Friday, August 30, 2013

The Oatmeal on Syria

Click on image for larger version

Saturday, August 24, 2013

Bird photographs

What one may aspire to.   {These species of birds visit my garden,  and surely I can grow such nice perches for them.}

America Creaks Along

As Pindelski puts it, to compare a low or middle income economy with that of the US is Arrant Nonsense.  And yes,  America is far from finished, and is still the envy of the developing world, including China.


The appropriate comparison of the US is with those OECD countries that have roughly equal levels of income.  In that respect, the US is falling behind.  Where it used to rank in the top three in various measures, it is now often in the bottom three of a list of twenty.

This includes things like:
  • language, science and math abilities of students on completion of high school.
  • completion rate of high school
    This despite being near the top in per student spending K-12.

  • percentage of people who complete a college degree
  • teenage pregnancy rate
  • people without adequate health care
  • life expectancy
  • infant mortality
  • incidence of various life-style diseases
    This despite spending more per person on health care - by a lot - than any other country.
  • lack of social mobility - it is now easier for people in the other OECD countries to climb the income ladder than it is in the US.
  • non-growth in the median income - other OECD countries are also afflicted with Chinese take-over of low-end manufacturing, but haven't succumbed to this.
  • poverty rate  (and the outcome for children born into poverty is apparently worse than children born crack-addicted because of their mothers' usage of the drug)
  • rates of violent crime
I can grow this list, but I hope the point is made. Let me be VERY clear - India or China would be eager to exchange their problems for those of the USA. China and India have large economies because they have lots of people, not because the average person is really well-off.

BUT - the US is sliding down the rankings of its peer group of nations. Perhaps part of the reason is that the US spends as much on defense as the next fifty nations combined. People should reflect that it is soft power - Pindelski's post is a paean to soft power - that keeps America admired, feared and safe, not its military power.

"America is not finished", "America is just getting started", a truth and a pious hope, respectively.  This hope may not be unfounded, BUT!

Pindelski talks about the resurgence of California.
With city finances rapidly recovering in California, I have noticed that many of the chewed up city streets in the SF Peninsula where I live are undergoing a transformation, and such was the case with mine.
But this recovery is because California threw out the Republicans, ended an era of bad governance and fixed the state's finances.  It is not at all clear that the nation as a whole is willing to do the same.  The Republicans will hold on to the House of Representatives in 2014, it is almost mathematically impossible to dislodge them; and the Republicans are given a better than even chance of winning the Senate in the 2014 elections.  The current set of Republicans are threatening to shut the government down, or even to force a default on its obligations by the Federal government (a default would put the world economy into a tailspin) in order to get their way.

PZ Myers on Pinker

Worth reading in full.

Repudiating scientism, rather than surrendering to it

Scientism is the idea that only science is the proper mode of human thought, and in particular, a blinkered, narrow notion that every human advance is the product of scientific, rational, empirical thinking. Much as I love science, and am personally a committed practitioner who also has a hard time shaking myself out of this path (I find scientific thinking very natural), I’ve got enough breadth in my education and current experience to recognize that there are other ways of progressing. Notice that I don’t use the phrase “ways of knowing” here — I have a rigorous enough expectation of what knowledge represents to reject other claims of knowledge outside of the empirical collection of information.

It’s the curse of teaching at a liberal arts university and rubbing elbows with people in the arts and humanities all the time.

I probably know more about the biological side of how the brain functions than Pinker does, with my background in neuroscience, cell biology, and molecular biology. But I have no illusions. If I could travel in time to visit Hume or Spinoza, I might be able to deliver the occasional enlightening fact that they would find interesting, but most of my knowledge would be irrelevant to their concerns, while their ideas would have broader applicability and would enlighten me. When I imagine visiting these great contributors to the philosophy of science (Hume and Bacon would be at the top of my list), I see myself as a supplicant, hoping to learn more, not as the font of wisdom come to deliver them from their errors. Alright, I might argue some with them, but Jesus…they have their own domains of understanding in which they are acknowledged masters, domains in which I am only a dabbler.

At the Salvia


Thursday, August 22, 2013

More on the Genomics Gartner Hype Cycle

Nicholas Wade,  The New York Times,  June 12, 2010:
In announcing on June 26, 2000, that the first draft of the human genome had been achieved, Mr. Clinton said it would “revolutionize the diagnosis, prevention and treatment of most, if not all, human diseases.”

At a news conference, Francis Collins, then the director of the genome agency at the National Institutes of Health, said that genetic diagnosis of diseases would be accomplished in 10 years and that treatments would start to roll out perhaps five years after that.

“Over the longer term, perhaps in another 15 or 20 years,” he added, “you will see a complete transformation in therapeutic medicine.”

The pharmaceutical industry has spent billions of dollars to reap genomic secrets and is starting to bring several genome-guided drugs to market. While drug companies continue to pour huge amounts of money into genome research, it has become clear that the genetics of most diseases are more complex than anticipated and that it will take many more years before new treatments may be able to transform medicine.

“Genomics is a way to do science, not medicine,” said Harold Varmus, president of the Memorial Sloan-Kettering Cancer Center in New York, who in July will become the director of the National Cancer Institute.

The last decade has brought a flood of discoveries of disease-causing mutations in the human genome. But with most diseases, the findings have explained only a small part of the risk of getting the disease. And many of the genetic variants linked to diseases, some scientists have begun to fear, could be statistical illusions.

Wednesday, August 21, 2013

The Gartner Hype Cycle

Gartner describes the technology hype cycle:

The hype cycle applies to science as well, it seems. 

Lewontin, 2011:  (agree or disagree with him, it is worth reading in full)
The genes for IQ have never been found. Ironically, at the same time that genetics has ceased to be a popular explanation for human intellectual and temperamental differences, genetic theories for the causation of virtually every physical disorder have become the mode. “DNA” has replaced “IQ” as the abbreviation of social import. The announcement in February 2001 that two groups of investigators had sequenced the entire human genome was taken as the beginning of a new era in medicine, an era in which all diseases would be treated and cured by the replacement of faulty DNA. William Haseltine, the chairman of the board of the private company Human Genome Sciences, which participated in the genome project, assured us that “death is a series of preventable diseases.” Immortality, it appeared, was around the corner. For nearly ten years announcements of yet more genetic differences between diseased and healthy individuals were a regular occurrence in the pages of The New York Times and in leading general scientific publications like Science and Nature.

Then, on April 15, 2009, there appeared in The New York Times an article by the influential science reporter and fan of DNA research Nicholas Wade, under the headline “Study of Genes and Diseases at an Impasse.” In the same week the journal Science reported that DNA studies of disease causation had a “relatively low impact.” Both of these articles were instigated by several articles in The New England Journal of Medicine, which had come to the conclusion that the search for genes underlying common causes of mortality had so far yielded virtually nothing useful. The failure to find such genes continues and it seems likely that the search for the genes causing most common diseases will go the way of the search for the genes for IQ.

Monday, August 19, 2013

Lewontin 1991: Scientific medicine

PS: Wiki defines Scientific medicine is a modern form of medicine stemming from the synthesis of the Flexnerian medical education reforms of the early 1900s and the Germ theory of disease.

In the Wiki sense, scientific medicine then dates to the Flexnerian reforms.


 Lewontin, Richard C., "A Reasonable Skepticism" from Biology as Ideology: The Doctrine of DNA (New York: HarperPerennial, 1991):
Yet it is remarkable how much important practical science has been quite independent of theory. In Chapter 3, I will consider one of the most famous examples of scientific agricultural change: the introduction of hybrid corn all over the world. Hybrid corn is said to be one of the great triumphs of modern genetics in action, helping to feed people and increase their well-being. Yet the development of hybrid corn and, indeed, almost all plant and animal breeding as it is actually practiced has been carried out in a way that is completely independent of any scientific theory. Indeed, a great deal of plant and animal breeding has been done in a way indistinguishable from the methods of past centuries before anyone had ever heard of genetics.

The same is true for our attempts to cope with killers like cancer and heart disease. Most cures for cancer involve either removing the growing tumor or destroying it with powerful radiation or chemicals. Virtually none of this progress in cancer therapy has occurred because of a deep understanding of the elementary processes of cell growth and development, although nearly all cancer research, above the purely clinical level, is devoted precisely to understanding the most intimate details of cell biology. Medicine remains, despite all the talk of scientific medicine, essentially an empirical process in which one does what works.
Already by 1991, the first genetically modified crops were appearing.   The number of drugs and disease treatments that have proceeded from at least some understanding of the fundamental biology involved have greatly increased.   In that sense the above is now somewhat dated.

But the reason for mentioning the quote above is that it gives a clue as to what Lewontin might mean by scientific medicine.   He seems to mean medicine based on deep understanding of the underlying biology.

For instance, as far as I know, we only know that high LDL cholesterol is correlated with heart disease, and that lowering cholesterol seems to reduce the risk of death from heart disease in many populations.  But the causal mechanisms are unclear.

Similarly, some cancer drugs are designed to attack the rapidly dividing cells of a tumor; but why the tumor cells have become that way in the first place is not clear. 

In that sense, we are still largely in the state of "essentially an empirical process in which one does what works". 

Sunday, August 18, 2013

Interview of Lewontin

A 2004 interview with Richard Lewontin.  The whole transcript is well worth reading.  Lewontin is eminently sensible, I suppose what annoys Pinker-types is views like this:
On the specific side, genetics, in particular, has for its entire history, since the beginning of the twentieth century, except for a very brief period during the Second World War, genetics has been extremely -- what shall I call it? -- deterministic in its view of the causes of human and social behavior. Geneticists have been, if you like, imperialistic in saying genes are responsible for everything.

Don't Text and Drive

The NYT Editorial Board weighs in on this Werner Herzog documentary.
While Mr. Herzog’s films are often ambiguous in nature, without a clear-cut editorial point, his message in this documentary is absolutely apparent. “Don’t ever text and drive.” Mr. Gerber says, “You get one chance, and you live with the choices you make.” 

The National Safety Council estimated that roughly 200,000 crashes in 2011 involved texting; and an AT&T Wireless survey found that 75 percent of teenagers say texting while driving is “common” among their friends. Whether or not Mr. Herzog’s film can actually reduce those figures, the project sets a high standard for how corporations can educate the public.

Saturday, August 17, 2013

More on Maudlin and Time

Douglas Kutach has a wiki, Project Line:
This is a repository of information on the Theory of Linear Structures (TLS) and a workspace for its further development. .....The Theory of Linear Structures is an alternative framework for describing physical geometry. It replaces the standard theory of point-set topology based on open sets with a version of point-set topology based on lines. ....The theory and its benefits are presented in Tim Maudlin's New Foundations for Physical Geometry, forthcoming from Oxford University Press.
Of interest to anyone who wants to sink their teeth into TLS are these problem sets.


Patience and Persistence

At the pixel level, these photos aren't great - and even with a 12mm extender tube, the minimum focus distance of the 400mm f/5.6 is large -  but I'm posting them as a reminder to self that the labor of growing hummingbird- and butterfly- friendly plants is worth it, patience is called for. Photography also requires patience :).


Friday, August 16, 2013

Lewontin - A Systems Thinker?

This review of Lewontin's book The Triple Helix (2000) makes it seem that Lewontin was a systems thinker.

Lewontin - "A Reasonable Skepticism"

Read the full essay.

For almost the entire history of European society since the empire of Charlemagne, the chief institution of social legitimation was the Christian Church. It was by the grace of God that each person had an appointed place in society. Kings ruled Dei gratia. Occasionally divine grace could be conferred on a commoner who was ennobled, and grace could be removed. Grace was removed from King Charles I, as Cromwell noted, and the proof was Charles's severed head. Even the most revolutionary of religious leaders pressed the claims of legitimacy for the sake of order. Martin Luther enjoined his flock to obey their lords, and in his famous sermon on marriage he asserted that justice was made for the sake of peace and not peace for the sake of justice. Peace is the ultimate social good, and justice is important only if it subserves peace.

Thursday, August 15, 2013

For People Who Have Read Too Much Pinker

H. Allen Orr in the NY Review of Books:
Fourth, I argued that Pinker minimized his debt to Enlightenment thought. One of his key claims in TBS {The Blank Slate} was that evolutionary psychology poses no threat to human decency. Another was that morality evolved. But I pointed out that the morality Pinker used at every turn to pacify evolutionary psychology was a product of Enlightenment liberalism, not evolution. Pinker now says that he is “the first to agree.” It’s too bad he couldn’t find room to agree in his 509-page book.
Which is exactly also why I who rarely agree with Douthat agree with him here. I read Pinker as saying that common sense (some unexceptionable conviction) + science provides us an adequate moral system.

The facts of science, by exposing the absence of purpose in the laws governing the universe, force us to take responsibility for the welfare of ourselves, our species, and our planet. For the same reason, they undercut any moral or political system based on mystical forces, quests, destinies, dialectics, struggles, or messianic ages. And in combination with a few unexceptionable convictions— that all of us value our own welfare and that we are social beings who impinge on each other and can negotiate codes of conduct—the scientific facts militate toward a defensible morality, namely adhering to principles that maximize the flourishing of humans and other sentient beings. This humanism, which is inextricable from a scientific understanding of the world, is becoming the de facto morality of modern democracies, international organizations, and liberalizing religions, and its unfulfilled promises define the moral imperatives we face today.

The problem, as H. Allen Orr points out is that those unexceptionable convictions that he has are really a specific product of a specific worldview.

Wednesday, August 14, 2013

A quote from Lewontin

Richard Lewontin, 1979. One can go and nitpick on the rest of his letter; but what would be interesting really is a refutation of what Lewontin claims to be facts below, leaving aside his extrapolations. That is, the statements below are not true; or that he has failed to mention significant other facts that change how we would interpret these statements.

In 1828, when causes of death were first systematically recorded in Britain, the death rate from tuberculosis was nearly 4,000 per million. The rate can only be appreciated in contrast to the present death rate in the US and Britain from all causes of only 9,000 per million. By 1855 the death rate from tuberculosis had fallen to about 2,700 and continued to fall steadily so that by the turn of the century it had reached about 1,200 per million. Koch’s discovery of the causal bacillus in the 1880s had no effect whatsoever on the rate of decline, and by 1925, after the Flexner revolution in medical schools, the rate was about 800, only 20 percent of its value in 1838. Totally unaffected by the arrival of modern medicine, the death rate continued its steady drop to 400 per million until 1948 when the introduction of chemotherapy on a broad scale did indeed accelerate the decline to its present negligible level. It is important to note that 57 percent of the decline had occurred by 1900 and 90 percent of the decline had occurred by the time of the introduction of chemotherapy. Extrapolation of the trend predicts that by 1970 death from tuberculosis would have reached its present low value even in the absence of chemotherapy.

The history of tuberculosis is the history of nearly all the major killers of the nineteenth century. Whooping cough, scarlet fever, and measles, all with death rates in excess of 1,000 per million children, and bronchitis, all declined steadily with no observable effect of the discovery of causative agents, of immunization or of chemotherapy. The sole exception was diphtheria which began its precipitous decline in 1900 with the introduction of anti-toxin and which was wiped out in five years after the national immunization campaign. The most revealing case is that of measles which killed about 1,200 in every million children in the nineteenth century. By 1960, despite the complete absence of any known medical treatment, it had disappeared as a cause of death in Britain and the US while in much of Africa it remains the chief cause of death of children.

The causes of the tremendous decline of mortality from infectious diseases in the last 100 years are not certain. All that is certain is that “scientific medicine” played no significant part. Water supply and sanitation are not involved, since water-borne diseases have not been the major killers. The suggestion that a reduction in crowding may have reduced the rate of transmission of respiratory diseases is not altogether convincing, since measles remains pandemic although it kills virtually no one in advanced countries. The most likely explanation, both for the historical trend and for the differences between regions of the world today, is in nutrition, although hard evidence is not easy to come by.

Proof Positive of Hummingbirds

Since this spring I've been regularly cleaning and refilling feeders, and occasionally excitedly reporting glimpses of hummingbirds, and now the season is running out.  It is mid-August, and soon the hummers will begin their migration south.  So with a now or never, this evening, I sat in wait with the 400mm f/5.6.  (Well, maybe it was because I really had other things to do, but was procrastinating.)

Here's the uncropped first proof:

Tuesday, August 13, 2013

Time and Tim Maudlin

Tim Maudlin seems to want to bake time into the topological structure of spacetime. E.g., see:

What I'm wondering is whether it gets him anything. More specifically - There is a theorem in "Analysis, Manifolds and Physics", Choquet-Bruhat and DeWitt-Morette, (chapter 5, page 293):

Hyperbolic structure.  A line element (direction) at x ∈ X is a 1-dimensional vector subspace of Tx (the tangent vector space at x).

Theorem: On a paracompact C1 manifold X the existence of a continuous line element field is equivalent to the existence of a hyperbolic riemannian structure on X.

This continuous line element field essentially gives the time dimension on X.

What does Maudlin obtain that this theorem does not give him? I guess I'll have to wait to see his book due next year. There is a very readable draft introduction here.  In fact, I think almost anyone can read the introduction.

PS: there is a more recent presentation here.

Monday, August 12, 2013

A significant point

Benjamin Fong in the NYT:

The real trouble with the Brain Initiative is not philosophical but practical. In short, the instrumental approach to the treatment of physiological and psychological diseases tends to be at odds with the traditional ways in which human beings have addressed their problems: that is, by talking and working with one another to the end of greater personal self-realization and social harmony.

In “Biology as Ideology,” Richard Lewontin points to the profound difference between the fact that one cannot get tuberculosis without a tubercle bacillus and the claim that the tubercle bacillus is the “cause” of tuberculosis. Registering that tuberculosis was a disease common in sweatshops in the 19th century, Lewontin contends: “We might be justified in claiming that the cause of tuberculosis is unregulated industrial capitalism, and if we did away with that system of social organization, we would not need to worry about the tubercle bacillus.” Having narrowed their view of “cause” to the biological realm, neuroscientists today are effectively chasing tubercle bacilli, drawing our focus away from the social practices and institutions that contribute to problems of mental health.

We know, for instance, that low socioeconomic status at birth is associated with a greater risk of developing schizophrenia, but the lion’s share of research into schizophrenia today is carried out by neurobiologists and geneticists, who are intent on uncovering the organic “cause” of the disease rather than looking into psychosocial factors. Though this research may very well bear fruit, its dominance over other forms of research, in the face of the known connection between poverty and schizophrenia, attests to a curious assumption that has settled into a comfortable obviousness: that socioeconomic status, unlike human biology, is something we cannot change “scientifically.” That it is somehow more realistic, “scientifically,” to find a way to change the human being itself than it is to work together to change the kind of environment that lends itself to the emergence of a disorder like schizophrenia.

Modern Hindu Mysticism

Eknath Easwaran, “The Dhammapada”, an excerpt, as an example of modern Hindu mysticism.


Despite the Buddha’s extraordinary capabilities, we must accept his own testimony that until the night of his enlightenment he saw life essentially the way the rest of us do.  Yet after that experience he lived in a world where concepts like time and space, causality, personality, death, all mean something radically different.  What happened to turn ordinary ways of seeing inside out?

In the Vinaya Pitika (III, 4) the Buddha left a concise roadmap of his journey to nirvana—a description of the course of his meditation that night cast in the kind of language a brilliant clinician might use in the lecture hall. In Buddhism the stages of this journey are called the “four dhyanas” from the Sanskrit word for meditation which later passed into Japanese as zen.  Scholars sometimes treat passage through the four dhyanas as a peculiarly Buddhist experience, but the Buddha’s description tallies not only with the Hindu authorities like Patanjali but also with Western mystics like John of the Cross, Teresa of Avila, Augustine, and Meister Eckhart.  What the Buddha is giving us is something of universal application: a precise account of levels of awareness beneath the everyday waking state.

On that night, he tells us, he seated himself for meditation with the resolve not to get up again until he had attained his goal.   Then, he continues,

Do not text and drive

Please view this Werner Herzog documentary: "From One Second To The Next".

MSNBC reported on it thus:

Part of AT&T's "It Can Wait" campaign and distributed Thursday to 40,000 high schools across the country, this 35-minute PSA by acclaimed German filmmaker Werner Herzog is nothing short of haunting. Focusing on four separate car accidents, "From One Second to the Next" is an unflinching look into the grief and guilt of both the victims and the drivers. It is a painful watch, but also an important one. "What AT&T proposed immediately clicked and connected inside of me," Herzog told the Associated Press. "I'm not a participant of texting and driving — or texting at all — but I see there's something going on in civilization which is coming with great vehemence at us." — By Michaela Gianotti [Source]

Sunday, August 11, 2013

Arctic Ice

Some Theodore Dalrymple

Thoughts on Woolwich
What these cases show is that it is not Islam that makes young converts violent; it is the violence within them that causes them to convert to Islam. The religion, in its most bloodthirsty form, supplies all their psychological needs and channels their anger into a supposedly higher purpose. It gives them moral license to act upon their rage; for, like many in our society, they do not realize that anger is not self-justifying, that one is not necessarily right because one is angry, and that in any case even justified anger does not entail a license to act violently. The hacking to death of Lee Rigby on a street in Woolwich tells us as much about the society that we have created, or allowed to develop, as it does about radical Islam preached by fat, middle-aged clerics.

Saturday, August 10, 2013

How the Buddha was turned Anti Hindu

Worth a read.
Far from being a revolutionary, the Buddha emphatically outed himself as a conservative, both in social and in religious matters. He was not a rebel or a revolutionary, but wanted the existing customs to continue.

Tuesday, August 06, 2013

The Robber State

Via, a New Yorker story, "Taken", tells us how civil forfeiture laws enable local police and law departments to extort property from innocent citizens who haven't been charged with anything.
In general, you needn’t be found guilty to have your assets claimed by law enforcement; in some states, suspicion on a par with “probable cause” is sufficient. Nor must you be charged with a crime, or even be accused of one. Unlike criminal forfeiture, which requires that a person be convicted of an offense before his or her property is confiscated, civil forfeiture amounts to a lawsuit filed directly against a possession, regardless of its owner’s guilt or innocence.
Over the past year, I spoke with more than a hundred police officers, defense attorneys, prosecutors, judges, and forfeiture plaintiffs from across the country. Many expressed concern that state laws designed to go after high-flying crime lords are routinely targeting the workaday homes, cars, cash savings, and other belongings of innocent people who are never charged with a crime.
Texas become Bihar, except that nobody in Bihar would pretend this is anything but corrupt.  India has a reputation for corruption, but that sometimes seems to simply mean that practices that are legal in Texas are illegal in India. (It is not just Texas that uses these laws, but that state prides itself in protecting the untrammeled rights of a property owner to do whatever; it seems to be true only if the property owner is rich, powerful and connected.)

And where is the Supreme Court of the USA in all of this?  It has no hesitation promoting the conservative majority's pet political causes, like installing a President Bush, allowing unlimited money in politics, in eviscerating voting rights, and so on.