The Daily Show on CNN’s coverage of Monday’s ‘debate’

I do not, of course, waste my time watching these ridiculous ‘debates’. Anyone who has taken part in actual debates will dismiss the idea that these events come anywhere close to the real thing. What they remind me of are circuses with a self-important host pacing the floor like a ringmaster and the ‘contestants’ (which is what they are, not candidates) waiting like animals to do their well-rehearsed tricks.

Some blog accounts of Monday’s event said that the contestants had been asked questions like ‘Coke or Pepsi?’ I assumed that the writers were being funny, parodying the triviality of the whole thing. It was only when I watched the above clip that I realized that this had actually happened. Why didn’t at least one contestant refuse to answer on the grounds that such questions were silly and beneath them? I am waiting for the day when one of the contestants tells the smug, overweening TV personalities that run these things (they are not journalists) to get serious or go to hell.

I find it hard to comprehend that we have sunk so low, that we have trivialized to such an extent such an important aspect of civic life as selecting the people who get to govern us. We have ceased to be a serious people and deserve the rotten governments that result.

Who am I?

In yesterday’s post, I wrote about the fact that different parts of our bodies keep regenerating themselves periodically. This fact alone should make nonsense of the belief of some religious people that our bodies become physically reconstituted after death in the afterlife, because if so, the resurrected body of a person who died at the age of 70 would be unrecognizably grotesque, consisting of around 70 livers and 7 full skeletons, all surrounded by hundreds, maybe thousands, of pounds of skin.

But leaving aside that, there is an interesting question raised by this constant regeneration of the body and that is how we retain a sense of having a single identity over our full life spans even as individual parts of us get replaced periodically. The average age of the molecules in my body is around 7 to 10 years and yet I have the strong sense of continuity, that I am in some fundamental sense the same person that I was as a child, even though almost none of those molecules have stayed with me over that time. How is it that we retain a strong sense of permanence in our identity while being so transient in our bodies?

The answer may lie in the fact that our brain seems to be the most permanent of our organs, undergoing little or no regeneration. In the same article in the New York Times that I referred to yesterday, Nicholas Wade says:

Dr. Frisen, a stem cell biologist at the Karolinska Institute in Stockholm, has also discovered a fact that explains why people behave their birth age, not the physical age of their cells: a few of the body’s cell types endure from birth to death without renewal, and this special minority includes some or all of the cells of the cerebral cortex.

The cerebral cortex is the thin sheet that forms the outer layer of the brain and is divided up into several zones that have different functional roles. If the cortex were removed and smoothed out to eliminate all the creases and folds, it would look like a dinner napkin. It is gray in color, the origin of its popular euphemism of ‘gray matter’. The network of nerve cells in the brain (called neurons) determines how the brain functions.

brain.jpg

While the brain seems to be the most enduring part of the body, even here there is variation. The cerebellum seems to contain non-neuronal cells that are close to the birth age (within three years or so) while the cerebral cortex (which is responsible for our cognitive capabilities and is thus most closely identified with our sense of self) has a slightly greater turnover of non-neuronal cells. But the researchers do not turn up any evidence that there is neuronal generation after birth, at least in the region known as the occipital cortex.

It was long believed that the number of neuronal connections in the brain grew rapidly during the first year or two of life and then got pruned and this was how our lives shaped our brains without new neurons being created. In 1999, there was research that found that new neurons were being created in the cerebral cortex of adult monkeys, suggesting that it could happen in adult humans too. This would complicate things somewhat as to how we retain a permanent sense of self but also provide hope that brains could regenerate. But this summary of later research (much of it by the same Karolinka group that I referred to yesterday) that appeared in the Proceedings of the National Academy of Sciences says that this does not happen with the neurons in the human cerebral cortex. (The neocortex referred to in the paper is the most recently evolved part of the cortex that is defined as containing the ‘higher’ functions and are “arranged in six layers, within which different regions permit vision, hearing, touch, the sense of balance, movement, emotional responses and every other feat of cognition.”)

The results show that the average age of the neurons (with respect to the age of the individual) is age 0.0 ± 0.4 years, i.e., the same as the age of the individual. In contrast, the nonneuronal cells have an average birth date of 4.9 ± 1.1 years after the birth of the individual.
…
Both of the experiments of Bhardwaj et al. indicate that there are no new neurons, either long-lived or transient, produced in the adult human for the neocortex. Importantly, these experiments are quantitative and indicate a theoretical maximum limit of 1% on the proportion of new neurons made over a 50-year period.
…
Bhardwaj et al. settle a hotly contested issue, unequivocally. The two-pronged experimental approach clearly establishes (i) that there is little or no continuous production of new neurons for long-term addition to the human neocortex and (ii) that there are few if any new neurons produced and existing transiently in the adult human neocortex. Importantly, the results are quantitatively presented, and a maximum limit to the amount of production of the new neurons can be established from the data presented. The data show that virtually all neurons (i.e., >99%) of the adult human neocortex are generated before the time of birth of the individual, exactly as suggested by Rakic, and the inescapable conclusion is that our neocortical neurons, the cell type that mediates much of our cognition, are produced prenatally and retained for our entire lifespan. [My italics]

So basically, even though every other part of us gets sloughed off and replaced at different points in time, for good or bad we are pretty much stuck with the brains that we have at birth. This may be crucial to our ability to retain a sense of a permanent identity that lasts all through our lives, although this is not yet established. Even if new research emerges that new neuronal cells could be generated over time replacing older ones, it may turn out to be able to do this seamlessly and provide cognitive continuity, just the way our other organs give us the illusion of being permanent even though they are not.

It seems like our brains are our essential selves with the rest of our bodies just superstructure. Rene Descartes famously said “I think, therefore I am.” We could also say, “My brain is who I am.”

How old are you?

In an article in the New York Times, Nicholas Wade points out that our bodies are younger than we think, because there is a discrepancy between our birth age and the age of the cells that make up our bodies

Whatever your age, your body is many years younger. In fact, even if you’re middle aged, most of you may be just 10 years old or less.

This heartening truth, which arises from the fact that most of the body’s tissues are under constant renewal, has been underlined by a novel method of estimating the age of human cells. Its inventor, Jonas Frisen, believes the average age of all the cells in an adult’s body may turn out to be as young as 7 to 10 years.

He quotes the work of Spalding, Bhardwaj, Buchhold, Druid, and Frisén of the Karolinska institute that uses the radioactive isotope carbon-14 to determine the age of the cells in bodies. Their paper appeared in the July 15, 2005 issue of Cell. They used carbon-14 dating to determine the age of cells. The carbon that forms organic matter is largely obtained from the atmosphere. Plants, for example, take in carbon dioxide from the air and exude oxygen as part of the process of photosynthesis. Hence the proportion of carbon-14 that is found in living organic matter is the same as that in the ambient atmosphere at the time it was absorbed. The level of the radioactive isotope carbon-14 that occurs in the atmosphere is fairly constant because its rate of production is balanced by the rate of decay. Once the plant dies, it does not take in any new carbon and the decay of the carbon-14 that it had at the moment of death results in a steadily smaller proportion of it and the difference can be used to measure how long it has been dead. The half-life of carbon-14 is 5,730 years and this method can be used to determine the age of dead organic matter up to about 50,000 years, which is a convenient range for archeological dating because it lies in the range required for those studies.

The way that Frisén and his co-workers used this knowledge to measure the age of cells in humans is quite clever. Carbon-14 is produced by cosmic rays and the level of carbon-14 in the atmosphere should be constant. This is why we can tell how long something has been dead but not when it was ‘born’, i.e., when the organic matter was created. But in the 1950s and 1960s, there was a sharp spike in carbon-14 levels because of the atmospheric testing of nuclear weapons. Once atmospheric test ban treaties came into came into being, the surge of carbon-14 that had been produced steadily became diffused in the atmosphere as it spread over the globe, and so there has been a steady decline in average carbon-14 levels over time. It is this that enables us to know when the carbon-14 was absorbed to create organic matter.

cell images_Page_02_Image_0001.jpg

The amount of carbon-14 in the genomic DNA can thus be used to measure when the DNA in the cell was created. The technique was checked against the age of trees which can be measured by the amounts of carbon-14 found in the various rings as the isotope is absorbed during photosynthesis. Their results and those of others show that different parts of the body get replaced after different durations, whose approximate values are given below. (I have included results from both the Wade newspaper article and the Frisen paper.)

Stomach lining: five days
Surface layer of skin: two weeks
Red blood cells: three months
Liver: one year
Skeleton: 10 years
Intestine: 11 years
Rib muscles: 15 years

This explains why our bodies seem so durable and able to withstand considerable abuse. [UPDATE: Later studies find that about 50% of our heart muscles are replaced over our lifetime, but the brain cells seem to be largely unchanged.]

So why do we die if parts of us keep getting regenerated? It seems as if the ability of stem cells to keep reproducing declines with age. In other words there seems to be a limit to the number of times that cells can reproduce and once we reach that limit, the ability of the body to regenerate itself ceases. What causes this limit is still an open question. As Wade writes:

Some experts believe the root cause is that the DNA accumulates mutations and its information is gradually degraded. Others blame the DNA of the mitochondria, which lack the repair mechanisms available for the chromosomes. A third theory is that the stem cells that are the source of new cells in each tissue eventually grow feeble with age.

Frisen thinks his research might be able to shed some light on this question, especially the third option, saying “The notion that stem cells themselves age and become less capable of generating progeny is gaining increasing support.”

The gays amongst us

I had never heard of Tracy Morgan until he appeared on The Daily Show a few weeks ago and I took an instinctive dislike to him. He seemed kind of obnoxious. I did not know if he was really like that or was playing a part and I did not really care.

The next thing I heard was that he had let loose a nasty homophobic rant during his stand up comedy routine.

Tina Fey, who plays his boss on a TV show, criticized his comments and in the process said something important that I hope all people will take to heart: “I hope for his sake that Tracy’s apology will be accepted as sincere by his gay and lesbian coworkers at 30 Rock, without whom Tracy would not have lines to say, clothes to wear, sets to stand on, scene partners to act with, or a printed-out paycheck from accounting to put in his pocket.”

Even if you don’t like gay people, you would be wise to keep your anti-gay bile to yourself, not because they will threaten you, but because they are all around us and we depend on them whether we are aware of it or not.

Informative budget chart

cbppdeficit.jpgWith all the talk of the deficit and national debt, it is illustrative to see the chart that the Center for Budget and Policy Priorities has published that shows the source of the projected budget deficits.

The main sources are the Bush-Obama wars and the Bush-Obama tax cuts for the rich, not ‘big government’, as is claimed by those who want to use the deficit as an excuse to further reduce government services and, more importantly, reduce government oversight over business.

This should come as no surprise to those who follow the numbers but it is worth periodically reiterating.

Patenting DNA and genetic tests

In an article titled Patently Unjust in the June 2010 issue of The Progressive (not available online), Kari Lydersen describes a similar issue to the one involving Henrietta Lacks, where private companies are making a bundle out of publicly funded research. In this case, the publicly funded Human Genome Project has made freely available the full human genome but some private companies have obtained patents over individual genes.

The particular case that Lydersen deals with involves the genes known as BRCA1 and BRCA2. Certain mutations in these genes are predictors of breast and ovarian cancer, since women with such mutations are five times more likely to develop breast cancer and ten to thirty times more likely to develop ovarian cancer. We are now able to test if a woman has these mutations in which case they have to make difficult decisions about whether to preemptively remove their breasts and ovaries. These genes were discovered as part of the genome project.

It turns out that a single company named Myriad Genetics holds several patents on the genes and as a result claims exclusive rights to the tests they developed to detect the mutations. They charge about $3,000 for the test, which prices many women out of the market. They claim that if companies could not make money, they would not have the incentive to develop the tests. There is some truth in this but it is also true that a huge amount of federal (i.e. public) research funding went into the research that provided the basis for the company’s work, which should also be a factor. If the public funds something, the public should also benefit.

The reasons given by the company’s founder for the high price they charge for the tests is revealing about the why medical costs are so high in the US. He says, “In the U.S. what you charge for a test is a complex equation of what it costs you to do it and what people will pay” (my italics). This is part of the problem in a system with employer-based private health insurance coupled with monopoly providers. Well-to-do groups with power can pressure their insurance companies to cover the costs of tests which enables the testing companies to charge higher prices than they need to merely cover costs and provide a reasonable profit. The price then becomes prohibitive for those without insurance and drives up the cost of health care. I have written about this before.

As Lydersen writes, this is a widespread problem.

Myriad is far from the only patent holder on human genes; about 20 percent of the human genome is patented. This basically means that only the patent holder can offer testing and other services related to a specific gene. Patents currently cover genes related to other diseases, including Alzheimer’s, asthma, colon cancer, muscular dystrophy, and spinal muscular atrophy, a hereditary disease that kills children at a young age.

What is worse, because the company claims exclusive rights to the genes, women cannot get a second opinion on such a major question. At a minimum, what is needed is at least for more than one company to be able to provide services so that they can compete with each other. Giving private companies monopoly power over the use of research results that were largely publicly funded seems wrong.

The intricacies of patent law are too subtle for me to get into but on the surface the U. S. Patent Office seems to have been too generous in allowing companies to patent genes. It is illegal to patent a product of nature but the US Patent Office has granted Myriad and similar outfits patents on the genes on the basis that they were able to isolate them from their natural state and purify them. But others argue that this is far too expansive a view. After all, just because you develop a technique to highly purify gold (say) should not enable you to claim the patent to gold. I can understand patents being awarded to the purifying process because that is something the company did develop. That would reward their intellectual contribution while yet preserving the right of other companies to invent alternative methods of purification of the same gene and thus develop competing tests.

The right of private companies to patent genes was litigated and Lydersen writes that in March of 2010 US District Judge judge Robert W. Sweet ruled that Myriad’s claims did not meet the test of what makes something derived from nature patentable and invalidated the patents, saying in his ruling:

“The patents issued by the USPTO are directed to a law of nature and therefore were improperly granted,” Sweet wrote. “DNA represents the physical embodiment of biological information, distinct in its essential characteristics from any other chemical found in nature…. DNAs existence in an ‘isolated’ form alters neither this fundamental quality of DNA as it exists in the body nor the information it encodes. Therefore, the patents at issue directed to ‘isolated DNA containing sequences found in nature are unsustainable as a matter of law and are deemed unpatentable subject matter.”

Patents are valuable things and protect the rights of inventors and other creative people but the Patent Office should be wary of taking the claims of private companies too much at face value, especially when it comes to patenting things in nature like bits of DNA.

Myriad has appealed the ruling to the US Court of Appeals and much hangs in the balance.