomerase I enzymes just nick one strand of the DNA, altering its helical winding- a much less complex proposition). It is interesting to consider how mere enzymes could effectively untangle DNA as they do. They don't have fingers or eyes, and they don't have any wider perspective on what is going on in the cell or in the DNA knots that evolution has fashioned them to resolve. They just cut DNA and reseal it, but in a clever way that leads, quite efficiently, to de-knotting of the cell's DNA.

The cycle of action is shown below, in cartoon form.

The enzyme grabs one segment of DNA (the G-segment), and bends it. This bend plays a critical role in funneling local knotted DNA segments (the T-segment in this case) which topologically "want" to pass through the G-strand towards the "mouth" of the enzyme, here shown in beige. When such a T-segment arrives, the enzyme, using ATP, cleaves the G-segment, opens its DNA gate (red, and see below), and allows the T-strand to pass through to the C-gate, the hollow area below the active site (green). Lastly, the G-strand is resealed, the T-segment is released, and everything is reset as it was at the start, minus one tangle. Incidentally, bent, stressed DNA induces increased activity by this enzyme.

Why does the C-gate exist? One might think that once the T-strand is through, then no problems- no need to keep it around rather then let it go on its way. I think the reason is for informational control- so that the enzyme knows to reseal the G-strand, rather than to cut it again. I assume there is a shape-dependent control by the occupied C-gate to enforce the direction of the overall cycle of the cutting/sealing active site.

The structure of the enzyme (just the core part, including only the colored areas of the protein cartoon in "A") is shown below. The C-gate is hard to miss. This large void is clearly able to hold the passed T-strand of DNA while the enzyme ligates the G-strand back to its pristine condition. Looking carefully, one can also see the strong bend of the G-segment DNA (backbone in blue), with both ends pointing sharply upwards.

One can imagine that the rest of the enzyme that was not solved or shown here (gray in part A) might help to form more of the funnel that brings the T-segment into proper position at the top. It might also help the enzyme hold tighly onto those DNA ends that, were they to get lost, would be virtually impossible to find again in the vast molecular soup of the cell and likely cause complete cellular arrest and death.

The cancer drug and topoisomerase II inhibitor, etoposide (in yellow) blocking the DNA strands within the topoisomerase II complex from being fully religated.

The paper devotes most of its time to the structure of the etoposide drug complex- how it locks the enzyme in an intermediate conformation and how these interactions might guide the design of better drugs. Given that this whole mode of therapy is rather crude, (hardly better than bombarding cells with radiation), it is hard to imagine how any "improvements" to the inhibitor would be helpful. Nevertheless, I find these structures immensely interesting- informative about how our bodies work at the molecular level, enlightening about obvious questions that arise with the advent of ever-longer DNA genomes, and indeed even artistic.

Here it is in 3D!

  • Yes, the crazies are really crazy.
  • Secular humanism, in the sentimental clutches of Paul Kurtz.
  • Is BofA the next Lehman, going over the event horizon? Parts I, II, III
  • Bernanke's speech, dedicated to do-nothing-ism.
  • Shalizi on macroeconomic models, with link to a critique.
  • Diplomatically speaking, talking is OK.
  • Economic quotes of the week, from Bill Mitchell
"Our real world laboratory is providing priceless data upon which we can assess basic propositions that mainstream macroeconomics provides and which Modern Monetary Theory (MMT) contests. A nation cannot have a fiscal contraction expansion when all other spending is flat or going backwards. Britain is up against an impossible equation."
  • And, on the "believers in laissez-faire". A Kuhnian expired paradigm is on its last legs, waiting for its proponents to die off.
"One thing that is clear – the majority of these economists never have to carry the costs of their denial and retire on nice pensions. The same cannot be said for the victims of their arrogance and denial."

Saturday, August 20, 2011

The worse, the better

The unemployment rate is not just a bummer, it is a sensitive gauge of social power.

The unemployment rate is disastrously high, and our government studiously dithers about doing nothing. The Republicans have cleverly diverted attention from the real problem onto the entirely chimerical problem of the federal "debt" at a time when people are saving like mad and only too happy to hold government bonds. The Democrats seem to have caved utterly to the forces of corporatism and finance, which got their bailouts and are now busily making war on labor. We (and other developed nations) are making precisely the same errors that we made during the Great Depression and in Japan's long-running recession, leaving the economy stalled so that the rich can widen their relative advantage.

It is as though Keynes and others who learned from economic history never existed. It is almost as though democracy doesn't exist either. Most of the problem is intellectual. This morning, a leading economist and conservative ideolog (John Taylor) lied through his teeth on NPR about how the Obama stimulus didn't work "at all", how corporations are not investing due to their fears of higher taxes, and other talking points of the Right. That such people are allowed to continue speaking as "experts" is unconscionable, however credentialed they are.

In this way, the intellectual waters are muddied, just as the tobacco industry, the fossil fuel industry, and the anti-evolution industries have muddied waters in their respective fields, freezing constructive public debate and action. What do conservative economists serve? The interests of wealth. At this moment, their lies serve variously to shield the powers of finance and corporate America from a reckoning for creating this enormous economic crisis in the first place, to forestall any constructive regulatory and fiscal solution to that crisis, (other than bailing out the banks, and the first dose of stimulus), and to entrench the power of wealth by floating the most self-serving "solutions" like lowering taxes and pulling saftey net programs from the poor, as well as, in effect, extending high unemployment for as long as possible.

For unemployment is a key indicator of our era. It is a barometer of the balance of power of capital vs labor. Low unemployment means that labor is hard to find and needs to be paid and treated well. High unemployment means the opposite- that employers can demand extraordinarily precise skill sets, provide no training, little security or benefits, all for low pay. Low unemployment is the most powerful promoter of worker's rights and middle class well-being, more than unions or legislative action.

Beware of economists who soft-pedel high unemployment as "natural" or "structural", as though the country were full of "lucky duckies" who prefer poverty to work, or losers who can't keep up with the jet setting workers of China. Whenever macro-economic times are good, people show that they can and want to work by working at high rates. Desire and training are not the issues.

It is more than ironic that the disaster caused by the financial sector as it oversold credit to the unworthy and leveraged itself to the stratosphere would result in yet greater power for those very financial and corporate malefactors. But there we are, and our only recourse is through the political system, which has  also duly been taken over by money, speaking with the forked tongue of right wing economics.

The Federal Reserve has the official mandate of maintaining low unemployment as well as low inflation- somewhat conflicting goals. But who runs the Fed? Bankers run the Fed, and bankers have had little regard for the employment mandate. Now they have none. The Fed poured money into the banks to restore their solvency, and took on vast quantities of their questionable debt. But for employment? They have hardly lifted a finger, lowering interest rates in case any bank might deign to lend to a worthy cause. There has been no mention of truly active policies like targeting higher inflation rates and negative real interest, forcing banks to lend or lose their charters, or forcing banks to eat some of their bad mortgage loans, as well as processing them more efficiently, to get consumers back on their feet.

We have little to hope from any of these quarters. The sad part is that high unemployment and a widening gap between rich and poor doesn't even serve the rich very well. The economy as a whole will become less productive, skills will be lost, infrastructure will continue to deteriorate, public goods will be shortchanged, political and social relations will fray, we will fall behind China, the dollar will slowly lose its reserve currency status, and even the rich will find that their heretofore advanced base of operations in the US is not nearly as attractive as it once was. It is a scandal and a shame.

Incidentally, today's title comes from the Russian revolution, whose instigators recognized that the worse conditions became within Russia, the more fertile they were for revolution. The analogy to our epoch may be double-edged.

"...people are more likely to get married if they have the things that make a union strong: mutual respect, problem-solving skills and — especially — economic security."
"So Karl Marx, it seems, was partly right in arguing that globalization, financial intermediation run amok, and redistribution of income and wealth from labor to capital could lead capitalism to self-destruct (though his view that socialism would be better has proven wrong). Firms are cutting jobs because there is not enough final demand. But cutting jobs reduces labor income, increases inequality and reduces final demand."
  • Graph of the week: Fed data on bank reserves. QE1,2 has been funnelled into banks, which sit on the money, doing no good to anyone, other than themselves by collecting interest courtesy of the Fed. The velocity of this money is zero. The Fed pays 0.25% on reserves, which adds up to real money on $2 trillion outstanding. This is quite apart from whatever Treasury bonds banks can buy paying 3%. Banks are well cared-for. Workers and homeowners.. not so much.


Saturday, August 13, 2011

Sex and the Red Queen

You knew sex was good. Now it is shown to fight disease and extinction too.

As studies of evolution progress, we often find papers dotting i's and crossing t's more often than opening new vistas of theory. This is one of those papers, showing with elegant experiments that reproduction via sex has significant advantages for a population of animals faced with pathogens that evolve quickly- as most of them do, and as most populations are.

In alchemy, the queen is typically white, and marries the red king to bring about the union of opposite natures, resulting in the birth of a unified hermaphrodite, the diamond body, the rubido, the golden flower, or the philosopher's stone. In psychological terms, enlightenment is achieved through such unifications when one has found the Jungian Self, or turned into the Nietzschean Übermensch. Given all this, I have no idea why Lewis Carroll chose the Red Queen as his character who runs and runs, but never gets anywhere- he was apparently more familiar with card play than with mystical esoterica.

At any rate, Carroll's Red Queen symbolizes an important feature of evolution, which is that a great deal may be going on genetically and physiologically over evolutionary time, with little changing on the surface (i.e, in  the fossils or other visible features). Even in the absence of selection and adaptation, evolution continues apace through neutral change, as mutations and other alterations accumulate, leading to the many forensic tools we have today to identify people and trace their lineages.

The most pressing source of non-neutral change, i.e. selection, is typically from microbial pathogens, which we may not think about very much in the developed world, but which pervade the evolutionary setting. Such pathogens evolve quickly, as we have learned from spectacular feats of antibiotic resistance. So, while we as animals possess a sophisticated multi-layer defense with an adaptive immune system, it isn't enough. Plagues of many kinds, and more chronic infections have wrought havok, keeping lifespans low, infant mortality high, and life generally perilous. Our salvation is genetic diversity, accumulated through mutation, kept in ready reserve in our diploid genomes where recessive genes are frequently not expressed, and shuffled continually by sexual reproduction.

For example, some people are resistant to AIDS. They may be infected by HIV, but do not become ill. They have a mutation that, when present in two copies, denies HIV access to the receptor it binds on the cell surface, and that is that.. complete protection. Were the AIDS epidemic to run to completion, those people might be the only ones left.

After several epidemics of this kind, (which cause genetic "sweeps" in the human population), a lot of evolution has happened, raising the proportion of previously rare gene alleles, but for little obvious gain- just to escape the next pathogen, and the next, and the next, in a never-ending arms race with those evil micro-terrorists who would do us ill. That is basically the Red Queen hypothesis.

The role of sex in this scenario is manifold. First, it keeps shuffling the genes around in the population, so that those animals that survive a genetic sweep should still harbor a fair proportion of the population's genetic variation at other loci, (genes), in preparation for the next pathogenic assault or other adaptive crisis.

Second, the shuffling uses the diploid nature of our genomes to "hide" recessive alleles of genes, so that even if such alleles have slightly deleterious effects most of the time, they persist in the population and can come to the rescue when they represent a key solution to an adaptive challenge.

Third, sex recombines genes that may in combination represent adaptive solutions that they do not in isolation. Fourth, the shuffling process deals out especially "bad hands" to a few organisms, which concentrates the bad genetic material and presumably kills it off by selection, counteracting the ever-rising level of mutations in the population at large, the large majority of which are deleterious- a process that goes by the name of Muller's Ratchet.

Very well- the theory behind all this is solid enough, biologists have deduced instances many times, and have tested it explicitly where it is easy to do- among microbes. But the current paper demonstrates the benefit of sex in particularly clear-cut fashon, using the nematode worm C. elegans. This tiny worm has a sexual choice- hermaphroditism and self-fertization, or maleness and obligatory sex, which can be enforced in the lab with appropriate genetic mutations when desired. In the wild, C. elegans are mostly hermaphroditic, with about 20% choosing the single-sex (male) lifestyle which carries the risk of not finding a partner and not reproducing at all. The choice is stochastic, but also a matter of genetics, so worm populations can evolve different rates of hermaphroditism when the trait matters.

The experimenters subjected worms to persistent infection with a bacterial species they typically contend with at much lower levels in the wild. In various experiments, the bacteria were either held constant or allowed to evolve along with the worms, in which case they evolved against each other through thirty worm generations. To maximize bacterial evolution, the bacteria for the next generation were taken from the dead carcasses of worms they had killed in the current generation. To help the worms along, they were mutagenized lightly before beginning, so their populations would have increased genetic variation.

One question was- if worms are genetically prevented from cross-fertilizing, can they keep up with an evolving pathogen? The answer turned out to be... no they can't. Such strains went extinct within about ten generations.

The metric for this work was bacterially-induced mortality rate of worms at the end of the experiment, at either generation ten (to accommodate those worm strains that went extinct shortly thereafter), or at generation thirty. The orginal mortality rate was 20% to 40% for all strains. For the obligately selfing (hermaphroditic) worms, this rose slightly against the non-evolving bacteria (to 40%), and rose dramatically- to 80%- against bacteria allowed to co-evolve, after which these worm strains went extinct.

On the other hand, wild-type worm strains ended up just where they began, no matter what the bacterial regimen- at about 30% mortality. And the obligately outcrossing worms succeeded by generation thirty in lowering their mortality from infection to about 15%, even in the face of co-evolving bacteria. The message is that sex strongly facilitates the rapid evolution that is required to outrun pathogens which have short generation times and rapid rates of evolution themselves.

An interesting extra analysis showed that among the wild-type strains put through this process, their rate of outcrossing increased markedly in response to bacterial infection, ending up at 90% in the face of co-evolving bacteria (see graph). This indicates that not only is sex helpful in staving off infection, but is itself a target of selection in organisms that have a choice in the matter, and is thus a sensitive gauge of sex's benefits.

Rate of outcrossing (sex) among wild-type C. elegans subjected to co-evolution with pathogenic bacteria (solid line), or to non-evolving bacteria (dashed line), or to no bacteria at all (dotted line).

"This increasing political pressure to destroy the foundations of the New Deal is bizarrely paradoxical. The right-wing coalition is on the verge of succeeding in its eighty-year quest to defeat the New Deal, not in spite of, but because it produced three-decades of economic failure and exploding deficits. It is the huge rise in government debt generated by the right-wing model that created the recent financial and political crisis that in turn spawned a wide-spread demand for austerity."

Saturday, August 6, 2011

Oolon Colluphid's God

An homage to Don Cupitt- a theologian I can deal with.

What is it about god? It drives some people nuts, and drives others to absurd feats of theological gymnastics. Dead for a hundred years, but your garden-variety theologian seemingly hasn't gotten the message. Don Cupitt offers an answer:
"... theology is the one subject whose practitioners are in constant danger of finding themselves becoming demythologized right out of their subject, and then being told by everyone that they have a duty to resign. The corollary is that you can be a theologian in good standing only for so long as you are not very good because you don't yet see your subject clearly and in an up-to-date way. You may plan to survive the difficulty by adopting the time-honoured strategies of being evasive, or sticking to history, and so avoiding ever actually having to come clean about your own personal views. But you cannot help but feel a little uncomfortable about the paradox: an academic must seek full, transparent understanding, but when you fully understand religion you are no longer a 'believer'."

Former Dean of Emanual College, Cambridge, radical theologian Don Cupitt takes modern science and philosophy seriously, and thus doesn't believe god is "real". And that is perfectly OK with him. In any case, the matter needs to be faced squarely. Due to his various heresies, he has both been sidelined in the Anglican church, and humorously mocked by Douglas Adams, who modeled the theologian Oolon Colluphid in his Hitchhiker's Guide to the Galaxy on Cupitt. Colluphid's putative titles include "Where God Went Wrong", "Some More of God's Greatest Mistakes", "Who Is This God Person Anyway?", and "Well That About Wraps It Up for God".

The title I am going to cover is "The Great Questions of Life", 2005, a book that puts Cupitt's various philosophical points across fairly briefly. Of the great questions, some are badly posed (What are we here for?), some not theological at all (Are we alone?), some infected with bad philosophy (What is real?), while some get a plain answer (Is there a God? No). The rub is that Cupitt still has great attachment to the Anglican traditions, and to some of the overall Christian culture, especially the revolutionary liberal teachings of Jesus himself.

The problem is simply to take in the higher level of knowledge we now have, and the separation of reality and fantasy that characterizes the modern state of philosophical understanding, including the sciences, arts, and humanities, and apply it to theology. Unfortunately, that means throwing a great deal out, and Cupitt has bitten the bullet and done so. The book is heavily philosophical, more so than Christian per se, which makes it interesting far beyond the Christian (or post-Christian) community. For instance, right off the bat, he has a passage on Hegel that did more to clarify Hegel's philosophy for me than reams of wiki pages:
"In Hegel's day people were coming to see the end of L'Ancien Régime as marking the end of the old hierarchical conception of reality, and its replacement by a new story that sees everything as developing historically within an entirely immanent process. In Hegel's interpretation of modernity, with the end of classical metaphysics the entire supernatural world of religion has come down from heaven and been dispersed into the unfolding common life of humanity. Ecclesiastical Christianity as we have known it hitherto reaches fulfilment and comes to an end. Instead of being routed through the heavenly world above, religion becomes immediate and beliefless, and the love of God is transposed into a new and ardent love of and commitment to life."

The main theme of this book is the "outsidelessness" of our situation. The universe is outsideless, there being no way we can ever peer beyond the shroud where our telescopes and cosmological theories reach, with spacetime being essentially closed (with a hat-tip to the multiverses, which are dubious). Supernaturalism is a matter, not of cosmology, but of psychology. His other example is language, which in any dictionary is defined solely in term of other language symbols- it is a self-contained, self-referential system. Similarly, our human, earthly world is outsideless as well, with no one handing down the rules and meaning. We are all we've got, and we had better take care of this, our precious world.
"As we have seen in looking at the great questions of life, even to this day, most people seem to assume that the purpose of life, the real meaning of life, the point of it all, the goal of life, what life is all about must be something great that hidden outside life. I thought the same myself, at first. Only very gradually, through the influence of figures like Hume and Darwin, did I gradually some to admit the superior beauty and clarity of naturalistic or immanent types of explanation in all fields."
"The general rule is that everything is contingent: everything is the product of time and chance. The cases of living organisms, of language, and of culture generally all pursuade us that complex, ordered, rule-governed, and self-maintaining or self-replicating systems can be formed and can develop just by the interplay of contingent forces within the world, over long periods of time. ... a broad, spreading network of purely contingent truths can be immensely strong without having to be based upon any sort of external support or founding certainties."

Cupitt makes the rather ironic point that conventional belief is in essence just as unrealist as his own more explicit formulation:
"Today, because of the decay of metaphysics, the ordinary believer's God is an imaginary Father- a finite being, in time- to whom one listens and with whom one talks. At the same time the ordinary believer invokes the God of non-realism, as when he or she says: 'My God is not a God of Judgement. My God is a God of Mercy, forgiveness, and love. Not a God of the respectable only, but also a God who takes the side of the outcast, etc.' In such talk (of which we hear a great deal) God functions as a personification of our most cherished values. So the God of the ordinary believer and the ordinary chuch leader clearly does not 'literally' exist. ... the believer is openly admitting that 'I posit a god whose job is to reflect my own cherished values, and in whom I can therefore believe.' Today's religion is therefore non-realist and will be quite happy to remain so- but with one qualification: it oddly insists upon its own realistic character, even though it is totally unable to spell out exactly what God's 'objective reality' is."

Ouch! No wonder Cupitt had to strike out on his own, founding the "Sea of faith" movement. And no wonder he tickled Douglas Adams.

Getting past the dissing of traditional religion, Cupitt's positive program consists of a very democratic and idiosyncratic approach to spirituality. Indeed, he is very sympathetic to those who term themselves "spiritual", without bothering with traditional dogma and theology. Glastonbury and all that. The purpose of religion becomes the generation of hope and health insofar as it battles the existential problem. He offers a creed:
"1. True religion is your own voice, if you can but find it.
2. True religion is in every sense to own one's own life.
3. True religion is the pure solar affirmation of life, 'in full acknowledgement of its utter gratuitousness, its contingency, its transience, and even its nothingness.'
4. True religion is productive, value-realizing action in the public world.
5. Faith is not a matter of holding onto anything. Faith is simply a letting go. It floats free."

I particularly liked his discussion of point 2, where he urges being and showing the values you have inside:
"You are your own life. Your personal identity is not a secret thing hidden inside you: it is your lived life and the roles you play. Thus your commitment to life and to the task of becoming yourself has to be read as the task of fully appropriating one's own life and assuming full responsibility for it. Here I reject the traditional idea that there is great virtue in obedience to religious law and to the direction of religious superiors. Instead I join all those young people who would rather die than put up with an arranged marriage or any career or life-path chosen for them by someone else. In traditional Christianity the  demand for radical personal religious freedom has always been condemned as deeply sinful, but I think we must now insist upon it. One must choose one's own life, both making it one's own and seeking fully to express oneself in it. One must come out in one's own life."

While this can be taken as vintage 70's self-actualization and self-fulfillment, even self-centeredness, (or, more probably, a redux of Nietzsche), it is also quite akin to the Buddhist program of fixing the world from the inside out, instead of finding and conquering outside demons. And yet, it communicates a love and gratitude for life, instead of a focus on asceticism and sufferance.

  • People take their own paths to reject reality.
  • Joseph Heller and the death of god.
  • And in Afghanistan, is it tradition, or is it religion? Whatever its name, it is patriarchy.
  • A southern tea party, a southern agenda.
  • We are still on FIRE.
  • Terror attack in the US- ho-hum.
  • Europe has set itself on course to repeat depression dynamics.
  • Economics quote of the week, today from a wealth fund manager, speaking of how differentiated wealth and power are, even within the top 1% of the wealthy.
"Most of those in the bottom half of the top 1% lack power and global flexibility and are essentially well-compensated workhorses for the top 0.5%, just like the bottom 99%. In my view, the American dream of striking it rich is merely a well-marketed fantasy that keeps the bottom 99.5% hoping for better and prevents social and political instability. The odds of getting into that top 0.5% are very slim and the door is kept firmly shut by those within it."
  • And a graph, on where gross income shares are headed, drawn from regular Fed reports: