Saturday, October 29, 2011

Evolution, revolution, or redistribution?

In evolution, losers die. What happens in capitalism?

Trite as it seems, comparing capitalism with evolution still makes sense to me. (And to others.) Companies struggle with each other to survive, and the losers disintegrate. But individuals (i.e. people, er, I mean humans) in our system are in a similar Darwinian struggle for jobs and income- now sharply accentuated with globalization. When individuals succeed, the results are clear- they get rich, maybe famous. But what happens when they fail?

That is a bit of a problem in capitalism- those who fail don't conveniently disappear, but linger in poverty, creating political and moral problems. They test a culture of pure rapacious competitive greed for the presence of human values. For her part, Ayn Rand couldn't give a fig for the fate of the losers- the proles, the leaches. That would be the orthodox capitalist position, though there is the small complication that after the money has all been taken from the losers, the winners still need workers to give them food and pedicures. Exactly how little can workers be paid and still arrive to work? And secondly, how can the moral claims of losers in unemployed poverty be best ignored and dismissed?

This brings us to our political moment and the Occupy Wall Street movement. The last few decades have featured a cult of the market and the demonization of human values in the name of supposed efficiency and just deserts. The result has been a well-oiled economic machine that transfers wealth upwards and glorifies the rich. Only, the market turned out to have a screw loose. Greed unleashed led to fraudulent banking on a cataclysmic scale, among many other pathologies in finance. Profligate lending to unqualified borrowers was not bumbling, generous, or inadvertant, but a pattern of fraud perpetrated by businessmen motivated by personal greed over organizational, not to mention systemic and public, responsibility.

They won, sure enough- took the money and ran. Virtually none have been called to account. It is the line where "winning" in the capitalist competition crosses from serving customers to fleecing them and destroying their lives. Obfuscating this basic dynamic is what current Washington politics is all about, especially on the Republican side. And exposing and resolving this dynamic is what OWS is all about.

The losers in capitalism don't quietly fade away, but linger on as citizens, voters, maybe protesters. This is where humans transcend evolution and the bare laws of competition. For all of biology's glories, it has been an extremely painful and slow process, and has resulted in sub-optimal solutions. The fact that humans, once evolved to have enormous brains, could take the world by storm, occupy all lands, commandeer all resources, and fly off into the solar system ... well, that shows how limited the scope of evolution had been up to that point in comparison. It testifies to a consciousness and intellect that reaches far beyond competitive narrow-mindedness- so faithfully modelled by market competition- to a revolutionary capability to foresee the future, to alter circumstances, and to adopt a whole new vision of humanity.

It is a humanity that engages in common effort, plans in common for future prosperity, and shares the fruits of that planning. It is a humanity that harnesses markets and competitive logic as tools, but not as a theology that places Mammon ahead of all else. Polls show that most people share this vision- one of rational forethought, mutual moral obligation, fundamental legal/political equality, and measured economic inequality. Everyone, perhaps, except the most stultified economists.

So, somehow, we have gotten blown off track by the ideology of greed and false efficiency, back to a Herbert Spencer-era economic Darwinism as an ideal of human affairs. Yes, some degree of competition and unequal reward is neccessary to make the economic wheels go around on a micro level. But other values are required as well: a democratic political system that directs the economic system, instead of being corrupted by it; recognition of public goods as essential goods; and progressive mechanisms (specifically, a financial transaction tax, among other means) to counteract the ratchet of wealth accumulation in the hands of the few so that other virtues besides greed can have a place in our society.

"The ECB has no statutory mission to protect the interests of Greece’s creditors. Its decision to side with the interests of Greece’s creditors (overwhelmingly European banks, particularly German banks) against the interests of a member nation makes clear why the ECB poses an enormous danger to Europe. The ECB is dominated by theoclassical economists who glory in their “independence” from democratic institutions but are slavish servants of the systemically dangerous institutions (SDIs) – the misnamed “too big to fail” banks."

Saturday, October 22, 2011

Evolutionary knob-twiddling and networking

Butterfly wings and waves of ancient innovation highlight the dynamism of transcriptional control in evolution.

When you hear about small changes during evolution.. the retreat of brow ridges from Neanderthals to Homo sapiens, or the growth of our brains over longer spans, you are typically hearing about changes in regulation of proteins that are themselves unchanged. A little more expression here, a little less there, and perhaps a few more years of expression during childhood.. it all adds up to just the kind of gradual change that Darwin had in mind when he saw that variation is pervasive in biology, and the raw material of evolution.

In our genomes, the locations most conserved over geological time are the protein-coding sections of genes. They are the raisins in the pudding, around which much less stable DNA swirls- the introns, promoters, enhancers, centromeres, telomeres, transposons, repetitive elements, and other material / junk, each of which have their own, typically faster, rate of change. When a protein sequence changes, its action everywhere changes immediately. In contrast, changing where and when it is expressed can have smaller and more subtle effects. More gradual effects, in an evolutionary sense.

Regulatory regions (promoters and enhancers) that control protein expression are dispersed, often spread over many times the length of the protein-coding DNA. They are also modular, composed of separable cassettes with specific control effects/patterns, in contrast to the mostly linear one-damn-amino-acid-after-the-next nature of protein-coding DNA. (Putting aside protein coding flexibility based on intron/exon dispersion). This pattern of dispersed controls is an inheritance from our Archeal ancestors, and is part of what made eukaryotes such revolutionary life forms, able to evolve rapidly relative to bacteria.

Example of a human gene (DAC1) of 2,274 protein-coding base pairs, itself a set of exons (B, in center, vertical black lines are exons) dispersed over 430,000 base pairs of introns. It is set within a 2,000,000 base pair region (A and B) with modules (B; red marks similarity to human) conserved in several species, and individually capable of driving gene expression in mouse embryos as shown in C. (H-human, M-mouse, F-frog, P-pufferfish, Z-zebrafish)

Two recent papers highlight this property in different ways- one about the patterning of butterfly wings among species that convergently evolve to mimic each other's designs, and the other tracing ancient innovation in the vertebrate lineage by bursts of regulatory change followed by conservation/stasis.

Taking the second article first, the regulatory regions of our genome are peppered with small modules (typically much smaller than protein-coding segments) that are somewhat conserved, for their regulatory role. Each module typically drives expression of its associated gene in response to an environmental event, or at a specific time and place in development, as in the above example.

The authors dredged up such modules en masse from several vertebrate genomes (about 10% of all gene regulatory elements, from two fish, cow, mouse, and human) and ask when they first became conserved in evolution, and what genes they associate with. Not being as well conserved as proteins, virtually none are traceable beyond 600 million years ago. The paper is mostly devoted to methods, since these sites are small, difficult to align across different species, and their times of origin are difficult to estimate. But I will leave the methods issues aside.

The interesting finding is that over this span of time, there were four distinct patterns of regulatory innovation (i.e. origination and conservation of regulatory modules) tied to different kinds of genes in vertebrates. The first wave, peaking at the very start of available data at 500+ million years ago, was of transcription regulators themselves, which bind to regulatory DNA sites. This indicates variation and evolution in the most basic programs driving animal function and development.

The second epoch ranged from 500 to 200 million years ago and is associated with developmental genes, reinforcing the finding above, but indicating that the deployment of transcriptional regulators was solidified well before the full palette of developmental possibilities was explored. Development is mostly regulated by the coordinated expression of genes, including transcription regulators, that go on to regulate other genes and proteins in a cascade or network.

A third epoch peaked sharply about 250 million years ago, being the fixation of regulatory sites near receptor genes (Figure below). Receptors play central roles in the nervous system, in smell and taste, and in hormonal control systems like the sex hormones. All these areas were important areas of innovation through the vertebrate lineage, but apparently concentrated at this era just as the age of dinosaurs began.

Lastly, the most recently fixed set of regulatory sites lie near genes involved in post-translational protein modification. This is the attachment of molecules ranging from tiny methyl and acetyl groups to fatty acids like palmitate up through whole mini-proteins like ubiquitin and its many relatives to an active protein.

Period during evolution (x-axis) when regulatory modules near specified classes of genes (noted at top) arose and became conserved (y-axis), indicating a function of increased importance,

These modifications exemplify evolutionary tinkering and jury-rigging. They originate in other processes, (markers for protein degradation in the case of ubiquitin), whose components (or copies thereof) were dragged into new regulatory roles, at first perhaps as just a tentative little tweek on top of the existing complexity, then over time used in more roles when other sources of variation and adaptation had already been so networked that they couldn't change. The evolutionary story suggests that in our lineage, the deeper and more central the system of regulation, the earlier it settled into a more-or-less stable, conserved, and unchangeable, state.

Turning from deep time to more recent events, butterflies in Northern South America are (for the time being) highly diverse. Yet some have converged from different lineages towards similar wing patterns in violation of the general rule of species divergence, and particularly the rule that different species need distinct markings to promote correct mate selection and ecological niche maintenance. This mimicry comes in two versions. Either a distasteful species is mimicked by another that is not distasteful in order to steal its advertising.. i.e. its protection from predators, (Batesian mimicry), or two distasteful species converge together in order to raise the level of advertising they share (Müllerian mimicry).

They would make car dealers proud! But what causes all this plasticity of wing patterning? How do butterflies find it so easy to create and then alter their beautiful patterns? Authors of this paper find one gene that seems to be in charge- a transcription regulator whose own regulation holds the key to variation in the Heliconius genus of butterflies, a distasteful genus (to predators that is, not to us).

Geographic distribution (B), lineages (A, horizontal), and mimicry (A, vertical) of selected Helioconius butterflies.

In this figure, the horizonal rows contain genetic close relatives, while the vertical columns show geographic co-occurence. The archetypal Müllerian mimics are H. melpomene and H. erato, which look very similar despite coming from distant lineages. The authors note that the Helioconius genus has hundreds of different wing pattern races and species. So they have helpfully lined up the various mimics that co-habit but arise from different lineages and thus presumably have converged to similar wing patterns from different ones originally. These are the butterflies they use to ask the question: what are the gene(s) responsible for this variation and convergence/mimicry?

A great deal of past genetics had already pointed to one large genomic region responsible for red wing variants in this genus. The authors drilled down further by using high-tech methods to measure the RNA expression from regularly-spaced 60 base pair segments throughout that ~500,000 base pair suspect genome region. The RNA was prepared from dissected pieces of wing, comparing gene expression in red-colored pieces to that in green or black pieces. Only one location spanning about 15,000 base pairs correlated in its expression closely with the observed color variation, surrounding a gene called "optix".

As one can tell from the name, this gene was already known for its role in eye development in flies. Indeed, earlier researchers found that "Ectopic expression of optix leads to the formation of ectopic eyes suggesting that optix has important functions in eye development." No kidding! "Ectopic" meaning that they engineered expression of the gene in novel places, and - holy moly! - saw eyes develop in those places.

Back to wings.. the authors then looked at full-wing patterns of expression of the optix gene, and indeed it seems to closely presage the appearance of red color, such as in these images:

Expression of optix in 72 hour pupal wings (blue patterns), compared with adult wings of the same species.

The authors also looked at the genetics of optix in more detail and found that not only was there high correlation, but there was complete correlation between the alleles of optix and the resulting wing patterns, using hybrids of various races, indicating that optix is not just a downstream reflection of some other patterning component, but that it drives the red patterning by its location of expression.

Now the interesting part was that they sequenced the optix gene from seven of their Heliconius species, and the protein code was identical in each of them. Twenty million years of evolutionary divergence hadn't made any difference. The authors thus deduce that the genetic variation at this optix locus all happens in the surrounding regulatory regions of the DNA, not the protein coding areas. And this makes sense if the function of the protein has remained the same - make red pigmented areas on the wing (or make eyes, in other settings) - while its deployment in space across the wing has varied with the evolutionary needs of the moment.

They state "optix provides a compelling example of a gene that drives adaptation because its various alleles are regulatory variants that have pronounced effects on complex large-scale patterns." Unfortunately, they have not yet found those regulatory regions. Someone's grant and future work surely hangs in the balance. But as noted above, these regions and their variants are sure to be small, modular, dispersed, and hard to detect, since they exist at the edge of efficacy; bordering on random noise, in a DNA sequence sense.

Control is the key. Just as electronics and computer science quickly gave rise to information theory and cybernetics, and our financial and political worlds depend on people knowing what they are doing and having effective management processes in place, (ahem!), biology too is drenched with management issues. The human genome has half the number of genes that soybean does.. so to paraphrase, it isn't how many you have, but how you use them.

"So the graph highlighted in the early stages of the crisis the importance of very large fiscal interventions. My Chinese contacts informed me that at the time there was no discussion over there about the country drowning in debt or that the government was going to “run out of money”. These ideas that crippled the recovery in the West were not allowed to germinate in China."
  • Occupy Marin at 12 noon- be there .. at the square.

Saturday, October 15, 2011

A Better Retirement

A modest proposal- cancel all retirement plans.

The US retirement system is a mess. It is grossly unfair, in that employers can choose whether to offer retirement benefits or not, with employees not able to say much about it. Whole fields of employment may have defined pensions or their miserable cousin, the 401K, or nothing, with little rhyme or reason. Workers unwittingly enter fields that either do or don't offer retirement benefits, for all sorts of unrelated reasons of interest and talent, and wind up forty years later either made in the shade, or dumpster diving. We need a better way.

Employers also are mistreated by the current system. Some misers offer the stingiest 401K (no, or token matching), while others offer generous defined benefits. The latter can be destroyed by their pension obligations if they undergo contraction in the ever-changing business landscape, rendering them disasterously uncompetitive against younger companies without large pools of retirees. Among 401K plans, the degree of matching is highly variable, presumably a gauge of labor power in that company or industry, with results that only come out in the wash when the worker is later hung out on the line.

This hidden part of pay packages should, like health insurance under the Obama reforms, be made more uniform, and also be brought into the light by a few fundamental reforms.

First would be to cancel all non-Social Security retirement plans offered in the US, whether by private or public entities. Retirement is not a job for the workplace. Instead, Social Security should be doubled, to provide a uniform and stable base to the retirement of every working American. Despite all the scare stories, there is plenty of scope to beef up Social Security, by raising the cap of income levels that are taxed, and increasing the tax rate.

Second would be to eliminate the employer role in 401K plans. If a company wants to pay employees more, it should put that in the top line of salary, while the employee takes responsibility for the saving, the investments, and the tax deduction. All employees should be treated equally, not given more or less money based on whether they wish to save. Employees would still be able, however, to get their desired savings automatically deducted from their paychecks. The switch would by law put the money previously hidden in retirement benefits into the employee's top-line pay.

For instance, an empoyee might decide to save 10% of income automatically from her paycheck, and have it sent to a specified investment account. Her company would pay her the extra 10% that it previously paid in matching 401K contributions. The employee would take over the tax benefits, being allowed up to $20,000 of annual income to be counted as pre-tax toward this 401K/IRA. The government would offer all workers a social-security-grade account to invest these savings, (as inflation-protected bonds), in case they don't want to gamble it at the Wall street casino, and might also insure special bank savings/CD accounts if desired.

All this would go a long way towards decoupling retirement from the corporations and other institutions we work for. They don't want to worry about our retirement- they have better things to do. They have also been willing to underfund and raid these retirement accounts. Retirement is just too important (and far too long-term) to leave to employers.

The paternalistic model of employment needs to be put out of its misery, instead of penalizing those employers with moral scruples. Companies deserve a level playing field where they compete on their productivity, and attract workers based on transparent offers of compensation. Such reforms will also promote workplace mobility, lowering the need for workers to wait out bad employment situations for their promised retirement. The various fiascos of early retirement programs (allowing retirement at 55, even 50) would no longer be an issue, since no one would get defined benefits that could be arbitrarily granted and started at early times.

Lastly, this proposal would also resolve the public pension crisis, which is truly dire. As investment returns head downwards in our Japan-decade, the extravagant promises made to public employees by various well-meaning but undisciplined public entities have become unsustainable, hollowing out municipal and state public services. This albatross of needs to be cut from our necks by clawing back promises that were so rashly, and sometimes corruptly, made. These costs should be transparent on the top line of salary, not in the sticker shock of hidden crises bequethed to future generations. Public employers need to get out of the retirement business as soon as possible, and into a fair, transparent, transportable, worker-centered system.

In the US case, adjustment will require a break with a credit-fuelled economy, which is the only way American capitalism has of dealing with the vast inequalities of wealth and income that it has created by outsourcing most of its manufacturing to low-wage countries. There is little sign, however, of the US being willing to rethink its version of capitalism.

Saturday, October 8, 2011

Evolved to blog

Is our reason good for thinking, or good for arguing?

Recent podcasts featured two researchers who propose a novel idea about the point of human reasoning. Their proposition is that it evolved not to reason silently to ourselves, but to support our side in arguments. (Hugo Mercier, on point of inquiry; Dan Sperber on philosophy bites.)

Acting in the world, we generally don't resort to pen and paper to work out complex trains of thought or future action. We go with our gut, and trust to our instincts. We also go by painstakingly cultivated cultural norms and other social frameworks, virtually all of which are implicit, not to say unconscious. It is only in the modern world that we have engineers working out complicated tasks by mathematical means, or management gurus leading by microsoft "project", for what that is worth.

A theme in recent shopping research is that the more we obsess about a decision, and the more we make lists of pros and cons, the less well the decision goes. It is another case of our unconscious guiding us very well through the vageries of life, while reason just can't keep up with the huge amount of information involved.

Our reason, when we choose to employ it, also has characteristic defects. We use it to rationalize existing preferences more than to lead us to new conclusions. We suffer from confirmation bias, which helps us (blindly) feel good about past decisions. We use it to criticize the positions of others relentlessly, with far more skepticism than we would ever train onto our own core ideas.

So what is its point? If reason is so biased and rarely used, why have it at all? Hugo Mercier thinks we reason to argue- it is a social skill far more than a solitary one. This hearkens back to the core pursuits of the ancients, one of which was rhetoric, a sadly abused discipline in our current politics. The citizen gathering, shura, or agora was where public policy was made, with momentous consequences for everyone in the society. Wars were begun, diplomats heard, crimes judged. This was where common action was commenced- that essential function of being human.

Today, through the magic of modern media, our attention spans have declined to soundbites, horseraces, gaffes, and gotchas, rendering reason in the public sphere virtually invisible. We are left with the vote as the final refuge of public will, virtually naked in its tattered clothing of discussion and debate, exercised as a pure, though often ignorant, expression of private interest, rather than public spirit.

Sorry to digress.. so, does arguing and public reason lead to better results? Sperber and Mercier argue that it does (if not on certain cable channels). This is mostly clearly seen in the scientific culture, where pet theories and self-serving authorities are raked over the coals of public critique, peer review, and independent confirmation. It is the public nature of science that is key to its success. Even lone geniuses like Newton and Eistein had their bad, even crackpot ideas, (alchemy in the case of Newton), judged and flushed down the drain of "irreproducible results".

Other animals do not reason together- it is a uniquely human activity as far as we know. Most animals reason implicitly, individually, and unconsciously, with only a few (perhaps jays, crows, higher mammals) able to reason their way around the most elementary problems in a way that appears strongly conscious. So this conscious reasoning capacity is a very recent layer atop the much more powerful unconscious systems that keep us alive and going most of the time.

A leading theory for human intelligence posits that it was mostly selected for its social virtues and attractiveness to mates. Language is of course a primary factor in our heightened consciousness and reasoning ability, to the point that we often reason privately by talking to ourselves or writing, (or doing math), to "bring out" thoughts that otherwise are inarticulate, unformed, or absent. The nexus between language and reasoning (and the other human virtues of art and imagination) seems very strong, supporting an interactive theory of how and why we reason.

Nothing turns on one's reasoning powers like a good argument. Our assumptions are questioned, our interests opposed, and in turn we call up latent resources of rhetoric and rationalization. The true target is typically onlookers in the disinterested middle who may lack preformed personal committment. It may be possible, ideally, to exhibit such a compelling argument that even those directly opposing one's argument must recognize its validity.

In my blogging travels, I have to say that such experiences are quite rare, especially in the area of religion where the most devout inaccessibility to reason prevails, whether public or private. Perhaps the ability to change one's mind needs to be better appreciated and cultivated in our society, particularly in our politics.

  • Bad loans- who is at fault?
  • Bad banks... mark-to-make-believe.
  • Warning- patriarchy at work.
  • Evil, finally vanquished.
  • Yet in Koch industries, it somehow persists.
  • Stiglitz on the need for lots of public spending.
  • Plastics, really vanquished.
  • Even China can't really stand Pakistan's duplicity.
  • OWS slogan of the week: "Tax the psychopaths".
  • Economics quote of the week, from Bill Mitchell, writing about the fundamental issue of economic distribution:
"In the past, the dilemma of capitalism was that the firms had to keep real wages growing in line with productivity to ensure that the consumption goods produced were sold. But in the lead up to the crisis, capital found a new way to accomplish this which allowed them to suppress real wages growth and pocket increasing shares of the national income produced as profits. Along the way, this munificence also manifested as the ridiculous executive pay deals and Wall Street gambling that we read about constantly over the last decade or so and ultimately blew up in our faces. 
The trick was found in the rise of “financial engineering” which pushed ever increasing debt onto the household sector. The capitalists found that they could sustain purchasing power and receive a bonus along the way in the form of interest payments. This seemed to be a much better strategy than paying higher real wages."

Saturday, October 1, 2011

What a REAL debt crisis looks like

Greece is in dire straights. We are not.

Economic discussion in the US is appallingly primitive. Boehner says that the federal debt "is the real jobs killer". This is taken seriously, and he continues to be invited to talk shows to spread his economic wisdom. No one is there to say that he is lying.

What does a debt crisis really look like? It looks like Greece, which is on the verge of exiting the Euro and defaulting on its Euro debts [Ed.- This may have happened already by publication]. Greece does not print its Euros, but has to borrow (or beg) Euros to cover its deficits.

It is in the same position as a Lehman or other company that borrows the state currency of issue from private lenders, who only buy the debt on free market terms- i.e. dependent on the perceived risk of default and insolvency. Last I heard, Greece was facing interest rates of 25%- truly astronomical and already a functional form of default. Recently, the central Euro bank extended Greece several extra emergency loans, but this was just putting off the inevitable, since the fundamental rules were not changed.

How do we look in comparison? The US government has unlimited dollars, so we are never subject to insolvency risk (with the exception of political or policy idiocy, where our leaders decide to withold dollars and lead us over a cliff). We face the different risk of inflation, if more dollars are printed than the economic system can handle. We definitely faced inflation through the seventies, after a binge of social and military spending in the preceding decade. But now? Now we are facing deflation, and all the work of the Fed to raise the "money supply" has lain idle as unlent bank reserves, awaiting a revival of animal spirits.

So inflation is telling us that the US federal deficit is not a problem at all, let alone a jobs killer. Indeed, the surest way to create more jobs is to fund them directly by government spending (with or without higher debt), killing two birds with one stone- raising employment, and also raising the perceived inflation target that will discourage passive investments, encourage active investments, and shrink fixed debt burdens.

The Republican economic rhetoric has become ever more confident and shrill as its snow job on the American public has gained traction. Surely its CEO supporters think that high taxes are hurting them, that government regulation is hurting them, and that labor unionization is hurting them. But that is not why they are not hiring. They are not hiring for lack of business. Macroeconomics should never be left in the hands of businessmen- that only leads to depression.

The point of public policy is not the care and feeding of the plutocracy, but the care of the general public interest, especially that of the lower and middle classes, which have been so abused over the last decades.

To put our current unemployment situation into perspective, the Apollo space program employed about 400,000 people at its height. Now, with unemployment plus the rate of discouraged workers standing at about 16%, and a civilian labor force of about 154 million, this works out to 62 Apollo programs. Granted, not everyone who is unemployed is a rocket scientist. But truly mind-blowing amounts of talent and energy are lying wasted, a casualty of free markets that don't work, ideology based on lies, and a general failure of political and intellectual will. We are choosing decline in the US, not suffering it.

  • Example of pure shilling.
  • Long term decline is setting in.
  • Skidelsky on indebtedness and Hayek.
  • Egregious waste in the oil fields, and how to end it.
  • Economics quote of the week Marriner Eccles, Chair of the Federal Reserve, 1933, via Bill Mitchell:
"We have a complete economic plant able to supply a superabundance of not only all of the necessities of our people, but the comforts and luxuries as well. Our problem, then, becomes one purely of distribution. This can only be brought about by providing purchasing power sufficiently adequate to enable the people to obtain the consumption goods which we, as a nation, are able to produce."