On the edge of chaos and some kind of order (Books - Europa, The Great Journey, At Home in the Universe)

I have the second of my comprehensive exams coming up. Although this has not resulted in reading nothing at all, it has meant that I have not finished anything. I guess I'm a less constant reader these days. Anyhoo, I thought I'd report on what's in the works.

Tim Parks's Europa (1997) concerns Jerry, a philandering middle-aged English professor and writer living in Milan, who considers the hash he has made of his life while he rides on a bus to the European Petition Committee to air grievances regarding his college's teaching contracts. With an international group of faculty and students who posture, who lecture, who flirt, drink, try to impress, to get into each others' pants, all while Dead Poet's Society plays on the bus video system in the background. It's written as a first-person monologue that switches from interior to exterior perspectives, a sort of string of pathetic parenthetical justifications for his screwed up marriage and loss of ambition, laced with bitter whining about "totties" who will and won't put out.

Ordinarily I detest novels with misogynist characters, set in academia (and that rules me out of quite a few). The fact that Tim Park's is himself an ex-pat Brit living in Milan translating Italian literature while teaching at a university adds an autobiographic layer that turns my impression of this book from a novel about misogynist characters to a misogynist novel, however, what I am finding impressive about the book is a) the ferocity of its voice: high-velocity sentences drive on and on in a rhythm that compels me to keep reading:

You should have a slug of this, boyo, Vikram Griffiths said, turning from trying to bribe the driver to take us into town in the evening of his own initiative without referring the time and expense to the coach company. You look terrible, he said, What's up? So, lying with the instinctive fluency that years of betrayal engender (and if one is lying one owes it to the world to do it well), I said the combination of the coach's movement and trying to watch Robin Williams seize the day had given me the most atrocious headache, and I told Vikram Griffiths, this feckless fragment of Empire (as he himself once described himself), this genius of broken marriage, bizarre manners and interminable good causes, this man who cam to my house just once, his dog only a puppy then, and frightened my wife with his life story - told him that I had come to the front of the coach to speak to him because I had heard, in the Chambersee Service Stations, Dimitra and Georg and her agreeing that he, Vikram, would have to be replaced, because incapable of putting a presentable face, I said (partly inventing, partly quoting), to our claims; he would make us look ridiculous, I said, they had said, with his unkempt baldness, his bushy sideburns and wild gestures.

and b) while this piece often feels grossly personal either about the narrator, the writer, or both, it also manages to be a novel about the European Union. The EU, as you probably already know, is a supra-national body of independent governments charged with negotiating political and economic decisions made for the good of all its members while at the same time maintaining their autonomy. It's an arrangement that is a lot like, well, this narrator's relationships - with his employment, his marriage, his lover, his daughter. That may make it sound trite, but actually, it is a book driven by ideas while not being a book of ideas. Jerry is mostly outraged because his ex-paramour is now having an affair with someone else. The bus (a subset of the institute where he teaches) is polyglot. Everyone speaks a different language, has different priorities, and in the end they are all out for themselves, so no satisfactory union (or at least no easy union) is possible, the book seems to imply.

I am finding it particularly interesting how the interior personal concerns of this novel interact with the exterior, geo-political - exemplified in the seating arrangements on the coach as each rider vies to pair off with a suitable other as their roommate in the hotel that evening. It is striking me as I read that, if this were an American novel, the personal would not interact with the political but rather with the pervasive metaphor of technology or, these days, the brain. It's a different zeitgeist 14 years later. Even as I find myself liking the characters less and less, I am compelled by how Parks makes a dialogue of these two realms, and so I read on.

Speaking of ex-pats, historian David McCullough's latest book The Greater Journey tells the story of mostly well-known American writers, painters, and doctors who came to Paris between 1830 and 1900, that is, post- Napoleon and pre-World War I, what drove them there, and how that visit contributed to what they became. As with his fantastic biography of John Adams, McCullough links places, personages, and ideas with seamless narrative that is a pleasure to read. The experience of the month-long oceanic voyage, the contrasting squalor and splendor of 1830s Paris, the cholera epidemic of 1831, are all vividly portrayed. I am finding the contrast of the shared political influences of France and the United States, what staunch allies we were, and the difference in what French and American culture value in living daily life striking, particularly in light of the recent Strauss-Kahn scandal.

Lastly, Stuart Kauffman is feeding me lots of beautiful narrative about how a certain degree of complexity in a system can perpetuate self-organization out of initial chaos, particularly in the context of biology. In his book At Home in the Universe, Kauffman offers these self-organizing principles as endemic to all kinds of systems - economies, cultures, microscopic molecules, and macroscopic universes. He speaks particularly of when systems, such a the molecular morass that makes up the biosphere, are balanced along the edge of order and chaos and is talented at turning complex mathematical ideas into visual metaphors:

This poised edge of chaos is a remarkable place. It is a close cousin of recent remarkable findings in a theory physicists Per Bak, Chao Tang, and Kurt Wiesenfeld called self-organized criticality. The central image here is of a sandpile on a table onto which sand is added at a constant slow rate. Eventually, the sand piles up and avalanches begin. What one finds are lots of small avalanches and few large ones. If the size of the avalanche is plotted on the familiar x-axis of a Cartesian coordinate system [that's a conventional graph with two axes], and the number of avalanches at that size are plotted on the y-axis, a curve is obtained. The result is a relationship called a power law. The particular shape of this curve, to which we shall return in later chapters, has the stunning implication that the same-sized grain of sand can unleash small or large avalanches. Although we can say that in general there will be more tiny avalanches and only a few big landslides (that is the nature of a power-law distribution), there is no way to tell whether a particular one will be insignificant or catastrophic. ... At this poised state between order and chaos, the players cannot fortell the unfolding consequences of their actions. While there is law in the distribution of avalanche sizes that arise in the posed state, there is unpredictablility in each individual case...

In other words, you are going to have to do some work to follow Kauffman's argument, he is writing at a fairly sophisticated level. But he combines complex mathematics and biology with a real appreciation for the beauty of the world, which phenomena in it can be predicted, as well as which cannot. I'm finding the reading well worth it and the concepts applicable to all sorts of observable phenomena.

The drudgery of field science reveals abundant evidence for the mechanisms of evolution (Books - The Beak of the Finch by Jonathan Weiner)

We've been back from vacation for almost a week but it has taken me until now to get back to writing. Our trip to the Dordogne, Paris, London, and Sussex allowed for far less reading than is typical of my vacations, but we did see The Cherry Orchard at the National Theatre in London, Die Meistersinger and L'Elisir D'Amore at Glyndebourne, and saw a wonderful new 3-D documentary film by Wim Wenders about the late choreographer Pina Bausch called Pina which I recommend looking out for. In addition, we drank some terrific wine, ate splendidly, saw some impressive chateaux - all in all, a lovely time.

Amidst all this, I finally had time to finish Jonathan Weiner's splendid The Beak of the Finch - a rich book detailing the work that evolutionary biologists Peter and Rosemary Grant have done on the Galapagos Islands. They have observed Darwin's theory of natural selection play out again and again and, in some cases, even observed how new species evolve, by watching the islands' famous finches.

It is the twenty-fifth of January, 1991. There are four hundred finches on the island at this moment, and the Grants know every one of the birds on sight, the way shepherds can tell every sheep in their flocks. In other years there have been more than a thousand finches on Daphne Major, and Peter and Rosemary could still recognize each one. The lock was down to three hundred once. The number is falling toward that now. The birds have gotten less than a fifth of an inch of rain the the last forty-four months: in 1,320 days, 5 millimeters of rain.

The Grants, and the Grants' young daughters, and a long line of assistants, keep coming back to this desert island like sentries on a watch. They have been observing Daphne Major for almost two decades, or about twenty generations of finches.

Aside from the pleasure of his lucid writing, Weiner elucidates the development of Darwin's own thinking as well as integrating his original work with that of contemporary scientists observing the forces of evolution in action. This book makes plain the great theory's relevance to the natural world in which we live and also reveals the unbelievable drudgery of painstaking observational field work. Holy cow. Months upon successive months on a small hot island of rock and guano, measuring finch beaks and seeds per square meter of island.

Peter Grant combined the measurements of seed size and seed hardness and rated each kind of birdseed as the finches might themselves, in a sort of Struggle Index. The small soft ones of Portulaca score lowest on this index, only 0.35. The big hard seeds of Cordia lutea score highest, almost 14. Any of the finches can handle Portulaca in its beak, but very few are up to Cordia.

The Grant team also kept a census of the numbers of each kind of seed on the lava. To do this objectively they used a random-number table to select a single plot of lava, one meter square, somewhere in each grid. Then they counter every single fruit and seed they could find on that square of lava, whether it was dangling from the top of a cactus tree or lying in the middle of a cactus patch. Next they chose a much smaller plot within that square meter, again at random, and they sifted the hot cindery soil, collecting every fruit and every seed they found. Finally they withdrew to their tents and spread out their trophies on white trays to count one by one. And they repeated the whole routine fifty times...

"People think fieldwork is so romantic," Boag says, "but a lot of it is real slog. This was absolutely the worst."

Seed hardness and beak size are important because, in certain environmental situations the length of a beak determines how much food a finch can access to get it through a dry season and a miniscule difference in size is literally the difference between living and dying in these cases. As Weiner so emphatically puts it:

...the birds were not simply magnified by the drought: they were reformed and revised. They were changed by their dead. Their beaks were carved by their losses.

But I have to say, my skin shrivels up just thinking about the work they did. Then again, the Grants might think the same of my measuring the brainwaves of 6 year old children. Weiner conveys the passion the Grants have about their data and the great satisfaction of seeing such painstaking collection and patient calculation yield a story, otherwise their slog would be the reader's as well.

The isolated Galapagos archipelago precipitated Darwin's theory because they hosted many unique creatures that clearly bore a resemblance to relatives on the South American mainland and a fossil record of extinct relatives of those living forms existed

to help reveal a Law of succession that links the living to the dead, the same law that links the fossils of one stratum of rock to the fossils in the strata below...

"It was evident that such facts as these, as well as many others, could be explained on the supposition that species gradually become modified"

Of course, the story of Darwin's monumental deduction has been told again and again. What is different about Weiner's book is that he observes contemporary scientists, the Grants, as well as their students, many of whom develop into credible scientists in their own right, collect the evidence needed to confirm the original hypotheses. The argument has been made time and again against evolution that the workings of natural selection and sexual selection cannot be observed, that the processes necessarily takes thousands of years and so one is left only being able to infer it from the trail of fossils left behind, as Darw.in did. They also argue that it is impossible to make quantitative predictions based on data in nature, i.e., "proof" is not possible. However, both of these statements are incorrect. The lifespan of many species is short enough to observe the infinitesimal changing of the frequency of a particular feature across a species in response to both the physical characteristics of the environment they inhabit and the amount of competition they face from similar other creatures, and how these small variations can diverge into new species under certain conditions. This is exactly what the Grants's work with finches as well as Endler's with guppies reveals. Furthermore, the Grants have successfully made quantitative predictions based on their work, and over time have seen them to be correct. Weiner is particularly strong in making clear how this can result from an undirected process of random mutations in individual animals. Weiner's talent for writing about natural science is making that story as palpable as well as exciting to the reader.

Weiner has a particularly good chapter on resistance, not only of certain ideological groups to teaching of evolution but also the resistance of moths or ticks to insecticide or E. coli to antibiotics. This is a particularly important part of the story, in my view, because it makes clear the ubiquity of evolution as it impacts our daily lives and the importance of seeing that a basic understanding of the process is gained in the general populace, as billions of dollars are thrown at developing insecticides and antibiotics when biology has clearly shown us that these are only temporary solutions. Bacteria and insects will not cease to evolve and eradication will not be achieved by these means. The target is always moving and these solutions are leading to more and more successfully resistant strains of streptococcus, tuberculosis, salmonella, pneumococcal pneumonia, and gonorrhea. We ignore the lessons of evolutionary biology at our own peril, so if you would like to read a book that depicts the mechanisms of this great theory via abundant example and does so in a style that feels very much like a good adventure story, I would recommend The Beak of the Finch by Jonathan Weiner.

We're a work in progress...

Carl Zimmer has an excellent post today on George Williams, a little known evolutionary biologist who made some important additions to our understanding of the mechanisms of natural selection.

Many scientists believed, for example, that natural selection often produced adaptations that benefited entire groups.Why did animals get old and die, for example? Why didn’t animals just keep humming along until they were killed by a predator or a pathogen? Death had to be good for something, and one popular idea was that death benefited entire groups of animals. By dying, older individuals stepped out of the way for younger ones.

One day, Williams heard this idea for the umpteenth time,during a lecture by a renowned ecologist named A.E. Emerson. “My reaction was that if Emerson’s presentation was acceptable biology, I would prefer another calling,” he later wrote.

Check out the post for more.

Correcting our misinterpretations of the world (Books - Full House by Stephen Jay Gould)

As a working scientist, Stephen Jay Gould had a good deal of practice thinking about trends in the natural world in the language of statistics. Statistics get a bad rap as merely a fancy way to lie, but really they are a system of tools that allows us to infer the likelihood of something occurring in our world as a rule (and hence in the future) given what has already happened before in some subset of that world. For example, the likelihood that Drug X will cure a case of malaria can't be tested in the abstract, it must be tested by actually administering the drug to a group of people with malaria for, say, two weeks. At the end of that period, the number of people who survived or succumbed to the disease are counted. But we still don't know everything because a certain portion of any group would live or die anyway, those numbers will be estimated by comparing them to a group who does not receive the drug. This group should, if they are like most, have the same chance of living or dying as the other group. Then we can begin to infer how many people as a rule will survive because of the drug. Some math is applied to adapt the number from that small group and apply it to everyone, since it is impossible to give everyone the drug. The result is stated as a probability, the language of science, as it acknowledges the ubiquity of error and the inferential nature of estimates, as we can never know all the cases of anything.

Paleontologist, biologist, and science writer Gould was diagnosed with peritoneal mesothelioma at age 40, a disease with the median mortality rate of eight months. As most general readers of probablistic statements would, Gould first interpreted this statistic to mean he was likely to be dead in eight months however, his training as a scientist made him think twice about this interpretation of the median or the mid point of a group of numbers. This is one of three ways statistics describe the central tendency of any group of numbers - baseball scores, people who earn $30,000/year or more, people who will vote for Charlie Rangel in the next election, etc. Central tendencies are statistics way of summarizing what is usual in nature with one number. However, after thinking, Gould realized:

I am not a measure of central tendency, either mean or median. I am one single human being with mesothelioma, and I want a best assessment of my own chances - for I have personal decisions to make, and my business cannot be dictated by abstract averages. I need to place myself in the most probable region of the variation based upon particulars of my own case; I must not simply assume that my personal fate will correspond to some measure of central tendency.

Full House is a 190-page disquisition of what one might assume to be dry and obscure notions - means, modes and medians, spreads of scores, skewed averages - but because they spring from a personal confrontation with mortality as well as Gould's love of baseball, and because they are written in Gould's down-to-earth prose, this book is anything but dry. It is a lively, entertaining narrative on our tendency to misinterpret the world given our misunderstandings about what statistics are telling us. The writing is cogent, the format concise, and the references various as they are learned. Plato, Shakespeare, Huxley, Darwin, nameless drunks weaving down the sidewalk, Bill Gates, and the Brooklyn Dodgers all put in an appearance in Gould's attempt to make plain to the lay-reader concepts like measures of excellence, the likelihood of survival, or whether development - of skills or species - means a trend toward greater complexity or less. These phenomena are continually misrepresented in everyday conversation and reporting about our world, sometimes unintentionally and sometimes with malice aforethought. If you have ever wanted a better understanding the daily missives we receive in the language of probability through our senses or our news sources then read this book. The next time I teach a class which would benefit from an understanding of statistics, Full House is going to be required reading.

Fish with legs and other predictable oddities of nature (Books - Your Inner Fish by Neil Shubin)

Paleontologist Neil Shubin, a discoverer of Tiktaalik - a fish with legs which is one of the many thousands of clear demonstrations in nature of the evolution of species - has written an entertaining and swift-moving book about the nature of his work collecting fossils and why it matters. If you can get past the gimmicky title, and I didn't find it too hard, Shubin writes in a modest, approachable style, provides down-to-earth examples (pun intended), and conveys to the reader the excitement he feels about his work.

The work traces three lines of evidence that Shubin offers as a way to better understand our own origins - fossils, genes, and embryos. Shubin builds our understanding in the book's first pages of how knowledge about anatomy and geology are necessary in the use of fossils to understand the evolution of species.

The order of fossils in the world's rocks is powerful evidence of our connections to the rest of life. If, digging in 600-million-year-old rocks, we found the earliest jellyfish lying next to the skeleton of a woodchuck, then we would have to rewrite our text. The woodchuck would have appeared earlier in the fossil record than the first mammal, reptile, or even fish - before even the first worm. Moreover, our ancient woodchuck would tell us that much of what we think we know about the history of the earth and life on it is wrong. Despite more than 150 years of people looking for fossils - on every continent of earth and in virtually every rock layer that is accessible - this observation has never been made.

Once a certain body of information has been amassed about the age of rocks and the structure of the skeletons of ancient creatures, a scientist can begin to make predictions about the layers of rock in which they are likely to find a particular kind of fossil - even if that fossil has yet to be discovered. This is, in fact, exactly what Shubin and his team did:

It took us six years to find it, but this fossil confirmed a prediction of paleontology: not only was the new fish an intermediate between two different kinds of animal, but we had found it also in the right time period in earth's history and in the right ancient environment...

Darwin's theory allows us to make very precise predictions.

Shubin's ushers us into the world of genes building the reader's understanding with simple, clear language. He does the same for developmental embryology, telling the story of how multi-celled creatures like the sponge or us humans evolved from single celled ones with the advent of intra-cellular communication and substances like collagens and proteoglycans - the glue that hold cells together. My favorite story in the book was about single-celled creatures known as choanoflagellates, their similarity to a particular type of cell in the sponge, many of which assemble to form the prototype of a mouth, and the genetic evidence to suggest that structures of multiple cells in bodies evolved from the collaboration of single-celled creatures in just this way. What are the advantages of the body plans that evolved since algae and single celled flagellates? What are the liabilities, since we all know that single celled creatures are still in abundance and there is ample evidence for our imperfections in thrombosis, and choking (one could not call the fact that we use the same tube to both inhale and swallow food particularly intelligent design.

Shubin is an amusing teacher, giving us a primer in how to extract DNA with just a kitchen blender, some dish soap, and rubbing alcohol. Talking about the origin of hiccups and hernias as misbegotten legacies of evolution, and offering a wonderful lesson in heredity with a family tree of clowns that arises from run-of-the-mill humans with the single mutation of a red rubber nose, followed in the next generation by floppy feet, and then orange curly hair. Once he has laid the groundwork, Shubin then launches into his point about what information we can derive from the family tree of a species:

The real power of this family tree lies in the predictions it allows us to make... We can now... confidently reconstruct the relationships among long-dead animals and the bodies and genes of recent ones[.] We look for the signature of descent with modification, we add characteristics, we evaluate the quality of the evidence, and we assess the degree to which our groups are represented in the fossil record.

Shubin is an effective teacher because he doesn't forget that to communicate his subject is more than impressing us with his knowledge, it is allowing us to see his wonder at the world, the vulnerability he feels when he perceives we have learned something new about who we are, this permits the reader to share his passion for his subject without becoming experts ourselves and he accomplishes this most effectively in Your Inner Fish.

The roots of communication are the roots of esthetics

Natalie Angier muses today in the Science Times about art - from whence it came and why. Is it the product of oversized brains that have too little to do? Some theorists have deemed art a way of preening. Having worked in the field for twenty-odd years, I can certainly see the connection. It starts with putting pictures up on the refrigerator and tales of great divas let us know where it can end up. Others see art as a social glue - like religion. Ellen Dissanayake, a scholar of evolution and art, believes that, given the amount of time and resources art consumer, it must be an evolutionary adaptation. Unfortunately this article skims along the surface of the subject without really getting into it. Does that mean if one person makes art then it uses a lot of their time or does that mean that it uses a lot of an entire society's time? Is that statement supportable? By resources does she mean material resources or cognitive ones? She also asserts :

Art also gives us pleasure...and activities that feel good tend to be those that evolution deems too important to leave to chance.

Stated this way, it seems spurious to me. Ice cream gives us pleasure, we are not evolutionarily adapted to it. We are adapted to consume calories where we can get them, a by-product supposedly left over from when we were roaming the earth more dependent on the whims of nature than on Safeway. This would point more to art being a by-product of our evolutionary attraction to bold colors and sounds, or to pattern recognition. Additionally, art is not necessarily just pleasurable - it is sometimes more deeply involving, intellectually stimulating, a complex synthesis, a way to represent things that are meaningful to us, a way to commemorate death, a way to leave a mark. However it may be all these things because it is the essence of what is engaging and attractive to us and that is exactly why Ms. Dissanayake has begun studying the communing rituals between mother and infant for signs that they might evolve to become the building blocks of choreography or music. It's an interesting notion that Ms. Dissanayake's book Art and Intimacy: How the Arts Began no doubt gets into it in more detail. It is interesting to ponder that we might be hardwired to be engaged and attracted by themes and variations on sound and movement and that that is the origin of our finding a textile design or a church spire esthetically pleasing.