The story of evolution-7: Genes, chromosomes, and DNA

In order to understand how inheritance works and the mathematics involved, it may be helpful to have a quick summary of some basic facts about genetics (a little simplified), using the human genome for concreteness.

All the genetic information in our bodies is found in the DNA, whose famous double helix structure was discovered in 1953. Thanks to the Human Genome Project, we now have a complete map of the DNA of humans, called the human genome, and know that it consists of a sequence of 3.1647 billion sites arranged in a row, each site containing one of four complex molecules (called bases) labeled A, C, T and G. It is this long arrangement of the four bases that define each of us genetically. Almost 99.9% of the arrangement of these bases is identical in all humans, and about 98% is identical between chimpanzees and us.
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Discussing health care seriously

In my discussions with people on serious and controversial topics, I have some simple rules of thumb to tell me tell whether the discussion is worth pursuing or whether the other person is not serious and talking further is a waste of time.

For example, when discussing evolution, as soon as someone says something along the lines of Mel Gibson’s “If we descended from monkeys, then how come there are still monkeys? How come apes aren’t people yet?” then you know that you are dealing with someone who is either being willfully dishonest or is so ignorant of the basic facts of the topic under discussion that it is not worth continuing unless one is willing to spend a lot of time to bring that person up to speed. The wrongful use of the second law of thermodynamics is another example of a warning sign.

A similar situation applies to global warming when, during a cold or snowy spell someone triumphantly suggests that this has conclusively proven that global warming is a myth.

In discussing politics, the signal is when one makes a criticism of some action of the US government (such as its decision to ignore habeas corpus, or to invade Iraq, or its numerous covert destabilization actions in other countries) and the other person replies “If you don’t like it, then why don’t you go to Russia/France/China/Cuba/Sweden/(fill in the blank for whatever other country the speaker does not like)?”

In all these cases, the signs are clear that there has been no attempt by the other person to really engage with the issue and he or she has resorted to what he or she thinks is a clever debating point but in actuality has little or no content behind it.

In the case of the debates over the merits of a universal, government run, single-payer health care system, the signal that someone is not serious is when he or she trots out the waiting times for hip replacements in Canada as an argument about how the Canadian system is so terrible in comparison to the US. In the wake of the release of Michael Moore’s film Sicko, we can expect to see this being trotted out repeatedly, as indeed it already has.

As Kevin Drum pointed out a few months ago, the hip replacement argument is a sign of egregious cherry picking of data.

When comparing huge and complex systems like the health care or education systems in different nations, making point-to-point comparisons of isolated cases is of little use. No system is going to be better at every single thing, so this kind of debate results in each side selecting just those pieces of data to suit its purposes. There are probably some elective procedures for which there are longer waiting times in other countries than for those with high quality insurance plans in the US. It would not surprise me in the least if access to tests using expensive equipment like MRI machines is easier in the US (for those who have the requisite insurance coverage, of course) than it is for people in other countries. Health care in the US is aimed at servicing the well-to-do, because it is they who are the decision and policy-makers and as long as they are kept content, they are unlikely to want to make changes that reduce the profits of the health care industry, let alone eliminate them entirely, even if the changes benefit the general public.

One needs to look at aggregate measures to better compare quality and cost across nations. For example, the World Health Organization in 2000 put out The world health report 2000 – Health systems: improving performance in which it used the following measures for the comparison for health systems, using measures of both goodness and fairness:

  1. overall good health (e.g., low infant mortality rates and high disability-adjusted life expectancy);
  2. a fair distribution of good health (e.g., low infant mortality and long life expectancy evenly distributed across population groups);
  3. a high level of overall responsiveness;
  4. a fair distribution of responsiveness across population groups; and
  5. a fair distribution of financing health care (whether the burden of health risks is fairly distributed based on ability to pay, so that everyone is equally protected from the financial risks of illness)

Based on these criteria, according to the WHO study (p. 152), the US comes in at #37 in rank internationally, compared to France (#1), England (#18), Canada (#30), and Cuba (#39).

Michael Moore’s Sicko (which you should really see) points out that on measures like life expectancy at birth and infant mortality rates (i.e., the number of infants who die before reaching the age of one year for each 1,000 births), the US lags behind its developed world counterparts, even though its spends far more on health care as a fraction of its GDP (13.6% in 1998) than its nearest competitor Germany (10.6%). Per capita spending is also highest is the US ($4,178) with the next highest being Switzerland ($2,794).

The reason the US gets so much less for the money it spends on health care is because of the vast amounts siphoned off to the insurance and drug companies, partly due to profits and partly due to a huge bureaucracy to handle the complex billing and processing process involved with private health insurance. Such costs account for between 19.3 and 24.1% of health care spending in the US compared with between 8.4 and 11.1% in (say) Canada.

image001.pngThere is a strong (negative) correlation between infant mortality and life expectancy, as can be seen from this graph, where each dot represents the data for a country, along with a linear regression line. The implication is clear that the best way to improve life expectancy is to reduce infant mortality. The reason that many developing countries have high infant mortality rates and resulting low life expectancy is that lack of access to clean water results in diarrhea and this leads to dehydration, which is often fatal for infants. (As an aside, the international conglomerate Nestle deserves widespread condemnation for its policy of marketing infant formula in the developing countries, despite the lack of easy access to clean water to prevent infection. Breastfeeding is always preferred except in exceptional cases, but because of the Nestle marketing campaign became perceived as inferior to formula.)

But when comparing the US to the rest of the developed world, access to clean water is not the main issue, so widespread access to health care emerges as the prime suspect for its low ranking. For example, infant mortality rates for non-whites in US cities are two to three times as high as the national average.

What really irks many people in the US about Moore’s film is perhaps not so much the adverse comparison with Canada, England and France. People who for some reason are enamored of the system here will complacently trot out once again hip replacement waiting times to claim a spurious superiority. It is the fact that among the 221 countries listed, Cuba’s infant mortality rate (6.04, rank 40) and life expectancy rates (77, rank 56) are almost identical with the US infant mortality (6.37, rank 42) and life expectancy (78, rank 45) that really rankles.

The US government’s implacable animosity to Cuba, trying to strangle its economy with boycotts and embargos and repeated attempts at destabilization and even assassination of its leaders, has to be one of the cruelest policies ever implemented towards a country that is not a threat to its security. And yet despite that deliberate attempt at destroying the Cuban economy, Cuba has managed to create a public health system that is a model for third world countries, and produces results in key indices that are comparable with the US. Cuba is legendary among third world countries in its generosity, sharing its medical personnel and expertise around the world.

Kevin Drum wonders if Moore’s use of Cuba in his film was a clever public relations strategy, knowing that it would trigger the almost reflexive anti-Cuba venom that exists in certain quarters in the US and that they would make a huge fuss, thus giving him free publicity. “Moore’s brilliance at getting his mortal enemies to do all his publicity for him is unparalleled.”

Drum may be right. In the weird media world we live in, it is not enough for Moore to accurately portray the scandal that is the US health system compared to its peer countries. That information has been out there for a long time, and ignored by the power elites. He had to create a fuss and by going to Cuba, he did so.

POST SCRIPT: This Modern World

Cartoonist Tom Tomorrow sums up the predictable responses to Sicko by the apologists for the US health care industry.

The story of evolution-6: The probabilities of natural selection

There are three mathematical ideas that one needs to come to terms with in order to get the full flavor of how natural selection works.

  1. One is the rate at which favorable mutations occur in organisms. These do occur by chance and the question is whether the frequency of such occurrences is sufficient to explain evolution.
  2. The second is the rate at which favorable mutations become more numerous in the population. It is not enough to produce a single favorable organism. The population of varieties with advantageous properties has to eventually grow to sufficiently high numbers that it dominates the population and can form the basis for yet further mutations.
  3. The third is whether the rate at which repeated small and favorable mutations build on each other is sufficient to produce major changes in complex systems (the eye, ear, and other organs for example) and even entirely new species.

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Defending the right of free speech and Dennis Kucinich

Since today is a holiday, there will be no original post today. Instead, here are some video clips.

One is of the late Frank Zappa of the group Mothers of Invention on Crossfire talking about the right of free speech.

It is always fun when someone appears on these idiotic talk/yell shows and simply says what he thinks. In this clip from 1986, Zappa drives the person from the Washington Times crazy with his quick-witted defense of free speech and his sardonic sense of humor.

Also, here is an interview of Dennis Kucinich on David Letterman’s show. Kucinich is the only candidate for president who takes the correct stands on the two most fundamental issues facing the US: The Iraq war and the need for single-payer universal health care.

On the pursuit of happiness

On this day before independence day, I wanted to reflect on what to me is one of the most intriguing phrases in the US Declaration of Independence, and is contained in the famous sentence:

We hold these truths to be self-evident, that all men are created equal, that they are endowed, by their Creator, with certain unalienable Rights, that among these are Life, Liberty, and the pursuit of Happiness.

I have always found the inclusion of the phrase “the pursuit of happiness” as a fundamental goal to be quaint and appealing. One does not expect to see such pleasing and innocently worded sentiment in a political document, and its inclusion sheds an interesting and positive light on the minds and aspirations of the people who signed that document.

But the problem has always been with how happiness is attained. And in one serious respect, Jefferson’s suggestion that we should pursue happiness, while laudable, may also be misguided. Happiness is not something to be pursued. People who pursue happiness as a goal are unlikely to find it. Happiness is what happens when you are pursuing other things. The philosopher Robert Ingersoll also valued happiness but had a better idea about what is would take to achieve it: “Happiness is the only good. The place to be happy is here. The time to be happy is now. The way to be happy is to make others so.”

Kurt Vonnegut in his last book A Man Without a Country suggests that the real problem is that we don’t realize when we are happy, and that we should get in the habit of noticing those moments and stop and savor them.

I apologize to all of you who are the same age as my grandchildren. And many of you reading this are probably the same age as my grandchildren. They, like you, are being royally shafted and lied to by our Baby Boomer corporations and government.

Yes, this planet is in a terrible mess. But it has always been a mess. There have never been any “Good Old Days,” there have just been days. And as I say to my grandchildren, “Don’t look at me, I just got here.”

There are old poops who will say that you do not become a grown-up until you have somehow survived, as they have, some famous calamity — the Great Depression, the Second World War, Vietnam, whatever. Storytellers are responsible for this destructive, not to say suicidal, myth. Again and again in stories, after some terrible mess, the character is able to say at last, “Today I am a woman. Today I am a man. The end.”

When I got home from the Second World War, my Uncle Dan clapped me on the back, and he said, “You’re a man now.” So I killed him. Not really, but I certainly felt like doing it.

Dan, that was my bad uncle, who said a man can’t be a man unless he’d gone to war.

But I had a good uncle, my late Uncle Alex. He was my father’s kid brother, a childless graduate of Harvard who was an honest life-insurance salesman in Indianapolis. He was well-read and wise. And his principal complaint about other human beings was that they so seldom noticed it when they were happy. So when we were drinking lemonade under an apple tree in the summer, say, and talking lazily about this and that, almost buzzing like honeybees, Uncle Alex would suddenly interrupt the agreeable blather to exclaim, “If this isn’t nice, I don’t know what is.”

So I do the same now, and so do my kids and grandkids. And I urge you to please notice when you are happy, and exclaim or murmur or think at some point, “If this isn’t nice, I don’t know what is.”

Good advice.

Film review: Sicko

When I was just six years old, I became gravely ill with polio. Although Sri Lanka had first-rate doctors, they felt at that time that they did not have the specialized services to provide the kind of treatment that was best for me and recommended that, if at all possible, my family take me to England. We were not wealthy, just middle class, and did not have the kind of money that would enable my parents to afford this. But by an incredible stroke of luck, my father just happened to work for the Sri Lankan state bank that just happened to have a branch in England. It was the bank’s practice to rotate their officers to that branch and my father was due to go in few years but because of the urgency of my illness, his bosses quickly arranged for him to be immediately transferred to the London branch. As a result we arrived in England and simply by virtue of the fact that we now lived there, I was able to get health care through the British National Health Service.
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The story of evolution-5: How probability intuition can lead us astray

One of life’s ironies is that the difficulty in understanding the mathematics of Darwin’s theory of natural selection may actually be caused by natural selection itself.

As we saw earlier, natural selection does not try for maximum benefit but instead works on a ‘just good enough for now’ principle. Steven Pinker in his book How the Mind Works (1997) is a cognitive scientist who believes that natural selection has been the driver for most aspects of our bodies and our behavior, and that the brain, being just another organ, has evolved to do what it does to effectively meet the challenges it faced at various times in our somewhat distant past. Pinker points out that humans, when compared with other animals, have unusually large brains compared to body size but that this rapid expansion in brain size occurred more than 100,000 years (or about 5,000 generations) ago (Pinker, p. 198) and then leveled off after that. This means that the structure of our present brains has been largely determined by a time when humans were hunter-gatherers and foragers. [Read more…]

Blowback

If you read some of the more thoughtful analyses of the reasons behind the 9/11 attacks, you may have noticed repeated use of the word ‘blowback’. Some may not be aware that this word is used by the CIA to denote the consequences that its covert activities abroad might cause, and the disasters they might someday bring down on the US.

The idea that one’s actions have repercussions is perfectly sensible. It is absurd to think that US foreign policy, especially when it is used aggressively and militarily and covertly to interfere in the internal affairs of other countries, will not give rise to opposition and antagonism that may manifest itself in unexpected and unconventional ways.

This rational view of how actors behave on the world stage is excoriated by those demagogues in the media (by which I mean the major political leaders and pundits) who prefer to couch foreign policy debates in simple dualistic good-and-evil terms, and to suggest that the ‘evil they’ hate the ‘good us’ simply because of our virtue.

The word ‘blowback’ and its associated meaning moved from the murky clandestine world and entered the popular culture when it was used as the title of an influential book Blowback: The Costs and Consequences of American Empire published in 2000 by Chalmers Johnson. Johnson is a former CIA consultant and a professor of Asian studies at Berkeley, and was an avowed cold-war warrior during the Vietnam war era.

Johnson has now written a very interesting article titled Evil Empire: Is Imperial Liquidation Possible for America? on the current state of affairs. The whole article is quite long but well worth reading but here are some excerpts:

The United States, today, suffers from a plethora of public ills. Most of them can be traced to the militarism and imperialism that have led to the near-collapse of our Constitutional system of checks and balances.
. . .
If these people actually believe a presidential election a year-and-a-half from now will significantly alter how the country is run, they have almost surely wasted their money. As Andrew Bacevich, author of The New American Militarism, puts it: “None of the Democrats vying to replace President Bush is doing so with the promise of reviving the system of check and balances…. The aim of the party out of power is not to cut the presidency down to size but to seize it, not to reduce the prerogatives of the executive branch but to regain them.”

George W. Bush has, of course, flagrantly violated his oath of office, which requires him “to protect and defend the constitution,” and the opposition party has been remarkably reluctant to hold him to account. Among the “high crimes and misdemeanors” that, under other political circumstances, would surely constitute the Constitutional grounds for impeachment are these: the President and his top officials pressured the Central Intelligence Agency to put together a National Intelligence Estimate (NIE) on Iraq’s nuclear weapons that both the administration and the Agency knew to be patently dishonest. They then used this false NIE to justify an American war of aggression. After launching an invasion of Iraq, the administration unilaterally reinterpreted international and domestic law to permit the torture of prisoners held at Abu Ghraib prison in Baghdad, at Guantánamo Bay, Cuba, and at other secret locations around the world.

Nothing in the Constitution, least of all the commander-in-chief clause, allows the president to commit felonies. Nonetheless, within days after the 9/11 attacks, President Bush had signed a secret executive order authorizing a new policy of “extraordinary rendition,” in which the CIA is allowed to kidnap terrorist suspects anywhere on Earth and transfer them to prisons in countries like Egypt, Syria, or Uzbekistan, where torture is a normal practice, or to secret CIA prisons outside the United States where Agency operatives themselves do the torturing.

On the home front, despite the post-9/11 congressional authorization of new surveillance powers to the administration, its officials chose to ignore these and, on its own initiative, undertook extensive spying on American citizens without obtaining the necessary judicial warrants and without reporting to Congress on this program. These actions are prima-facie violations of the Foreign Intelligence Surveillance Act of 1978 (and subsequent revisions) and of Amendment IV of the Constitution.

These alone constitute more than adequate grounds for impeachment, while hardly scratching the surface.

It is a measure of how weakened the Congress has become that it has failed to seriously consider impeachment of the President despite having a very strong case for doing so. Only Congressman and Democratic presidential candidate Dennis Kucinich has made any moves to at least impeach Vice President Cheney.

POST SCRIPT: The flourishing of nonsense

Not heard about best selling self-help book The Secret? These two funny guys from Australia explain what it is all about and take the correct attitude towards it. (Thanks to Onegoodmove.)

One reason that religion is a negative influence in society is that it enables other evidence-free beliefs to flourish in its wake, because it creates a climate where vague mystical and supernatural forces are given credibility. How else can one explain the vast numbers of people who take stuff like The Secret seriously?

Materialists can dismiss this stuff as nonsense because it invokes some mysterious and unknown agency that intervenes in the world in response to human requests. But on what basis can someone who believes in a personal god do so, even if they wanted to? Isn’t The Secret based on prayer and faith, just like religion?

The story of evolution-4: Darwin gets an idea from Malthus

In Darwin’s travels to distant lands from 1831 to 1836 on the Beagle, the different climates and environmental conditions he encountered made him aware of the weakness of the existing theory of ‘special creation’, where god was assumed to have created creatures best suited for their environment. Darwin saw for himself that very similar climates could produce hugely different kinds of species, and that the nature of these species seemed to be more influenced by the species in nearby areas than by anything else. This seemed to him to suggest that new species arose from the modifications of the old.

The discovery that the Earth was much older than had been previously thought, and the evidence for which was in the geology book by Charles Lyell that he had read on the boat, told him that it may be possible for these changes to occur gradually by very small steps provided that there was enough time for the changes to accumulate.
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The mixed views of candidate Ron Paul

If anyone had any doubts that the US is ruled by a single pro-war, pro-business party, recent Congressional action should dispel them. It is clear that the wheels are already being oiled for starting a war with Iran, and the Democrats are complicit in this pre-war demagoguery, just as they were before the war with Iraq, when many voted for the Iraq war authorization resolution.
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