perfect pitch and just temperament

One gene may be key to coveted perfect pitch
A tantalizing headline for a musical biologist, about a new study published in PNAS:

Dichotomy and perceptual distortions in absolute pitch ability
E. Alexandra Athos, Barbara Levinson, Amy Kistler, Jason Zemansky, Alan Bostrom, Nelson Freimer & Jane Gitschier.
PNAS 11 September 2007 104(37): 14795-14800

Disappointingly, this study in no way tested a genetic basis for perfect pitch - no DNA was cloned or sequenced, no family trees analyzed, nothing that might actually help to identify a gene for perfect pitch. This is a typical case of the headline not representing the content of the study. The authors only make this surmise based on a bimodal distribution (either you have it or you don't), rather than perfect pitch being one extreme of a continuous variation in pitch perception ability. There could well be some genetic basis of absolute pitch perception, but other mechanisms could conceivably give the same bimodal distribution, such as having a specific development window of opportunity for nurturing this ability. Perhaps we are all born with the inherent capability to perceive absolute pitch, but without conscious training at a specific point in our brain development, the neural connections are not stabilized, and the ability is lost.

In any case, this is a very nice study. It shows a systematic bias towards erring on the sharp side with increasing age, suggesting possible mechanical changes in the cochlea, like altered elasticity of the membrane or reduction in the density of hair cells.

What was really interesting to me was the distribution of accuracy in note perception. Subjects with absolute pitch uniformly nailed the A and had high reliability on other 'white key' notes, but there were subtle yet systematic errors in identifying the 'black key' notes. The authors propose a kind of 'magnet' effect around A, due to heightened perception caused by orchestras tuning to A at various pitch standards, which is an intriguing idea, but remains to be tested.

These systematic variations in perception, even in people with perfect pitch, could actually tell us as much about our tuning system as about the neurobiology of pitch perception. Our standard equal tempered tuning forces our scale into evenly sized intervals, rather than optimizing the primary intervals depending on the key of the music, as with various just tuning systems. Just temperament, as Bach so beautifully demonstrated with his Well Tempered Clavier (generally incorrectly descibed as modern equal temperament), brings out different 'colours' in the harmonies of each different key, when played on an appropriately tuned keyboard.

So I wonder: is the relative difficulty in identifying chromatic pitches a consequence of being habituated to music with a compromised equal tuning system? What would this study have measured in 18th century musicians, or in people brought up listening to non-western music, based on entirely different scales?

Proponents of just temperament have argued that we have done music a huge disservice by switching from just to equal temperament. Here is an excerpt from composer Kyle Gann's Just Intonation Explained pages:

...equal temperament chords do have a kind of active buzz to them, a level of harmonic excitement and intensity. By contrast, just-intonation chords are much calmer, more passive; you literally have to slow down to listen to them. (As Terry Riley says, Western music is fast because it's not in tune.) ... I've learned to hear equal temperament music as a kind of aural caffeine, overly busy and nervous-making. If you're used to getting that kind of buzz from music, you feel the lack of it as a deprivation when it's not there. But do we need it? Most cultures use music for meditation, and ours may be the only culture that doesn't. With our tuning, we can't. My teacher, Ben Johnston, was convinced that our tuning is responsible for much of our cultural psychology, the fact that we are so geared toward progress and action and violence and so little attuned to introspection, contentment, and acquiesence. Equal temperament could be described as the musical equivalent to eating a lot of red meat and processed sugars and watching violent action films. The music doesn't turn your attention inward, it makes you want to go out and work off your nervous energy on something.

Perhaps this study provides the first biological evidence that equal temperament doesn't quite resonate naturally with our brains.

more dangers of creationism

I wonder if the current resistance to acknowledging a human role in climate change in the US is related to the lack of acceptance of evolution. Studying evolution entails: challenging the mind to contemplate geological timescales, far beyond the timescale of our everyday experience; understanding life as a dynamic, ever-changing process; realizing that organisms not only adapt to their environment, but also contribute to the active construction of their environment; seeing that there are limits to adaptation. Someone who has pondered these aspects of life will surely be better equipped to imagine possible future scenarios, given our current trajectory, and to engage in meaningful debate about the role (and responsibility) of human society in constructing our collective environment.

a misplaced debate

The debate between evolutionists and creationists is alive and well, and seem to be never-ending, as neither side has any desire to be converted to the other way of thinking.

Science is a process of incremental learning, with current ideas continually being updated or replaced as new evidence or interpretations emerge. The asymmetry of hypothesis testing means that while theories not standing up to evidence get discarded, no theory can be definitively proven, once and for all. On the other hand, religious belief is structured in such a way that any piece of evidence can be taken as support for a creator (it exists, therefore it must have been created), yet the existence of a higher power cannot be disproven. Thanks to these contrary modes of understanding, evolution biology is a dynamic and progressive field, while creationism is as static as its underlying beliefs. Still, debate can be stalled, because in a metaphysical sense, evolution cannot be absolutely proven any more than a creator be absolutely disproven.

So perhaps it would be best to leave the creationists in peace with their own beliefs, and save our energy for what I think is a much more important issue: the teaching of science. Students who approach creationism on an equal footing with evolution cannot be learning the real meaning of the scientific process, and those who push for teaching 'creation science' clearly don't understand what is meant by the scientific method. Science is one means of coming to an understanding of life, by a particular process of hypothesis testing. Creationism was not arrived at by the scientific method, and is not subject to the rules of science. Therefore it is not science, and absolutely should not be taught as such. This is not to say that religion has no place in our society, just that science class is not an appropriate forum for religious discussion.

As scientists we don't claim that science has all the answers: every scientific theory is subject to continual revision. Our current understanding of evolution has served us well since Darwin's time, but of course will become outdated as new ideas develop. Perhaps one day we will even develop a more efficient learning process, at which time science will become a historical discipline. But in the mean time, the scientific method is our means of generating knowledge about the world, and teaching science in a rigorous way is necessary for future scientists and laypeople alike to understand and participate in 21st century society.

A time for change

Cancer: is it due to spontaneous genetic mutations or to karyotype and tissue disorganization? Inborn genetic factors or external environmental factors?

AIDS: a new disease resulting from HIV infection, or a collection of old diseases caused by drugs and malnutrition?

Heart disease: is it really caused by high cholesterol, or could it be a consequence of the replacement of traditional foods by processed foods?

Mad cow & Creutzfeld-Jacob disease: due to hyper-infectious prions or metallotoxins?


In each of these examples, the minority dissenters from the scientific mainstream make a very convincing case, but the scientific mainstream is an extremely powerful force, backed by industrial profits, political will, scientific reputations, as well as the hopes and expectations of the general public.

I see two main problems here. One is the failure of genetic reductionism as an approach to human biology. We need to return to studying multiple levels of organization, from the genes of a single cell, to tissues, to organ systems, to individuals, to societies, to our external environment. The other problem is how quickly and extensively non-scientific factors come to entangle issues that should be decided for their own merit based on careful experimentation and observation.

We are conceivably spending trillions of dollars, representing the majority of our healthcare spending and research investment over years or decades, on chasing elusive genetic causes for what are clearly environmental diseases. How many more decades of 'war on cancer' genetic research will we fund while the incidence of, and mortality from, cancer continues to skyrocket? How many more millions of impoverished people will die of AIDS before we decide to spend the money on basic nutrition and sanitation instead of on toxic patented antiviral drugs?

The community of physicists was forced to face the greater social implications of their work once nuclear war became a reality. Perhaps it is time for the community of molecular biologists to face the current social reality, to admit that our work has also been corrupted by corporate and political factors, and actively promote the chanelling of our collective energy towards more productive humanitarian aims.

my little mutant

Last week I found what looks a homeotic mutant in my drosophila stocks. She had only one wing, with her head on the side of the thorax where the other wing should have been. She seemed otherwise healthy, and laid at least a couple of eggs, but unfortunately none survived.

The Dreaded Shrinks!

Here is a letter I sent recently to CBC news, in response to a disturbing article based around Bush's recent medical examination:


Your recent article 'shrinking through the ages' (www.cbc.ca/news/background/health/aging.html) erroneously portrays the loss of bone mass in elderly people as an inevitability of the human condition. In fact, reduction in bone mass can be primarily attributed to our modern diet, and is easily avoided, given sufficient knowledge. There are four related features of a typical modern diet which together contribute to loss of bone mass:

Low dietary mineral content:
Foods traditionally valued for outstanding mineral content, such as organ meats and bone broths, are rarely consumed by the average modern Canadian. Fresh milk from healthy grass-fed cows, once the primary daily source of minerals, has been replaced by milk from cows fed a grain-based diet, and bred to produce high quantity but not high quality milk, from which the already poor mineral content is further depleted through intensive processing. Mineral-rich butter from grass-fed cows has largely been replaced by processed vegetable oils. Sea salt, with a large and balanced spectrum of trace elements, has given way to refined sodium chloride. The vegetables which once provided a significant contribution to our mineral intake are now likely to be grown in soils depleted of nutrients, thanks to industrial scale monocropping agricultural practices.

Low intake of nutrients which promote mineral absorption:
Even if sufficient minerals are present in our diets, our bodies cannot absorb and utilize them correctly without the necessary cofactors: the fat soluble vitamins A and D, and cholesterol. Changes in our eating habits, fuelled to a large degree by an aggressive yet unfounded anti-cholesterol and anti-saturated fat campaign, have led to a drastic reduction in consumption of these necessary cofactors. Without eating high quality fresh whole milk dairy products and unprocessed animal fats, we are undoubtedly not absorbing a significant fraction of the minerals already present in our diets.

High intake of factors which inhibit mineral absorption:
The increasing consumption of carbohydrates in modern diets, without the traditional methods of preparation, has greatly increased our intake of 'anti-nutrients'. Soybeans and many grains contain phytic acid, which unless neutralized by fermenting, sprouting or soaking, will actively prevent absorption of minerals. Unfortunately, infants whose mothers can't or won't breast feed are instead given soy-based formula containing phytic acid, and so begin life with poor mineral supplies. The oxalic acid present in some leafy greens (which can be neutralized by cooking) and the tannins in black tea, have a similar effect on blocking mineral absorption.

High intake of foods that actively deplete mineral stores:
Metabolic acidosis is increasingly being recognized as a widespread result of poor modern diets, and as an underlying factor in many modern diseases, including osteoporosis. The pH balance of the body is shifted due to excessive intake of acidifying foods (such as refined carbohydrates and processed foods) and a deficit of alkalizing foods (those rich in minerals and antioxidants). In order to maintain the physiological blood pH of 7.4 (slightly alkaline), our bodies use as a buffer the mineral stocks in our bones. If those reserves are not continually replenished, metabolic acidosis occurs, with consequent loss of bone mass over time. The two worst offenders in the modern diet for contributing to metabolic acidosis are coffee and soft drinks, followed by most, if not all, processed and fast foods. To balance a diet that includes regular consumption of any of these culprits, an extremely high intake of minerals is required, otherwise the minerals in our bones are used as a buffer to prevent immediate damage to our bodies, resulting, of course, in the widespread phenomenon of shrinking through the ages.

Only by learning once again how to sustain ourselves on a diet of natural, carefully prepared, nutrient-dense foods, will we be able to maintaint our default healthy state throughout life, and 'the dreaded shrinks' can return to being merely a figment of Roald Dahl's imagination!




Further reading:

Weston A Price Foundation

Better Bones

The International Network of Cholesterol Sceptics

21st century alchemy

A colleague asked me the other day what I thought was the raison d'etre of molecular biology. Though it had never occurred to me before, one possible answer was immediately clear: immortality.

The acknowledged goals of molecular biology are to cure disease, to live healthy into our old age, giving all members of our society an equal chance at a productive life, no matter what their genetic makeup; to engineer our food sources to provide what we naively think we need to improve our health. But what are the unspoken, and perhaps even unconscious driving forces? Is all this technology really an altruistic act on the part of we scientists to help those less fortunate?

Our scientific ancestors were the alchemists, whose ostensible pursuit was the transformation of materials, the quest for gold. But buried between the lines of alchemical texts, one finds the true underlying motivation: the transformation of the soul, the quest for eternal life.

Technology now in the hands of modern scientists is vastly more complex than that of our alchemical forefathers, but have our human desires really evolved in parallel with our means of investigation? Is this hugely complex undertaking we call molecular biology, now racing towards the generation of a human clone, simply the age-old pursuit of eternal life in a 21st century disguise?